ALLOGRAFT TOLERANCE WITHOUT THE NEED FOR SYSTEMIC IMMUNE SUPPRESSION

FIELD OF THE DISCLOSURE

The disclosure relates generally to the field of transplantation. The disclosure further relates to methods for generating local immunosuppression in the environment of transplanted cells.

BACKGROUND OF THE DISCLOSURE

The advent of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells has had a paradigm-shifting effect on regenerative and translational medicine. These cells have can self-renew indefinitely in a pluripotent state while retaining the ability to differentiate into any cell type in the human body. Such properties have allowed researchers to better understand human development and the etiology of developmental disorders. They have also given modern medicine a powerful new tool against diseases that have been intractable or impossible to treat with conventional medicine, including spinal cord injury, diabetes, blindness, multiple sclerosis, and cancer, to name a few. The efficacy and range of applicable diseases for cell therapies will only increase with our growing understanding of how to control stem cell differentiation and the biology of the differentiated cell products.

With these applications come important and critical challenges. Along with cell safety, one of the most important concerns is immune rejection of cells from a different genetic background. Immune rejection remains a critical barrier because the immune system has evolved a complex set of mechanisms to recognize and eliminate “non-self” cells that express specific protein fragments—especially those from the major histocompatibility complex (MHC in mouse, HLA in humans)—that differ between donor and recipient (Yang et al., Nat Rev Genet. 18:309-26 (2017)). This response is almost certainty a by-product of the evolutionary pressure to protect against opportunistic infections and malignancies, which are often defined by the presence of “foreign” proteins and epitopes. Depending on the context, rejection of transplanted cells or tissues can occur over the timescale of minutes/hours (hyperacute), days/months (acute), and months/years (chronic) (LaRosa et al., J Immunol. 178:7503-9 (2007)). This rejection results from the complex and coordinated effects of cell types from both innate (Murphy et al., Immunol Rev. 241:39-48 (2011)) and adaptive immunity (Issa et al., Expert Rev Clin Immunol. 6:155-69 (2010)).

One of the most important pathways to rejection is the priming of the adaptive immune system and activation of CD8+ cytotoxic T-cells. This occurs after antigen presenting cells process donor-specific peptides and then activate recipient T-cells that are specific for the same peptides in secondary lymph organs (Lechler et al., J Exp Med. 155:31-41 (1982); Guermonprez et al., Annu Rev Immunol. 20:621-67 (2002); Stockwin et al., Immunol Cell Biol. 78:91-102 (2000)). These T-cells then migrate to and kill transplanted cells or tissues with the release of cytolytic factors like perforin and granzyme. NK-cells can also induce apoptosis in donor cells based on foreign or no MHC expression (Kitchens et al., Transplantation. 81:811-7 (2006); Benichou et al., Curr Opin Organ Transplant. 16:47-53 (2011)), and other cell types like macrophages can support rejection with the release of pro-inflammatory cytokines at the engraftment site (Mannon, Curr Opin Organ Transplant. 17:20-5 (2012)). Many other cell types and subtypes also have a role in allograft rejection. Since these are the same immune pathways used to eliminate common viral and bacterial pathogens, they are—along with rejection of an allograft—highly conserved across vertebrate species.

A current solution to prevent rejection of an allograft involves the following two options: find a donor with a matched histocompatibility haplotype (mostly likely from genetically-related family), and much more commonly, use broadly-directed immunosuppressant drugs (Wiseman, Clin J Am Soc Nephrol. 11:332-43 (2016); Malaise et al., Transplant Proc. 37:2840-2 (2005)). Common drugs include those from the families of calcineurin inhibitors (Flechner et al., Clin Transplant. 22:1-15 (2008); Casey et al., Curr Opin Nephrol Hypertens. 20:610-5 (2011)), anti-proliferative agents (Hardinger et al., World J Transplant. 3:68-77 (2013)), mTOR inhibitors (Macdonald, Expert Rev Clin Immunol. 3:423-36 (2007); Neuhaus et al., Liver Transpl. 7:473-84 (2001)), and steroids (Steiner et al., Semin lmmunopathol. 33:157-67 (2011))—all of which suppress T-cell proliferation or function (particularly the former three). These drugs need to be taken every day for life, and even a single missed dose can increase the risk of rejection. Yet they do not always work, and when they do, rates of chronic rejection still continually climb over time (Demetris et al., Ann Transplant. 2:27-44 (1997); Libby et al., Immunity. 14:387-97 (2001)). Most importantly, they are systemically-acting and ultimately leave patients immunocompromised with increased rates of cancer and life-threatening infections (Gallagher et al., J Am Soc Nephroi. 21:852-8 (2010)). Pertaining to ES cells, these drugs have shown only marginal improvements in permitting survival across an MHC barrier (Swijnenburg et al., Proc Natl Acad Sci USA. 105:12991-6 (2008); Toriumi et al., Neurol Res. 31:220-7 (2009)). While newer and more targeted immunosuppressant reagents are becoming available and tested in skin and cardiac (Larsen et al., Nature. 381:434-8 (1996)), as well as ES cell allograft settings (Pearl et al., Cell Stem Cell. 8:309-17 (2011)), they are still systemically-acting and therefore likely to leave hosts immune compromised.

One proposed benefit to the discovery of iPS cells was that they could be created from, and for, each patient. These cells should, in theory, be protected from immune rejection by the corresponding patient (Pearl et al., Sci Transl Med. 4:164p525 (2012)). However, the induction of an iPS cell state involves epigenetic alterations and in-vitro-culture pressures that can create abnormalities and malignancies, so each cell line would need to be vigorously tested and/or genetically modified to achieve safety as well as function (Hussein et al., Nature. 471:58-62 (2011); Laurent et al., Cell Stem Cell. 8:106-18 (2011); Lister et al., Nature. 471:68-73 (2011)). Ultimately, the cost and time needed to create and test an iPS cell line for each individual patient makes this approach practically and economically unrealistic. Even if the costs were dramatically reduced, it would not help those patients who need immediate treatment for conditions like burns, heart attacks, strokes, and spinal cord injury (among many others). Furthermore, given recent findings, it remains controversial whether IFS cell-derived cell types are truly protected from immune rejection even when transplanted into the same host from where they were derived (Zhao et al., Nature. 474:212-5 (2011)).

One proposed solution in this regard has been to use naturally suppressive or regulatory immune cells, like Tregs or others, that are expanded and/or transferred before, during, or after transplant of therapeutic cells or tissues (Cobbold et al., Cold Spring Harb Perspect Med. 3(6) (2013); Wood et al., Nature reviews Immunology. 12:417-30 (2012)). These strategies have been suggested based on the recognition of suppressive immune pathways, in particular the discovery of the master regulator FoxP3 that programs a subset of CD4+ cells regulatory T-cells (Hort et al., 299:1057-61 (2003); Fontenot et al., Nat Immunol. 4:330-6 (2003)) and proof of their critical importance in promoting tolerance to allografts (Kendal et al., J Exp Med. 208:2043-53 (2011)). This thinking is in contrast to some of the first tolerance-inducing strategies which focused almost exclusively on depletion of effector T-cells with monoclonal antibodies, coupled with bone marrow transplant and the creation of donor chimerism (Cobbold et al., Nature. 323:164-6 (1986); Qin et al., J Exp Med. 169:779-94 (1989)). The importance of suppressive T-cell phenotypes was later appreciated with strategies that did not kill the cells, but blocked critical T-cell receptors in a way that left them unresponsive to allografts (Cobbold et al., J Immunol. 172:6003-10 (2004)), yet simultaneously able to suppress naïve T-cells of other specificities (Cobbold et al., Immunol Rev. 129:165-201 (1992); Qin et al., Eur J Immunol. 20:2737-45 (1990)). These cells, now recognized as Tregs, may promote tolerance by a number of mechanisms, including (but not limited to) the expression of suppressive factors like TGF beta (Nakamura et al., The Journal of experimental medicine. 194:629-44 (2001); Nakamura et al., J Immunol. 172:834-42 (2004)), CTLA4 (Tang et al., J Immunol. 181:1806-13 (2008); Walker et al., Trends (mmunol. 36:63-70 (2015)), IL10 (O'Garra et al., J Clin Invest. 114:1372-8 (2004); Chaudhry et al., Immunity. 34:566-78 (2011)), and IL35 (Collison et al., Nature. 450:566-9 (2007)), as well as the preferential consumption of IL-2 (Shevach et al., Immunity. 30:636-45 (2009); Setoguchi et al., J Exp Med. 201:723-35 (2005)), manipulation or killing of antigen presenting cells (Mahnke et al., Cell Immunol. 250:1-13 (2007); Shevach et al., Immunol Rev. 212:60-73 (2006)), and depletion of local ATP (Regateiro et al., Eur J Immunol. 41:2955-65 (2011); Regateiro et al., Clin Exp Immunol. 171:1-7 (2013)) or essential amino acids (Cobbold et al., Proc Natl Aced Sci USA. 106:12055-60 (2009)).

Two approaches for potential therapeutic uses of Tregs involve either in-vitro expansion using donor antigens coupled with transplantation, or selective in-vivo expansion that leverages differences between regulatory and effector T-cells. While these strategies are interesting, to date no long term of acceptance of an allograft has been demonstrated solely with the use of in-vitro or in-vivo expanded Tregs. There remain many complications and unknown facets to Treg biology, including the optimal methodology for in-vitro or in-vivo expansion, as well as the therapeutically-relevant dosage and timing. It has also been shown that antigen-specific Treg suppression can be “defeated” depending on the inflammatory context (Korn et al., Nat Med. 13:423-31 (2007)) and that Tregs can be killed by NK-cells (Roy et al., J Immunol. 180:1729-36 (2008)).

In addition to Tregs, other suppressive cell types have also been explored to induce allograft tolerance, such as antigen presenting cells like dendritic cells (DCs) (Walker et al., Trends Immunol. 36:63-70 (2015)). DCs are the link between innate and adaptive immunity, and they can induce both effector and suppressive immune responses depending on contexts like their maturation state and the local inflammatory cues. During allograft rejection, DCs present allograft antigens inside the binding grooves of MHC (mouse) or HLA (human) molecules on their surface, along with costimulatory molecules like CD80, CD86, and CD40 (among others), which allograft-specific T-cell clones recognize to become activated (Walker et al., Trends Immunol. 36:63-70 (2015)). Tolerogenic DCs can be induced from the immature state by exposure to suppressive cues, which keep expression levels of MHC and costimulatory molecules low and in turn promote naïve T-cells into anergic or even Tregulatory subtypes upon DC-Tcell interactions. Therapeutically, one application of this biology is to expand DCs in vitro exposed simultaneously to specific allograft antigens of interest and immunosuppressive factors—many of which have been tested including TGF-beta, IL10, cAMP, prostaglandin E2, histamine, neuropeptides, vitamin D2, B2 agonists, HLA-G, glucosamine, as well drugs like corticosteroids, cyclosporine, tacrolimus, rapamycin, aspirin, mecophenolate mofetil, sanglifehrin, and deoxyspergualin (Hackstein et al., Nat Rev Immunol. 4:24-34 (2004)). Alternatively, DCs have been genetically engineered to directly express immunomodulatory factors like TGF-beta, IL-10, VEGF, FasL, CTLA4-Ig, IDO, NFKb decoy receptors, soluble TNFR, CCR7, as well as siRNA-induced silencing of IL-12 (Morelli et al., Immunol Rev. 196:125-46 (2003)). These cultured or engineered DCs are then transferred into recipients concomitantly with an allograft to test whether they can prolong the survival of an allograft, with the assumption that they suppress allograft-specific T-cells, or increase the number of allograft-focused Tregulatory cells.

In one prototypical approach of this kind, bone-marrow derived DCs were transduced with SOCS1 (preventing upregulation of costimulatory molecules and MHCII), which prolonged mouse cardiac allografts (Fu et al., Cell Mol Immunol. 6:87-95 (2009)). In another demonstration, FasL-expressing DCs were also able to prolong mouse cardiac allografts (Min et al., J Immunol. 164:161-7 (2000)). In general there have been many singular and combinatorial approaches using tolerogenic DCs along these lines (Bjorck et al., J Heart Lung Transplant. 24:1118-20 (2005): Sun et al., PLoS One. 7:e52096 (2012); Li et al., J Immunol. 178:5480-7 (2007); Xu et al., Transplant Proc. 38:1561-3 (2006); Lan et al., J Immunol. 177:5868-77 (2006); Lutz et al., Eur J Immunol. 30:1813-22 (2000); Fischer et al., Transpl Immunol. 25:20-6 (2011)), and the outcomes are highly variable depending on the type of modification to the DCs, culture conditions, timing, and type of allograft being tested (Zhou et al., J Immunol Res. 2016:5730674 (2016); Xia et al., J Evid Based Med. 7:135-46 (2014)). Almost all of these studies have been done in mouse, although recent human testing has begun including testing for safety in healthy volunteers (Dhodapkar et al., J Exp Med. 193:233-8 (2001); Dhodapkar et al., Blood. 100:174-7 (2002)) as well as a phase I clinical trial in 10 patients with diabetes (Giannoukakis et al., Diabetes Care. 34:2026-32 (2011)).

There remain many unknowns to both adoptive Treg and tolerogenic DC therapies, and one of the most important is the duration of their efficacy. While in-vivo studies show that prolonged allograft survival is possible using these two approaches (with or without additional immunosuppressive drugs), it is not long-term, and in almost every case the allograft eventually dies. This is fitting with the fact that both Tregs and DCs have a finite time-span. Also, it is possible for tolerogenic phenotypes, especially among DCs, to “convert” and instead promote inflammatory pathways (Delamarre et al., Semin Immunol. 23:2-11 (2011); Schreibelt et al., Cancer Immunol Immunother. 59:1573-82 (2010); Satpathy et al., Nat Immunol. 14:937-48 (2013)). This is likely due to the highly adaptive nature of DCs, and their ability to sense and respond to a large breadth of inflammatory cues. It has also been shown that these cells can die very quickly after in-vivo adoptive transfer. There are also many subsets of suppressive Tregs and tolerogenic DCs that have been described, and it is still unclear which is the ideal subtype, or if it will entirely depend on the context of the allograft transplant.

Additionally, there is a huge practical and economical barrier to these kinds of approaches in that they require clinicians to manipulate and work with a complicated immune cell type in addition to the therapeutic one. Given their finite lifespan, it is still unclear if these cells would need to be continuously and/or repeatedly delivered to confer long-term tolerance to an allograft. This would compound the already expensive and timely methodology for culturing, expanding, or transducing the cells with critical immunomodulatory factors, and ultimately impede the uses for treatments that are extremely time-sensitive.

Another approach for inducing tolerance is the use of Hematopoietic Cell transplantation (HCT), in which recipients of an HLA-mismatched organ receive an HCT using hematopoietic cells from the same donor (Gozzo et al., Surg Forum. 21:281-4 (1970); Ildstad et al., Nature. 307:168-70 (1984); Sayegh et al., Ann Intern Med. 114:954-5 (1991); Huang et al., J Clin Invest. 105:173-81 (2000); Kawai et al., N Engl J Med. 358:353-61 (2008); Sachs et al., Semin Immunol. 23:165-73 (2011)). This results in a chimerism that can allow newly developing T and B-cells in the recipient to be tolerant of both the recipient and the donor antigens (Tomita et al., J Immunol. 153:1087-98 (1994); Tomita et al., Transplantation. 61:469-77 (1996); Tomita et al., Transplantation. 61:477-85 (1996); Khan et al., Transplantation. 62:380-7 (1996); Manilay et al., Transplantation. 66:96-102 (1998)). This is due to the role that hematopoietic cells play in positive and negative selection in the thymus, where they eliminate cells with an affinity for hematopoietic cell-containing antigens that might also be present in the allograft, ultimately leading to their rejection. (Griesemer et al., Transplantation. 90:465-74 (2010)). However, the inherent and dangerous risk of this approach is the potential for Graft vs. Host Disease (GVHD), in which transplanted hematopoietic cells recognize and systemically attack the recipient tissues as foreign (Sun et al., PLoS One. 7:e52096 (2012)). Since its inception, several variants of HCT to dampen rejection have been developed, including the use of nonmyeloablative strategies. These strategies use altered chemotherapy regimens, often involving lower dosages, so that the recipient receiving the HCT does not receive total ablation of their hematopoietic compartment. The most recent of these strategies, for instance, used a tolerance-promoting facilitating cell (FC)-based HCT to promote tolerance in HLA-mismatched kidney recipients while largely avoiding GHVD (Leventhal et al., Sci Transl Med. 4:124ra28 (2012)).

Besides the risk of GHVD and risk of a secondary HCT procedure, the general limitation to these chimerism-inducing approaches is the need to have the HLA-matched donor available for the collection of marrow. While this is easily accomplished in rodent studies, it is quite demanding in humans. Donor organs should ideally be taken from the donor as soon as possible, which leaves an incredibly short window from which to collect marrow, if at all possible. It is also an expensive and logistically demanding procedure that requires a very patient and operation-specific approach. And, as with regulatory cell approaches, it is not clear how it would be practically applied to those situations where the patient could benefit from or needs therapy immediately for treatment of acute injuries or disease.

Another approach that has been tested for reducing allorejection in vivo is the removal of histocompatibility molecules (Torikai et al. Blood. 122:1341-9 (2013)), which are the major antigenic source of “non-self” recognition in allorejection. This fits with the empirical data that HLA-matched donors and recipients have greatly improved rates of organ survival after transplantation (Opelz et al., Rev Immunogenet. 1:334-42 (1999)). While there have been some positive results with this approach, removal of MHC class I renders cells extremely susceptible to NK cells (Pegram et al., Immunol Cell Biol. 89:216-24 (2011); Raulet et al., Nat Rev Immunol. 6:520-31 (2006); Huntington, Immunol Cell Biol. 92:208-9 (2014)). It also leaves MHC-independent killing pathways among CD8+ T-cells intact (Haspot et al., Am J Transplant. 14:49-58 (2014)) and does not address antigenic differences (minor antigens) outside the MHC/HLA gene family (Roopenian et al., Immunol Rev. 190:86-94 (2002)).

An employment of this approach involved the deletion of all classical HLA class I molecules from pluripotent stem cells, coupled with the introduction of the gene encoding HLA-E, a minimally polymorphic HLA that inhibits NK-cells (Gornalusse et al., Nat Biotechnol. (2017)). While this approach showed short-term resistance to NK and CD8 T-cell attack in partially immune compromised humanized mice, it was not demonstrated that these cells could survive long term in a fully immune-competent host. In another approach ES cells were engineered to express PD-L1 and CTLA4-Ig, which improved survival in allogenic hosts (Rong et al., Cell Stem Cell. 14:121-30 (2014)), but with the severe limitation that CTLA4-Ig can lead to systemic immune suppression. It has not yet been demonstrated that a set of modifications to ES or iPS cells allows them to escape allorejection without the potential for systemic immunosuppression and without the need for immunosuppressive drugs.

It is an object of the present disclosure to mitigate and/or obviate one or more of the above deficiencies.

SUMMARY OF THE DISCLOSURE

In an aspect, a cell genetically modified to comprise at least one mechanism for providing a local immunosuppression at a transplant site when transplanted in an allogeneic host is provided. The genetically modified cell comprises: a set of transgenes, each transgene encoding a gene product that is cytoplasmic, membrane bound, or local acting, and has one or more of the following functions: a) to mitigate antigen presenting cell activation and function; b) to mitigate graft attacking leukocyte activity or cytolytic function; c) to mitigate macrophage cytolytic function and phagocytosis of allograft cells; d) to induce apoptosis in graft attacking leukocytes; e) to mitigate local inflammatory proteins; and f) to protect against leukocyte-mediated apoptosis.

In an embodiment of the cell, the set of transgenes comprises one or more (e.g., one, two, three, four, five, six, seven, or all eight) of the following genes: PD-L1, HLA-G (or the mouse version of HLA-G, H2-M3), Cd47, Cd200, FASLG (or the mouse version of FASLG, FasL), Ccl21 (or the mouse version of Ccl21, Ccl21b), Mfge8, and Serpin B9 (or the mouse version of Serpin B9, Spi6).

In an embodiment of the cell, the set of transgenes comprises two or more of the following genes: PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In an embodiment of the cell, the set of transgenes genes comprises PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) or a gene encoding a biologic that acts as an agonist of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In an embodiment of the cell, the cell further comprises one or more (e.g., one, two, three, four, five, six, seven, eight, nine, ten, or all eleven) of the following transgenes: TGF-β, Cd73, Cd39, Lag3, Il1r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, and IFNγR1 d39 or a gene encoding a biologic that acts as an agonist of TGF-β, Cd73, Cd39, Lag3, Il1r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, or IFNγR1 d39.

In an embodiment of the cell, the TGF-β or the biologic is local acting in the graft environment. In an embodiment of the cell, the TGF-β or the biologic is local acting in the graft environment with minimal systemic effect.

In various embodiments of the cell, the cell is a stem cell, a cell amenable for genome editing, and/or a source of a therapeutic cell type (e.g., a cell that can be differentiated into a therapeutic cell type, or a cell of a desired target tissue). In various embodiments, the cell is an embryonic stem cell, a pluripotent stem cell, an induced pluripotent stem cell, a hematopoietic stem cell, a mesenchymal stem cell, an endothelial stem cell, an epithelial stem cell, an adipose stem or progenitor cell, a germline stem cell, a lung stem or progenitor cells, a mammary stem cell, an olfactory adult stem cell, a hair follicle stem cell, an intestinal stem or progenitor cell, a multipotent stem cell, an amniotic stem cell, a cord blood stem cell, a neural stem or progenitor cell, an adult stem cell, a somatic stem cell, a tissue-specific stem cell, a totipotent stem cell, a fibroblast, a monocytic precursor, a B cell, an exocrine cell, a pancreatic progenitor, an endocrine progenitor, a hepatoblast, a myoblast, a preadipocyte, a hepatocyte, a chondrocyte, a smooth muscle cell, a K562 human erythroid leukemia cell line, a bone cell, a synovial cell, a tendon cell, a ligament cell, a meniscus cell, an adipose cell, a dendritic cell, a natural killer cell, a skeletal muscle cell, a cardiac muscle cell, an erythroid-megakaryocytic cell, an eosinophil, a macrophage, a T cell, an islet beta-cell, a neuron, a cardiomyocyte, a blood cell, an exocrine progenitor, a ductal cell, an acinar cell, an alpha cell, a beta cell, a delta cell, a PP cell, a cholangiocyte, a white or brown adipocyte, a hormone-secreting cell, an epidermal keratinocyte, an epithelial cell, a kidney cell, a germ cell, a skeletal joint synovium cell, a periosteum cell, a perichondrium cell, a cartilage cell, an endothelial cell, a pericardium cell, a meningeal cell, a keratinocyte precursor cell, a keratinocyte stem cell, a pericyte, a glial cell, an ependymal cell, a cell isolated from an amniotic or placental membrane, a serosal cell, a somatic cell, or a cell derived from skin, heart, brain or spinal cord, liver, lung, kidney, pancreas, bladder, bone marrow, spleen, intestine, or stomach.

In an embodiment of the cell, the cell is further genetically modified to comprise at least one (e.g., one, two, three, or more) mechanism for controlling cell proliferation (e.g., to reduce the tumorigenic potential of the modified cell or to reduce proliferation of a modified cell that has become tumorigenic). The genetically modified cell comprises: a genetic modification of one or more (e.g., one, two, three, or more) cell division locus/loci (CDL), the CDL being one or more loci whose transcription product(s) is expressed by dividing cells (e.g., all dividing cells containing one or more of the immunosuppressive transgenes), the genetic modification being one or more of: a) an ablation link (ALINK) system, the ALINK system comprising a DNA sequence encoding a negative selectable marker that is transcriptionally linked to a DNA sequence encoding the CDL; and b) an exogenous activator of regulation of a CDL (EARC) system, the EARC system comprising an inducible activator-based gene expression system that is operably linked to the CDL.

In an embodiment of the cell, the genetic modification of the CDL comprises performing targeted replacement of the CDL with one or more of: a) a DNA vector comprising the ALINK system; b) a DNA vector comprising the EARC system; and c) a DNA vector comprising the ALINK system and the EARC system; wherein the ALINK and/or EARC systems are each operably linked to the CDL.

In various embodiments of the cell, the ALINK genetic modification of the CDL is homozygous, heterozygous, hemizygous or compound heterozygous and/or the EARC genetic modification ensures that functional CDL modification can only be generated through EARC-modified alleles.

In various embodiments of the cell, the CDL is one or more (e.g., one, two, three, or more) of the loci recited in Table 5. In various embodiments, the CDL encodes a gene product that functions in one or more of: cell cycle, DNA replication, RNA transcription, protein translation, and metabolism. In various embodiments, the CDL is one or more of Cdk1/CDK1, Top2A/TOP2A, Cenpa/CENPA, Birc5/BIRC5, and Eef2/EEF2, preferably the CDL is Cdk1 or CDK1. In some embodiments, the CDL is Top2A. In some embodiments, the CDL is Eef2. In various embodiments, the CDL is two or more of Cdk1/CDK1, Top2A/TOP2A, Cenpa/CENPA, Birc5/BIRC5, and Eef2/EEF2, preferably the CDL is Cdk1 and Top2A or Cdk1 and Eef2.

In various embodiments of the cell, the ALINK system comprises a herpes simplex virus-thymidine kinase/ganciclovir system, a cytosine deaminase/5-fluorocytosine system, a carboxyl esterase/irinotecan system or an iCasp9/AP1903 system, preferably the ALINK system is a herpes simplex virus-thymidine kinase/ganciclovir system.

In various embodiments of the cell, the EARC system is a doxycycline inducible “dox-bridge” system, a cumate switch inducible system, an ecdysone inducible system, a radio wave inducible system, or a ligand-reversible dimerization system, preferably the EARC system is a dox-bridge system.

In an aspect, a method for providing a local immunosuppression at a transplant site in an allogeneic host is provided. The method comprises providing a cell; and expressing in the cell a set of transgenes, each transgene encoding a gene product that is cytoplasmic, membrane bound, or local acting, and has one or more of the following functions: a) to mitigate antigen presenting cell activation and function; b) to mitigate graft attacking leukocyte activity or cytolytic function; c) to mitigate macrophage cytolytic function and phagocytosis of allograft cells; d) to induce apoptosis in graft attacking leukocytes; e) to mitigate local inflammatory proteins; and f) to protect against leukocyte-mediated apoptosis.

In an embodiment of the method, the set of transgenes comprises one or more (e.g., one, two, three, four, five, six, seven, or all eight) of the following genes: PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6) or a gene encoding a biologic that acts as an agonist of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, or Serpin B9 (Spi6).

In an embodiment of the method, the set of transgenes comprises two or more of the following genes: PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In an embodiment of the method, the set of transgenes genes comprises PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6) or a gene encoding a biologic that acts as an agonist of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6).

In an embodiment of the method, the method further comprises expressing one or more (e.g., one, two, three, four, five, six, seven, eight, nine, ten, or all eleven) of the following transgenes: TGF-β, Cd73, Cd39, Lag3, Il1r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, and IFNγR1 d39 or a gene encoding a biologic that acts as an agonist of TGF-β, Cd73, Cd39, Lag3, 111r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, or IFNγR1 d39. In an embodiment, the TGF-β or the biologic is local acting in the graft environment. In an embodiment of the cell, the TGF-β or the biologic is local acting in the graft environment with minimal systemic effect.

In various embodiments of the method, the cell is a stem cell, a cell amenable to genome editing, and/or a source of a therapeutic cell type (e.g., a cell that can be differentiated into a therapeutic cell type, or a cell of a desired target tissue). In various embodiments, the cell is an embryonic stem cell, a pluripotent stem cell, an induced pluripotent stem cell, a hematopoietic stem cell, a mesenchymal stem cell, an endothelial stem cell, an epithelial stem cell, an adipose stem or progenitor cell, a germline stem cell, a lung stem or progenitor cells, a mammary stem cell, an olfactory adult stem cell, a hair follicle stem cell, an intestinal stem or progenitor cell, a multipotent stem cell, an amniotic stem cell, a cord blood stem cell, a neural stem or progenitor cell, an adult stem cell, a somatic stem cell, a tissue-specific stem cell, a totipotent stem cell, a fibroblast, a monocytic precursor, a B cell, an exocrine cell, a pancreatic progenitor, an endocrine progenitor, a hepatoblast, a myoblast, a preadipocyte, a hepatocyte, a chondrocyte, a smooth muscle cell, a K562 human erythroid leukemia cell line, a bone cell, a synovial cell, a tendon cell, a ligament cell, a meniscus cell, an adipose cell, a dendritic cell, a natural killer cell, a skeletal muscle cell, a cardiac muscle cell, an erythroid-megakaryocytic cell, an eosinophil, a macrophage, a T cell, an islet beta-cell, a neuron, a cardiomyocyte, a blood cell, an exocrine progenitor, a ductal cell, an acinar cell, an alpha cell, a beta cell, a delta cell, a PP cell, a cholangiocyte, a white or brown adipocyte, a hormone-secreting cell, an epidermal keratinocyte, an epithelial cell, a kidney cell, a germ cell, a skeletal joint synovium cell, a periosteum cell, a perichondrium cell, a cartilage cell, an endothelial cell, a pericardium cell, a meningeal cell, a keratinocyte precursor cell, a keratinocyte stem cell, a pericyte, a glial cell, an ependymal cell, a cell isolated from an amniotic or placental membrane, a serosal cell, a somatic cell, or a cell derived from skin, heart, brain or spinal cord, liver, lung, kidney, pancreas, bladder, bone marrow, spleen, intestine, or stomach.

In various embodiments of the method, the cell is provided (e.g., injected) to or near the transplant site. In various embodiments of the method, the cell is provided (e.g., injected or implanted) into the transplant (e.g., injected or implanted into the tissue or organ transplant before, during, or after transplantation). In some embodiments, the cell in which the transgenes are expressed is a cell of the transplant (e.g., a cell of the tissue or organ that is being transplanted is modified to express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)).

In an aspect, a method of controlling proliferation of a cell at a transplant site in an allogeneic host is provided (e.g., to reduce the tumorigenic potential of the cell at the transplant site or to reduce proliferation of the cell that has become tumorigenic at the transplant site). The method comprises: a) genetically modifying in the cell one or more (e.g., one, two, three, or more) cell division locus/loci (CDL), the CDL being one or more loci whose transcription product(s) is expressed by dividing cells (e.g., all dividing cells containing one or more of the immunosuppressive transgenes), the genetic modification of the CDL comprising one or more of: i) an ablation link (ALINK) system, the ALINK system comprising a DNA sequence encoding a negative selectable marker that is transcriptionally linked to a DNA sequence encoding the CDL; and i) an inducible exogenous activator of regulation of a CDL (EARC) system, the EARC system comprising an inducible activator-based gene expression system that is operably linked to the CDL; b) genetically modifying the cell to comprise at least one mechanism for providing a local immunosuppression at a transplant site; c) transplanting the cell or a population of the cells at a transplantation site in an allogeneic host; and d) permitting proliferation of the genetically modified cell comprising the ALINK system by maintaining the genetically modified cell comprising the ALINK system in the absence of an inducer of the negative selectable marker or ablating and/or inhibiting proliferation of the genetically modified cell comprising the ALINK system by exposing the cell comprising the ALINK system to the inducer of the negative selectable marker; and/or permitting proliferation of the genetically modified cell comprising the EARC system by exposing the genetically modified cell comprising the EARC system to an inducer of the inducible activator-based gene expression system or preventing or inhibiting proliferation of the genetically modified cell comprising the EARC system by maintaining the cell comprising the EARC system in the absence of the inducer of the inducible activator-based gene expression system.

In an embodiment of the method, the genetic modification of the CDL comprises performing targeted replacement of the CDL with one or more of: a) a DNA vector comprising the ALINK system; b) a DNA vector comprising the EARC system; and c) a DNA vector comprising the ALINK system and the EARC system; wherein the ALINK and/or EARC systems are each operably linked to the CDL.

In various embodiments of the method the ALINK genetic modification of the CDL is homozygous, heterozygous, hemizygous or compound heterozygous and/or the EARC genetic modification ensures that functional CDL modification can only be generated through EARC-modified alleles.

In various embodiments of the method, the CDL is one or more (e.g., one, two, three, or more) of the loci recited in Table 5. In various embodiments, the CDL encodes a gene product whose function is involved with one or more of: cell cycle, DNA replication, RNA transcription, protein translation, and metabolism. In various embodiments, the CDL is one or more of Cdk1/CDK1, Top2A/TOP2A, Cenpa/CENPA, Birc5/BIRC5, and Eef2/EEF2, preferably the CDL is Cdk1 or CDK1. In some embodiments, the CDL is Top2A. In some embodiments, the CDL is Eef2. In various embodiments, the CDL is two or more of Cdk1/CDK1, Top2A/TOP2A, Cenpa/CENPA, Birc5/BIRC5, and Eef2/EEF2, preferably the CDL is Cdk1 and Top2A or Cdk1 and Eef2.

In various embodiments of the method, the ALINK system comprises a herpes simplex virus-thymidine kinase/ganciclovir system, a cytosine deaminase/5-fluorocytosine system, a carboxyl esterase/irinotecan system or an iCasp9/AP1903 system, preferably the ALINK system is a herpes simplex virus-thymidine kinase/ganciclovir system.

In various embodiments of the method, the EARC system is a doxycycline inducible “dox-bridge” system, a cumate switch inducible system, an ecdysone inducible system, a radio wave inducible system, or a ligand-reversible dimerization system, preferably the EARC system is a dox-bridge system.

In an embodiment of the method, the genetically modified cell comprises: a set of transgenes, each transgene encoding a gene product that is cytoplasmic, membrane bound, or local acting and has one or more of the following functions: a) to mitigate antigen presenting cell activation and function; b) to mitigate graft attacking leukocyte activity or cytolytic function; c) to mitigate macrophage cytolytic function and phagocytosis of allograft cells; d) to induce apoptosis in graft attacking leukocytes; e) to mitigate local inflammatory proteins; and f) to protect against leukocyte-mediated apoptosis.

In an embodiment of the method, the set of transgenes comprises one or more (e.g., one, two, three, four, five, six, seven, or all eight) of the following genes: PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) or a gene encoding a biologic that acts as an agonist of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, or Serpin B9 (Spi6).

In an embodiment of the method, the set of transgenes comprises two or more of the following genes: PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In an embodiment of the method, the set of transgenes genes comprises PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) or a gene encoding a biologic that acts a as an agonist of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In an embodiment of the method, the cell further comprises one or more (e.g., one, two, three, four, five, six, seven, eight, nine, ten, or all eleven) of the following transgenes: TGF-β, Cd73, Cd39, Lag3, Il1r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, and IFNγR1 d39 or a gene encoding a biologic that acts as an agonist of TGF-β, Cd73, Cd39, Lag3,111r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, or IFNγR1 d39.

In an embodiment of the method, the TGF-β or the biologic is local acting in the graft environment. In an embodiment, the TGF-β or the biologic is local acting in the graft environment with minimal systemic effect

In various embodiments of the method, the cell is a stem cell, a cell amenable to genome editing, and/or a source of therapeutic cell type (e.g., a cell that can be differentiated into a therapeutic cell type, or a cell of a desired target tissue). In various embodiments, the cell is an embryonic stem cell, a pluripotent stem cell, an induced pluripotent stem cell, a hematopoietic stem cell, a mesenchymal stem cell, an endothelial stem cell, an epithelial stem cell, an adipose stem or progenitor cell, a germline stem cell, a lung stem or progenitor cells, a mammary stem cell, an olfactory adult stem cell, a hair follicle stem cell, an intestinal stem or progenitor cell, a multipotent stem cell, an amniotic stem cell, a cord blood stem cell, a neural stem or progenitor cell, an adult stem cell, a somatic stem cell, a tissue-specific stem cell, a totipotent stem cell, a fibroblast, a monocytic precursor, a B cell, an exocrine cell, a pancreatic progenitor, an endocrine progenitor, a hepatoblast, a myoblast, a preadipocyte, a hepatocyte, a chondrocyte, a smooth muscle cell, a K562 human erythroid leukemia cell line, a bone cell, a synovial cell, a tendon cell, a ligament cell, a meniscus cell, an adipose cell, a dendritic cell, a natural killer cell, a skeletal muscle cell, a cardiac muscle cell, an erythroid-megakaryocytic cell, an eosinophil, a macrophage, a T cell, an islet beta-cell, a neuron, a cardiomyocyte, a blood cell, an exocrine progenitor, a ductal cell, an acinar cell, an alpha cell, a beta cell, a delta cell, a PP cell, a cholangiocyte, a white or brown adipocyte, a hormone-secreting cell, an epidermal keratinocyte, an epithelial cell, a kidney cell, a germ cell, a skeletal joint synovium cell, a periosteum cell, a perichondrium cell, a cartilage cell, an endothelial cell, a pericardium cell, a meningeal cell, a keratinocyte precursor cell, a keratinocyte stem cell, a pericyte, a glial cell, an ependymal cell, a cell isolated from an amniotic or placental membrane, a serosal cell, a somatic cell, or a cell derived from skin, heart, brain or spinal cord, liver, lung, kidney, pancreas, bladder, bone marrow, spleen, intestine, or stomach.

In various embodiments of the method, the allogeneic host is a mammal. In various embodiments of the method, the allogeneic host is a mouse or a human.

In various embodiments of the method, the host has a degenerative disease or condition that can be treated with cell therapy. In various embodiments, the disease or condition is blindness, arthritis (e.g., osteoarthritis or rheumatoid arthritis), ischemia, diabetes (e.g., Type 1 or Type 2 diabetes), multiple sclerosis, spinal cord injury, stroke, cancer, a lung disease, a blood disease, a neurological disease, such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and ALS, an enzyme or hormone deficiency, a metabolic disorder (e.g., a lysosomal storage disorder, Galactosemia, Maple syrup urine disease, Phenylketonuria, a glycogen storage disease, a mitochondrial disorder, Friedrich's ataxia, a peroxisomal disorder, a metal metabolism disorder, or an organic academia), an autoimmune disease (e.g., Psoriasis, Systemic Lupus Erythematosus, Grave's disease, Inflammatory Bowel Disease, Addison's Diseases, Sjogren's Syndrome, Hashimoto's Thyroiditis, Vasculitis, Autoimmune Hepatitis, Alopecia Areata, Autoimmune pancreatitis, Crohn's Disease, Ulcerative colitis, Dermatomyositis), age-related macular degeneration, retinal dystrophy, an infectious disease, hemophilia, a degenerative disease (e.g., Charcot-Marie-Tooth disease, chronic obstructive pulmonary disease, chronic traumatic encephalopathy, Creutzfeldt-Jakob disease, Cystic Fibrosis, Cytochrome C Oxidase deficiency, Ehlers-Danlos syndrome, essential tremor, Fribrodisplasia Ossificans Progressiva, infantile neuroaxonal dystrophy, keratoconus, keratoglobus, muscular dystrophy, neuronal ceroid lipofuscinosis, a prior disease, progressive supranuclear palsy, sandhoff disease, spinal muscular atrophy, retinitis pigmentosa), or an age-related disease (e.g., atherosclerosis, cardiovascular disease (e.g., angina, myocardial infarction), cataracts, osteoporosis, or hypertension).

In some embodiments of any of the foregoing aspects, one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) is expressed at a level that is greater than the expression level of the corresponding endogenous gene in a wild-type stem cell (e.g., a wild-type ES cell from the same species, e.g., the expression level of the cloaking transgene is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100, 500, 1,000-fold or more higher in cloaked cells compared to expression of the endogenous gene in unmodified wild-type ES cells from the same species). In some embodiments, all 8 of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) are expressed at a level that is greater (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or 100-fold higher or more) than the expression level of the endogenous gene in a wild-type stem cell (e.g., an embryonic stem cell from the same species as the cloaked cell). In some embodiments, one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) is expressed at a level that is in the top 5% of gene expression for all genes in the ES cell genome. In some embodiments, one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) is expressed at a level that is in the top 1% of gene expression for all genes in the ES cell genome. In some embodiments, all of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) are expressed at a level that is in the top 5% of gene expression for all genes in the ES cell genome.

In some embodiments of any of the foregoing aspects, the PD-L1 transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 12.

In some embodiments of any of the foregoing aspects, the HLA-G (H2-M3) transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 16 or SEQ ID NO: 15.

In some embodiments of any of the foregoing aspects, the Cd47 transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 4.

In some embodiments of any of the foregoing aspects, the CD200 transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 5 or SEQ ID NO: 6.

In some embodiments of any of the foregoing aspects, the FASLG (FasL) transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 9.

In some embodiments of any of the foregoing aspects, the Ccl21 (Ccl21b) transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 2 or SEQ ID NO: 1.

In some embodiments of any of the foregoing aspects, the Mfge8 transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 13 or SEQ ID NO: 14.

In some embodiments of any of the foregoing aspects, the Serpin B9 (Spi6) transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 7.

In some embodiments of any of the foregoing aspects, the IFNγR1 d39 transgene encodes a protein having at least 85% identity (e.g., 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence identity or more) to the amino acid sequence of SEQ ID NO: 17.

In some embodiments of any of the foregoing aspects, the one or more transgenes is operably linked to a constitutive promoter. In some embodiments, the constitutive promoter is selected from the group consisting of the CAG promoter, the cytomegalovirus (CMV) promoter, the EF1α promoter, the PGK promoter, adenovirus late promoter, vaccinia virus 7.5K promoter, SV40 promoter, tk promoter of HSV, mouse mammary tumor virus (MMTV) promoter, LTR promoter of HIV, promoter of moloney virus, Epstein barr virus (EBV) promoter, and the Rous sarcoma virus (RSV) promoter.

In some embodiments of any of the foregoing aspects, the cell further comprises (e.g., the cell is further modified to include) a transgene encoding a therapeutic agent. In some embodiments, the therapeutic agent is a protein or antibody. In some embodiments, the antibody is an inhibitory antibody or agonist antibody. In some embodiments, the therapeutic agent is an agent listed in Table 2. In some embodiments, the therapeutic agent is the wild-type version of a gene that is mutated in the subject (e.g., the wild-type version of the mutated gene that is associated with the disease or condition in the subject, e.g., a genetic mutation that is associated with cancer, an enzyme or hormone deficiency, a metabolic disorder, or a degenerative disease). In some embodiments, the therapeutic agent is expressed using an inducible expression system selected from the group consisting of a tetracycline response element, a light inducible system, a radiogenetic system, a cumate switch inducible system, an ecdysone inducible system, a destabilization domain system, or a ligand-reversible dimerization system. In some embodiments, the therapeutic agent is expressed using a constitutive promoter selected from the group consisting of the CAG promoter, the cytomegalovirus (CMV) promoter, the EF1α promoter, the PGK promoter, adenovirus late promoter, vaccinia virus 7.5K promoter, SV40 promoter, tk promoter of HSV, mouse mammary tumor virus (MMTV) promoter, LTR promoter of HIV, promoter of moloney virus, Epstein barr virus (EBV) promoter, and the Rous sarcoma virus (RSV) promoter.

In another aspect, there is provided a population of genetically modified cells according to any of the cells described above.

In an aspect, a method for providing a local immunosuppression at a transplant site in an allogeneic host is provided. The method comprises transplanting a genetically modified cell as described above or a population of genetically modified cells as described above at a transplantation site in an allogeneic host.

In another aspect, the invention features a composition containing a cell of the invention. In some embodiments, the composition further includes a pharmaceutically acceptable excipient.

In another aspect, featured is a kit including a cell of the invention or a pharmaceutical composition of the invention.

In another aspect, featured is a method of treating a disease or condition in a subject in need thereof by administering to the subject the cell of the invention or a composition of the invention. In some embodiments, the disease or condition is blindness, arthritis (e.g., osteoarthritis or rheumatoid arthritis), ischemia, diabetes (e.g., Type 1 or Type 2 diabetes), multiple sclerosis, spinal cord injury, stroke, cancer, a lung disease, a blood disease, a neurological disease, such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and ALS, an enzyme or hormone deficiency, a metabolic disorder (e.g., a lysosomal storage disorder, Galactosemia, Maple syrup urine disease, Phenylketonuria, a glycogen storage disease, a mitochondrial disorder, Friedrich's ataxia, a peroxisomal disorder, a metal metabolism disorder, or an organic academia), an autoimmune disease (e.g., Psoriasis, Systemic Lupus Erythematosus, Grave's disease, Inflammatory Bowel Disease, Addison's Diseases, Sjogren's Syndrome, Hashimoto's Thyroiditis, Vasculitis, Autoimmune Hepatitis, Alopecia Areata, Autoimmune pancreatitis, Crohn's Disease, Ulcerative colitis, Dermatomyositis), age-related macular degeneration, retinal dystrophy, an infectious disease, hemophilia, a degenerative disease (e.g., Charcot-Marie-Tooth disease, chronic obstructive pulmonary disease, chronic traumatic encephalopathy, Creutzfeldt-Jakob disease, Cystic Fibrosis, Cytochrome C Oxidase deficiency, Ehlers-Danlos syndrome, essential tremor, Fribrodisplasia Ossificans Progressiva, infantile neuroaxonal dystrophy, keratoconus, keratoglobus, muscular dystrophy, neuronal ceroid lipofuscinosis, a prior disease, progressive supranuclear palsy, sandhoff disease, spinal muscular atrophy, retinitis pigmentosa), or an age-related disease (e.g., atherosclerosis, cardiovascular disease (e.g., angina, myocardial infarction), cataracts, osteoporosis, or hypertension), or a disease or condition listed in Table 2 and/or the cell further includes a transgene encoding a corresponding therapeutic agent listed in Table 2 or the wild-type version of a gene that is mutated in the subject (e.g., the wild-type version of the mutated gene that is associated with the disease or condition in the subject, e.g., a genetic mutation associated with cancer, an enzyme or hormone deficiency, a metabolic disorder, or a degenerative disease). In some embodiments, the disease or condition is age-related macular degeneration (e.g., wet AMD) or retinal dystrophy and the therapeutic agent is a VEGF inhibitor (e.g., a soluble form of a VEGF receptors (e.g., soluble VEGFR-1 or NRP-1), platelet factor-4, prolactin, SPARC, a VEGF inhibitory antibody (e.g., bevacizumab or ranibizumab), or a soluble decoy receptor described in Holash et al., Proc Natl Acad Sci U.S.A. 99:11383-11398, 2002, e.g., VEGF-Trap_parental, VEGF-Trap_ΔB1, VEGF-Trap_ΔB2, VEGF-Trap_R1R2, e.g., aflibercept). In some embodiments, the disease or condition is osteoarthritis or rheumatoid arthritis and the therapeutic agent is an anti-inflammatory biologic (e.g. a TNFα inhibitor (e.g., adalimumab, etanercept, infliximab, golimumab, or certolizumab), an interleukin-6 (IL6) receptor inhibitor (e.g., tocilizumab), an IL1 receptor inhibitor (e.g., anakinra), or another agent used to treat rheumatoid arthritis (e.g., abatacept, rituximab)). In some embodiments, the disease or condition is diabetes (e.g., Type 1 diabetes or Type 2 diabetes) and the therapeutic agent is insulin. In some embodiments, the disease or condition is hemophilia and the therapeutic agent is Factor VIII. In some embodiments, the disease or condition is a metabolic deficiency and the therapeutic agent is a transgene having the nucleic acid sequence of the wild-type version of the gene that is mutated in the subject or a transgene encoding an enzyme that is deficient in the subject.

In some embodiments of any of the foregoing aspects, the cells are differentiated into a lineage restricted cell type prior to administration to the subject. In some embodiments, the disease or condition is myocardial infarction and the cells are differentiated into cardiac muscle cells. In some embodiments, the disease or condition is blindness and the cells are differentiated into photoreceptor cells. In some embodiments, the disease or condition is spinal cord injury, Parkinson's disease, Huntington's disease, or Alzheimer's disease and the cells are dissociated into neurons. In some embodiments, the disease or condition is multiple sclerosis and the cells are differentiated into glial cells.

In some embodiments of any of the foregoing aspects, the cells are administered (e.g., injected or implanted) locally to the tissue or body site in need of cells or the therapeutic agent.

In some embodiments of any of the foregoing aspects, the cells are administered intravenously, subcutaneously, intramuscularly, percutaneously, intradermally, parenterally, intraarterially, intravascularly, or by perfusion.

In some embodiments of any of the foregoing aspects, the cells are administered by subcutaneous injection to produce a cloaked subcutaneous tissue.

In some embodiments of any of the foregoing aspects, the cells are administered as a tissue. In some embodiments, the tissue is administered with a gel, biocompatible matrix, or cellular scaffold.

In some embodiments of any of the foregoing aspects, the cells are administered in an amount of 25,000 to 5,000,000,000 cells (e.g., 2.5×10⁴, 5×10⁴, 7.5×10⁴, 1×10⁵, 2×10⁵, 3×10⁵, 4×10⁵, 6×10⁵, 6×10⁵, 7×10⁵, 8×10⁵, 9×10⁵, 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, 3×10⁹, 4×10⁹, or 5×10⁹cells).

In some embodiments of any of the foregoing aspects, the cells are administered in an amount of 800,000,000 to 100,000,000,000 cells (e.g., 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹, 4×10⁹, 5×10⁹, 6×10⁹, 7×10⁹, 8×10⁹, 9×10⁹, 1×10¹⁰, 2×10¹⁰, 3×10¹⁰, 4×10¹⁰, 5×10¹⁰, 6×10¹⁰, 7×10¹⁰, 8×10¹⁰, 9×10¹⁰, or 1×10¹¹, cells).

In some embodiments of any of the foregoing methods, the method further includes administering an additional therapeutic agent. In some embodiments, the additional therapeutic agent is administered prior to administration of the cells. In some embodiments, the additional therapeutic agent is administered after administration of the cells. In some embodiments, the additional therapeutic agent is administered concurrently with administration of the cells. In some embodiments, the additional therapeutic agent is an immunosuppressive agent, a disease-modifying anti-rheumatic drug (DMARD), a biologic response modifier (a type of DMARD), a corticosteroid, or a nonsteroidal anti-inflammatory medication (NSAID), prednisone, prednisolone, methylprednisolone, methotrexate, hydroxychloroquine, sulfasalazine, leflunomide, cyclophosphamide, azathioprine, tofacitinib, adalimumab, abatacept, anakinra, kineret, certolizumab, etanercept, golimumab, infliximab, rituximab or tocilizumab, 6-mercaptopurine, 6-thioguanine, abatacept, adalimumab, alemtuzumab, an aminosalicylate, an antibiotic, an anti-histamine, Anti-TNFα, azathioprine, belimumab, beta interferon, a calcineurin inhibitor, certolizumab, a corticosteroid, cromolyn, cyclosporin A, cyclosporine, dimethyl fumarate, etanercept, fingolimod, fumaric acid esters, glatiramer acetate, golimumab, hydroxyurea, IFNγ, IL-11, leflunomide, leukotriene receptor antagonist, long-acting beta2 agonist, mitoxantrone, mycophenolate mofetil, natalizumab, ocrelizumab, pimecrolimus, a probiotic, a retinoid, salicylic acid, short-acting beta2 agonist, sulfasalazine, tacrolimus, teriflunomide, theophylline, tocilizumab, ustekinumab, or vedolizumab, bevacuzimab, ranibizumab, or aflibercept), photodynamic therapy, photocoagulation, carbidopa-levodopa, a dopamine agonist, an MAO-B inhibitor, a catechol-O-methyltransferase inhibitor, an anticholinergic, amantadine, deep brain stimulation, an anticoagulant, an anti-platelet agent, an angiotensin-converting enzyme inhibitor, an angiotensin II receptor blocker, an angiotensin receptor neprilysin inhibitor, a beta blocker, a combined alpha and beta blocker, a calcium channel blocker, a cholesterol lowering medication, a nicotinic acid, a cholesterol absorption inhibitor, a digitalis preparation, a diuretic, a vasodilator, a dual anti-platelet therapy, a cardiac procedure, an antiviral compound, a nucleoside-analog reverse transcriptase inhibitor (NRTI), a non-nucleoside reverse transcriptase inhibitor (NNRTI), a protease inhibitor, an antibacterial compound, an antifungal compound, an antiparasitic compound, insulin, a sulfonylurea, a biguanide, a meglitinide, a thiazolidinedione, a DPP-4 inhibitor, an SGLT2 inhibitor, an alpha-glucosidase inhibitor, a bile acid sequestrant, aspirin, a dietary regimen, a clotting factor, desmopressin, a clot-preserving medication, a fibrin sealant, physical therapy, a coenzyme, a bone marrow transplant, an organ transplant, hemodialysis, hemofiltration, exchange transfusion, peritoneal dialysis, medium-chain triacylglycerols, miglustat, enzyme supplementation therapy, a checkpoint inhibitor, a chemotherapeutic drug, a biologic drug, radiation therapy, cryotherapy, hyperthermia, surgical excision or tumor tissue, or an anti-cancer vaccine.

In some embodiments of any of the foregoing methods, the method further comprises controlling proliferation of the cell. In some embodiments, the cell comprises an ALINK system, and the method of controlling proliferation comprises: i) permitting proliferation of the cell comprising the ALINK system by maintaining the cell comprising the ALINK system in the absence of an inducer of the negative selectable marker; or ii) ablating or inhibiting proliferation of the cell comprising the ALINK system by exposing the cell comprising the ALINK system to the inducer of the negative selectable marker. In some embodiments, the cell comprises an EARC system, and the method of controlling cell proliferation comprises: i) permitting proliferation of the cell comprising the EARC system by exposing the cell comprising the EARC system to an inducer of the inducible activator-based gene expression system; or ii) preventing or inhibiting proliferation of the cell comprising the EARC system by maintaining the cell comprising the EARC system in the absence of the inducer of the inducible activator-based gene expression system.

In some embodiments of any of the foregoing methods, the cell is removed after completion of the therapy. Removal of the cell(s) can be by surgery (e.g., to remove transplanted tissue or organs, or to remove cloaked subcutaneous tissue) or by the use of the ALINK and/or EARC systems. In some embodiments, one or more (e.g., one, two, three, four, or more) ALINK and/or EARC systems are used to eliminate all of the cloaked cells.

In another aspect, the invention provides a cell of the invention or a composition of the invention for use in treating a disease or condition in a subject in need thereof. In some embodiments, disease or condition is blindness, arthritis (e.g., osteoarthritis or rheumatoid arthritis), ischemia, diabetes (e.g., Type 1 or Type 2 diabetes), multiple sclerosis, spinal cord injury, stroke, cancer, a lung disease, a blood disease, a neurological disease, such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and ALS, an enzyme or hormone deficiency, a metabolic disorder (e.g., a lysosomal storage disorder, Galactosemia, Maple syrup urine disease, Phenylketonuria, a glycogen storage disease, a mitochondrial disorder, Friedrich's ataxia, a peroxisomal disorder, a metal metabolism disorder, or an organic academia), an autoimmune disease (e.g., Psoriasis, Systemic Lupus Erythematosus, Grave's disease, Inflammatory Bowel Disease, Addison's Diseases, Sjogren's Syndrome, Hashimoto's Thyroiditis, Vasculitis, Autoimmune Hepatitis, Alopecia Areata, Autoimmune pancreatitis, Crohn's Disease, Ulcerative colitis, Dermatomyositis), age-related macular degeneration, retinal dystrophy, an infectious disease, hemophilia, a degenerative disease (e.g., Charcot-Marie-Tooth disease, chronic obstructive pulmonary disease, chronic traumatic encephalopathy, Creutzfeldt-Jakob disease, Cystic Fibrosis, Cytochrome C Oxidase deficiency, Ehlers-Danlos syndrome, essential tremor, Fribrodisplasia Ossificans Progressiva, infantile neuroaxonal dystrophy, keratoconus, keratoglobus, muscular dystrophy, neuronal ceroid lipofuscinosis, a prior disease, progressive supranuclear palsy, sandhoff disease, spinal muscular atrophy, retinitis pigmentosa), or an age-related disease (e.g., atherosclerosis, cardiovascular disease (e.g., angina, myocardial infarction), cataracts, osteoporosis, or hypertension), or a disease or condition listed in Table 2.

In another aspect, the invention provides a cell of the invention or a composition of the invention for use in providing a local immunosuppression at a transplant site in an allogeneic host.

In some embodiments of any of the foregoing aspects, the cell is comprises two of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) (e.g., PD-L1 and HLA-G (H2-M3); PD-L1 and Cd47; PD-L1 and Cd200; PD-L1 and FASLG (FasL); PD-L1 and Ccl21 (Ccl21b); PD-L1 and Mfge8; PD-L1 and Serpin B9 (Spi6); HLA-G (H2-M3) and Cd47; HLA-G (H2-M3) and Cd200; HLA-G (H2-M3) and FASLG (FasL); HLA-G (H2-M3) and Ccl21 (Ccl21b); HLA-G (H2-M3) and Mfge8; HLA-G (H2-M3) and Serpin B9 (Spi6); Cd47 and Cd200; Cd47 and FASLG (FasL); Cd47 and Ccl21 (Ccl21b); Cd47 and Mfge8; Cd47 and Serpin B9 (Spi6); Cd200 and FASLG (FasL); Cd200 and Ccl21 (Ccl21b); Cd200 and Mfge8; Cd200 and Serpin B9 (Spi6); FASLG (FasL) and Ccl21 (Ccl21b); FASLG (FasL) and Mfge8; FASLG (FasL) and Serpin B9 (Spi6); Ccl21 (Ccl21b) and Mfge8; Ccl21 (Ccl21b) and Serpin B9 (Spi6); or Mfge8 and Serpin B9 (Spi6)).

In some embodiments of any of the foregoing aspects, the cell comprises three of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) (e.g., PD-L1, HLA-G (H2-M3), and Cd47; PD-L1, HLA-G (H2-M3), and Cd200; PD-L1, HLA-G (H2-M3), and FASLG (FasL); PD-L1, HLA-G (H2-M3), and Ccl21 (Ccl21b); PD-L1, HLA-G (H2-M3), and Mfge8; PD-L1, HLA-G (H2-M3), and Serpin B9 (Spi6); PD-L1, Cd47, and Cd200; PD-L1, Cd47, and FASLG (FasL); PD-L1, Cd47, and Ccl21 (Ccl21b); PD-L1, Cd47, and Mfge8; PD-L1, Cd47, and Serpin B9; PD-L1, Cd200, and FASLG (FasL); PD-L1, Cd200, and Ccl21 (Ccl21b); PD-L1, Cd200, and Mfge8; PD-L1, Cd200, and Serpin B9 (Spi6); PD-L1, FASLG (FasL), and Ccl21 (Ccl21b); PD-L1, FASLG (FasL), and Mfge8; PD-L1, FASLG (FasL), and Serpin B9 (Spi6); PD-L1, Ccl21 (Ccl21b), and Mfge8; PD-L1, Ccl21 (Ccl21b), and Serpin B9 (Spi6); PD-L1, Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, and Cd200; HLA-G (H2-M3), Cd47, and FASLG (FasL); HLA-G (H2-M3), Cd47, and Ccl21 (Ccl21 b); HLA-G (H2-M3), Cd47, and Mfge8; HLA-G (H2-M3), Cd47, and Serpin B9; HLA-G (H2-M3), Cd200, and FASLG (FasL); HLA-G (H2-M3), Cd200, and Ccl21 (Ccl21b); HLA-G (H2-M3), Cd200, and Mfge8; HLA-G (H2-M3), Cd200, and Serpin B9; HLA-G (H2-M3), FASLG (FasL), and Ccl21 (Ccl21b); HLA-G (H2-M3), FASLG (FasL), and Mfge8; HLA-G (H2-M3), FASLG (FasL), and Serpin B9 (Spi6); HLA-G (H2-M3), Ccl21 (Ccl21b), and Mfge8; HLA-G (H2-M3), Ccl21 (Ccl21b), and Serpin B9 (Spi6); HLA-G (H2-M3), Mfge8, and Serpin B9 (Spi6); Cd47, Cd200, and FASLG (FasL); Cd47, Cd200, and Ccl21 (Ccl21b); Cd47, Cd200, and Mfge8; Cd47, Cd200, and Serpin B9 (Spi6); Cd47, FASLG (FasL), and Ccl21 (Ccl21b); Cd47, FASLG (FasL), and Mfge8; Cd47, FASLG (FasL), and Serpin B9 (Spi6); Cd47, Ccl21 (Ccl21b), and Mfge8; Cd47, Ccl21 (Ccl21b), and Serpin B9 (Spi6); Cd47, Mfge8, and Serpin B9 (Spi6); Cd200, FASLG (FasL), and Ccl21 (Ccl21b); Cd200, FASLG (FasL), and Mfge8; Cd200, FASLG (FasL), and Serpin B9 (Spi6); Cd200, Ccl21 (Ccl21b), and Mfge8; Cd200, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); Cd200, Mfge8, and Serpin B9 (Spi6); FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)).

In some embodiments of any of the foregoing aspects, the cell comprises four of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6) (e.g., PD-L1, HLA-G (H2-M3), Cd47, and Cd200; PD-L1, HLA-G (H2-M3), Cd47, and FASLG (FasL); PD-L1, HLA-G (H2-M3), Cd47, and Ccl21 (Ccl21 b); PD-L1, HLA-G (H2-M3), Cd47, and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, and FASLG (FasL); PD-L1, HLA-G (H2-M3), Cd200, and Ccl21 (Ccl21b); PD-L1, HLA-G (H2-M3), Cd200, and Mfge8; PD-L1, HLA-G (H2-M3), Cd200, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), FASLG (FasL), and Ccl21 (Ccl21 b); PD-L1, HLA-G (H2-M3), FASLG (FasL), and Mfge8; PD-L1, HLA-G (H2-M3), FASLG (FasL), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Ccl21(Ccl21b), and Mfge8; PD-L1, HLA-G (H2-M3), Ccl21(Ccl21b), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, and FASLG (FasL); PD-L1, Cd47, Cd200, and Ccl21 (Ccl21 b); PD-L1, Cd47, Cd200, and Mfge8; PD-L1, Cd47, Cd200, and Serpin B9 (Spi6); PD-L1, Cd47, FASLG (FasL), and Ccl21 (Ccl21b); PD-L1, Cd47, FASLG (FasL), and Mfge8; PD-L1, Cd47, FASLG (FasL), and Serpin B9 (Spi6); PD-L1, Cd47, Ccl21 (Ccl21b), and Mfge8; PD-L1, Cd47, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); PD-L1, Cd47, Mfge8, and Serpin B9 (Spi6); PD-L1, Cd200, FASLG (FasL), and Ccl21 (Ccl21 b); PD-L1, Cd200, FASLG (FasL), and Mfge8; PD-L1, Cd200, FASLG (FasL), and Serpin B9 (Spi6); PD-L1, Cd200, Ccl21 (Ccl21 b), and Mfge8; PD-L1, Cd200, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); PD-L1, Cd200, Mfge8, and Serpin B9 (Spi6); PD-L1, FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; PD-L1, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); PD-L1, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Cd200, and FASLG (FasL); HLA-G (H2-M3), Cd47, Cd200, and Ccl21 (Ccl21 b); HLA-G (H2-M3), Cd47, Cd200, and Mfge8; HLA-G (H2-M3), Cd47, Cd200, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, FASLG (FasL), and Ccl21 (Ccl21b); HLA-G (H2-M3), Cd47, FASLG (FasL), and Mfge8; HLA-G (H2-M3), Cd47, FASLG (FasL), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Ccl21 (Ccl21 b), and Mfge8; HLA-G (H2-M3), Cd47, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd200, FASLG (FasL), and Ccl21 (Ccl21 b); HLA-G (H2-M3), Cd200, FASLG (FasL), and Mfge8; HLA-G (H2-M3), Cd200, FASLG (FasL), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd200, Ccl21 (Ccl21 b), and Mfge8; HLA-G (H2-M3), Cd200, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd200, Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; HLA-G (H2-M3), FASLG (FasL), Ccl21 (Ccl21 b), and Serpin B9 (Spi6); HLA-G (H2-M3), FASLG (FasL), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); Cd47, Cd200, FASLG (FasL), and Ccl21 (Ccl21 b); Cd47, Cd200, FASLG (FasL), and Mfge8; Cd47, Cd200, FASLG (FasL), and Serpin B9 (Spi6); Cd47, Cd200, Ccl21 (Ccl21 b), and Mfge8; Cd47, Cd200, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); Cd47, Cd200, Mfge8, and Serpin B9 (Spi6); Cd47, FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; Cd47, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); Cd47, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); or FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)).

In some embodiments of any of the foregoing aspects, the cell comprises five of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6) (e.g., PD-L1, HLA-G (H2-M3), Cd47, Cd200, and FASLG (FasL); PD-L1, HLA-G (H2-M3), Cd47, Cd200, and Ccl21 (Ccl21b); PD-L1, HLA-G (H2-M3), Cd47, Cd200, and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, Cd200, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, FASLG (FasL), and Ccl21 (Ccl21b); PD-L1, HLA-G (H2-M3), Cd47, FASLG (FasL), and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, FASLG (FasL), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, Ccl21 (Ccl21 b), and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, FASLG (FasL), and Ccl21 (Ccl21b); PD-L1, HLA-G (H2-M3), Cd200, FASLG (FasL), and Mfge8, PD-L1, HLA-G (H2-M3), Cd200, FASLG (FasL), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, Ccl21 (Ccl21 b), and Mfge8; PD-L1, HLA-G (H2-M3), Cd200, Ccl21 (Ccl21b), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; PD-L1, HLA-G (H2-M3), FASLG (FasL), Ccl21 (Ccl21 b), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, FASLG (FasL), and Ccl21 (Ccl21b); PD-L1, Cd47, Cd200, FASLG (FasL), and Mfge8, PD-L1, Cd47, Cd200, FASLG (FasL), and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, Ccl21 (Ccl21b), and Mfge8; PD-L1, Cd47, Cd200, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; PD-L1, Cd47, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); PD-L1, Cd47, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; PD-L1, Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); PD-L1, Cd200, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); PD-L1, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), and Ccl21 (Ccl21 b); HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), and Mfge8; HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21b), and Mfge8; HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21 b), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Cd200, Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; HLA-G (H2-M3), Cd47, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; HLA-G (H2-M3), Cd200, FASLG (FasL), Ccl21 (Ccl21 b), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd200, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), and Serpin B9 (Spi6); Cd47, Cd200, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); Cd47, Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); Cd47, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); or Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6)),In some embodiments of any of the foregoing aspects, the cell comprises six of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) (e.g., PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), and Ccl21 (Ccl21 b); PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21 b), and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21b), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, Cd200, Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, FASLG (FasL), Ccl21 (Ccl21 b), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; PD-L1, HLA-G (H2-M3), Cd200, FASLG (FasL), Ccl21 (Ccl21b),and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; PD-L1, Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21 b), and Mfge8; HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd47, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); HLA-G (H2-M3), Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); or Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)).

In some embodiments of any of the foregoing aspects, the cell comprises seven of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) (e.g., PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Mfge8; PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd47, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); PD-L1, HLA-G (H2-M3), Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); PD-L1, Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6); or HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)).

In some embodiments of any of the foregoing aspects, the cell comprises all eight of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In some embodiments of any of the foregoing aspects, the cell comprises one or more (e.g., one, two, three, four, five, six, or all seven) of the set of transgenes HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In some embodiments of any of the foregoing aspects, the cell comprises one or more (e.g., one, two, three, four, five, six, or all seven) of the set of transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In some embodiments of any of the foregoing aspects, the cell comprises one or more (e.g., one, two, three, four, five, or all six) of the set of transgenes HLA-G (H2-M3), Cd47, Cd200, Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

In some embodiments of any of the foregoing aspects, the cell is not modified to express PD-L1.

In some embodiments of any of the foregoing aspects, the cell is not modified to express FasL.

In some embodiments of any of the foregoing aspects, the cell is not modified to express TGF-β. In some embodiments of any of the foregoing aspects, the cell is not modified to express CTLA4 or CLTA4-Ig. In some embodiments of any of the foregoing aspects, the cell is not modified to express IDO. In some embodiments of any of the foregoing aspects, the cell is not modified to express IL-35. In some embodiments of any of the foregoing aspects, the cell is not modified to express IL-10. In some embodiments of any of the foregoing aspects, the cell is not modified to express VEGF. In some embodiments of any of the foregoing aspects, the cell is not modified to express an NFκb decoy receptor. In some embodiments of any of the foregoing aspects, the cell is not modified to express soluble TNFR. In some embodiments of any of the foregoing aspects, the cell is not modified to express CCR7. In some embodiments of any of the foregoing aspects, the cell is not modified to express SOCS1. In some embodiments of any of the foregoing aspects, the cell is not modified to express HLA-E. In some embodiments of any of the foregoing aspects, the cell is not modified to express siRNA directed to IL-12.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.

As used herein, the term “about” refers to a value that is no more than 10% above or below the value being described. For example, the term “about 5 nM” indicates a range of from 4.5 nM to 5.5 nM.

As used herein, the term “activated leukocyte” refers to the state of a leukocyte (e.g., a granulocyte, such as a neutrophil, eosinophil, or basophil; a monocyte, or a lymphocyte, such as a B or T cell) caused by response to a perceived insult. When leukocytes become activated, they can proliferate, secrete cytokines, differentiate, present antigens, become more polarized, become more phagocytic, and/or become more cytotoxic. Factors that stimulate immune cell activation include pro-inflammatory cytokines, pathogens, and non-self antigen presentation. Activated leukocytes can be isolated from lymphoid organs. Leukocytes, such as T cells, can also be activated in vitro using anti-CD3/CD28 beads or other methods employed by those of skill in the art (see, e.g., Frauwith and Thompson, J. Clin Invest 109:295-299 (2002); and Trickett and Kwan, J Immunol Methods 275:251-255 (2003)).

As used herein, “allogeneic” means cells, tissue, DNA, or factors taken or derived from a different subject of the same species.

As used herein, the term “stem cell” refers to a cell that can differentiate into one or more specialized cells and has the capacity for self-renewal. Stem cells include pluripotent stem cells (PSCs), such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), and multipotent stem cells, such as cord blood stem cells, mesenchymal stromal cells and adult stem cells, which are found in various tissues. The term “stem cell” also includes cells amenable for genome editing, cells that can serve as a source of a therapeutic cell type (e.g., cells that can be directed to differentiate into a lineage restricted or terminally differentiated cell that is used for cell therapy, or cells of a desired target tissue), and cells with “artificial” cell acquired stem cell properties (e.g., pluripotency or multipotency or self-renewal).

As used herein, the terms “embryonic stem cell” and “ES cell” refer to an embryo-derived totipotent or pluripotent stem cell, derived from the inner cell mass of a blastocyst that can be maintained in an in vitro culture under suitable conditions. ES cells are capable of differentiating into cells of any of the three vertebrate germ layers, e.g., the endoderm, the ectoderm, or the mesoderm. ES cells are also characterized by their ability propagate indefinitely under suitable in vitro culture conditions. See, for example, Thomson et al., Science 282:1145 (1998).

As used herein, the terms “induced pluripotent stem cell,” “iPS cell,” and “iPSC” refer to a pluripotent stem cell that can be derived directly from a differentiated somatic cell. Human iPS cells can be generated by introducing specific sets of reprogramming factors into a non-pluripotent cell that can include, for example, Oct3/4, Sox family transcription factors (e.g., Sox1, Sox2, Sox3, Sox15), Myc family transcription factors (e.g., c-Myc, 1-Myc, n-Myc), Kruppel-like family (KLF) transcription factors (e.g., KLF1, KLF2, KLF4, KLF5), and/or related transcription factors, such as NANOG, LIN28, and/or Glis1. Human iPS cells can also be generated, for example, by the use of miRNAs, small molecules that mimic the actions of transcription factors, or lineage specifiers. Human iPS cells are characterized by their ability to differentiate into any cell of the three vertebrate germ layers, e.g., the endoderm, the ectoderm, or the mesoderm. Human iPS cells are also characterized by their ability propagate indefinitely under suitable in vitro culture conditions. See, for example, Takahashi and Yamanaka, Cell 126:663 (2006).

As used herein, the term “mitigate antigen presenting cell activation and function” refers to a transgene that encodes a gene product whose function is to inhibit antigen presenting cell activation or the ability of an antigen presenting cell to promote the activation of graft attacking leukocytes (Fiorentino et al., J Immunol. 146:3444-51 (1991); Salio et al., Eur J Immunol. 29:3245-53 (1999)). In an embodiment, mitigation of antigen presenting cell activation and function refers to a decrease in APC activation and function of at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%, relative to a control (e.g., as determined using an assay for antigen presenting cell activation, such as reduced proliferation, reduced secretion of pro-inflammatory cytokines (e.g., interleukin-1 (IL-1, e.g., IL-1β), IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, tumor necrosis factor (TNF, e.g., TNFα), interferon gamma (IFNγ), and granulocyte macrophage colony stimulating factor (GMCSF), which can be measured using an ELISA or Western Blot analysis of culture media or a patient sample, such as a blood sample), or reduced levels of cell surface markers (e.g., CD11c, CD11b, HLA molecules (e.g., MHC-II), CD40, B7, IL-2, CD80 or CD86, which can be assessed using flow cytometry, immunohistochemistry, in situ hybridization, and other assays that allow for measurement of cell surface markers)). Antigen presenting cells include dendritic cells, B cells, and macrophages. Mast cells and neutrophils can also be induced to present antigens. Methods for determining mitigation of antigen presenting cell activation and function are known in the art. Examples of gene products that mitigate antigen presenting cell activation and function include, but are not limited to: Ccl21 (Ccl21b) and PD-L1. Such transgenes may be referred herein to “cloaking” or “cloaked” genes.

As used herein, the term “mitigate graft attacking leukocyte activity or cytolytic function” refers to a transgene that encodes a gene product whose function is to inhibit or prevent graft attacking leukocyte activity or cytolytic function near allograft cells (MacDonald et al., J Immunol. 126:1671-5 (1981); Bongrand et al., Eur J Immunol. 13:424-9 (1983); MacDonald et al., Eur J Immunol. 9:466-70 (1979)). In an embodiment, mitigation of graft attacking leukocyte activity or cytolytic function refers to a decrease in leukocyte activity or cytolytic function of at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%, relative to a control (e.g., as determined using an assay for leukocyte activation, such as reduced proliferation, reduced secretion of pro-inflammatory cytokines (e.g., interleukin-1 (IL-1, e.g., IL-1, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, tumor necrosis factor (TNF, e.g., TNFα), interferon gamma (IFNγ), and granulocyte macrophage colony stimulating factor (GMCSF), which can be measured using an ELISA or Western Blot analysis of culture media or a patient sample, such as a blood sample), or reduced polarization (e.g., a reduction in the level of IL-12, TNF, IL-1β, IL-6, IL-23, MARCO, MHC-II, CD86, iNOS, CXCL9, and CXCL10 in a macrophage or monocyte, or a reduction in the level of a TM-specific marker (e.g., T-bet, IL-12R, STAT4), a chemokine receptor (e.g., CCRS, CXCR6, or CXCR3); or a Th2-specific marker: (e.g., CCR3, CXCR4, STATE, GATA3, or IL-4Ra) in a T cell, which can be assessed using flow cytometry, immunohistochemistry, situ hybridization, qPCR, or western blot analysis for cell surface markers or intracellular proteins, and ELISA or western blot analysis for secreted proteins); or as determined using an assay for cytolytic function (e.g., by incubating leukocytes with a target cell line that has been pre-coated with antibodies to a surface antigen expressed by the target cell line and measuring the number of surviving target cells with a fluorescent viability stain, or by measuring the secretion of cytolytic granules (e.g., perforin, granzymes, or other cytolytic proteins released from immune cells) from the leukocytes). Methods for determining mitigation of graft attacking leukocyte activity or cytolytic function are known in the art. Examples of gene products that mitigate graft attacking leukocyte activity or cytolytic function include, but are not limited to: PD-L1, HLA-G (H2-M3), Cd39, Cd73, and Lag3. Such transgenes may be referred herein to “cloaking” or “cloaked” genes.

As used herein, the term “mitigate macrophage cytolytic function and phagocytosis of allograft cells” refers to a transgene that encodes a gene product whose function is to inhibit or prevent macrophage cytolytic function and/or phagocytosis of allograft cells (Fish et al., Toxicology. 19:127-38. (1981); Sung et al., J Biol Chem. 260:546-54 (1985); Amash et al., J Immunol. 196:3331-40 (2016)). In an embodiment, mitigation of macrophage cytolytic function and phagocytosis of allograft cells refers to a decrease in macrophage cytolytic function and/or phagocytosis of allograft cells of at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%, relative to a control (e.g., as determined using an assay for macrophage cytolytic function (e.g., by incubating macrophages with a target cell line that has been pre-coated with antibodies to a surface antigen expressed by the target cell line and measuring the number of surviving target cells with a fluorescent viability stain, or by measuring the secretion of cytolytic granules (e.g., perforin, granzymes, or other cytolytic proteins released from immune cells) released from the macrophages; or as determined using an assay for macrophage phagocytosis (e.g., culturing macrophages with fluorescent beads or a target cell line that has been pre-coated with antibodies to a surface antigen expressed by the target cell line and measuring fluorescence inside the immune cell or quantifying the number of beads or cells engulfed)). Methods for determining mitigation of macrophage cytolytic function and phagocytosis of allograft cells are known in the art. Examples of gene products that mitigate macrophage cytolytic function include, but are not limited to: Cd47, Cd200, Mfge8, and ill r2. Such transgenes may be referred herein to “cloaking” or “cloaked” genes.

As used herein, the term “induce apoptosis in graft attacking leukocytes” refers to a transgene that encodes a gene product whose function is to kill graft attacking leukocytes near allograft cells (Huang et al., Proc Natl Acad Sci USA. 96:14871-6 (1999); Suzuki et al., Proc Natl Acad Sci USA. 97:1707-12 (2000); Simon et al., Proc Natl Acad Sci USA. 98:5158-63 (2001)). In an embodiment, induction of apoptosis in graft attacking leukocytes refers to an increase in apoptosis in graft attacking leukocytes of at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%, relative to a control (e.g., as determined using an assay for apoptosis, such as TUNEL staining, caspase staining, or Annexin-V staining, or use of fluorescent viability stains). Methods for determining induction of apoptosis in graft attacking leukocytes are known in the art. Examples of gene products that can induce apoptosis in graft attacking leukocytes include, but are not limited to: FASLG (FasL) and Infsf10. Such transgenes may be referred herein to “cloaking” or “cloaked” genes.

As used herein, the term “mitigate local inflammatory proteins” refers to a transgene that encodes a gene product whose function is to inhibit the activity of local proteins, where the function of said proteins is to promote graft attacking leukocyte accumulation, and/or their cytolytic function (Felix et al., Nat Rev Immunol. 17:112-29 (2017)). In an embodiment, mitigation of local inflammatory proteins refers to a reduction in local inflammatory proteins of at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%, relative to a control (e.g., as determined using an assay for inflammatory proteins that promote leukocyte activation or migration to a site of inflammation (e.g., a chemokine, such as CCL2, CCL3, CCLS, CXCL1, CXCL2, and CXCL8, or a pro-inflammatory cytokine, such as IL-1β, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-18, TNFα, IFNγ, or GMCSF, which can be measured using an ELISA, Western blot analysis, or other techniques known in the art for measuring secreted proteins)). Methods for determining mitigation of local inflammatory proteins are known in the art. Examples of gene products that mitigate local inflammatory proteins include, but are not limited to: PD-L1, Il1r2, and Ackr2. Such transgenes may be referred herein to “cloaking” or “cloaked” genes.

As used herein, the term “protect against leukocyte-mediated apoptosis” refers to a transgene that encodes a gene product whose function is to inhibit any cell component that may induce apoptosis or cytolysis of an allograft cell (Abdullah et al., J Immunol. 178:3390-9 (2007)). In an embodiment, protection against leukocyte-mediated apoptosis refers to a decrease in leukocyte-mediated apoptosis of at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100%, relative to a control (e.g., as determined using an assay for leukocyte-mediated apoptosis (e.g., by incubating leukocytes with a target cell line that has been pre-coated with antibodies to a surface antigen expressed by the target cell line and measuring the number of surviving target cells with a fluorescent viability stain, or by measuring the secretion of cytolytic granules (e.g., perforin, granzymes, or other cytolytic proteins released from immune cells) released from the leukocyte). Methods for determining protection against leukocyte-mediated apoptosis are known in the art. Examples of gene products that protect against leukocyte-mediated apoptosis include, but are not limited to: Serpin B9 (Spi6) and Dad1. Such transgenes may be referred herein to “cloaking” or “cloaked” genes.

As used herein, the term “biologic” refers to a designed polypeptide and corresponding encoding DNA, which can be expressed as a transgene. The polypeptide may agonize or inhibit the function of an endogenous gene or inhibit or activate a biological process. Methods for determining whether a polypeptide has agonist or antagonist activity or function are generally known in the art. In an embodiment, the agonist function is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90, 95% or 100% of the function, relative to the function of a control. In an embodiment, the antagonist function is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90, 95% or 100% of the function, relative to the function of a control.

As used herein, the term “operably linked” refers to a first molecule joined to a second molecule, wherein the molecules are so arranged that the first molecule affects the function or expression of the second molecule. The two molecules may or may not be part of a single contiguous molecule and may or may not be adjacent. For example, a promoter is operably linked to a transcribable polynucleotide molecule if the promoter modulates transcription of the transcribable polynucleotide molecule of interest in a cell. Additionally, two portions of a transcription regulatory element are operably linked to one another if they are joined such that the transcription-activating functionality of one portion is not adversely affected by the presence of the other portion. Two transcription regulatory elements may be operably linked to one another by way of a linker nucleic acid (e.g., an intervening non-coding nucleic acid) or may be operably linked to one another with no intervening nucleotides present.

As used herein, the term “promoter” refers to a recognition site on DNA that is bound by an RNA polymerase. The polymerase drives transcription of the transgene.

“Percent (%) sequence identity” with respect to a reference polynucleotide or polypeptide sequence is defined as the percentage of nucleic acids or amino acids in a candidate sequence that are identical to the nucleic acids or amino acids in the reference polynucleotide or polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid or amino acid sequence identity can be achieved in various ways that are within the capabilities of one of skill in the art, for example, using publicly available computer software such as BLAST, BLAST-2, or Megalign software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For example, percent sequence identity values may be generated using the sequence comparison computer program BLAST. As an illustration, the percent sequence identity of a given nucleic acid or amino acid sequence, A, to, with, or against a given nucleic acid or amino acid sequence, B, (which can alternatively be phrased as a given nucleic acid or amino acid sequence, A that has a certain percent sequence identity to, with, or against a given nucleic acid or amino acid sequence, B) is calculated as follows:

100 multiplied by (the fraction X/Y)

where X is the number of nucleotides or amino acids scored as identical matches by a sequence alignment program (e.g., BLAST) in that program's alignment of A and B, and where Y is the total number of nucleic acids in B. It will be appreciated that where the length of nucleic acid or amino acid sequence A is not equal to the length of nucleic acid or amino acid sequence B, the percent sequence identity of A to B will not equal the percent sequence identity of B to A.

As used herein, the term “pharmaceutical composition” refers to a mixture containing a therapeutic agent, optionally in combination with one or more pharmaceutically acceptable excipients, diluents, and/or carriers, to be administered to a subject, such as a mammal, e.g., a human, in order to prevent, treat or control a particular disease or condition affecting or that may affect the subject.

As used herein, the term “pharmaceutically acceptable” refers to those compounds, materials, compositions and/or dosage forms, which are suitable for contact with the tissues of a subject, such as a mammal (e.g., a human) without excessive toxicity, irritation, allergic response and/or other problem complications commensurate with a reasonable benefit/risk ratio.

As used herein, the term “wild-type” refers to a genotype with the highest frequency for a particular gene in a given organism.

The terms “cell division locus”, “cell division loci”, and “CDL” as used herein, refer to a genomic locus (or loci) whose transcription product(s) is expressed by dividing cells. When a CDL comprises a single locus, absence of CDL expression in a cell (or its derivatives) means that tumour initiation and/or formation is prohibited either because the cell(s) will be ablated in the absence of CDL expression or because proliferation of the cell(s) will be blocked or compromised in the absence of CDL expression. When a CDL comprises multiple loci, absence of expression by all or subsets of the loci in a cell (or its derivatives) means that tumour initiation and/or formation is prohibited either because the cell(s) will be ablated in the absence of CDL expression or because proliferation of the cell(s) will be blocked or compromised in the absence of CDL expression. A CDL may or may not be expressed in non-dividing and/or non-proliferating cells. A CDL may be endogenous to a host cell or it may be a transgene. If a CDL is a transgene, it may be from the same or different species as a host cell or it may be of synthetic origin. In an embodiment, a CDL is a single locus that is transcribed during cell division. For example, in an embodiment, a single locus CDL is CDK1. In an embodiment, a CDL comprises two or more loci that are transcribed during cell division. For example, in an embodiment, a multi-locus CDL comprises two MYC genes (c-Myc and N-myc) (Scognamiglio et al., 2016). In an embodiment, a multi-locus CDL comprises AURORA B and C kinases, which may have overlapping functions (Fernandez-Miranda et al., 2011). Cell division and cell proliferation are terms that may be used interchangeably herein.

The terms “normal rate of cell division”, “normal cell division rate”, “normal rate of cell proliferation”, and “normal cell proliferation rate” as used herein, refer to a rate of cell division and/or proliferation that is typical of a non-cancerous healthy cell. A normal rate of cell division and/or proliferation may be specific to cell type. For example, it is widely accepted that the number of cells in the epidermis, intestine, lung, blood, bone marrow, thymus, testis, uterus and mammary gland is maintained by a high rate of cell division and a high rate of cell death. In contrast, the number of cells in the pancreas, kidney, cornea, prostate, bone, heart and brain is maintained by a low rate of cell division and a low rate of cell death (Pellettieri and Sanchez Alvarado, 2007).

The terms “inducible negative effector of proliferation” and “iNEP” as used herein, refer to a genetic modification that facilitates use of CDL expression to control cell division and/or proliferation by: i) inducibly stopping or blocking CDL expression, thereby prohibiting cell division and proliferation; ii) inducibly ablating at least a portion of CDL-expressing cells (i.e., killing at least a portion of proliferating cells); or iii) inducibly slowing the rate of cell division relative to a cell's normal cell division rate, such that the rate of cell division would not be fast enough to contribute to tumor formation.

The terms “ablation link” and “ALINK” as used herein, refer to an example of an iNEP, which comprises a transcriptional link between a CDL and a sequence encoding a negative selectable marker. The ALINK modification allows a user to inducibly kill proliferating host cells comprising the ALINK or inhibit the host cell's proliferation by killing at least a portion of proliferating cells by exposing the ALINK-modified cells to an inducer of the negative selectable marker. For example, a cell modified to comprise an ALINK at a CDL may be treated with an inducer (e.g., a prodrug) of the negative selectable marker in order to ablate proliferating cells or to inhibit cell proliferation by killing at least a portion of proliferating cells.

The terms “exogenous activator of regulation of CDL” and “EARC” as used herein, refer to an example of an iNEP, which comprises a mechanism or system that facilitates exogenous alteration of non-coding or coding DNA transcription or corresponding translation via an activator. An EARC modification allows a user to inducibly stop or inhibit division of cells comprising the EARC by removing from the EARC-modified cells an inducer that permits transcription and/or translation of the EARC-modified CDL. For example, an inducible activator-based gene expression system may be operably linked to a CDL and used to exogenously control expression of a CDL or CDL translation, such that the presence of a drug inducible activator and corresponding inducer drug are required for CDL transcription and/or translation. In the absence of the inducer drug, cell division and/or proliferation would be stopped or inhibited (e.g., slowed to a normal cell division rate). For example, the CDL Cdk1/CDK1 may be modified to comprise a dox-bridge, such that expression of Cdk1/CDK1 and cell division and proliferation are only possible in the presence of an inducer (e.g., doxycycline).

The term “proliferation antagonist system” as used herein, refers to a natural or engineered compound(s) whose presence inhibits (completely or partially) proliferation of a cell.

The term “dox-bridge” as used herein, refers to a mechanism for separating activity of a promoter from a target transcribed region by expressing rtTA (Gossen et al., 1995) by the endogenous or exogenous promoter and rendering the transcription of target region under the control of TRE. As used herein, “rtTA” refers to the reverse tetracycline transactivator elements of the tetracycline inducible system (Gossen et al., 1995) and “TRE” refers to a promoter consisting of TetO operator sequences upstream of a minimal promoter. Upon binding of rtTA to the TRE promoter in the presence of doxycycline, transcription of loci downstream of the TRE promoter increases. The rtTA sequence may be inserted in the same transcriptional unit as the CDL or in a different location of the genome, so long as the transcriptional expression's permissive or non-permissive status of the target region is controlled by doxycycline. A dox-bridge is an example of an EARC.

As used herein, the term “fail-safe cell” refers to a cell that contains one or more homozygous, heterozygous, hemizygous or compound heterozygous ALINKs or EARCs in one or more CDLs (e.g., at least two, three, four, or five CDLs). Fail-safe cells may contain either ALINKs or EARCs or both ALINK and EARC modifications (e.g., ALINK and EARC modifications in different CDLs or in a single CDL).

As used herein, the term “fail-safe” refers to a property of a cell that is unlikely to exhibit uncontrolled (e.g., tumorigenic) proliferation. A cell can be considered “fail safe” when cell proliferation is under the control of a negative regulator or inducer, and the possibility of the cell losing the activity of the system that controls proliferation due to genetic mutation is low. The fail-safe volume will depend on the number of ALINKs and the number of ALINK-targeted CDLs (e.g., a cell with homozygous modifications of two different CDLs has a higher fail safe volume (e.g., it is less likely to lose all systems that control proliferation through genetic mutation) than a cell with a heterozygous modification of a single CDL). The fail-safe property is further described in Table 3.

DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.

These and other features of the disclosure will become more apparent in the following detailed description in which reference is made to the appended drawings wherein:

FIGS. 1A-1D depict representative images showing the expression of cloaking proteins (Cd200 (FIG. 1A), FasL (FIG. 1B), H2-M3 (FIG. 1C) and Cd47 (FIG. 1D)) in C57BL/6 mouse embryonic stem cell line C2 using immunohistochemistry.

FIGS. 2A-2E are flow cytometry plots showing T-cell activation using splenocytes (FIG. 2A), wt B16 melanoma cells (FIG. 2B), cloaked B16 melanoma cells (FIG. 2C), wt ES cells (FIG. 2D), and cloaked ES cells (FIG. 2E) in a mixed lymphocyte reaction.

FIGS. 3A-3B are schematics and images showing that cloaked (FIG. 3B) B16F10 cancer cells in an allogenic model are protected from rejection compared to their WT counterparts (FIG. 3A). Representative images of uncloaked cells in C57BL/6 (n=5) and uncloaked cells in FVB/N (n=4) (FIG. 3A); cloaked cells in C57BL/6 (n=5) and cloaked cells in FVB/N (n=6) (FIG. 3B).

FIG. 4 is a schematic showing that cloaked embryonic stem cells form tumors in isogenic B6 mouse recipients (upper panel) and in FVB allogenic recipients (lower panel).

FIGS. 5A-5C are a series of photographs depicting allogenic mice bearing teratomas formed from subcutaneous injection of cloaked C57BL/6 ES cells. Red arrows indicate teratomas.

FIG. 5A shows teratomas in C3H mice, FIG. 5B shows teratomas in FVB/N mice, and FIG. 5C shows teratomas in CD1 mice.

FIG. 6 is a schematic and series of images showing that animals with cloaked tissue are not immune compromised.

FIG. 7 is a series of images of FVB/N mice showing additional results showing that animals with cloaked tissues are not immune compromised.

FIGS. 8A-8H show transgene expression in clonal FailSafe containing embryonic stem cells derived from C57BL/6 mice. FIG. 8A shows FasL expression, FIG. 8B shows Ccl21 b expression, FIG. 8C shows Cd200 expression, FIG. 8D shows Cd47 expression, FIG. 8E shows Mfge8 expression, FIG. 8F shows Spi6 expression, FIG. 8G H2-M3 expression, and FIG. 8H shows PD-L1 expression.

FIG. 9 is a series of graphs depicting cloaking transgene expression in ES cell clones. Each cloaking transgene is depicted in a different color. Concentric circles represent expression level on a log 10 scale. The thick black circle represents ix expression normalized to positive controls (activated leukocytes isolated from murine lymph organs), with the next outer ring representing 10× and 100× expression compared to positive controls, respectively. The innermost ring is 0.1× expression compared to positive controls. Clones NT2 and 15 (indicated with red squares) had the highest expression of the cloaking genes. These clones survived in allogenic hosts.

FIG. 10 is a graph depicting the expression of the cloaking transgenes among the whole genome gene expression level distribution for the whole genome of ES cells. All 8 cloaking transgenes in the NT2 cell line and NT2-derived teratoma had an expression level that was among the top 5% of all genes in the ES cell genome, with 5 of the cloaking transgenes having an expression level in the top 1% of all genes in the ES cell genome. The expression levels of the transgenes in the NT2 line and NT2-derived teratoma succeeded to achieve allograft tolerance.

FIGS. 11A-11B are photographs showing C57BL/6 derived teratomas in FVB/N mice. The transgenic line, NT2, resulted in 9 teratomas out of 10 injection sites. Images were taken 3 months post injection. FIG. 11B is an enlarged image of the teratoma indicated by the arrow in FIG. 11A.

FIGS. 12A-12B are graphs showing the teratoma tumor size in isogenic (FIG. 12A) and allogenic (FIG. 12B) mice treated with ganciclovir.

FIGS. 13A-13B are a series of photomicrographs showing that cloaked embryonic stem cells, injected into both isogenic (FIG. 13A) and allogenic (FIG. 13B) hosts, can differentiate into all three cell lineages.

FIGS. 14A-140 are photomicrographs showing the formation of all three germ layers in a teratoma formed from subcutaneous injection of cloaked ES cells into a mouse. FIG. 14A, FIG. 14B, and FIG. 14C show the three germ layers (ec=ectoderm, shown in FIG. 14A; en=endoderm, shown in FIG. 140; me=mesoderm, shown in FIG. 14B). FIG. 14D shows a blood vessel, indicated by the red arrow, confirming that the tissues are well vascularized.

FIG. 15 is a schematic showing the construction of vectors that express target genes essential for allo-tolerance.

FIGS. 16A-16H are fluorescent photomicrographs showing the expression of proteins encoded by the cloaking transgenes in ES cells. FIG. 16A shows the expression of PD-L1, FIG. 16B shows the expression of CD200, FIG. 16C shows the expression of CD47, FIG. 16D shows the expression of FasL, FIG. 16E shows the expression of H2-M3, FIG. 16F shows the expression of Ccl21, FIG. 16G shows the expression of Mfge8, and FIG. 16H shows the expression of Spi6.

FIGS. 17A-17B are photomicrographs showing that cloaked ES cells have typical ES cell morphology (FIG. 17A) and express the ES cell marker alkaline phosphatase (FIG. 17B).

FIGS. 18A-18B are fluorescent photomicrographs showing the expression of markers of pluripotent ES cells (Oct4 (FIG. 18A) and SSEA1 (FIG. 18B)) in cloaked ES cells. The insets in FIGS. 18A-18B show single channel images of the fluorescent micrographs for the ES cell markers (Oct4 and SSEA) and DAPI, which labels the nucleus, to demonstrate that staining for the ES cell markers colocalizes with the cloaked cells.

FIG. 19 is a schematic depicting the immune processes that are inhibited by the cloaking transgenes (top) and the expression cassette (bottom) used to express the cloaking transgenes in ES cells.

FIG. 20 is a series of graphs depicting the effect of interferon gamma (IFNγ) on MHC levels in ES cells. IFNγ increased MHC levels in wild-type ES cells and ES cells overexpressing the wild-type IFNγ receptor IFNγR1, but did not increase MHC levels in ES cells overexpressing a dominant negative form of the IFNγ receptor (IFNγR1 d39), indicating that IFNγR1 d39 completely inhibited the IFNγ-mediated upregulation of MHCs in ES cells.

DETAILED DESCRIPTION OF THE DISCLOSURE
Description of Cells and Methods

Featured are tools, such as genetically modified cells, and methods for providing a local immune suppression at a transplant site using the cells, e.g., when the cells are transplanted in an allogeneic host. The genetically modified cell comprises: one or a set of transgenes, each transgene encoding a gene product that is cytoplasmic, membrane bound, or local acting and whose function is to mitigate function of the host immune system (e.g., graft attacking leukocyte and NK cell activation) or act as a defense mechanism against attacking leukocytes.

Various cytoplasmic, membrane-bound, or local acting immune factors have been found to regulate the local immune compartment and local immune populations. Immune factors like PD-L1 (Brown et al., J Immunol. 170:1257-66 (2003: Curie) et al., Nat Med. 9:562-7 (2003); Dong et al., Nat Med. 8:793-800 (2002)), CD47 ((Willingham et al., Proc Natl Aced Sci USA. 109:6662-7 (2012); Liu et al., PLoS One. 10:e0137345 (2015); Demeure et al., J Immunol. 164:2193-9 (2000)), CD200 (Jenmalm et al., J Immunol. 176:191-9 (2006); Cherwinski et al., J Immunol. 174:1348-56 (2005); Kretz-Rommel et al., J Immunol. 178:5595-605 (2007)), FasL (O'Connell et al., J Exp Med. 184:1075-82 (1996); Ju et al., Nature. 373:444-8 (1995); Mazar et al., J Biol Chem. 284:22022-8 (2009)), and Spi6 (Medema Proceedings of the National Academy of Sciences of the United States of America. 98:11515-20 (2001); Zhang et al., Immunity. 24:451-61 (2006); Soriano et al., Lung Cancer. 77:38-45 (2012)) are among the very many that have been described, including their role in immune modulation. We discovered that expression of one or more of these immune regulatory factors in an allogenic cell can be used to provide local immune suppression and/or reduce allorejection in a host to which the cells are administered.

We modified allogenic cells through the use of specific immunomodulatory factors introduced into a cell or population of cells. The modified cells evade immune rejection through the simultaneous modulation of many different local immune pathways. Such genetically engineered cells can be transplanted “off the shelf” into many recipients regardless of genetic background and without rejection by the recipient's immune system. This immunomodulatory approach overcomes the requirement for systemic immunosuppression of the transplant recipient, which can be dangerous to the recipient. Thus, although an immunosuppressive agent(s) can be administered to a patient that receives the modified cells described herein, the therapy need not include the administration of an immunosuppressive agent(s). This immunomodulatory approach also overcomes the costly and impractical methodology of deriving patient-specific iPS cells, manipulating regulatory cells, or inducing chimerism through hematopoietic cell transplantation (HCT).

Cells can be genetically modified to express a set of transgenes encoding gene products that are cytoplasmic, membrane bound, or local acting, and whose function is to mitigate immune function (e.g., graft attacking leukocyte and NK cell activation) or to act as a defense mechanism against the immune response (e.g., attacking leukocytes). The set of transgenes may be selected from the genes having a role in the immune modulatory pathways described above. Such genes include, but are not limited to those provided in Table 1.

TABLE 1

Genes that can be expressed by

allogenic cells for local immunosuppression

Gene
Function

PD-L1
Induces cell death in PD-L1 expressing T cells and

macrophages

HLA-G
Inhibits NK cells from attacking cells lacking MHC

(mouse
molecules

gene:

H2-M3)

Cd47
Negative regulator of macrophages and killer T cells

Cd200
Inhibits macrophage activation

FASLG
Induces apoptosis in Fas expressing CD8+ T cells

(mouse

gene: FasL)

Clc21
Chemo-attractant for antigen presenting cells (APCs)

(mouse

gene:

Ccl21b)

Mfge8
Inhibition of macrophage phagocytosis

Serpin B9
Inhibition of granzyme/perforin attack

(mouse

gene: Spi6)

Dad1
Negative regulator of programmed cell death

Tnfrsf10
Induces apoptosis in leukocytes expressing the TRAIL

receptor

Cd39
Converts ATP to AMP, inhibits T-cells

Cd73
Converts AMP to adenosine, inhibits T-cells, suppresses

cells
dendritic

Lag3
Inhibits T-cell activation, proliferation, function

II1r2
Blocks IL-1B activity, blocks inflammation and innate

cell activation

Ackr2
Decoy receptor for chemokines, prevents leukocyte

accumulation

Tnfrsf22
Decoy receptor, blocks TRAIL-induced apoptosis

from T-cells

Tnfrsf23
Decoy receptor, blocks TRAIL-induced apoptosis

from T-cells

IFNγR1
Dominant negative interferon gamma receptor 1, prevents

d39
IFNγ-mediated upregulation of MHCs in ES cells

C-C motif chemokine ligand 21(Ccl21) is expressed by local lymph nodes where it acts to attract activated antigen presenting cells (APCs). This key function offers an opportunity to “reverse” the migration of APCs by overexpressing this gene on grafted cells. Indeed, some melanomas express Ccl21 and recruit CCR7⁺ cells that, in turn, can reorganize portions of their tumor stroma as “self”. This leads to a stromal reconstruction that directs the recruitment and maintenance of Cd4⁺ Tregs (Zindl et al., Science. 328:697-8 (2010)). In fact, the expression of Ccl21 on tumors can protect co-implanted Ccl21 deficient tumor cells from rejection in a syngeneic allograft setting (Shields et al., Science. 328:749-52(2010)). Ccl21 b is the mouse ortholog of human Ccl21.

The amino acid sequences of mouse and human Ccl21 are:

Mouse Ccl21

(SEQ ID NO: 1)

MAQMMTLSLLSLVLALCIPWTQGSDGGGQDCCLKYSQKKIPYSIVRG

YRKQEPSLGCPIPAILFLPRKHSKPELCANPEEGWVQNLMRRLDQPP

APGKQSPGCRKNRGTSKSGKKGKGSKGCKRTEQTQPSRG

Human Ccl21

(SEQ ID NO: 2)

MAQSLALSLLILVLAFGIPRTQGSDGGAQDCCLKYSQRKIPAKVVRS

YRKQEPSLGCSIPAILFLPRKRSQAELCADPKELWVQQLMQHLDKTP

SPQKPAQGCRKDRGASKTGKKGKGSKGCKRTERSQTPKGP

Expression of Cd47 in umbilical cord blood can promote the development of hyporesponsive T-cells (Avice et al., J Immunol. 167:2459-68 (2001)). Erythrocytes also up-regulate Cd47 to avoid dendritic cell activation due to their lack of “self” presentation (van den Berg et al., Immunity. 43:622-4 (2015)). More recently, it was shown that expression of human Cd47 increases engraftment in a mouse model of pig-to-human hematopoietic cell transplantation (Tena et al., Am J Transplant. 14:2713-22 (2014)).

The amino acid sequences of mouse and human Cd47 are:

Mouse Cd47

(SEQ ID NO: 3)

MWPLAAALLLGSCCCGSAQLLFSNVNSIEFTSCNETVVIPCIVRNVE

AQSTEEMFVKWKLNKSYIFIYDGNKNSTTTDQNFTSAKISVSDLING

IASLKMDKRDAMVGNYTCEVTELSREGKTVIELKNRTVSWFSPNEKI

LIVIFPILAILLFWGKFGILTLKYKSSHTNKRIILLLVAGLVLTVIV

VVGAILLIPGEKPVKNASGLGLIVISTGILILLQYNVFMTAFGMTSF

TIAILITQVLGYVLALVGLCLCIMACEPVHGPLLISGLGIIALAELL

GLVYMKFVASNQRTIQPPRNR

Human Cd47

(SEQ ID NO: 4)

MWPLVAALLLGSACCGSAQLLFNKTKSVEFTFCNDTVVIPCFVTNME

AQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKG

DASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRVVSWFSPNE

NILIVIFPIFAILLFWGQFGIKTLKYRSGGMDEKTIALLVAGLVITV

IVIVGAILFVPGEYSLKNATGLGLIVTSTGILILLHYYVFSTAIGLT

SFVIAILVIQVIAYILAVVGLSLCIAACIPMHGPLLISGLSILALAQ

LLGLVYMKFVASNQKTIQPPRKAVEEPLNAFKESKGMMNDE

Cd200 is also as an important immunoregulatory molecule; increased expression can reduce the severity of allograft rejection, autoimmunity, and allergic disease (Gorczynski et al., J Immunol. 172:7744-9 (2004)). It has been shown that, in vitro, APC expression of Cd200 suppresses production of interferon gamma (IFN-γ) and cytolytic granules by activated Cd8+ T-cells (Misstear et al., J Virol. 86:6246-57 (2012)). Most interestingly, overexpression of Cd200 increases the survival of skin and cardiac allografts in mice by promoting of Foxp3+ Treg cells (Gorczynski et al., Transplantation. 98:1271-8 (2014)).

The amino acid sequences of mouse and human Cd200 are:

Mouse Cd200

(SEQ ID NO: 5)

MGSLVFRRPFCHLSTYSLIWGMAAVALSTAQVEVVTQDERKALHTTA

SLRCSLKTSQEPLIVTWQKKKAVSPENMVTYSKTHGVVIQPAYKDRI

NVTELGLWNSSITFWNTTLEDEGCYMCLFNTFGSQKVSGTACLTLYV

QPIVHLHYNYFEDHLNITCSATARPAPAISWKGIGTGIENSTESHFH

SNGTTSVISILRVKDPKTQVGKEVICQVLYLGNVIDYKQSLDKGFWF

SVPLLLSIVSLVILLVLISILLYWKRHRNQERGESSQGMQRMK

Human Cd200

(SEQ ID NO: 6)

MERLVIRMPFSHLSTYSLVWVMAAVVLCTAQVQVVTQDEREQLYTPA

SLKCSLQNAQEALIVTWQKKKAVSPENMVTFSENHGVVIQPAYKDKI

NITQLGLQNSTITFWNITLEDEGCYMCLFNTFGFGKISGTACLTVYV

QPIVSLHYKFSEDHLNITCSATARPAPMVFWKVPRSGIENSTVTLSH

PNGTTSVTSILHIKDPKNQVGKEVICQVLHLGTVTDFKQTVNKGYWF

SVPLLLSIVSLVILLVLISILLYWKRHRNQDRGELSQGVQKMT

Spi6 is an endogenous inhibitor of the cytotoxic effector molecule granzyme B released by activated Cd8+ T-cells (Sun et al., J Biol Chem. 272:15434-41 (1997)). Some data shows that Mesenchymal Stem Cells (MSCs) escape immune rejection by upregulating this molecule (El Haddad et al., Blood. 117:1176-83 (2011)). It has also recently been demonstrated that the ability of dendritic cells to present antigen to cytotoxic T cells without themselves being killed through contact mediated cytotoxicity is mediated by Spi6 (Lovo et al., J Immunol. 188:1057-63 (2012)). Spi6 is also known as Serpin B9.

The amino acid sequences of mouse Spi6 and the human counterpart, Serpin B9, are:

Mouse Spi6

(SEQ ID NO: 7)

MNTLSEGNGTFAIHLLKMLCQSNPSKNVCYSPASISSALAMVLLGAK

GQTAVQISQALGLNKEEGIHQGFQLLLRKLNKPDRKYSLRVANRLFA

DKTCEVLQTFKESSLHFYDSEMEQLSFAEEAEVSRQHINTWVSKQTE

GKIPELLSGGSVDSETRLVLINALYFKGKWHQPFNKEYTMDMPFKIN

KDEKRPVQMMCREDTYNLAYVKEVQAQVLVMPYEGMELSLVVLLPDE

GVDLSKVENNLTFEKLTAWMEADFMKSTDVEVFLPKFKLQEDYDMES

LFQRLGVVDVFQEDKADLSGMSPERNLCVSKFVHQSVVEINEEGTEA

AAASAIIEFCCASSVPTFCADHPFLFFIRHNKANSILFCGRFSSP

Human Serpin B9

(SEQ ID NO: 8)

METLSNASGTFAIRLLKILCQDNPSHNVFCSPVSISSALAMVLLGAK

GNTATQMAQALSLNTEEDIHRAFQSLLTEVNKAGTQYLLRTANRLFG

EKTCQFLSTFKESCLQFYHAELKELSFIRAAEESRKHINTWVSKKTE

GKIEELLPGSSIDAETRLVLVNAIYFKGKWNEPFDETYTREMPFKIN

QEEQRPVQMMYQEATFKLAHVGEVRAQLLELPYARKELSLLVLLPDD

GVELSTVEKSLTFEKLTAVVTKPDCMKSTEVEVLLPKFKLQEDYDME

SVLRHLGIVDAFQQGKADLSAMSAERDLCLSKFVHKSFVEVNEEGTE

AAAASSCFVVAECCMESGPRFCADHPFLFFIRHNRANSILFCGRFSS

P

Activated, cytotoxic, Cd8+ can kill target cells by expression of FasL, which binds to the FAS receptor and activates a caspase-mediated apoptosis in targeted cells. However, many tumors have developed a “counterattack” by upregulating FasL on their surface (Chen et al., J Immunol. 171:1183-91 (2003)). Selective expression of FasL in the vasculature of human and mouse solid tumors has been associated with scarce Cd8+ T-cell infiltration and a predominance of FoxP3+ Treg cells (Motz et al. Nat Med. 20:607-15 (2014)). Most recently, it was shown that B-lymphocytes also use the expression of FasL to kill T helper cells at the effector stage of immune responses (Lundy et al., Front Immunol. 6:122 (2015)). FasL is the mouse ortholog of human FASLG.

The amino acid sequences of mouse FasL and the human counterpart, FASLG, are:

Mouse FasL

(SEQ ID NO: 9)

MQQPMNYPCPQIFWVDSSATSSVVTPPGSVFPCPSSGPRGPDQRRPP

PPPPPVSPLPPPSQPLPLPPLTPLKKKIDHNTNLWLPVVFFMVLVAL

VGMGLGMYQLFHLQKELAELREFTNQSLKVSSFEKQIANPSTPSEKK

ELRSVAHLTGNPHSRSIPLEWEDTYGTALISGVKYKKGSLVINEAGL

YFVYSKVYFRGQSCNNQPLNHKVYMRNSKYPGDLVLMEEKRLNYCTT

GQIWAHSSYLGAVFNLTSADHLYVNISQLSLINFEESKTFFGLYKL

Human FASLG

(SEQ ID NO: 10)

MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPP

PPPPPPLPPPPPPPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVAL

VGLGLGMFQLFHLQKELAELRESTSQMHTASSLEKQIGHPSPPPEKK

ELRKVAHLTGKSNSRSMPLEWEDTYGIVLLSGVKYKKGGLVINETGL

YFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLVMMEGKMMSYCTT

GQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGLYKL

PD-L1 is a critical immune modulatory molecule that binds to Programmed Cell Death 1 (PD-1). PD-1 is expressed on T-cells, and binding to PD-L1 results in T-cell anergy (MacDonald et al., J Immunol. 126:1671-5 (1981)).

The amino acid sequences of mouse and human PD-L1 are:

Mouse PD-L1

(SEQ ID NO: 11)

MRIFAGIIFTACCHLLRAFTITAPKDLYVVEYGSNVTMECRFPVERE

LDLLALVVYWEKEDEQVIQFVAGEEDLKPQHSNFRGRASLPKDQLLK

GNAALQITDVKLQDAGVYCCIISYGGADYKRITLKVNAPYRKINQRI

SVDPATSEHELICQAEGYPEAEVIVVTNSDHQPVSGKRSVTTSRTEG

MLLNVTSSLRVNATANDVFYCTFWRSQPGQNHTAELIIPELPATHPP

QNRTHWVLLGSILLFLIVVSTVLLFLRKQVRMLDVEKCGVEDTSSKN

RNDTQFEET

Human PDL1 (CD274)

(SEQ ID NO: 12)

MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQ

LDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSL

GNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKINQRI

LVVDPVTSEHELTCQAEGYPKAEVIVVTSSDHQVLSGKITTINSKRE

EKLFNVISTLRINTTINEIFYCTFRRLDPEENHTAELVIPELPLAHP

PNERTHLVILGAILLCLGVALTFIFRLRKGRMMDVKKCGIQDTNSKK

QSDTHLEET

Inflammatory environments, like those induced by allograft transplants, attracts macrophages and inflammatory monocytes, among many other innate immune cells. The milk fat globule epidermal growth factor-8 (Mfge-8) is expressed by many murine tumours (Neutzner et al., Cancer Res. 67:6777-85 (2007)) and has been shown to contribute to local immune suppression by polarizing incoming monocytes to suppressive, M2-like macrophages (Soki et al., J Biol Chem. 289:24560-72 (2014)).

The amino acid sequences of mouse and human MFGE-8 are:

Mouse MFGE8

(SEQ ID NO: 13)

MQVSRVLAALCGMLLCASGLFAASGDFCDSSLCLNGGTCLTGQDNDI

YCLCPEGFTGLVCNETERGPCSPNPCYNDAKCLVTLDTQRGDIFTEY

ICQCPVGYSGIHCETETNYYNLDGEYMFTTAVPNTAVPTPAPTPDLS

NNLASRCSTQLGMEGGAIADSQISASSVYMGFMGLQRWGPELARLYR

TGIVNAVVTASNYDSKPWIQVNLLRKMRVSGVMTQGASRAGRAEYLK

TFKVAYSLDGRKFEFIQDESGGDKEFLGNLDNNSLKVNMFNPTLEAQ

YIKLYPVSCHRGCTLRFELLGCELHGCSEPLGLKNNTIPDSQMSASS

SYKTWNLRAFGWYPHLGRLDNQGKINAVVTAQSNSAKEWLQVDLGTQ

RQVTGIITQGARDFGHIQYVASYKVAHSDDGVQVVIVYEEQGSSKVF

QGNLDNNSHKKNIFEKPFMARYVRVLPVSWHNRITLRLELLGC

Human MFGE8

(SEQ ID NO: 14)

MPRPRLLAALCGALLCAPSLLVALDICSKNPCHNGGLCEEISQEVRG

DVFPSYTCTCLKGYAGNHCETKCVEPLGMENGNIANSQIAASSVRVT

FLGLQHWVPELARLNRAGMVNAVVTPSSNDDNPWIQVNLLRRMWVTG

VVTQGASRLASHEYLKAFKVAYSLNGHEFDFIHDVNKKHKEFVGNWN

KNAVHVNLFETPVEAQYVRLYPTSCHTACTLRFELLGCELNGCANPL

GLKNNSIPDKQITASSSYKTWGLHLFSWNPSYARLDKQGNFNAWVAG

SYGNDQWLQVDLGSSKEVTGIITQGARNFGSVQFVASYKVAYSNDSA

NVVTEYQDPRTGSSKIFPGNWDNHSHKKNLFETPILARYVRILPVAW

HNRIALRLELLGC

The potent killing potential of NK cells is also absolutely critical in graft rejection. NK cells can kill targets cells that lack MHC class I molecules, as well as other cells within an inflammatory setting. H2-M3, the murine homologue of human HLA-G has recently been shown to have a regulatory effect on NK cells, licensing them to ignore cells that lack “self molecules” (Andrews et al., Nat Immunol. 13:1171-7 (2012)). This is thought to be achieved by binding of HLA-G, immunosuppressive receptors on both NK and T-cells (Carosella et al., Adv Immunol. 127:33-144 (2015)). H2-M3 is the mouse ortholog of human HLA-G.

The amino acid sequences of mouse H2-M3 and the human counterpart, HLA-G, are:

Mouse H2-M3

(SEQ ID NO: 15)

SIEEIPRMEPRAPWMEKERPEYWKELKLKVKNIAQSARANLRTLLRY

YNQSEGGSHILQWMVSCEVGPDMRLLGAHYQAAYDGSDYITLNEDLS

SVVTAVDMVSQITKSRLESAGTAEYFRAYVEGECLELLHRFLRNGKE

ILQRADPPKAHVAHHPRPKGDVTLRCWALGFYPADITLTWQKDEEDL

TQDMELVETRPSGDGTFQKWAAVVVPSGEEQRYTCYVHHEGLTEPLA

LKWGRSSQSSVVIMV

Human HLA-G

(SEQ ID NO: 16)

MVVMAPRTLFLLLSGALTLTETWAGSHSMRYFSAAVSRPGRGEPRFI

AMGYVDDTQFVRFDSDSACPRMEPRAPWVEQEGPEYWEEETRNTKAH

AQTDRMNLQTLRGYYNQSEASSHTLQWMIGCDLGSDGRLLRGYEQYA

YDGKDYLALNEDLRSVVTAADTAAQISKRKCEAANVAEQRRAYLEGT

CVEWLHRYLENGKEMLQRADPPKTHVTHHPVFDYEATLRCWALGFYP

AEIILTWQRDGEDQTQDVELVETRPAGDGTFQKWAAVVVPSGEEQRY

TCHVQHEGLPEPLMLRWKQSSLPTIPIMGIVAGLVVLAAVVTGAAVA

AVLWRKKSSD

A set of transgenes that includes one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, H2-M3, Cd47, Cd200, FasL, Ccl21 b, Mfge8, and Spi6A can be expressed in cells. The cells may be, for example, stem cells or a cell that is amenable to genome editing, such as a cell that can be used for therapy and/or differentiated into a therapeutic cell type. The stem cells may be, for example, embryonic stem (ES) cells or induced pluripotent stem (iPS) cells. The set of transgenes may comprise 1, 2, 3, 4, 5, 6, 7, or all 8 of these genes or may comprise at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 of these genes. The cell may be further genetically modified to express one or more of TGF-β, Cd73, Cd39, Lag3, Il1r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, and/or IFNγR1 d39. The TGF-β transgene may be modified to express the gene product in a membrane-bound form (i.e., such that the gene product is expressed on the cell surface of the allograft), using methods known to those skilled in the art. For example, a method for localizing TGF-β to the membrane is to co-express TGF-β with an additional transgene encoding the LRRC32 protein or any other polypeptide that results in localization of TGF-β to the cell membrane. This protein anchors TGF-β to the membrane. (Tran D Q et al., Proc Natl Acad Sci U.S.A 106:13445-50 (2009)).

The amino acid sequence of IFNγR1 d39 is:

(SEQ ID NO: 17)

MGPQAAAGRMILLVVLMLSAKVGSGALTSTEDPEPPSVPVPTNVLIK

SYNLNPVVCWEYQNMSQTPIFTVQVKVYSGSVVTDSCTNISDHCCNI

YGQIMYPDVSAWARVKAKVGQKESDYARSKEFLMCLKGKVGPPGLEI

RRKKEEQLSVLVFHPEVVVNGESQGTMFGDGSTCYTFDYTVYVEHNR

SGEILHTKHTVEKEECNETLCELNISVSTLDSRYCISVDGISSFWQV

RTEKSKDVCIPPFHDDRKDSIWILVVAPLTVFTVVILVFAYVVYTKK

NSFKRKSIMLPKSLLSVVKSATLETKPESKYSLVTPHQPAVLESETV

ICEEPLSTVTAPDSPEAAEQEELSKETKALEAGGSTSAMTPDSPPTP

TQRRSFSLLSSNQSGPCSLTAYHSRNGSDSGLVGSGSSISDLESLPN

NNSETKMAEHDPPPVRKA

The genes may be human genes or murine genes. In an embodiment, the gene is of the same species as the recipient of the allograft recipient in which the cell is to be transplanted. In an embodiment, the gene is of any species in which the function of the gene is conserved or in which a designed biologic has the agonist function of the endogenous counterpart. Methods for introducing and expressing these transgenes in cells are described herein and are also known to those skilled in the art. Cells expressing these transgenes may be referred to as “cloaked” due to their ability to evade allorejection without systemic immunosuppression and without the need for immunosuppressive drugs.

It is contemplated herein that populations of cells derived from the above-described cloaked cells can also be used to produce a local immunosuppression when transplanted at a transplant site of an allogeneic recipient.

Before or after generating the cloaked cells of the disclosure, the cells can first be modified to be fail-safe cells. Fail-safe cells use cell division loci (CDLs) to control cell proliferation in animal cells. CDLs, as provided herein, are loci whose transcription product(s) are expressed during cell division. CDLs may be genetically modified, as described herein, to comprise a negative selectable marker and/or an inducible activator-based gene expression system, which allows a user to permit, ablate, and/or inhibit proliferation of the genetically modified cell(s) by adding or removing an appropriate inducer. Methods for making and using fail-safe cells are described, for example, in WO 2016/141480, the entire teachings of which are incorporated herein by reference. A cell may be made fail-safe first and then cloaked afterwards. Alternatively, a cell may be cloaked first and then made fail-safe afterwards.

The cell may be a vertebrate cell, for example, a mammalian cell, such as a human cell or a mouse cell. The cell may also be a vertebrate stem cell, for example, a mammalian stem cell, such as a human stem cell or a mouse stem cell. Preferably, the cell or stem cell is amenable to genetic modification. Preferably, the cell or stem cell is deemed by a user to have therapeutic value, meaning that the cell or stem cell may be used to treat a disease, disorder, defect or injury in a subject in need of treatment for same.

In some embodiments, the cell is a stem cell or progenitor cell (e.g., iPSC, embryonic stem cell, hematopoietic stem cell, mesenchymal stem cell, endothelial stem cell, epithelial stem cell, adipose stem or progenitor cells, germline stem cells, lung stem or progenitor cells, mammary stem cells, olfactory adult stem cells, hair follicle stem cells, multipotent stem cells, amniotic stem cells, cord blood stem cells, or neural stem or progenitor cells). In some embodiments, the stem cells are adult stem cells (e.g., somatic stem cells or tissue specific stem cells). In some embodiments, the stem or progenitor cell is capable of being differentiated (e.g., the stem cell is totipotent, pluripotent, or multipotent). In some embodiments, the cell is isolated from embryonic or neonatal tissue. In some embodiments, the cell is a fibroblast, monocytic precursor, B cell, exocrine cell, pancreatic progenitor, endocrine progenitor, hepatoblast, myoblast, preadipocyte, progenitor cell, hepatocyte, chondrocyte, smooth muscle cell, K562 human erythroid leukemia cell line, bone cell, synovial cell, tendon cell, ligament cell, meniscus cell, adipose cell, dendritic cells, or natural killer cell. In some embodiments, the cell is manipulated (e.g., converted or differentiated) into a muscle cell, erythroid-megakaryocytic cell, eosinophil, iPS cell, macrophage, T cell, islet beta-cell, neuron, cardiomyocyte, blood cell, endocrine progenitor, exocrine progenitor, ductal cell, acinar cell, alpha cell, beta cell, delta cell, PP cell, hepatocyte, cholangiocyte, or brown adipocyte. In some embodiments, the cell is a muscle cell (e.g., skeletal, smooth, or cardiac muscle cell), erythroid-megakaryocytic cell, eosinophil, iPS cell, macrophage, T cell, islet beta-cell, neuron, cardiomyocyte, blood cell (e.g., red blood cell, white blood cell, or platelet), endocrine progenitor, exocrine progenitor, ductal cell, acinar cell, alpha cell, beta cell, delta cell, PP cell, hepatocyte, cholangiocyte, or white or brown adipocyte. In some embodiments, the cell is a hormone-secreting cell (e.g., a cell that secretes insulin, oxytocin, endorphin, vasopressin, serotonin, somatostatin, gastrin, secretin, glucagon, thyroid hormone, bombesin, cholecystokinin, testosterone, estrogen, or progesterone, renin, ghrelin, amylin, or pancreatic polypeptide), an epidermal keratinocyte, an epithelial cell (e.g., an exocrine secretory epithelial cell, a thyroid epithelial cell, a keratinizing epithelial cell, a gall bladder epithelial cell, or a surface epithelial cell of the cornea, tongue, oral cavity, esophagus, anal canal, distal urethra, or vagina), a kidney cell, a germ cell, a skeletal joint synovium cell, a periosteum cell, a bone cell (e.g., osteoclast or osteoblast), a perichondrium cell (e.g., a chondroblast or chondrocyte), a cartilage cell (e.g., chondrocyte), a fibroblast, an endothelial cell, a pericardium cell, a meningeal cell, a keratinocyte precursor cell, a keratinocyte stem cell, a pericyte, a glial cell, an ependymal cell, a cell isolated from an amniotic or placental membrane, or a serosal cell (e.g., a serosal cell lining body cavities). In some embodiments, the cell is a somatic cell. In some embodiments, the cells are derived from skin or other organs, e.g., heart, brain or spinal cord, liver, lung, kidney, pancreas, bladder, bone marrow, spleen, intestine, or stomach. The cells can be from humans or other mammals (e.g., rodent, non-human primate, bovine, or porcine cells). It is contemplated herein that cloaked cells may be of use in cell-based therapies wherein it may be desirable to evade allorejection at a localized transplant site.

In some embodiments, the cloaked cells described herein survive in a host without stimulating the host immune response for one week or more (e.g., one week, two weeks, one month, two months, three months, 6 months, one year, two years, three years, four years, five years or more, e.g., for the life of the cell and/or its progeny). The cells maintain expression of the cloaking transgenes for as long as they survive in the host (e.g., if cloaking transgenes are no longer expressed, the cloaked cells may be removed by the host's immune system). In some embodiments, the cloaked cells further express a transgene encoding a protein that allows the cloaked cells to be detected in vivo (e.g., a fluorescent protein, such as GFP or other detectable marker).

It is contemplated herein that the combination of cloaked and fail-safe cells may be of use in cell-based therapies wherein it may be desirable to evade allorejection at a localized transplant site, while also being able to eliminate cells exhibiting undesirable growth rates, irrespective of whether such cells are generated before or after grafting the cells into a host. The combined cloaking and fail-safe technologies allows for localized immunoprotection while addressing the risk that the recipient will develop a malignancy because the cells are providing local immunosuppression.

Methods of Producing Cloaked Cells

The compositions and methods described herein can be used to reduce rejection of allogenic cells through expression of cloaking transgenes. A wide array of methods has been established for the delivery of proteins to mammalian cells and for the stable expression of genes encoding proteins in mammalian cells, which can be used to produce the cloaked cells described herein.

Polynucleotides Encoding Cloaking Proteins or Therapeutic Agents

One platform that can be used to achieve therapeutically effective expression of cloaking proteins or therapeutic agents in mammalian cells is via the stable expression of a gene encoding a cloaking protein or therapeutic agent (e.g., by integration into the nuclear or mitochondrial genome of a mammalian cell, or by episomal concatemer formation in the nucleus of a mammalian cell). The gene is a polynucleotide that encodes the primary amino acid sequence of the corresponding protein. In order to introduce exogenous genes into a mammalian cell, genes can be incorporated into a vector. Vectors can be introduced into a cell by a variety of methods, including transformation, transfection, transduction, direct uptake, projectile bombardment, and by encapsulation of the vector in a liposomes. Examples of suitable methods of transfecting or transforming cells include calcium phosphate precipitation, electroporation, microinjection, infection, lipofection and direct uptake. Such methods are described in more detail, for example, in Green, et al., Molecular Cloning: A Laboratory Manual, Fourth Edition (Cold Spring Harbor University Press, New York 2014); and Ausubel, et al., Current Protocols in Molecular Biology (John Wiley & Sons, New York 2015), the disclosures of each of which are incorporated herein by reference.

Cloaking proteins or therapeutic agents can also be introduced into a mammalian cell by targeting vectors containing portions of a gene encoding a cloaking protein or therapeutic agent to cell membrane phospholipids. For example, vectors can be targeted to the phospholipids on the extracellular surface of the cell membrane by linking the vector molecule to a VSV-G protein, a viral protein with affinity for all cell membrane phospholipids. Such a construct can be produced using methods well known to those of skill in the field.

Recognition and binding of the polynucleotide encoding a cloaking protein or therapeutic agent by mammalian RNA polymerase is important for gene expression. As such, one may include sequence elements within the polynucleotide that exhibit a high affinity for transcription factors that recruit RNA polymerase and promote the assembly of the transcription complex at the transcription initiation site. Such sequence elements include, e.g., a mammalian promoter, the sequence of which can be recognized and bound by specific transcription initiation factors and ultimately RNA polymerase.

Polynucleotides suitable for use in the compositions and methods described herein also include those that encode a cloaking protein or therapeutic agent downstream of a mammalian promoter. Promoters that are useful for the expression of a cloaking protein or therapeutic agent in mammalian cells include constitutive promoters. Constitutive promoters include the CAG promoter, the cytomegalovirus (CMV) promoter, the EF1α promoter, and the PGK promoter. Alternatively, promoters derived from viral genomes can also be used for the stable expression of these agents in mammalian cells. Examples of functional viral promoters that can be used to promote mammalian expression of these agents include adenovirus late promoter, vaccinia virus 7.5K promoter, SV40 promoter, tk promoter of HSV, mouse mammary tumor virus (MMTV) promoter, LTR promoter of HIV, promoter of moloney virus, Epstein barr virus (EBV) promoter, and the Rous sarcoma virus (RSV) promoter.

Once a polynucleotide encoding a cloaking protein or a therapeutic agent described herein below has been incorporated into the nuclear DNA of a mammalian cell, the transcription of this polynucleotide can be induced by methods known in the art. For example expression can be induced by exposing the mammalian cell to an external chemical reagent, such as an agent that modulates the binding of a transcription factor and/or RNA polymerase to the mammalian promoter and thus regulates gene expression. The chemical reagent can serve to facilitate the binding of RNA polymerase and/or transcription factors to the mammalian promoter, e.g., by removing a repressor protein that has bound the promoter. Alternatively, the chemical reagent can serve to enhance the affinity of the mammalian promoter for RNA polymerase and/or transcription factors such that the rate of transcription of the gene located downstream of the promoter is increased in the presence of the chemical reagent. Examples of chemical reagents that potentiate polynucleotide transcription by the above mechanisms include tetracycline and doxycycline. These reagents are commercially available (Life Technologies, Carlsbad, Calif.) and can be administered to a mammalian cell in order to promote gene expression according to established protocols.

Other DNA sequence elements that may be included in the nucleic acid vectors for use in the compositions and methods described herein include enhancer sequences. Enhancers represent another class of regulatory elements that induce a conformational change in the polynucleotide containing the gene of interest such that the DNA adopts a three-dimensional orientation that is favorable for binding of transcription factors and RNA polymerase at the transcription initiation site. Thus, polynucleotides for use in the compositions and methods described herein include those that encode a cloaking protein or therapeutic agent and additionally include a mammalian enhancer sequence. Many enhancer sequences are now known from mammalian genes, and examples include enhancers from the genes that encode mammalian globin, elastase, albumin, α-fetoprotein, and insulin. Enhancers for use in the compositions and methods described herein also include those that are derived from the genetic material of a virus capable of infecting a eukaryotic cell. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. Additional enhancer sequences that induce activation of eukaryotic gene transcription are disclosed in Yaniv, et al., Nature 297:17 (1982). An enhancer may be spliced into a vector containing a polynucleotide encoding a cloaking protein or therapeutic agent, for example, at a position 5′ or 3′ to this gene. In a preferred orientation, the enhancer is positioned at the 5′ side of the promoter, which in turn is located 5′ relative to the polynucleotide encoding a cloaking protein or therapeutic agent.

The nucleic acid vectors described herein may include a Woodchuck Posttranscriptional Regulatory Element (WPRE). The WPRE acts at the transcriptional level, by promoting nuclear export of transcripts and/or by increasing the efficiency of polyadenylation of the nascent transcript, thus increasing the total amount of mRNA in the cell. The addition of the WPRE to a vector can result in a substantial improvement in the level of transgene expression from several different promoters, both in vitro and in vivo.

In some embodiments, the nucleic acid vectors for use in the compositions and methods described herein include a reporter sequence, which can be useful in verifying gene expression, for example, in specific cells and tissues. Reporter sequences that may be provided in a transgene include DNA sequences encoding β-lactamase, β-galactosidase (LacZ), alkaline phosphatase, thymidine kinase, green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), luciferase, and others well known in the art. When associated with regulatory elements which drive their expression, the reporter sequences provide signals detectable by conventional means, including enzymatic, radiographic, colorimetric, fluorescence or other spectrographic assays, fluorescent activating cell sorting assays and immunological assays, including enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and immunohistochemistry. For example, where the marker sequence is the LacZ gene, the presence of the vector carrying the signal is detected by assays for β-galactosidase activity. Where the transgene is green fluorescent protein or luciferase, the vector carrying the signal may be measured visually by color or light production in a luminometer.

Techniques for Introducing Transgenes into Cells

Transfection

Techniques that can be used to introduce a transgene, such as a cloaking transgene or a therapeutic transgene described herein, into a target cell (e.g., a mammalian cell) are well known in the art. For instance, electroporation can be used to permeabilize mammalian cells (e.g., human target cells) by the application of an electrostatic potential to the cell of interest. Mammalian cells, such as human cells, subjected to an external electric field in this manner are subsequently predisposed to the uptake of exogenous nucleic acids. Electroporation of mammalian cells is described in detail, e.g., in Chu et al., Nucleic Acids Research 15:1311 (1987), the disclosure of which is incorporated herein by reference. A similar technique, Nucleofection™, utilizes an applied electric field in order to stimulate the uptake of exogenous polynucleotides into the nucleus of a eukaryotic cell. Nucleofection™ and protocols useful for performing this technique are described in detail, e.g., in Distler et al., Experimental Dermatology 14:315 (2005), as well as in US 2010/0317114, the disclosures of each of which are incorporated herein by reference.

Additional techniques useful for the transfection of target cells include the squeeze-poration methodology. This technique induces the rapid mechanical deformation of cells in order to stimulate the uptake of exogenous DNA through membranous pores that form in response to the applied stress. This technology is advantageous in that a vector is not required for delivery of nucleic acids into a cell, such as a human target cell. Squeeze-poration is described in detail, e.g., in Sharei et al., Journal of Visualized Experiments 81:e50980 (2013), the disclosure of which is incorporated herein by reference.

Lipofection represents another technique useful for transfection of target cells. This method involves the loading of nucleic acids into a liposome, which often presents cationic functional groups, such as quaternary or protonated amines, towards the liposome exterior. This promotes electrostatic interactions between the liposome and a cell due to the anionic nature of the cell membrane, which ultimately leads to uptake of the exogenous nucleic acids, for instance, by direct fusion of the liposome with the cell membrane or by endocytosis of the complex. Lipofection is described in detail, for instance, in U.S. Pat. No. 7,442,386, the disclosure of which is incorporated herein by reference. Similar techniques that exploit ionic interactions with the cell membrane to provoke the uptake of foreign nucleic acids include contacting a cell with a cationic polymer-nucleic acid complex. Exemplary cationic molecules that associate with polynucleotides so as to impart a positive charge favorable for interaction with the cell membrane include activated dendrimers (described, e.g., in Dennig, Topics in Current Chemistry 228:227 (2003), the disclosure of which is incorporated herein by reference) polyethylenimine, and diethylaminoethyl (DEAE)-dextran, the use of which as a transfection agent is described in detail, for instance, in Gulick et al., Current Protocols in Molecular Biology 40:1:9.2:9.2.1 (1997), the disclosure of which is incorporated herein by reference. Magnetic beads are another tool that can be used to transfect target cells in a mild and efficient manner, as this methodology utilizes an applied magnetic field in order to direct the uptake of nucleic acids. This technology is described in detail, for instance, in US 2010/0227406, the disclosure of which is incorporated herein by reference.

Another useful tool for inducing the uptake of exogenous nucleic acids by target cells is laserfection, also called optical transfection, a technique that involves exposing a cell to electromagnetic radiation of a particular wavelength in order to gently permeabilize the cells and allow polynucleotides to penetrate the cell membrane. The bioactivity of this technique is similar to, and in some cases found superior to, electroporation.

Impalefection is another technique that can be used to deliver genetic material to target cells. It relies on the use of nanomaterials, such as carbon nanofibers, carbon nanotubes, and nanowires. Needle-like nanostructures are synthesized perpendicular to the surface of a substrate. DNA containing the gene, intended for intracellular delivery, is attached to the nanostructure surface. A chip with arrays of these needles is then pressed against cells or tissue. Cells that are impaled by nanostructures can express the delivered gene(s). An example of this technique is described in Shalek et al., PNAS 107: 1870 (2010), the disclosure of which is incorporated herein by reference.

Magnetofection can also be used to deliver nucleic acids to target cells. The magnetofection principle is to associate nucleic acids with cationic magnetic nanoparticles. The magnetic nanoparticles are made of iron oxide, which is fully biodegradable, and coated with specific cationic proprietary molecules varying upon the applications. Their association with the gene vectors (DNA, siRNA, viral vector, etc.) is achieved by salt-induced colloidal aggregation and electrostatic interaction. The magnetic particles are then concentrated on the target cells by the influence of an external magnetic field generated by magnets. This technique is described in detail in Scherer et al., Gene Therapy 9:102 (2002), the disclosure of which is incorporated herein by reference.

Another useful tool for inducing the uptake of exogenous nucleic acids by target cells is sonoporation, a technique that involves the use of sound (typically ultrasonic frequencies) for modifying the permeability of the cell plasma membrane permeabilize the cells and allow polynucleotides to penetrate the cell membrane. This technique is described in detail, e.g., in Rhodes et al., Methods in Cell Biology 82:309 (2007), the disclosure of which is incorporated herein by reference.

Microvesicles represent another potential vehicle that can be used to modify the genome of a target cell according to the methods described herein. For instance, microvesicles that have been induced by the co-overexpression of the glycoprotein VSV-G with, e.g., a genome-modifying protein, such as a nuclease, can be used to efficiently deliver proteins into a cell that subsequently catalyzes the site-specific cleavage of an endogenous polynucleotide sequence so as to prepare the genome of the cell for the covalent incorporation of a polynucleotide of interest, such as a gene or regulatory sequence. The use of such vesicles, also referred to as Gesicles, for the genetic modification of eukaryotic cells is described in detail, e.g., in Quinn et al., Genetic Modification of Target Cells by Direct Delivery of Active Protein [abstract]. In: Methylation changes in early embryonic genes in cancer [abstract], in: Proceedings of the 18th Annual Meeting of the American Society of Gene and Cell Therapy; 2015 May 13, Abstract No. 122.

Viral Infection

In addition to achieving high rates of transcription and translation, stable expression of an exogenous gene in a mammalian cell can be achieved by integration of the polynucleotide containing the gene into the nuclear genome of the mammalian cell. A variety of vectors for the delivery and integration of polynucleotides encoding exogenous proteins into the nuclear DNA of a mammalian cell have been developed. Examples of expression vectors are disclosed in, e.g., WO 1994/011026 and are incorporated herein by reference. Expression vectors for use in the compositions and methods described herein contain a cloaking transgene or therapeutic transgene, as well as, e.g., additional sequence elements used for the expression of these agents and/or the integration of these polynucleotide sequences into the genome of a mammalian cell. Certain vectors that can be used for the expression of cloaking transgenes or therapeutic transgenes include plasmids that contain regulatory sequences, such as promoter and enhancer regions, which direct gene transcription. Other useful vectors for expression of cloaking transgenes or therapeutic transgenes contain polynucleotide sequences that enhance the rate of translation of these genes or improve the stability or nuclear export of the mRNA that results from gene transcription. These sequence elements include, e.g., 5′ and 3′ untranslated regions and a polyadenylation signal site in order to direct efficient transcription of the gene carried on the expression vector. The expression vectors suitable for use with the compositions and methods described herein may also contain a polynucleotide encoding a marker for selection of cells that contain such a vector. Examples of a suitable marker include genes that encode resistance to antibiotics, such as ampicillin, chloramphenicol, kanamycin, or nourseothricin.

Viral Vectors for Nucleic Acid Delivery

Viral genomes provide a rich source of vectors that can be used for the efficient delivery of a gene of interest into the genome of a target cell (e.g., a mammalian cell, such as a human cell). Viral genomes are particularly useful vectors for gene delivery because the polynucleotides contained within such genomes are typically incorporated into the nuclear genome of a mammalian cell by generalized or specialized transduction. These processes occur as part of the natural viral replication cycle, and do not require added proteins or reagents in order to induce gene integration. Examples of viral vectors include a retrovirus (e.g., Retroviridae family viral vector), adenovirus (e.g., Ad5, Ad26, Ad34, Ad35, and Ad48), parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g. measles and Sendai), positive strand RNA viruses, such as picornavirus and alphavirus, and double stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, modified vaccinia Ankara (MVA), fowlpox and canarypox). Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, human papilloma virus, human foamy virus, and hepatitis virus, for example. Examples of retroviruses include: avian leukosis-sarcoma, avian C-type viruses, mammalian C-type, B-type viruses, D-type viruses, oncoretroviruses, HTLV-BLV group, lentivirus, alpharetrovirus, gammaretrovirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, Virology, Third Edition (Lippincott-Raven, Philadelphia, 1996)). Other examples include murine leukemia viruses, murine sarcoma viruses, mouse mammary tumor virus, bovine leukemia virus, feline leukemia virus, feline sarcoma virus, avian leukemia virus, human T-cell leukemia virus, baboon endogenous virus, Gibbon ape leukemia virus, Mason Pfizer monkey virus, simian immunodeficiency virus, simian sarcoma virus, Rous sarcoma virus and lentiviruses. Other examples of vectors are described, for example, U.S. Pat. No. 5,801,030, the disclosure of which is incorporated herein by reference as it pertains to viral vectors for use in gene therapy.

AAV Vectors for Nucleic Acid Delivery

In some embodiments, cloaking transgenes or therapeutic transgenes described herein are incorporated into rAAV vectors and/or virions in order to facilitate their introduction into a cell. rAAV vectors useful in the compositions and methods described herein are recombinant nucleic acid constructs that include (1) a promoter, (2) a heterologous sequence to be expressed (e.g., a cloaking transgene or therapeutic transgene described herein), and (3) viral sequences that facilitate integration and expression of the heterologous genes. The viral sequences may include those sequences of AAV that are required in cis for replication and packaging (e.g., functional ITRs) of the DNA into a virion. Such rAAV vectors may also contain marker or reporter genes. Useful rAAV vectors have one or more of the AAV WT genes deleted in whole or in part, but retain functional flanking ITR sequences. The AAV ITRs may be of any serotype suitable for a particular application. Methods for using rAAV vectors are described, for example, in Tal et al., J. Biomed. Sci. 7:279 (2000), and Monahan and Samulski, Gene Delivery 7:24 (2000), the disclosures of each of which are incorporated herein by reference as they pertain to AAV vectors for gene delivery.

The transgenes and vectors described herein (e.g., a promoter operably linked to a cloaking transgene or therapeutic transgene) can be incorporated into a rAAV virion in order to facilitate introduction of the polynucleotide or vector into a cell. The capsid proteins of AAV compose the exterior, non-nucleic acid portion of the virion and are encoded by the AAV cap gene. The cap gene encodes three viral coat proteins, VP1, VP2 and VP3, which are required for virion assembly. The construction of rAAV virions has been described, for instance, in U.S. Pat. Nos. 5,173,414; 5,139,941; 5,863,541; 5,869,305; 6,057,152; and 6,376,237; as well as in Rabinowitz et al., J. Virol. 76:791 (2002) and Bowles et al., J. Virol. 77:423 (2003), the disclosures of each of which are incorporated herein by reference as they pertain to AAV vectors for gene delivery.

rAAV virions useful in conjunction with the compositions and methods described herein include those derived from a variety of AAV serotypes including AAV 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, rh10, rh39, rh43, and rh74. Construction and use of AAV vectors and AAV proteins of different serotypes are described, for instance, in Chao et al., Mol. Ther. 2:619 (2000); Davidson et al., Proc. Natl. Acad. Sci. USA 97:3428 (2000); Xiao et al., J. Virol. 72:2224 (1998); Halbert et al., J. Virol. 74:1524 (2000); Halbert et al., J. Virol. 75:6615 (2001); and Auricchio et al., Hum. Molec. Genet. 10:3075 (2001), the disclosures of each of which are incorporated herein by reference as they pertain to AAV vectors for gene delivery.

Also useful in conjunction with the compositions and methods described herein are pseudotyped rAAV vectors. Pseudotyped vectors include AAV vectors of a given serotype (e.g., AAV9) pseudotyped with a capsid gene derived from a serotype other than the given serotype (e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, etc.). Techniques involving the construction and use of pseudotyped rAAV virions are known in the art and are described, for instance, in Duan et al., J. Virol. 75:7662 (2001); Halbert et al., J. Virol. 74:1524 (2000); Zolotukhin et al., Methods, 28:158 (2002); and Auricchio et al., Hum. Molec. Genet. 10:3075 (2001).

AAV virions that have mutations within the virion capsid may be used to infect particular cell types more effectively than non-mutated capsid virions. For example, suitable AAV mutants may have ligand insertion mutations for the facilitation of targeting AAV to specific cell types. The construction and characterization of AAV capsid mutants including insertion mutants, alanine screening mutants, and epitope tag mutants is described in Wu et al., J. Virol. 74:8635 (2000). Other rAAV virions that can be used in methods described herein include those capsid hybrids that are generated by molecular breeding of viruses as well as by exon shuffling. See, e.g., Soong et al., Nat. Genet., 25:436 (2000) and Kolman and Stemmer, Nat. Biotechnol. 19:423 (2001).

Genome Editing

In addition to the above, a variety of tools have been developed that can be used for the incorporation of a gene of interest into a target cell, such as a mammalian cell. One such method that can be used for incorporating polynucleotides encoding target genes into target cells involves the use of transposons. Transposons are polynucleotides that encode transposase enzymes and contain a polynucleotide sequence or gene of interest flanked by 5′ and 3′ excision sites. Once a transposon has been delivered into a cell, expression of the transposase gene commences and results in active enzymes that cleave the gene of interest from the transposon. This activity is mediated by the site-specific recognition of transposon excision sites by the transposase. In some instances, these excision sites may be terminal repeats or inverted terminal repeats. Once excised from the transposon, the gene of interest can be integrated into the genome of a mammalian cell by transposase-catalyzed cleavage of similar excision sites that exist within the nuclear genome of the cell. This allows the gene of interest to be inserted into the cleaved nuclear DNA at the complementary excision sites, and subsequent covalent ligation of the phosphodiester bonds that join the gene of interest to the DNA of the mammalian cell genome completes the incorporation process. In certain cases, the transposon may be a retrotransposon, such that the gene encoding the target gene is first transcribed to an RNA product and then reverse-transcribed to DNA before incorporation in the mammalian cell genome. Exemplary transposon systems are the piggybac transposon (described in detail in, e.g., WO 2010/085699) and the sleeping beauty transposon (described in detail in, e.g., US 2005/0112764), the disclosures of each of which are incorporated herein by reference as they pertain to transposons for use in gene delivery to a cell of interest.

Another tool for the integration of target genes into the genome of a target cell is the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, a system that originally evolved as an adaptive defense mechanism in bacteria and archaea against viral infection. The CRISPR/Cas system includes palindromic repeat sequences within plasmid DNA and an associated Cas9 nuclease. This ensemble of DNA and protein directs site specific DNA cleavage of a target sequence by first incorporating foreign DNA into CRISPR loci. Polynucleotides containing these foreign sequences and the repeat-spacer elements of the CRISPR locus are in turn transcribed in a host cell to create a guide RNA, which can subsequently anneal to a target sequence and localize the Cas9 nuclease to this site. In this manner, highly site-specific cas9-mediated DNA cleavage can be engendered in a foreign polynucleotide because the interaction that brings cas9 within close proximity of the target DNA molecule is governed by RNA:DNA hybridization. As a result, one can design a CRISPR/Cas system to cleave any target DNA molecule of interest. This technique has been exploited in order to edit eukaryotic genomes (Hwang et al., Nature Biotechnology 31:227 (2013)) and can be used as an efficient means of site-specifically editing target cell genomes in order to cleave DNA prior to the incorporation of a gene encoding a target gene. The use of CRISPR/Cas to modulate gene expression has been described in, for example, U.S. Pat. No. 8,697,359, the disclosure of which is incorporated herein by reference as it pertains to the use of the CRISPR/Cas system for genome editing. Alternative methods for site-specifically cleaving genomic DNA prior to the incorporation of a gene of interest in a target cell include the use of zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Unlike the CRISPR/Cas system, these enzymes do not contain a guiding polynucleotide to localize to a specific target sequence. Target specificity is instead controlled by DNA binding domains within these enzymes. The use of ZFNs and TALENs in genome editing applications is described, e.g., in Urnov et al., Nature Reviews Genetics 11:636 (2010); and in Joung et al., Nature Reviews Molecular Cell Biology 14:49 (2013), the disclosure of each of which are incorporated herein by reference as they pertain to compositions and methods for genome editing.

Additional genome editing techniques that can be used to incorporate polynucleotides encoding target genes into the genome of a target cell include the use of ARCUS™ meganucleases that can be rationally designed so as to site-specifically cleave genomic DNA. The use of these enzymes for the incorporation of genes encoding target genes into the genome of a mammalian cell is advantageous in view of the defined structure-activity relationships that have been established for such enzymes. Single chain meganucleases can be modified at certain amino acid positions in order to create nucleases that selectively cleave DNA at desired locations, enabling the site-specific incorporation of a target gene into the nuclear DNA of a target cell. These single-chain nucleases have been described extensively in, for example, U.S. Pat. Nos. 8,021,867 and 8,445,251, the disclosures of each of which are incorporated herein by reference as they pertain to compositions and methods for genome editing.

Expression of Cloaking Transgenes

The cloaking transgenes described herein (e.g., one of, or any combination of, PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)) are expressed in an amount sufficient to produce a cloaking effect (e.g., in an amount sufficient to prevent rejection when injected into a subject, e.g., a mammalian subject, such as a mouse, rat, or human). Transgene expression can be considered to produce a cloaking effect if subcutaneous injection of cloaked cells generates a teratoma that is not removed by the subject's immune system. The cloaking transgenes are also expressed at a level that is sufficient to promote production of the proteins encoded by said transgenes. Protein production can be detected using routine methods known to those of skill in the art (e.g., immunohistochemistry, Western Blot analysis, or other methods that allow for visualization or proteins). Preferably, the expression of the cloaking transgenes is such that all 8 proteins encoded by the cloaking transgenes (PD-L1, H2-M3, Cd47, Cd200, FasL, Ccl21 b, Mfge8, and Spi6) can be detected in cloaked cells (e.g., detected by immunohistochemistry using antibodies directed against the proteins encoded by the cloaking transgenes).

In some embodiments, cloaking transgenes are expressed at similar levels in cloaked cells to levels of endogenous gene expression in activated leukocytes, such as T cells (e.g., activated leukocytes from the same species, such as an activated leukocyte isolated from a lymph organ, for example expression in a cloaked mouse cell is similar to expression in an activated leukocyte isolated from a murine lymphoid organ). The expression of one or more cloaking transgenes (e.g., 1, 2, 3, 4, 5, 6, 7, or 8 of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)) is greater than or equal to expression of the endogenous gene in activated leukocytes (e.g., T cells) from the same species (e.g., expression level of the cloaking transgene is equal to the level of expression of the endogenous gene in activated leukocytes, or is 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10-fold or more higher than the level of expression of the endogenous gene in activated leukocytes). In some embodiments, all 8 cloaking transgenes are expressed at a level that is greater than or equal to the expression level of the endogenous gene in an activated leukocyte from the same species. Activated leukocytes can be isolated from lymphoid organs, or leukocytes, such as T cells, can activated in vitro using anti-CD3/CD28 beads or other methods employed by those of skill in the art (see, e.g., Frauwith and Thompson, J.Clin Invest 109:295-299 (2002); and Trickett and Kwan, J Immunol Methods 275:251-255 (2003)). Transgene expression in cloaked cells can also be compared to gene expression levels reported in profiling studies of activated T cells (see, e.g., Palacios et al., PLOSone 2:e1222 (2007)). In some embodiments, cloaking transgene expression is compared to expression of the endogenous gene in a wild-type version of the cell (e.g., a stem cell, e.g., an embryonic stem cell from the same species as the cloaked cell). The expression of one or more cloaking transgenes (e.g., 1, 2, 3, 4, 5, 6, 7, or 8 of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)) is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100, 500, 1,000-fold or more higher in cloaked cells compared to expression of the endogenous gene in unmodified wild-type cells of the same cell type as the cloaked cell (e.g., stem cells, such as embryonic stem cells from the same species). In some embodiments, all 8 cloaking transgenes are expressed at a level that is greater (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or 100-fold higher or more) than the expression level of the endogenous gene in a wild-type version of the cell (e.g., a stem cell, e.g., an embryonic stem cell from the same species as the cloaked cell). Gene expression can be evaluated through direct comparison to isolated ES cells, or compared to stem cell expression (e.g., ES cell expression) in the Project Grandiose dataset (www.stemformatics.org/project_grandiose). Gene expression can be measured using techniques known in the art (e.g., quantitative polymerase chain reaction (qPCR)).

Methods of Providing a Local Immunosuppression at a Transplant Site

Also featured is a method of providing local immunosuppression at a transplant site.

The method comprises providing a cell; and expressing in the cell a set of transgenes, each transgene encoding a gene product that is cytoplasmic, membrane bound, or local acting and whose function is to mitigate function of graft attacking leukocyte and NK cell activation or act as a defense mechanism against attacking leukocytes.

The set of transgenes comprises one or more (e.g., two, three, four, five, six, seven, or all eight) of the following genes: PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6). In an embodiment, the set of transgenes genes comprises Pd-L1, H2-M3, Cd47, Cd200, FasL, Ccl21 b, Mfge8, and Spi6.

Optionally, the method further comprises expressing one or more of the following transgenes in the cell: TGF-β, Cd73, Cd39, Lag3, Il1r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1, and IFNγR1 d39. In an embodiment, the TGF-β or the biologic is local acting.

Techniques for introducing into animal cells various genetic modifications, such as transgenes are described herein and are generally known in the art.

In an embodiment of the method, the cell is a stem cell, a cell amenable to genome editing, and/or a source of therapeutic cell type (e.g., a cell that can be differentiated into a lineage restricted cell for cell therapy, or a cell of a desired target tissue). In an embodiment, the cell is an embryonic stem cell, an induced pluripotent stem cell, an adult stem cell, a tissue-specific stem cell, a hematopoietic stem cell, a mesenchymal stem cell, an endothelial stem cell, an epithelial stem cell, an adipose stem or progenitor cells, germline stem cell, a lung stem or progenitor cell, a mammary stem cell, an olfactory adult stem cell, a hair follicle stem cell, a multipotent stem cell, an amniotic stem cell, a cord blood stem cell, or a neural stem or progenitor cell. In some embodiments, the cell is derived from a target tissue, e.g., skin, heart, brain or spinal cord, liver, lung, kidney, pancreas, bladder, bone marrow, spleen, intestine, or stomach. In some embodiments, the cell is a fibroblast, an epithelial cell, or an endothelial cell. The cell may be a vertebrate cell, for example, a mammalian cell, such as a human or mouse cell. In some embodiments, the cell that is modified to express one or more (e.g., two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) is a cell in the tissue or organ to be transplanted. In some embodiments, the cloaked cells (e.g., cloaked stem cells) are differentiated in vitro using methods known by those of skill in the art into a tissue or organ for transplantation.

In some embodiments, one million to one hundred billion cloaked cells (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10°, 2×10°, 3×10°, 4×10⁹, 5×10⁹, 6×10°, 7×10⁹, 8×10⁹, 9×10⁹, 1×10¹⁰, 2×10¹⁰, 3×10¹⁰, 4×10¹°, 5×10¹°, 6×10¹°, 7×10¹⁰, 8×10¹°, 9×10¹⁰, or 1×10¹¹cloaked cells) are administered to or near a transplant site in a subject, or into an organ or tissue to be transplanted.

Techniques for transplanting the genetically modified cells into a transplant site of an allogeneic host are described herein and are generally known in the art.

Expression of Therapeutic Agents by Cloaked Cells

The cloaked cells described herein can be further modified to express a therapeutic agent. In some embodiments, the therapeutic agent is a protein. The therapeutic protein can be a wild type form of a protein that is deficient in a subject, such as a protein that is mutated or produced in insufficient quantity (e.g., produced at low levels or not produced) by the subject's cells. In some embodiments, the therapeutic protein is an inhibitory antibody (e.g., an antibody that blocks or neutralizes protein function). The cloaked cells may be modified to produce an inhibitory antibody to treat a subject having or at risk of developing a disease or condition related to overproduction or aberrant production of a protein (e.g., production by cells that do not normally produce the protein, production of a protein at a time or in a location at which the protein is not normally produced, or production of an excessive amount of a protein). In some embodiments, the therapeutic antibody is an agonist antibody (e.g., an activating antibody). The agonist antibody can act by binding to and activating an endogenous receptor (e.g., inducing or increasing signaling downstream of receptor activation or changing the conformation of the endogenous receptor to an open or active state). The cloaked cells may be modified to produce an agonist antibody to treat a subject having or at risk of developing a disease or condition related to under activation of a receptor or signaling pathway. The cloaked cells can be modified to produce the therapeutic protein or antibody using the methods described herein or using other methods known by those of skill in the art. Cloaked cells that produce a secreted protein or antibody can be delivered as circulating cells, injected into the tissue, organ, or body site in need of the therapeutic protein or antibody, or injected subcutaneously to produce a cloaked subcutaneous tissue. Cloaked cells that produce a transmembrane or membrane-bound protein, can be injected at or near the site of the endogenous cells that respond to the therapeutic protein.

In some embodiments, the cloaked cells described herein provide a wild-type copy of a gene that is mutated in the subject (e.g., the cloaked cell is a “wild-type cell” that does not have the genetic cause of the disease and that expresses one, two, three, four, five, six, seven or all eight of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6)). Such cells can be used to treat subjects having a disease or condition caused by a mutation in an endogenous gene (e.g., subjects having a metabolic disorder associated with one or more mutations described herein below).

A list of exemplary therapeutic agents that can be administered with or produced by cloaked cells and the associated diseases or conditions that can be treated using these therapeutic agents are provided in Table 2 below.

TABLE 2

Exemplary therapeutic agents that can be administered

with or expressed by cloaked cells to treat disease

Disease or Condition
Therapeutic Agent

Diabetes, altered
Insulin, insulotropin, glucagon

glycemic states

Skeletal growth
Human growth hormone

retardation

Anemia
Erythropoietin (EPO), hemoglobins

Obesity
Ob gene translation product (leptin)

Immunodeficiency
Adenosine deaminase, purine nucleoside

(e.g., AIDS)
phosphorylase, CD-4

Hemophilia A
Factor VIII

Hemophilia B
Factor IX

Emphysema
α₁-antitrypsin

Hypercholesterolemia
LDL receptor protein

Disease or Condition
Therapeutic Agent

Pernicious anemia
Intrinsic factor

Hypoalbuminemia
Albumin

Gaucher's disease
B-glucosidase (glucocerebrosidase)

Cystic fibrosis
CF transmembrane conductance regulator

Cardiovascular
Tissue Plasminogen Activator (tPA),

disease
urokinase, streptokinase, antithrombin III,

Apolipoproteins (e.g., APO B48, A1), Low

Density lipoprotein receptor, vascular

endothelial growth factor (VEGF)

Calcium mineral
Calcitonin, parathyroid hormone (PTH), PTH-

diseases
like hormone

Severe Combined
Adenosine deaminase

Immunodeficiency

(SCID)

Phenylketonuria
Phenylalanine hydroxylase

von Willebrand's
von Willebrand Factor

disease

Cancers, cancer
Tumor Necrosis Factors (TNFs), cytokines,

suppression
anti-neoplastic agents (e.g., vincristine,

doxorubicin, tamoxifen, methotrexate),

interleukins (ILs), interferons (INFs), p53 and

related, anti-BRCAs, anti-VEGF (bevacizumab),

anti-

Epidermal Growth Factor (EGF), oncogene

anti-sense RNAs, antibodies (e.g., Rituximab;

Daclizumab; Basiliximab; Palivizumab;

Infliximab; Trastuzumab; Gemtuzumab

ozogamicin; Alemtuzumab; Ibritumomab

tiuxetan; Adalimumab; Omalizumab;

Tositumomab-I-131; Efalizumab; Cetuximab;

Bevacizumab; Natalizumab; Tocilizumab;

Panitumumab; Ranibizumab; Eculizumab;

Certolizumab pegol; Golimumab; Canakinumab;

Ustekinumab; Ofatumumab; Denosumab;

Motavizumab; Raxibacumab; Belimumab;

Ipilimumab; Brentuximab Vedotin; Pertuzumab;

Ado-trastuzumab emtansine; or Obinutuzumab),

or checkpoint inhibitors (e.g., nivolumab,

pidilizumab/CT-011, pembrolizumab,

ipilimumab, or tremelimumab)

Peripheral vascular
VEGF, endothelins

disease

Neurodegenerative
Ciliary Neurotrophic Factor (CNTF), Brain

states, and post neural
Derived Neurite Factor (BDNF), Nerve Growth

trauma conditions
Factor (NGF), tyrosine hydroxylase

Retarded fracture
Bone morphogenic proteins (BMP)

healing

Lactose insufficiency
Lactase

Wound healing
Epidermal Growth Factors, Transforming

Growth Factors, Granulocyte-Colony

Stimulating Factors, Fibroblast Growth

Factors, Interferons, Interleukins, Insulin-like

growth Factors

Thrombosis,
Antithrombins, urokinases, tPAs , hirudins,

hypercoagulability
streptokinase

Diabetes insipidus
Antidiuretic hormone (ADH)

Psychiatric Disorders
Selective Serotonin Reuptake Inhibitors, anti-

psychotic bio-substances

Pain Control
Endorphins

Endocrineopathies
Estrogens, Androgens, mineralocorticoids,

glucocorticoids, anabolic steroids, etc.

Hypothyroidism
Thyroid hormones, thyroglobulins

Muscular dystrophy
Dystrophin

Infections (bacterial,
Anti-microbial polypeptides

fungal, viral)

Shock, Sepsis
Lipid Binding Protein (LBP)

Leukemia
L-asparaginase

Disorders of digestive,
Pepsin, trypsin, chymotrypsin, cholecystokinin,

pancreatic states
sucrase carboxypeptidase

Oxidative Stress,
Catalase

Neurodegenerative

Disorders

Hypouricasemia, Gout
Uricase

Ehlers Danlos
Elastase

Thrombocytopenia
Thrombopoietin (TPO)

SCID/ADA deficiency
Adenosine deamidase

Porphyria
Porphobilinogen deaminase

Inborn errors of
Specific enzymes catalyzing transformations at

carboxylic and amino
genetic block points, (e.g., glutaryl CoA

acid metabolism, (e.g.,
dehydrogenase)

glutaric acidemia)

Homocystinuria
Cystathionine B-synthase

Wilson's Disease,
Specific copper transporting ATPase's

Menkes Disease

Thalassemia
β-globin

Sickle Cell Anemia
α-globin

Baldness
Sonic hedgehog gene products

Hashimoto's
Thyroid hormone

Thyroiditis,

Wet Age-Related
VEGF trap (e.g., a soluble decoy receptor

Macular Degeneration
described in Holash et al., Proc Natl Acad Sci

or Retinal Dystrophy
U.S.A. 99: 11383-11398, 2002, e.g., VEGF-

Trap_parental, VEGF-Trap_ΔB1, VEGF-Trap_ΔB2,

VEGF-Trap_R1R2, e.g., aflibercept), soluble forms

of VEGF receptors (e.g., soluble VEGFR-1 or

NRP-1), platelet factor-4, prolactin, SPARC,

VEGF inhibitory antibodies (e.g.,

bevacizumab or ranibizumab).

Osteoarthritis or
TNFα inhibitors (adalimumab, etanercept,

Rheumatoid Arthritis
infliximab, golimumab, certolizumab), interleukin-

6 (IL6) receptor inhibitors (e.g., tocilizumab), IL1

receptor inhibitors (e.g., anakinra), or other

agents used to treat RA (e.g., abatacept,

rituximab)

Inflammatory Bowel
TNFα inhibitors (adalimumab, etanercept,

Disease, Crohn's
infliximab, golimumab, certolizumab),

disease,
mesalazine, prednisone, azathioprine,

Ulcerative Colitis
methotrexate

Addison's Disease
Aldosterone, cortisol, glucocorticoids,

mineralocorticoids, androgens

Hurler syndrome
Alpha-L iduronidase

Niemann-Pick
Sphingomyelin phosphodiesterasel (SMPD1),

disease
NPC1 protein, or NPC2 protein

Tay-Sachs disease
beta-hexosaminidase A

Fabry disease
alpha galactosidase

Krabbe disease
Galactosylceramidase

Galactosemia
Galactokinase or galactose-1-phosphate

uridyltransferase

Maple syrup urine
Enzymes of the branched-chain alpha-keto acid

disease
dehydrogenase complex

Phenylketonuria
Phenylalanine hydroxylase

Glycogen storage
GSD0: Glycogen synthase (GYS2);

diseases (GSDs)
GSD1/von Gierke's disease: Glucose-6-

phosphatase (G6PC);

GSD 2/Pompe's disease: Acid alpha-glucosidase

(GAA);

GSD 3/Cori's disease or Forbes' disease:

Glycogen debranching enzyme (AGL);

GSD 4/Andersen disease: Glycogen branching

enzyme (GBE1);

GSD 5/McArdle disease: Muscle glycogen

phosphorylase (myophosphorylase) (PYGM);

GSD 6/Hers' disease: Liver glycogen

phosphorylase (PYGL) or muscle

phosphoglycerate mutase (PGAM2);

GSD 7/Tarui's disease: Muscle

phosphofructokinase (PKFM);

GSD 9: Glycogen phosphorylase kinase B

(PHKA2, PHKB, PHKG2, or PHKA1),

GSD 10: Enolase 3 (ENO3);

GSD 11: Muscle lactate dehydrogenase (LDHA);

Fanconi-Bickel syndrome: Glucose transporter 2

(GLUT2);

GSD 12: Aldolase A (ALDOA);

GSD 13: β-enolase (ENO3);

GSD 15: Glycogenin-1 (GYG1)

Mitochondrial
Leber's hereditary optic neuropathy (LHON):

disorders
NADH dehydrogenase;

Leigh syndrome: thiamine-diphosphate kinase,

thiamine triphosphate, or pyruvate

dehydrogenase;

Neuropathy, ataxia, retinitis pigmentosa, and

ptosis (NARP: ATP synthase;

Myoneurogenic gastrointestinal encephalopathy

(MNGIE): thymidine phosphorylase (TYMP);

Mitochondria myopathy, encephalomyopathy,

lactic acidosis, stroke-like symptoms (MELAS):

NADH dehydrogenase

Friedrich's ataxia
Frataxin (FXN)

Peroxisomal
Zellweger syndrome: Proteins encoded by PEX1,

disorders
PEX2, PEX3, PEX5, PEX6, PEX10, PEX12,

PEX13, PEX14, PEX16, PEX19, or PEX26;

Adrenoleukodystrophy: protein encoded by

ABCD1

Metal metabolism
Wilson disease: Wilson disease protein (ATP7B);

disorders
Hemochromatosis: Human hemochromatosis

protein (HFE)

Organic acidemias
Methylmalonic acidemia: methylmalonyl CoA

mutase, methylmalonyl CoA epimerase,

adenosylcobalamin

Propionic academia: propionyl-CoA carboxylase

Urea cycle disorders
Ornithine transcarbamylase (OTC), deficiency:

Ornithine transcarbamylase;

Arginase (ARG1) deficiency: Arginase;

Argininosuccinate lyase (ASL) deficiency:

Argininosuccinate lyase;

Argininosuccinate synthase 1 (ASS1) deficiency:

Argininosuccinate synthase 1;

Citrin deficiency: Citrin;

Carbamoyl phosphate synthase 1 (CPSI)

deficiency: Carbamoyl phosphate synthase 1;

N-acetylglutamate synthase (NAGS) deficiency:

N-acetylglutamate synthase;

Ornithine translocase (ORNT1) deficiency:

Ornithine translocase

Inducible Systems for Expression of Therapeutic Agents

If continuous administration of a therapeutic agent expressed by cloaked cells is needed to treat a disease or condition, the therapeutic agent can be expressed using a constitutive promoter described herein or known by those of skill in the art (e.g., CAG, CMV, or another constitutive promoter). If the therapeutic agent is needed intermittently (e.g., needed during a period of relapse or flare up that occurs during a disease or condition, but not needed when a subject is asymptomatic), it can be expressed by an inducible promoter, which provides the capability of expressing the therapeutic agent only when it is needed. One exemplary class of therapeutic agents that could be delivered using an inducible promoter is TNFα inhibitors. TNFα inhibitors are currently used to treat rheumatoid arthritis, but are only administered intermittently during flare-ups of joint inflammation as constitutive administration of TNFα can lead to systemic immunosuppression. If cloaked cells are modified to express TNFα inhibitors under the control of an inducible promoter, cloaked cells can be used to deliver TNFα intermittently, thus, obviating the need for repeated injections. Other therapeutic agents that have potentially adverse effects if administered continuously can also be expressed intermittently using inducible promoters as described herein. Exemplary inducible expression systems are described below.

Tetracycline Response Element

One widely used inducible expression system is based on tetracycline-controlled transcriptional activation. In this system, the antibiotic tetracycline, or one of its derivatives (e.g., doxycycline), is used to reversibly activate or inhibit gene expression. To use this system, a tetracycline response element (TRE) is placed upstream of a gene of interest (e.g., a therapeutic transgene to be expressed by cloaked cells), typically along with a minimal promoter that has very low basal expression. A protein called rtTA, which also needs to be expressed by the cloaked cells, binds to the TRE and activates transcription in the presence of tetracycline or doxycycline. When tetracycline or doxycycline is removed, rtTA no longer binds to the TRE and the gene of interest is no longer expressed. Advanced versions of this system, Tet-On Advanced transactivator (rtTA2⁵-M2) and Tet-On 3G, may be particularly useful for human therapy as they are human codon optimized and respond to low concentrations of doxycycline,

Light Inducible Systems

Another method for inducible activation of gene expression involves the use of optogenetics, which uses light sensitive proteins to manipulate gene expression. A recent development in optogenetics that can be used to inducibly express therapeutic agents in cloaked cells involves a class of proteins that undergo a conformational change and dimerize in response to blue light. These proteins have been fused to DNA-binding and transcriptional components that have been shown to bind to specific promoter sequences and activate transcription when brought together by exposure to blue light (Wang et al., Nat Methods, 9:266-269, 2012). This method of inducibly activating gene expression could be used to control the production of therapeutic agents in cloaked cells that are administered subcutaneously, as blue light can be shone onto the skin near the cloaked subcutaneous tissue to induce production of a therapeutic agent by the cloaked cells.

Radiogenetics

A third method of inducibly activating gene expression (e.g., expression of a therapeutic agent by cloaked cells) involves the use of radio waves. In one version of a radio wave-inducible expression system, the TRPV1 receptor is fused to a GFP binding domain and co-expressed with a form of ferritin that is linked to GFP (Stanley et al., Nat Med 21:92-98, 2015). The GFP-ferritin binds to the GFP binding domain of the TRPV1 receptor. When a radio wave of a specific frequency is applied to the cell, ferritin interacts with TRPV1 and allows for an influx of calcium, which activates the transcription factor NFAT. Therapeutic agents can be inducibly expressed using this system if they are operably linked to an NFAT-sensitive promoter element, such as SRE-CRE-NFATRE, and co-expressed with TRPV1-GFP and GFP-ferritin. Radio wave-induced expression provides the advantage of being able to induce expression in cells that are further from the outside of the body, as radio waves can pass through tissue. For example, radiogenetics could be used to regulate gene expression in the retina. This method could, therefore, be used to inducibly express therapeutic transgenes in cloaked cells with non-invasive and non-harmful radio waves.

Destabilization Domain System

Gene expression can also be regulated using destabilization domain systems. A transgene encoding a protein of interest (e.g., a therapeutic agent described herein) can also include destabilizing domains, such that the resulting protein product includes the protein of interest fused to a destabilizing domain. Exemplary destabilizing domains include mutants of the human FK506- and rapamycin-binding protein (FKBP12), which confer instability to the proteins to which they are fused. FKBP12 mutants include N-terminal mutants F15S, V24A, H25R, E60G, and L106P, and C-terminal mutants M66T, R71G, 0100G, 0100N, E102G, and K1051, as characterized in Banaszynski et al., Cell 126:995 (2006), the disclosure of which is incorporated herein by reference as it pertains to FKBP12 destabilizing domains. Destabilizing domains promote protein degradation. A small molecule synthetic ligand can be used to stabilize the destabilizing domain-containing proteins when expression of the protein of interest (e.g., a therapeutic agent) is desired. The small molecule ligand Shield-1 (Shld1) can be used to stabilize FKBP12 mutant-containing proteins by protecting them from degradation. Other destabilizing domains that can be used to regulate expression proteins of interest include mutants of the E. coli dihydrofolate reductase (ecDHFR) and mutants of the human estrogen receptor ligand binding domain (ERLBD), which confer instability resulting in degradation when fused to a protein of interest and can be stabilized by small molecule ligand trimethoprim (TMP), or by CMP8 or 4-hydroxytamoxifen (4OHT), respectively, as described in Iwamoto et al., Chem Biol. 17:981 (2010) and Miyazaki et al., J Am Chem Soc., 134:3942 (2012), the disclosures of each of which are incorporated herein by reference as they pertain to destabilization domain systems.

Cumate Switch Inducible System

Another method for inducible activation of gene expression involves the use of the cumate gene-switch system. In the repressor configuration of this system, regulation is mediated by the binding of the repressor (CymR) to the operator site (CuO), placed downstream of a strong constitutive promoter. Addition of cumate, a small molecule, relieves the repression, allowing for expression of the transgene. Alternatively, a reverse-cumate-Trans-Activator (rcTA) may be inserted upstream of a minimal CMV promoter that is operably linked to a transgene encoding a therapeutic agent. A 6-times repeat of a Cumate Operator (6×CuO) may be inserted just before the translational start (ATG) of the therapeutic transgene. In the absence of cumate, rcTA cannot bind to the 6×CuO, so the transgene encoding the therapeutic agent will not be transcribed because the 6×CuO is not active. When cumate is added, it will form a complex with rcTA, which allows for binding to 6×CuO and transcription of the transgene encoding the therapeutic agent (Mullick et al., 2006).

Ecdysone Inducible System

Another example of an inducible gene expression system is the ecdysone inducible system, in which a retinoid X receptor (RXR) and an N-terminal truncation of ecdysone receptor (EcR) fused to the activation domain of Vp16 (VpEcR) are inserted in the 5′ untranslated region of a gene expressed by the cloaked cell such that they are co-expressed by an endogenous promoter. An ecdysone responsive element (EcRE), with a downstream minimal promoter, can be inserted just upstream of the start codon of the transgene encoding the therapeutic agent. Co-expressed RXR and VpEcR can heterodimerize with each other. In the absence of ecdysone or synthetic drug analog muristerone A, dimerized RXR/VpEcR cannot bind to EcRE, so the transgene encoding the therapeutic agent is not transcribed. In the presence of ecdysone or muristerone A, dimerized RXR/VpEcR can bind to EcRE, such that the transgene encoding the therapeutic agent is transcribed (No et al., 1996). As ecdysone administration has no apparent effect on mammals, its use for regulating genes should be excellent for transient inducible expression of any gene.

Ligand-Reversible Dimerization System

In another example, the transgene encoding a therapeutic agent can be modified so that it is functionally divided in to parts/domains, such as a 5′ portion and a 3′ portion, and an FKBP peptide sequence can be inserted into each domain. An IRES (internal ribosomal entry site) sequence may be placed between the two domains, which allows for simultaneous transcription of the two different domains to generate two separate proteins. In the absence of a dimerization agent, the two separate domains of the therapeutic agent will be functionally inactive. Upon introduction of a dimerization agent, such as rapamycin or AP20187, the FKBP peptides will dimerize, bringing together the 5′ and 3′ domains of the therapeutic agent and reconstituting an active protein (Rollins et al., 2000).

Cell-Based Delivery of a Therapeutic Agent

Treatment of Age-Related Macular Degeneration or Retinal Dystrophy

In one example, cloaked cells can be modified to produce a VEGF inhibitor, such as VEGF trap (e.g., a soluble decoy receptor described in Holash et al., Proc Natl Acad Sci U.S.A. 99:11383-11398, 2002, incorporated herein by reference, such as aflibercept) to treat age-related macular degeneration (AMD) or retinal dystrophy. VEGF trap is a biologic that binds to and inhibits VEGF, an angiogenic protein that can promote the formation of aberrant blood vessels. VEGF trap is used to treat wet AMD, which features aberrant growth of blood vessels beneath the retina that can lead to retinal detachment and progressive vision loss. To treat AMD, VEGF trap is typically delivered by regular injection into the eye. Cloaked cells can be modified to produce VEGF trap or another VEGF inhibitor by expression of a transgene encoding VEGF trap or another VEGF inhibitor operably linked to a constitutive or inducible promoter. Cloaked cells (e.g., stem cells) that express a VEGF inhibitor (e.g., VEGF trap) can be differentiated into retinal pigmented epithelium (RPE) cells before administration to the eye using methods known by those of skill in the art, or isolated RPE cells can be modified to express cloaking transgenes and a VEGF inhibitor. Twenty five thousand to one hundred thousand cloaked RPE cells (e.g., 25,000, 50,000, 75,000 or 100,000 cloaked RPE cells) expressing a VEGF inhibitor (e.g., VEGF trap) can be injected into the subretinal space of each eye to treat wet AMD or retinal dystrophy. Other VEGF inhibitors suitable for use in the compositions and methods described herein include soluble forms of VEGF receptors (e.g., soluble VEGFR-1 or NRP-1), platelet factor-4, prolactin, SPARC, and VEGF inhibitory antibodies (e.g., bevacizumab and ranibizumab).

Treatment of Parkinson's Disease

In another example, cloaked cells, such as dopaminergic neurons or cells (e.g., stem cells) that can be differentiated in vitro to produce dopaminergic neurons using methods known by those of skill in the art, can be administered to subjects suffering from Parkinson's disease, which is characterized by loss of dopaminergic neurons. Twenty five thousand to one hundred thousand cloaked dopaminergic neurons (e.g., 25,000, 50,000, 75,000 or 100,000 cloaked dopaminergic neurons) can be administered to the brain of a subject suffering from Parkinson's disease (e.g., stereotactically injected into the substantia nigra).

Treatment of Cardiac Infarction

The cloaked cells described herein can also be used to treat cardiac infarction (e.g., myocardial infarction, commonly known as a heart attack). Cardiac infarction occurs when blood flow decreases or stops to a part of the heart, causing damage to the heart muscle. To treat subjects who have suffered a cardiac infarction, cloaked cells (e.g., stem cells) can be differentiated into cardiac muscle cells using methods known by those of skill in the art, or isolated cardiac muscle cells can be modified to express cloaking transgenes. Five hundred million to five billion cloaked cardiac muscle cells (e.g., 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, 3×10⁹, 4×10⁹, or 5×10⁹cloaked cardiac muscle cells) can be administered to a subject by injection into the cardiac muscle to treat a subject who has suffered a cardiac infarction (e.g., to replace dead or damaged cardiac muscle cells).

Treatment of Osteoarthritis and Rheumatoid Arthritis

In another example, the cloaked cells described herein can be used to treat osteoarthritis or rheumatoid arthritis. Osteoarthritis and rheumatoid arthritis (RA) are characterized by joint inflammation, and are commonly treated with anti-inflammatory therapeutics. To treat subjects suffering from osteoarthritis or RA, cloaked cells can be modified to express anti-inflammatory biologics, such as inhibitors of TNFα (e.g., TNFα inhibitory antibodies), which are already in clinical use for the treatment of RA. Cloaked cells can be modified to produce an anti-inflammatory biologic, such as a TNFα inhibitor, by expression of a transgene encoding an anti-inflammatory biologic operably linked to a constitutive or inducible promoter. Cloaked cells (e.g., stem cells) that express an anti-inflammatory biologic (e.g., a TNFα inhibitor) can be differentiated into articular fibroblasts before administration to a joint using methods known by those of skill in the art, or isolated articular fibroblasts can be modified to express cloaking transgenes and an anti-inflammatory biologic. One million to one hundred million cloaked articular fibroblasts (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸cloaked articular fibroblasts) expressing an anti-inflammatory biologic can be injected into an arthritic or inflamed joint (depending on joint size) to treat osteoarthritis or RA. Anti-inflammatory biologics that can be expressed by cloaked cells to treat osteoarthritis or RA include TNFα inhibitors (adalimumab, etanercept, infliximab, golimumab, certolizumab), interleukin-6 (IL6) receptor inhibitors (e.g., tocilizumab), IL1 receptor inhibitors (e.g., anakinra), or other agents used to treat RA (e.g., abatacept, rituximab).

Treatment of Diabetes

The cloaked cells can be used to treat diabetes (e.g., Type 1 or Type 2 diabetes). Type 1 diabetes results from a failure of the pancreas to produce enough insulin. Type 2 diabetes begins with insulin resistance, but a lack of insulin may develop as the disease progresses. To treat subjects suffering from diabetes, cloaked cells can be modified to express insulin, or insulin-expressing cells from a healthy subject (e.g., pancreatic beta cells from a subject without diabetes) can be modified to express one or more (e.g., one, two, three, four, five, six, seven or all eight) of cloaking transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) and administered to a subject with diabetes. Cloaked cells can be modified to produce insulin by expression of a transgene encoding insulin operably linked to a constitutive or inducible promoter. Cloaked cells (e.g., stem cells) that express insulin can be differentiated into insulin producing cells (e.g., pancreatic beta cells) prior to administration using methods known by those of skill in the art or can be administered without differentiation, or isolated pancreatic beta cells can be modified to express cloaking transgenes and, optionally, to express a transgene encoding insulin. Eight hundred million to three billion cloaked pancreatic beta cells (e.g., 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹cloaked pancreatic beta cells) expressing insulin (e.g., expressing insulin endogenously or expressing insulin due to expression of a transgene encoding insulin) to can be injected subcutaneously in a subject to create a cloaked subcutaneous tissue that produces insulin for treating diabetes.

Treatment of Hemophilia

In another example, the cloaked cells described herein can be used to treat hemophilia. Patients with hemophilia do not produce a functional Factor VIII protein, which is a critical blood component needed for blood clotting. These patients can have severe bleeding, and the standard of care involved multiple injections per week of a purified Factor VIII protein. To treat subjects suffering from hemophilia, cloaked cells can be modified to express an additional transgene that encodes Factor VIII. Factor VIII would be expressed constitutively in cloaked cells by being operably linked to a constitutive promoter, such as CMV or CAG. Cloaked cells (e.g., stem cells) that express Factor VIII can be differentiated into cells that produce blood coagulation factors (e.g., liver sinusoidal cells or endothelial cells) prior to administration using methods known by those of skill in the art or can be administered without differentiation, or isolated Factor VIII-expressing liver sinusoidal cells or endothelial cells from a healthy subject (e.g., a subject without hemophilia) can be modified to express one or more (e.g., one, two, three, four, five, six, seven or all eight) of cloaking transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) and administered to a subject with hemophilia. Isolated Factor VIII-expressing liver sinusoidal cells or endothelial cells from a healthy subject that are modified to express one or more cloaking transgenes, can be further modified to express a transgene encoding Factor VIII, if desired to ensure that Factor VIII is expressed at high levels. Eight hundred million to three billion cloaked cells (e.g., 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹cloaked cells) expressing Factor VIII (e.g., expressing Factor VIII endogenously or expressing Factor VIII due to expression of a transgene encoding Factor VIII) can be injected subcutaneously in a subject to create a cloaked subcutaneous tissue that produces Factor VIII for treating hemophilia.

Treatment of Metabolic Disorders

The cloaked cells of the invention can also be used to treat inherited metabolic disorders. In most inherited metabolic disorders, a single enzyme is not produced by the body or it is produced in a form that is defective. Inherited metabolic disorders include lysosomal storage disorders, such as Hurler syndrome (deficiency in alpha-L iduronidase), Niemann-Pick disease (mutations in SMPD1, NPC1, or NPC2), Tay-Sachs disease (mutation in HEXA), Gaucher's disease (mutation in GBA gene), Fabry disease (deficiency in alpha galactosidase due to mutation in GLA), and Krabbe disease (deficiency in galactosylceramidase due to mutations in GALC); Galactosemia (deficiency in Galactokinase or galactose-1-phosphate uridyltransferase); Maple syrup urine disease (deficiency in enzyme BCKD); Phenylketonuria (deficiency in enzyme PAH); glycogen storage diseases (GSDs), such as GSD0 (deficiency in glycogen synthase (GYS2)), GSD1/von Gierke's disease (deficiency in glucose-6-phosphatase (G6PC)), GSD 2/Pompe's disease (deficiency in acid alpha-glucosidase (GAA)), GSD 3/Cori's disease or Forbes' disease (deficiency in glycogen debranching enzyme AGL), GSD 4/Andersen disease (deficiency in glycogen branching enzyme (GBE1)), GSD 5/McArdle disease (deficiency in muscle glycogen phosphorylase (PYGM)), GSD 6/Hers' disease (deficiency in liver glycogen phosphorylase (PYGL) or muscle phosphoglycerate mutase (PGAM2)), GSD 7/Tarui's disease (deficiency in muscle phosphofructokinase (PKFM)), GSD 9 (deficiency in phosphorylase kinase (PHKA2, PHKB, PHKG2, or PHKA1)), GSD 10 (deficiency in enolase 3 (ENO3)), GSD 11 (deficiency in muscle lactate dehydrogenase (LDHA)), Fanconi-Bickel syndrome (deficiency in glucose transporter 2 (GLUT2)), GSD 12 (deficiency in aldolase A (ALDOA)), GSD 13 (deficiency in β-enolase (ENO3)), or GSD 15 (deficiency in glycogenin-1 (GYG1)); mitochondrial disorders, such as mitochondrial myopathy (Kearns-Sayre syndrome (KSS, caused by a deletion in mitochondrial DNA) and Chronic progressive external opthalmoplegia (CPEO, caused by a deletion or duplication in mitochondrial DNA or a mutation in ANTI, POLG, POLG2, or PEO1), diabetes mellitus and deafness (DAD, caused by a mutation in mitochondrial DNA at position 3243, which encodes tRNALeu(UUR)), Leber's hereditary optic neuropathy (LHON, caused by mutations in MT-ND1, MT-ND4, MT-ND4L, and MT-ND6), Leigh syndrome (associated with mutations in SURF1, MT-ATP6, MT-ND2, MT-ND3, MT-ND5, MT-ND6, BCS1L, NDUFA10, SDHA, NDUFS4, NDUFAF2, NDUFA2, NDUFAF6, COX15, NDUFS3, NDUFS8, FOXRED1, NDUFA9, NDUFA12, NDUFS7), Neuropathy, ataxia, retinitis pigmentosa, and ptosis (NARP, caused by mutations in MT-ATP6), myoneurogenic gastrointestinal encephalopathy (MNGIE, caused by mutations in TYMP), myoclonic epilepsy with ragged red fibers (MERRF, caused by mutation sin MT-TK, MT-TL1, MT-TH, MT-TS1, MT-TS2, or MT-TF), or mitochondria myopathy, encephalomyopathy, lactic acidosis, stroke-like symptoms (MELAS, caused by mutations in MT-ND1, MT-ND5, MT-TH, MT-TL1, or MT-TV); Friedrich's ataxia (mutation in FXN); peroxisomal disorders, such as Zellweger syndrome (mutations in PEX1, PEX2, PEX3, PEX5, PEX6, PEX10, PEX12, PEX13, PEX14, PEX16, PEX19, or PEX26) and adrenoleukodystrophy (mutations in ABCD1); metal metabolism disorders, such as Wilson disease (mutation in Wilson disease protein ATP7B) and hemochromatosis (mutation in human hemochromatosis protein HFE); organic acidemias, such as methylmalonic acidemia (mutations in MUT, MMAA, MMAB, MMADHC, or MCEE) and propionic academia (mutations in PCCA or PCCB); urea cycle disorders, such as ornithine transcarbamylase (OTC), deficiency, arginase (ARG1) deficiency, argininosuccinate lyase (ASL) deficiency, argininosuccinate synthase 1 (ASS1) deficiency, citrin deficiency, carbamoyl phosphate synthase 1 (CPSI) deficiency, N-acetylglutamate synthase (NAGS) deficiency, and ornithine translocase (ORNT1) deficiency.

To treat subjects suffering from a metabolic disorder, cloaked cells can be modified to express the wild-type form of the gene that is mutated in the subject or a transgene encoding the enzyme that is missing or deficient in the subject (see Table 2), or cells from a healthy subject (e.g., a subject that does not have a metabolic disorder) that express the wild-type form of the gene that is mutated in the subject or the enzyme that is deficient in the subject can be modified to express one or more (e.g., one, two, three, four, five, six, seven or all eight) of cloaking transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) and administered to a subject with a metabolic disorder. The wild-type form of the gene that is mutated in the subject or a transgene encoding the enzyme that is missing or deficient in the subject can be expressed constitutively in cloaked cells by being operably linked to a constitutive promoter, such as CMV or CAG, or can be inducibly expressed using one of the inducible expression systems described herein. Cloaked cells (e.g., stem cells) that are modified to express the wild-type form of the gene that is mutated in the subject or the enzyme that is missing or deficient in the subject can be differentiated into cells that normally express the gene or enzyme prior to administration using methods known by those of skill in the art or can be administered without differentiation, or isolated cells from a healthy subject that express the wild-type form of the gene or enzyme that is mutated or deficient in the subject can be modified to express one or more (e.g., one, two, three, four, five, six, seven or all eight) of cloaking transgenes PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) and administered to a subject with a metabolic disorder. If the subject has not already been diagnosed as having a particular mutation prior to treatment, the subject can be evaluated using standard methods to identify the mutated gene related to the metabolic disorder, to ensure that the cloaked cells express the corresponding wild-type gene. Eight hundred million to three billion cloaked cells (e.g., 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹cloaked cells) expressing the wild-type form of the gene that is mutated in the subject can be injected subcutaneously to create a cloaked subcutaneous tissue that produces the corresponding wild-type protein.

Methods of Controlling Division of a Cloaked Cell

In an aspect, a method of controlling proliferation of cell at a transplant site in an allogeneic host is provided (e.g., to reduce the tumorigenic potential of a cell at the transplant site or to reduce proliferation of a cell that has become tumorigenic at a transplant site).

The method comprises: providing a cell genetically modified to comprise at least one mechanism for providing a local immunosuppression at a transplant site when transplanted in an allogeneic host the cell or a population of such cells; genetically modifying in the cell a cell division locus/loci (CDL), the CDL being one or more loci whose transcription product(s) is expressed by dividing cells (e.g., all dividing cells containing one or more of the immunosuppressive transgenes), the genetic modification of the CDL comprising one or more of: a) an ablation link (ALINK) system, the ALINK system comprising a DNA sequence encoding a negative selectable marker that is transcriptionally linked to a DNA sequence encoding the CDL; and b) an inducible exogenous activator of regulation of a CDL (EARC) system, the EARC system comprising an inducible activator-based gene expression system that is operably linked to the CDL; permitting proliferation of the genetically modified cell comprising the ALINK system by maintaining the genetically modified cell comprising the ALINK system in the absence of an inducer of the negative selectable marker or ablating and/or inhibiting proliferation of the genetically modified cell comprising the ALINK system by exposing the cell comprising the ALINK system to the inducer of the negative selectable marker; and/or permitting proliferation of the genetically modified cell comprising the EARC system by exposing the genetically modified cell comprising the EARC system to an inducer of the inducible activator-based gene expression system or preventing or inhibiting proliferation of the genetically modified cell comprising the EARC system by maintaining the cell comprising the EARC system in the absence of the inducer of the inducible activator-based gene expression system; and transplanting the cell or a population of the cells at a transplantation site in an allogeneic host. Cells that have been modified to control cell division using one or more ALINK and/or EARC systems in one or more CDLs (e.g., 2, 3, 4, or more CDLs) may be referred to as “fail-safe cells”. The number of cells that can be grown from a single fail-safe cell (clone volume) before the cell loses activity of all of the systems (e.g., ALINKs or EARCs) that control cell division through genetic mutation (e.g., the number of cell divisions it would take for a cell to “escape” from control and exhibit uncontrollable cell proliferation based on mathematical modeling) determines the fail-safe volume. The fail-safe volume will depend on the number of ALINKs and the number of ALINK-targeted CDLs. The fail-safe property is further described in Table 3.

TABLE 3

Fail-safe cell volumes and their relationship to a human body were

calculated using mathematical modeling. The model did not take

into account an event in which CDL expression was co-lost with

the loss of negative selectable marker activity, compromising cell

proliferation. Therefore the values are underestimates and were

calculated assuming 10⁶forward mutation rate for the negative

selectable marker. The estimated number of cells in a human body

as 3.72 × 10¹³was taken from (Bianconi et al., 2013).

Geno-
Fail-safe
Relative (x) to
Estimated

CDL
ALINK
type
volume
a human body =
weight of

#
#
in CDLs
(#cells)
3.72 × 10¹³cells
clones

1
1
het
512
0.0000000000137
1
μg

1
2
hom
16777216
0.000000451
31
mg

2
3
het, hom
1.374E+11
0.004
0.26
kg

2
4
hom, hom
1.13E+15
30
2100
kg

In various embodiments, a CDL is a locus identified as an “essential gene” as set forth in Wang et al., 2015, which is incorporated herein by reference as if set forth in its entirety. Essential genes in Wang et al., 2015, were identified by computing a score (i.e., a CRISPR score) for each gene that reflects the fitness cost imposed by inactivation of the gene. In an embodiment, a CDL has a CRISPR score (CS) of less than about −1.0 (Table 5, column 5).

In various embodiments, a CDL is a locus/loci that encodes a gene product that is relevant to cell division and/or replication (Table 5, column 6). For example, in various embodiments, a CDL is a locus/loci that encodes a gene product that is relevant to one or more of: i) cell cycle; ii) DNA replication; iii) RNA transcription and/or protein translation; and iv) metabolism (Table 5, column 7).

In an embodiment, a CDL is one or more cyclin-dependent kinases that are involved with regulating progression of the cell cycle (e.g., control of G1/S G2/M and metaphase-to-anaphase transition), such as CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9 and/or CDK11 (Morgan, 2007). In an embodiment, a CDL is one or more cyclins that are involved with controlling progression of the cell cycle by activating one or more CDK, such as, for example, cyclinB, cyclinE, cyclinA, cyclinC, cyclinD, cyclinH, cyclinC, cyclinT, cyclinL and/or cyclinF (FUNG and POON, 2005). In an embodiment, a CDL is one or more loci involved in the anaphase-promoting complex that controls the progression of metaphase to anaphase transition in the M phase of the cell cycle (Peters, 2002). In an embodiment, a CDL is one or more loci involved with kinetochore components that control the progression of metaphase to anaphase transition in the M phase of the cell cycle (Fukagawa, 2007). In an embodiment, a CDL is one or more loci involved with microtubule components that control microtubule dynamics required for the cell cycle (Cassimeris, 1999).

In various embodiments, a CDL is a locus/loci involved with housekeeping. As used herein, the term “housekeeping gene” or “housekeeping locus” refers to one or more genes that are required for the maintenance of basic cellular function. Housekeeping genes are expressed in all cells of an organism under normal and patho-physiological conditions.

In various embodiments, a CDL is a locus/loci that encodes a gene product that is relevant to cell division and/or proliferation and has a CRISPR score of less than about −1.0. For example, in an embodiment, a CDL is a locus/loci that encodes a gene product that is relevant to one or more of: i) cell cycle; ii) DNA replication; iii) RNA transcription and/or protein translation; and iv) metabolism, and has a CRISPR score of less than about −1.0. In an embodiment, the CDL may also be a housekeeping gene.

In some embodiments, the CDL is Cdk1/CDK1, Top2A/TOP2A, Cenpa/CEPNA, Birc5/BIRC5, or Eef2/EEF2. In some embodiments, the CDL is Cdk1/CDK1. In some embodiments, the CDL is Top2A/TOP2A. In some embodiments, the CDL is Eef2/EEF2. In some embodiments, the CDLs are Cdk1/CDK1 and Top2A/TOP2A or Cdk1/CDK1 and Eef2/EEF2.

A cell can be modified to be a “fail-safe” cell by linking the expression of a CDL with that of a DNA sequence encoding a negative selectable marker, thereby allowing drug-induced ablation of mitotically active cells expressing both the CDL and the negative selectable marker. Ablation of proliferating cells may be desirable, for example, when cell proliferation is uncontrolled and/or accelerated relative to a cell's normal division rate (e.g., uncontrolled cell division exhibited by cancerous cells), or when therapeutic need for the cells has passed. Ablation of proliferating cells may be achieved via a genetic modification to the cell, referred to herein as an “ablation link” (ALINK), which links the expression of a DNA sequence encoding a negative selectable marker to that of a CDL, thereby allowing elimination or sufficient inhibition of ALINK-modified proliferating cells consequently expressing the CDL locus (sufficient inhibition being inhibition of cell expansion rate to a rate that is too low to contribute to tumour formation). In the presence of a pro-drug or other inducer of the negatively selectable system, cells expressing the negative selectable marker will stop proliferating or die, depending on the mechanism of action of the selectable marker. Cells may be modified to comprise homozygous, heterozygous, hemizygous or compound heterozygous ALINKS. In one embodiment, to improve fidelity of ablation, a negative selectable marker may be introduced into all alleles functional of a CDL. In one preferred embodiment, a negative selectable marker may be introduced into all functional alleles of a CDL. The fail-safe system can be used to eliminate all of the cloaked cells, if desired.

An ALINK may be inserted in any position of CDL, which allows co-expression of the CDL and the negative selectable marker.

In some embodiments, the ALINK system comprises a herpes simplex virus-thymidine kinase/ganciclovir system, a cytosine deaminase/5-fluorocytosine system, a carboxyl esterase/irinotecan system or an iCasp9/AP1903 system.

DNA encoding a negatively selectable marker (e.g., HSV-TK), may be inserted into a CDL (e.g., CDK1) in a host cell, such that expression of the negative selectable marker causes host cells expressing the negative selectable marker and, necessarily, the CDL, to be killed in the presence of an inducer (e.g., prodrug) of the negative selectable marker (e.g., ganciclovir (GCV)). In this example, host cells modified with the ALINK will produce thymidine kinase (TK) and the TK protein will convert GCV into GCV monophosphate, which is then converted into GCV triphosphate by cellular kinases. GCV triphosphate incorporates into the replicating DNA during S phase, which leads to the termination of DNA elongation and cell apoptosis (Halloran and Fenton, 1998).

A modified HSV-TK gene (PreuR et al., 2010) is disclosed herein as one example of DNA encoding a negative selectable marker that may be used in an ALINK genetic modification to selectively ablate cells comprising undesirable cell division rate.

It is contemplated herein that alternative and/or additional negative selectable systems could be used in the tools and/or methods provided herein. Various negative selectable marker systems are known in the art (e.g., dCK.DM (Neschadim et al., 2012)).

For example, various negative selectable system having clinical relevance have been under active development in the field of “gene-direct enzyme/prodrug therapy” (GEPT), which aims to improve therapeutic efficacy of conventional cancer therapy with no or minimal side-effects (Hedley et al., 2007; Nawa et al., 2008). Frequently, GEPT involves the use of viral vectors to deliver a gene into cancer cells or into the vicinity of cancer cells in an area of the cancer cells that is not found in mammalian cells and that produces enzymes, which can convert a relatively non-toxic prodrug into a toxic agent.

HSV-TK/GCV, cytosine deaminase/5-fluorocytosine (CD/5-FC), and carboxyl esterase/irinotecan (CE/CPT-11) are examples of negative selectable marker systems being evaluated in GEPT pre- and clinical trials (Danks et al., 2007; Shah, 2012).

To overcome the potential immunogenicity of a Herpes Simplex Virus type 1 thymidine kinase/ganciclovir (TK/GCV) system, a “humanized” suicide system has been developed by engineering the human deoxycytidine kinase enzyme to become thymidine-active and to work as a negative selectable (suicide) system with non-toxic prodrugs: bromovinyl-deoxyuridine (BVdU), L-deoxythymidine (LdT) or L-deoxyuridine (LdU) (Neschadim et al., 2012).

The CD/5-FC negative selectable marker system is a widely used “suicide gene” system. Cytosine deaminase (CD) is a non-mammalian enzyme that may be obtained from bacteria or yeast (e.g., from Escherichia coli or Saccharomyces cerevisiae, respectively) (Ramnaraine et al., 2003). CD catalyzes conversion of cytosine into uracil and is an important member of the pyrimidine salvage pathway in prokaryotes and fungi, but it does not exist in mammalian cells. 5-fluorocytosine (5-FC) is an antifungal prodrug that causes a low level of cytotoxicity in humans (Denny, 2003). CD catalyzes conversion of 5-FC into the genotoxic agent 5-FU, which has a high level of toxicity in humans (Ireton et al., 2002).

The CE/CPT-11 system is based on the carboxyl esterase enzyme, which is a serine esterase found in a different tissues of mammalian species (Humerickhouse et al., 2000). The anti-cancer agent CPT-11 is a prodrug that is activated by CE to generate an active referred to as 7-ethyl-10-hydroxycamptothecin (SN-38), which is a strong mammalian topoisomerase I inhibitor (Wierdl et al., 2001). SN-38 induces accumulation of double-strand DNA breaks in dividing cells (Kojima et al., 1998).

Another example of a negative selectable marker system is the iCasp9/AP1903 suicide system, which is based on a modified human caspase 9 fused to a human FK506 binding protein (FKBP) to allow chemical dimerization using a small molecule AP1903, which has tested safely in humans. Administration of the dimerizing drug induces apoptosis of cells expressing the engineered caspase 9 components. This system has several advantages, such as, for example, including low potential immunogenicity, since it consists of human gene products, the dimerizer drug only effects the cells expressing the engineered caspase 9 components (Straathof et al., 2005). The iCasp/AP1903 suicide system is being tested in clinical settings (Di Stasi et al., 2011).

It is contemplated herein that the negative selectable marker system of the ALINK system could be replaced with a proliferation antagonist system. The term “proliferation antagonist” as used herein, refers to a natural or engineered compound(s) whose presence inhibits (completely or partially) division of a cell. For example, Omomyc^ERis the fusion protein of MYC dominant negative Omomyc with mutant murine estrogen receptor (ER) domain. When induced with tamoxifen (TAM), the fusion protein Omomyc^ERlocalizes to the nucleus, where the dominant negative Omomyc dimerizes with C-Myc, L-Myc and N-Myc, sequestering them in complexes that are unable to bind the Myc DNA binding consensus sequences (Soucek et al., 2002). As a consequence of the lack of Myc activity, cells are unable to divide (Oricchio et al., 2014). Another example of a proliferation antagonist is A-Fos, a dominant negative to activation protein-1 (AP1) (a heterodimer of the oncogenes Fos and Jun) that inhibits DNA binding in an equimolar competition (Olive et al., 1997). A-Fos can also be fused to ER domain, rendering its nuclear localization to be induced by TAM. Omomyc^ER/tamoxifen or A-Fos^ER/tamoxifen could be a replacement for TK/GCV to be an ALINK.

A cell can also be modified to be “fail-safe” by operably linking the CDL with an EARC, such as an inducible activator-based gene expression system. Under these conditions, the CDL will only be expressed (and the cell can only divide) in the presence of the inducer of the inducible activator-based gene expression system. Under these conditions, EARC-modified cells stop dividing, significantly slow down, or die in the absence of the inducer, depending on the mechanism of action of the inducible activator-based gene expression system and CDL function. Cells may be modified to comprise homozygous or compound heterozygous EARCs or may be altered such that only EARC-modified alleles can produce functional CDLs. In an embodiment, an EARC modification may be introduced into all alleles of a CDL, for example, to provide a mechanism for cell division control.

An EARC may be inserted in any position of CDL that permits co-expression of the CDL and the activator component of the inducible system in the presence of the inducer.

In an embodiment, an “activator” based gene expression system is preferable to a “repressor” based gene expression system. For example, if a repressor is used to suppress a CDL a loss of function mutation of the repressor could release CDL expression, thereby allowing cell proliferation. In a case of an activation-based suppression of cell division, the loss of activator function (mutation) would shut down CDL expression, thereby disallowing cell proliferation.

In some embodiments, the EARC system is a dox-bridge system, a cumate switch inducible system, an ecdysone inducible system, a radio wave inducible system, or a ligand-reversible dimerization system.

A dox-bridge may be inserted into a CDL (e.g., CDK1) in a host cell, such that in the presence of an inducer (e.g., doxycycline or “DOX”) the dox-bridge permits CDL expression, thereby allowing cell division and proliferation. Host cells modified with a dox-bridge EARC may comprise a reverse tetracycline Trans-Activator (rtTA) gene (Urlinger et al., 2000) under the transcriptional control of a promoter, which is active in dividing cells (e.g., in the CDL). This targeted insertion makes the CDL promoter no longer available for CDL transcription. To regain CDL transcription, a tetracycline responder element promoter (for example TRE (Agha-Mohammadi et al., 2004)) is inserted in front of the CDL transcript, which will express the CDL gene only in a situation when rtTA is expressed and doxycycline is present. When the only source of CDL expression is dox-bridged alleles, there is no CDL gene expression in the absence of doxycycline. The lack of CDL expression causes the EARC-modified cells to be compromised in their proliferation, either by death, stopping cell division, or by rendering the cell mitotic rate so slow that the EARC-modified cell could not contribute to tumor formation.

The term “dox-bridge” as used herein, refers to a mechanism for separating activity of a promoter from a target transcribed region by expressing rtTA (Gossen et al., 1995) by the endogenous or exogenous promoter and rendering the transcription of target region under the control of TRE. As used herein, “rITA” refers to the reverse tetracycline transactivator elements of the tetracycline inducible system (Gossen et al., 1995) and “TRE” refers to a promoter consisting of TetO operator sequences upstream of a minimal promoter. Upon binding of rITA to the TRE promoter in the presence of doxycycline, transcription of loci downstream of the TRE promoter increases. The rITA sequence may be inserted in the same transcriptional unit as the CDL or in a different location of the genome, so long as the transcriptional expression's permissive or non-permissive status of the target region is controlled by doxycycline. A dox-bridge is an example of an EARC.

Introduction of an EARC system into the 5′ regulatory region of a CDL is also contemplated herein.

It is contemplated herein that alternative and/or additional inducible activator-based gene expression systems could be used in the tools and or methods provided herein to produce EARC modifications. Various inducible activator-based gene expression systems are known in the art.

For example, destabilizing protein domains (Banaszynski et al., 2006) fused with an acting protein product of a coding CDL could be used in conjunction with a small molecule synthetic ligand to stabilize a CDL fusion protein when cell division and/or proliferation is desirable. In the absence of a stabilizer, destabilized-CDL-protein will be degraded by the cell, which in turn would stop proliferation. When the stabilizer compound is added, it would bind to the destabilized-CDL-protein, which would not be degraded, thereby allowing the cell to proliferate.

For example, transcription activator-like effector (TALE) technology (Maeder et al., 2013) could be combined with dimerizer-regulated expression induction (Pollock and Clackson, 2002). The TALE technology could be used to generate a DNA binding domain designed to be specific to a sequence, placed together with a minimal promoter replacing the promoter of a CDL. The TALE DNA binding domain also extended with a drug dimerizing domain. The latter can bind to another engineered protein having corresponding dimerizing domain and a transcriptional activation domain.

For example, a reverse-cumate-Trans-Activator (rcTA) may be inserted in the 5′ untranslated region of the CDL, such that it will be expressed by the endogenous CDL promoter. A 6-times repeat of a Cumate Operator (6×CuO) may be inserted just before the translational start (ATG) of CDL. In the absence of cumate in the system, rcTA cannot bind to the 6×CuO, so the CDL will not be transcribed because the 6×CuO is not active. When cumate is added, it will form a complex with rcTA, enabling binding to 6×CuO and enabling CDL transcription (Mullick et al., 2006).

For example, a retinoid X receptor (RXR) and an N-terminal truncation of ecdysone receptor (EcR) fused to the activation domain of Vp16 (VpEcR) may be inserted in the 5′ untranslated region of a CDL such that they are co-expressed by an endogenous CDL promoter. Ecdysone responsive element (EcRE), with a downstream minimal promoter, may also be inserted in the CDL, just upstream of the starting codon. Co-expressed RXR and VpEcR can heterodimerize with each other. In the absence of ecdysone or a synthetic drug analog muristerone A, dimerized RXR/VpEcR cannot bind to EcRE, so the CDL is not transcribed. In the presence of ecdysone or muristerone A, dimerized RXR/VpEcR can bind to EcRE, such that the CDL is transcribed (No et al., 1996).

For example, a transient receptor potential vanilloid-1 (TRPV1), together with ferritin, may be inserted in the 5′ untranslated region of a CDL and co-expressed by an endogenous CDL promoter. A promoter inducible by NFAT (NFATre) may also be inserted in the CDL, just upstream of the starting codon. In a normal environment, the NFAT promoter is not active. However, upon exposure to low-frequency radio waves, TRPV1 and ferritin create a wave of Ca⁺⁺ entering the cell, which in turn converts cytoplasmatic-NFAT (NFATc) to nuclear-NFAT (NFATn), that ultimately will activate the NFATre and transcribe the CDL (Stanley et al., 2015).

For example, a CDL may be functionally divided in to parts/domains: 5′-CDL and 3′CDL, and a FKBP peptide sequence may be inserted into each domain. An IRES (internal ribosomal entry site) sequence may be placed between the two domains, which will be transcribed simultaneously by a CDL promoter but will generate two separate proteins. Without the presence of an inducer, the two separate CDL domains will be functionally inactive. Upon introduction of a dimerization agent, such as rapamycin or AP20187, the FKBP peptides will dimerize, bringing together the 5′ and 3′ CDL parts and reconstituting an active protein (Rollins et al., 2000).

In an embodiment of the method, the genetically modified cell comprises: a set of transgenes, each transgene encoding a gene product that is cytoplasmic, membrane bound, or local acting and whose function is to mitigate function of graft attacking leukocyte and NK cell activation or act as a defense mechanism against attacking leukocytes.

Methods for genetically modifying cell to comprise at least one mechanism for providing a local immunosuppression at a transplant site when transplanted in an allogeneic host the cell or a population of such cells are described, for example, in WO 2016/141480, the entire teachings of which are incorporated herein by reference.

The set of transgenes comprises one or more of the following genes: PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6). In an embodiment, the set of transgenes genes comprises PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6).

Techniques for introducing into animal cells various genetic modifications, such as transgenes are described herein and are generally known in the art.

In an embodiment of the method, the cell is a stem cell, a cell amenable to genome editing, or a cell that can serve as a source of a therapeutic cell type (e.g., a cell that can be directed to differentiate into a lineage restricted or terminally differentiated cell that can be used for cell therapy, or a cell of a desired target tissue). In an embodiment, the cell is an embryonic stem cell, an induced pluripotent stem cell, an adult stem cell, a tissue-specific stem cell, a hematopoietic stem cell, a mesenchymal stem cell, an endothelial stem cell, an epithelial stem cell, an adipose stem or progenitor cells, germline stem cell, a lung stem or progenitor cell, a mammary stem cell, an olfactory adult stem cell, a hair follicle stem cell, a multipotent stem cell, an amniotic stem cell, a cord blood stem cell, or a neural stem or progenitor cell. In some embodiments, the cell is derived from a target tissue, e.g., skin, heart, brain or spinal cord, liver, lung, kidney, pancreas, bladder, bone marrow, spleen, intestine, or stomach. In some embodiments, the cell is a fibroblast, an epithelial cell, or an endothelial cell. The cell may be a vertebrate cell, for example a mammalian cell, such as a human or mouse cell.

Techniques for transplanting the genetically modified cells into a transplant site of an allogeneic host are described herein and are generally known in the art.

In various embodiments of any of the methods of the disclosure, the host has a degenerative disease or a condition that can be treated with cell therapy. Examples of such diseases or conditions include, but are not limited to: blindness, arthritis (e.g., osteoarthritis or rheumatoid arthritis), ischemia, diabetes (e.g., Type 1 or Type 2 diabetes), multiple sclerosis, spinal cord injury, stroke, cancer, a lung disease, a blood disease, a neurological disease, such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and ALS, an enzyme or hormone deficiency, a metabolic disorder (e.g., a lysosomal storage disorder, Galactosemia, Maple syrup urine disease, Phenylketonuria, a glycogen storage disease, a mitochondrial disorder, Friedrich's ataxia, a peroxisomal disorder, a metal metabolism disorder, or an organic academia), an autoimmune disease (e.g., Psoriasis, Systemic Lupus Erythematosus, Grave's disease, Inflammatory Bowel Disease, Addison's Diseases, Sjogren's Syndrome, Hashimoto's Thyroiditis, Vasculitis, Autoimmune Hepatitis, Alopecia Areata, Autoimmune pancreatitis, Crohn's Disease, Ulcerative colitis, Dermatomyositis), age-related macular degeneration, retinal dystrophy, an infectious disease, hemophilia, a degenerative disease (e.g., Charcot-Marie-Tooth disease, chronic obstructive pulmonary disease, chronic traumatic encephalopathy, Creutzfeldt-Jakob disease, Cystic Fibrosis, Cytochrome C Oxidase deficiency, Ehlers-Danlos syndrome, essential tremor, Fribrodisplasia Ossificans Progressiva, infantile neuroaxonal dystrophy, keratoconus, keratoglobus, muscular dystrophy, neuronal ceroid lipofuscinosis, a prior disease, progressive supranuclear palsy, sandhoff disease, spinal muscular atrophy, retinitis pigmentosa), or an age-related disease (e.g., atherosclerosis, cardiovascular disease (e.g., angina, myocardial infarction), cataracts, osteoporosis, or hypertension).

Pharmaceutical Compositions

The cloaked cells described herein may be incorporated into a vehicle for administration into a patient, such as a human patient receiving a transplant or suffering from a disease or condition described herein. Pharmaceutical compositions containing cloaked cells can be prepared using methods known in the art. For example, such compositions can be prepared using, e.g., physiologically acceptable carriers, excipients or stabilizers (Remington: The Science and Practice of Pharmacology 22nd edition, Allen, L. Ed. (2013); incorporated herein by reference), and in a desired form, e.g., in the form of aqueous solutions.

The cloaked cells described herein can be administered in any physiologically compatible carrier, such as a buffered saline solution. Pharmaceutically acceptable carriers and diluents include saline, aqueous buffer solutions, solvents and/or dispersion media. The use of such carriers and diluents is well known in the art. Other examples include liquid media, for example, Dulbeccos modified eagle's medium (DMEM), sterile saline, sterile phosphate buffered saline, Leibovitz's medium (L15, Invitrogen, Carlsbad, Calif.), dextrose in sterile water, and any other physiologically acceptable liquid. Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. The solution is preferably sterile and fluid to the extent that easy syringability exists. Preferably, the solution is stable under the conditions of manufacture and storage and preserved against the contaminating action of microorganisms such as bacteria and fungi through the use of, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosol, and the like. Solutions of the invention can be prepared by using a pharmaceutically acceptable carrier or diluent and, as required, other ingredients enumerated above, followed by filtered sterilization, and then incorporating the cloaked cells as described herein.

For example, a solution containing a pharmaceutical composition described herein may be suitably buffered, if necessary, and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous, and intraperitoneal administration. In this connection, sterile aqueous media that can be employed will be known to those of skill in the art in light of the present disclosure. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Moreover, for human administration, preparations may meet sterility, pyrogenicity, general safety, and purity standards as required by FDA Office of Biologics standards.

Pharmaceutical compositions comprising cloaked cells in a semi-solid or solid carrier are typically formulated for surgical implantation at the site of transplantation or at the affected site of a disease or condition in the subject. It will be appreciated that liquid compositions also may be administered by surgical procedures. In particular embodiments, semi-solid or solid pharmaceutical compositions may comprise semi-permeable gels, matrices, cellular scaffolds and the like, which may be non-biodegradable or biodegradable. For example, in certain embodiments, it may be desirable or appropriate to sequester the cloaked cells from their surroundings, yet enable the cells to secrete and deliver biological molecules (e.g., a therapeutic agent listed in Table 2) to surrounding cells.

In other embodiments, different varieties of degradable gels and networks are utilized for the pharmaceutical compositions of the invention. For example, degradable materials include biocompatible polymers, such as poly(lactic acid), poly(lactic acid-co-glycolic acid), methylcellulose, hyaluronic acid, collagen, and the like.

In another embodiment, one or more hydrogels are used for the pharmaceutical compositions. The one or more hydrogels may include collagen, atelocollagen, fibrin constructs, hydrophilic vinyl and acrylic polymers, polysaccharides such as calcium alginate, and poly(ethylene oxide). Further, the hydrogel may be formed of poly(2-hydroxyethyl methacrylate), poly(acrylic acid), self-assembling peptides (e.g., RAD16), poly(methacrylic acid), poly(N-vinyl-2-pyrrolidinone), poly(vinyl alcohol) and their copolymers with each other and with hydrophobic monomers such as methyl methacrylate, vinyl acetate, and the like. Also preferred are hydrophilic polyurethanes containing large poly(ethylene oxide) blocks. Other preferred materials include hydrogels comprising interpenetrating networks of polymers, which may be formed by addition or by condensation polymerization, the components of which may comprise hydrophilic and hydrophobic monomers such as those just enumerated. In situ-forming degradable networks are also suitable for use in the invention (see, e.g., Anseth, K S et al. J. Controlled Release, 2002; 78:199-209; Wang, D. et al., Biomaterials, 2003; 24:3969-3980; U.S. Patent Publication 2002/0022676). These in situ forming materials are formulated as fluids suitable for injection; then may be induced to form a hydrogel by a variety of means such as change in temperature, pH, and exposure to light in situ or in vivo. In one embodiment, the construct contains fibrin glue containing gels. In another embodiment, the construct contains atelocollagen containing gels.

A polymer used to form a matrix may be in the form of a hydrogel. In general, hydrogels are cross-linked polymeric materials that can absorb more than 20% of their weight in water while maintaining a distinct three-dimensional structure. This definition includes dry cross-linked polymers that will swell in aqueous environments, as well as water-swollen materials. A host of hydrophilic polymers can be cross-linked to produce hydrogels, whether the polymer is of biological origin, semi-synthetic or wholly synthetic. The hydrogel may be produced from a synthetic polymeric material. Such synthetic polymers can be tailored to a range of properties and predictable lot-to-lot uniformity, and represent a reliable source of material that generally is free from concerns of immunogenicity. The matrices may include hydrogels formed from self assembling peptides, such as those discussed in U.S. Pat. Nos. 5,670,483 and 5,955,343, U.S. Patent Application No. 2002/0160471, and PCT Application No. WO 02/062969.

Properties that make hydrogels valuable in drug delivery applications include the equilibrium swelling degree, sorption kinetics, solute permeability, and their in vivo performance characteristics. Permeability to compounds depends, in part, upon the swelling degree or water content and the rate of biodegradation. Since the mechanical strength of a gel may decline in proportion to the swelling degree, it is also well within the contemplation of the present invention that the hydrogel can be attached to a substrate so that the composite system enhances mechanical strength. In some embodiments, the hydrogel can be impregnated within a porous substrate, so as to gain the mechanical strength of the substrate, along with the useful delivery properties of the hydrogel.

In other embodiments, the pharmaceutical composition comprises a biocompatible matrix made of natural, modified natural or synthetic biodegradable polymers, including homopolymers, copolymers and block polymers, as well as combinations thereof.

Examples of suitable biodegradable polymers or polymer classes include any biodegradable polymers discussed within this disclosure, including but not limited to, fibrin, collagen types I, II, III, IV and V, elastin, gelatin, vitronectin, fibronectin, laminin, thrombin, poly(aminoacid), oxidized cellulose, tropoelastin, silk, ribonucleic acids, deoxyribonucleic acids; proteins, polynucleotides, gum arabic, reconstituted basement membrane matrices, starches, dextrans, alginates, hyaluron, chitin, chitosan, agarose, polysaccharides, hyaluronic acid, poly(lactic acid), poly(glycolic acid), polyethylene glycol, decellularized tissue, self-assembling peptides, polypeptides, glycosaminoglycans, their derivatives and mixtures thereof. Suitable polymers also include poly(lactide) (PLA) which can be formed of L(+) and D(−) polymers, polyhydroxybutyrate, polyurethanes, polyphoshazenes, poly(ethylene glycol)-poly(lactide-co-glycolide) co-polymer, degradable polycyanoacrylates and degradable polyurethanes. For both glycolic acid and lactic acid, an intermediate cyclic dimer is may be prepared and purified prior to polymerization. These intermediate dimers are called glycolide and lactide, respectively.

Other useful biodegradable polymers or polymer classes include, without limitation, aliphatic polyesters, poly(alkylene oxalates), tyrosine derived polycarbonates, polyiminocarbonates, polyorthoesters, polyoxaesters, polyamidoesters, polyoxaesters containing amine groups, poly(propylene fumarate), polyfumarates, polydioxanones, polycarbonates, polyoxalates, poly(alpha-hydroxyacids), poly(esters), polyurethane, poly(ester urethane), poly(ether urethane), polyanhydrides, polyacetates, polycaprolactones, poly(orthoesters), polyamino acids, polyamides and blends and copolymers thereof. Additional useful biodegradable polymers include, without limitation stereopolymers of L- and D-lactic acid, copolymers of bis(para-carboxyphenoxy)propane and sebacic acid, sebacic acid copolymers, copolymers of caprolactone, poly(lactic acid)/poly(glycolic acid)/polyethyleneglycol copolymers, copolymers of polyurethane and poly(lactic acid), copolymers of alpha-amino acids, copolymers of alpha-amino acids and caproic acid, copolymers of alpha-benzyl glutamate and polyethylene glycol, copolymers of succinate and poly(glycols), polyphosphazene, poly(hydroxyalkanoates) and mixtures thereof. Binary and ternary systems also are contemplated.

In general, the material used to form a matrix is desirably configured so that it: (1) has mechanical properties that are suitable for the intended application; (2) remains sufficiently intact until tissue has in-grown and healed; (3) does not invoke an inflammatory or toxic response; (4) is metabolized in the body after fulfilling its purpose; (5) is easily processed into the desired final product to be formed; (6) demonstrates acceptable shelf-life; and (7) is easily sterilized.

In another embodiment, the population of cloaked cells can be administered by use of a scaffold. The composition, shape, and porosity of the scaffold may be any described above. Typically, these three-dimensional biomaterials contain the living cells attached to the scaffold, dispersed within the scaffold or incorporated in an extracellular matrix entrapped in the scaffold. Once implanted into the target region of the body, these implants become integrated with the host tissue, wherein the transplanted cells gradually become established.

Non-limiting examples of scaffolds that may be used include textile structures, such as weaves, knits, braids, meshes, non-wovens, and warped knits; porous foams, semi-porous foams, perforated films or sheets, microparticles, beads, and spheres and composite structures being a combination of the above structures. Nonwoven mats may, for example, be formed using fibers comprised of a synthetic absorbable copolymer of glycolic and lactic acids (PGA/PLA), sold under the tradename VICRYL sutures (Ethicon, Inc., Somerville, N.J.). Foams, composed of, for example, poly(epsilon-caprolactone)/poly(glycolic acid) (PCL/PGA) copolymer, formed by processes such as freeze-drying, or lyophilized, as discussed in U.S. Pat. No. 6,355,699, also may be utilized.

In another embodiment, the framework is a felt, which can be composed of a multifilament yarn made from a bioabsorbable material. The yarn can be made into a felt using standard textile processing techniques consisting of crimping, cutting, carding and needling. In another embodiment, cells are seeded onto foam scaffolds that may be used as composite structures.

The framework may be molded into a useful shape, such as to fill a tissue void. The framework can therefore be shaped to not only provide a channel for neural growth, but also provide a scaffold for the supporting and surrounding tissues, such as vascular tissue, muscle tissue, and the like. Furthermore, it will be appreciated that the population of cells may be cultured on pre-formed, non-degradable surgical or implantable devices.

Pharmaceutical compositions may include preparations made from cloaked cells that are formulated with a pharmaceutically acceptable carrier or medium. Suitable pharmaceutically acceptable carriers include any discussed within this disclosure, including but not limited to, water, salt solution (such as Ringers solution), alcohols, oils, gelatins, polyvinyl pyrrolidine, carbohydrates such as lactose, amylose, or starch, fatty acid esters, and hydroxymethylcellulose. Such preparations can be sterilized, and if desired, mixed with auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, and coloring agents. Pharmaceutical carriers suitable for use in the present invention are known in the art and are described, for example, in Pharmaceutical Sciences (17^thEd., Mack Pub. Co., Easton, Pa.) and WO 96/05309.

Methods of Treatment

The cloaked cells and compositions described herein may be administered to a subject in need thereof (e.g., a subject who is receiving or has received a transplant, or a subject having a disease or condition described herein) by a variety of routes, such as local administration to or near the site of a transplant, local administration to the site affected by the disease or condition (e.g., injection to a joint for treating RA, injection into the subretinal space for treating wet AMD, direct administration to the central nervous system (CNS) (e.g., intracerebral, intraventricular, intrathecal, intracisternal, or stereotactic administration) for treating a neurological disease, such as Parkinson's disease, direct injection into the cardiac muscle for treating cardiac infarction), intravenous, parenteral, intradermal, transdermal, intramuscular, intranasal, subcutaneous, percutaneous, intratracheal, intraperitoneal, intraarterial, intravascular, inhalation, perfusion, lavage, and oral administration. The most suitable route for administration in any given case will depend on the particular cells or composition administered, the patient, pharmaceutical formulation methods, administration methods (e.g., administration time and administration route), the patient's age, body weight, sex, severity of the disease being treated, the patient's diet, and the patient's excretion rate. Compositions may be administered once, or more than once (e.g., once annually, twice annually, three times annually, bi-monthly, or monthly). For local administration, the cloaked cells may be administered by any means that places the population of cells in a desired location, including catheter, syringe, shunt, stent, microcatheter, pump, implantation with a device, or implantation with a scaffold.

As described herein, before administration, the population of cells can be incubated in the presence of one or more factors, or under conditions, that stimulate stem cell differentiation into a desired cell type (e.g., a neuron, a cardiac muscle cell, an RPE cell, an insulin producing cell, a blood coagulation factor producing cell, an articular fibroblast, or other cell types described herein). Such factors are known in the art and the skilled artisan will appreciate that determination of suitable conditions for differentiation can be accomplished with routine experimentation. Such factors include growth or trophic factors, chemokines, cytokines, cellular products, demethylating agents, and other stimuli which are known to stimulate differentiation, for example, of stem cells along angiogenic, hemangiogenic, vasculogenic, skeletal muscle, vascular smooth muscle, pericyte, neuronal, or vascular endothelial pathways or lineages. Alternatively, the composition administered to the patient includes a population of cloaked cells with one or more factors that stimulate cell differentiation into a desired cell type, where the cell differentiation occurs in vivo at the tissue site. In some embodiments, the cloaked cells can be differentiated into an organ or tissue in vitro using methods known by those of skill in the art and administered to a subject in need of an organ or tissue transplant.

In some embodiments, cells of a specific cell type are collected from the patient or from a donor (e.g., from an HLA-matched or mis-matched donor that is, e.g., free of the disease or condition), modified to express one or more (e.g., one, two, three, four, five, six, seven, or eight) cloaking transgenes, and subsequently administered to a subject. Such an approach is useful for treating subjects carrying a mutation in a particular gene, as the cloaked donor cells can endogenously express the wild-type version of the gene, or for subjects deficient in a particular secreted protein or enzyme (e.g., using cloaked donor cells that endogenously express the protein or enzyme that is deficient in the subject). This approach can also be used for treatment of subjects receiving an organ or tissue transplant, as cells in the organ or tissue transplant can be modified to express one or more (e.g., one, two, three, four, five, six, seven, or eight) of the cloaking transgenes before the transplant is performed.

Subjects that may be treated as described herein are subjects that have received a transplant, or subjects having a disease or condition described herein (e.g., wet AMD or retinal dystrophy, a neurodegenerative disease, such as Parkinson's disease, cardiac infarction, osteoarthritis or RA, diabetes, hemophilia, a metabolic disorder, or a disease or condition listed in Table 2). The cells, compositions, and methods described herein can be used to treat a disease or condition caused by or associated with loss of cells, a mutation or deficiency in a protein, or aberrant production of a protein, which could be treated using cell replacement protein or cellular therapy, production of a therapeutic protein, production of an agonist antibody, or production of an inhibitory antibody. The methods described herein may include a step of screening a subject for mutations in genes associated with deficient protein production prior to treatment with or administration of the compositions described herein. A subject can be screened for a genetic mutation using standard methods known to those of skill in the art (e.g., genetic testing). The methods described herein may also include a step of evaluating the symptoms of the disease or condition in a subject prior to treatment with or administration of the cloaked cells or compositions described herein. The subject can then be evaluated using the same diagnostic tests after administration of the cloaked cells or compositions to determine whether the subject's condition has improved. The compositions and methods described herein may be administered as a preventative treatment to patients who have received a tissue or organ transplant before the patient shows any signs of tissue or organ rejection.

The cloaked cells, compositions, and methods described herein can be used to replace dead or dying cells in a subject (e.g., to replace neurons in a subject suffering from a neurodegenerative disease, or to replace cardiac muscle cells in a subject who has had a myocardial infarction). The cloaked cells, compositions, and methods described herein can also be used to provide immunosuppression in the region of a tissue or organ transplant, or to reduce the risk of rejection of the tissue or organ transplant. Cloaked cells that express a therapeutic agent, such as a protein or agonist antibody, compositions including such cells, or methods of administering such cells, may be used to replace or supply wild type versions of proteins that are mutated or deficient in a subject (e.g., proteins that are produced but do not function correctly due to a genetic mutation, such as truncated proteins or proteins with altered charge, polarity, or binding properties; or proteins that are not produced or that are produced in insufficient quantities, e.g., deficient protein production that is associated with a disease or condition in Table 2). Cloaked cells that express a therapeutic agent, such as an inhibitory or neutralizing antibody, compositions including such cells, or methods of administering such cells, may be used to block or neutralize proteins that are overexpressed in a subject or proteins that are aberrantly produced (e.g., proteins that are produced in at a time or in a location that differs from production of that protein in healthy subjects, e.g., aberrant protein production that is associated with a disease or condition listed in Table 2).

Treatment may include administration of cloaked cells or a composition containing cloaked cells in various unit doses. Each unit dose will ordinarily contain a predetermined-quantity of the cloaked cells described herein. The quantity to be administered, and the particular route of administration and formulation, are within the skill of those in the clinical arts. A unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time. Dosing may be performed using a catheter, syringe, shunt, stent, microcatheter, pump, implantation with a device, or implantation with a scaffold. The number of cells administered may vary depending on whether the cells are administered to a tissue, organ, or body site associated with a disease or injury, or are administered subcutaneously to produce a cloaked subcutaneous tissue. For administration to a tissue, organ, or body site, the cloaked cells may be administered to the patient at a dose of, for example 1×10⁴cells to 1×10¹⁰cells (e.g., 1×10⁴, 2×10⁴, 3×10⁴, 4×10⁴, 5×10⁴, 6×10⁴, 7×10⁴, 8×10⁴, 9×10⁴, 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, 3×10⁹, 4×10⁹, 5×10⁹, 6×10⁹, 7×10⁹, 8×10⁹, 9×10⁹, 1×10¹⁰cells). The number of cells administered will depend on the size of the recipient tissue, organ, or body site. For example, 2.5×10⁴to 1×10⁶cells (e.g., 2.5×10⁴, 3×10⁴, 4×10⁴, 5×10⁴, 6×10⁴, 7×10⁴, 8×10⁴, 9×10⁴, or 1×10⁶cells) can be administered (e.g., injected) to the subretinal space of the eye or to a specific brain region; 1×10⁶to 1×10⁸cells (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸cells) can be administered (e.g., injected) to a joint, with the quantity of cells depending on the size of the joint; and 5×10⁸to 5×10⁹cells(e.g., 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, 3×10⁹, 4×10⁹, or 5×10⁹cells) can be administered to the cardiac muscle. For creating cloaked subcutaneous tissue, 8×10⁸cells to 3×10⁹cells (e.g., 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, 3×10⁹cells) can be administered (e.g., injected) subcutaneously. Cloaked cells can be administered in two or more doses (e.g., two, three, four, five, or more different doses, e.g., to joints of different sizes in a patient with RA) or at the same dose two or more times (e.g., two, three, four, five, six, or more times over the course of an hour, day, week, month, or year). In some embodiments, the cloaked cells described herein are administered as a tissue (e.g., a tissue that has been grown and/or differentiated in vitro from cloaked cells). In some embodiments, the cloaked tissue is administered (e.g., implanted) with a gel, biocompatible matrix, or scaffold.

The compositions described herein are administered in an amount sufficient to prevent or reduce transplant rejection or to improve symptoms of a disease or condition listed in Table 2 (e.g., to reduce symptoms of osteoarthritis or RA (e.g., reduce inflammation, joint pain, stiffness, or immobility); reduce symptoms of retinal dystrophy or wet AMD (e.g., improve vision, slow or reduce vascularization of the eye); reduce symptoms of Parkinson's disease (e.g., reduce tremors, rigidity, bradykinesia, or improve posture or gait); reduce symptoms of diabetes (e.g., improve insulin levels, reduce the need for regular insulin injections); reduce symptoms of cardiac infarction (e.g., improve heart function, reduce infarct size); reduce symptoms of hemophilia (e.g., increase level of blood coagulation factors, such as Factor VIII, reduce excessive bleeding, reduce bruising, reduce nosebleeds, reduce joint pain or swelling); or reduce symptoms of metabolic disorders (e.g., increase appetite, growth, or weight gain, or reduce lethargy, weight loss, jaundice, seizures, abdominal pain, or vomiting)). Transplant rejection may be evaluated using standard methods known by those of skill in the art and may be reduced by 5% or more (e.g., 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or more) compared to rates of transplant rejection typically observed without treatment. In some embodiments, administration of the cloaked cells or compositions described herein results in an equivalent outcome in transplant rejection as that observed in subjects administered immunosuppressive agent(s). Symptoms of diseases and conditions described herein can be evaluated using standard methods known to those of skill in the art and may be reduced (e.g., the subject's condition may be improved) by 5% or more (e.g., 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or more) compared to symptoms prior to administration of the cloaked cells or compositions described herein. These effects may occur, for example, within 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 15 weeks, 20 weeks, 25 weeks, or more, following administration of the compositions described herein. The patient may be evaluated 1 month, 2 months, 3 months, 4 months, 5 months, 6 months or more following administration of the cloaked cell or composition depending on the dose and route of administration used for treatment. Depending on the outcome of the evaluation, the patient may receive additional treatments.

Combination Therapy

In some embodiments, the cloaked cells described herein are administered in combination with one or more additional therapeutic agents. The additional therapeutic agent(s) can be administered prior to administration of the cloaked cells, after administration of the cloaked cells, or concurrently with administration of the cloaked cells. The cloaked cells and additional therapeutic agents can also be administered simultaneously via co-formulation. The cloaked cells and therapeutic agent(s) can also be administered sequentially, such that the action of the cloaked cells and therapeutic agent(s) overlaps and their combined effect is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with the cloaked cells or therapeutic agent delivered alone or in the absence of the other. The effect of the cloaked cells and therapeutic agent(s) can be partially additive, wholly additive, or greater than additive (e.g., synergistic). Sequential or substantially simultaneous administration of cloaked cells and therapeutic agent(s) can be effected by any appropriate route including, but not limited to oral routes, intravenous routes, intramuscular routes, local routes, or subcutaneous routes. The cloaked cells and therapeutic agent(s) can be administered by the same route or by different routes. For example, cloaked cells may be administered by subcutaneous injection while the additional therapeutic agent is administered orally. The cloaked cells may be administered immediately, up to 1 hour, up to 2 hours, up to 3 hours, up to 4 hours, up to 5 hours, up to 6 hours, up to 7 hours, up to, 8 hours, up to 9 hours, up to 10 hours, up to 11 hours, up to 12 hours, up to 13 hours, 14 hours, up to hours 16, up to 17 hours, up 18 hours, up to 19 hours up to 20 hours, up to 21 hours, up to 22 hours, up to 23 hours up to 24 hours or up to 1-7, 1-14, 1-21 or 1-30 days before or after the additional therapeutic agent.

In one example, the additional therapeutic agent is an immunosuppressive agent(s) commonly given for organ or tissue transplant. The immunosuppressive agent(s) may be an agent that is given immediately after transplantation to prevent acute rejection (e.g., methylprednisolone, atgam, thymoglobulin, OKT3, basiliximab, or daclizumab) or an immunosuppressive agent(s) used for maintenance (e.g., prednisone, a calcineurin inhibitor (e.g., cyclosporine, tacrolimus), Mycophenolate Mofetil, Azathioprine or Rapamycin). Other immunosuppressive agents given after organ transplantation include corticosteroids (e.g., methylprednisolone, dexamethasone, prednisolone), cytotoxic immunosuppressants (e.g., azathioprine, chlorambucil, cyclophosphamide, mercaptopurine, methotrexate), immunosuppressant antibodies (e.g., antithymocyte globulins, basiliximab, infliximab), sirolimus derivatives (e.g., everolimus, sirolimus), and anti-proliferative agents (e.g., mycophenolate mofetil, mycophenolate sodium, and azathioprine). In this case, the cloaked cell(s) is administered to or near the transplant site, or the tissue to be transplanted is modified to express one or more (e.g., one, two, three, four, five, six, seven, or eight) cloaking transgenes, and the immunosuppressive agent(s) is administered as an additional source of immunosuppression, if needed.

For use in treating inflammatory and autoimmune related diseases or conditions, the additional agent may be a disease-modifying anti-rheumatic drug (DMARD), a biologic response modifier (a type of DMARD), a corticosteroid, or a nonsteroidal anti-inflammatory medication (NSAID). In some embodiments, the additional agent is prednisone, prednisolone, methylprednisolone, methotrexate, hydroxychloroquine, sulfasalazine, leflunomide, cyclophosphamide, azathioprine, or a biologic such as tofacitinib, adalimumab, abatacept, anakinra, kineret, certolizumab, etanercept, golimumab, infliximab, rituximab or tocilizumab. In some embodiments, the additional agent is 6-mercaptopurine, 6-thioguanine, abatacept, adalimumab, alemtuzumab (Lemtrada), an aminosalicylate (5-aminoalicylic acid, sulfasalazine, mesalamine, balsalazide, olsalazine), an antibiotic, an anti-histamine, Anti-TNFα (infliximab, adalimumab, certolizumab pegol, natalizumab), azathioprine, belimumab, beta interferon, a calcineurin inhibitor, certolizumab, a corticosteroids, cromolyn, cyclosporin A, cyclosporine, dimethyl fumarate (tecfidera), etanercept, fingolimod (Gilenya), fumaric acid esters, glatiramer acetate (Copaxone), golimumab, hydroxyurea, IFNγ, IL-11, infliximab, leflunomide, leukotriene receptor antagonist, long-acting beta2 agonist, mitoxantrone, mycophenolate mofetil, natalizumab (tysabri), ocrelizumab, pimecrolimus, a probiotic (VSL #3), a retinoid, rituximab, salicylic acid, short-acting beta2 agonist, sulfasalazine, tacrolimus, teriflunomide (Aubagio), theophylline, tocilizumab, ustekinumab (anti-IL-12/IL-23), or vedolizumab (Anti alpha3 beta7 integrin). In this case, the cloaked cell(s) could be administered to replace a tissue or organ damaged by the inflammatory or autoimmune-related disease or condition. In another example, the cloaked cell(s) administered could be modified to express a biologic therapeutic agent (e.g., an antibody) directed to treatment of a particular inflammatory or autoimmune-related disease or condition, and the additional agent could be a compound or general anti-inflammatory agent (e.g., an NSAID or corticosteroid).

For example, if the disease is rheumatoid arthritis, the additional agent may be one or more of: prednisone, prednisolone and methylprednisolone, methotrexate, hydroxychloroquine, sulfasalazine, leflunomide, cyclophosphamide and azathioprine, tofacitinib, adalimumab, abatacept, anakinra, kineret, certolizumab, etanercept, golimumab, infliximab, rituximab or tocilizumab. The cloaked cell(s) administered could be cartilage or bone producing cells of the joints. In some embodiments, the cloaked cell(s) can be modified to produce an anti-TNFα antibody and can be administered in combination with an anti-inflammatory agent (e.g., a corticosteroid).

In another example, for use in treating AMD or retinal dystrophy, the additional therapeutic agent may be an additional biologic agent (e.g., bevacuzimab, ranibizumab, or aflibercept), photodynamic therapy, or photocoagulation. The cloaked cell(s) administered could be retinal cells (e.g., RPE cells). In some embodiments, the cloaked cell(s) can be modified to produce a VEGF inhibitor and can be administered in combination with photodynamic therapy or photocoagulation.

For use in treating Parkinson's disease, the cloaked cells described herein can be administered with carbidopa-levodopa, a dopamine agonist (e.g., pramipexole, ropinirole, rotigotine, or apomorphine), an MAO-B inhibitor (e.g., selegiline or rasagiline), a catechol-O-methyltransferase inhibitor (e.g., entacapone or tolcapone), anticholinergic (e.g., benztropine or trihexyphenidyl), amantadine, or deep brain stimulation. The cloaked cell(s) administered could be dopaminergic neurons.

Additional agents for treating cardiac infarction include anticoagulants (e.g., rivaroxaban, dabigatran, apixaban, heparin, warfarin), anti-platelet agents (e.g., aspirin, clopidogrel, dipyramidole, prasugrel, ticagrelor), angiotensin-converting enzyme inhibitors (e.g., benazepril, captopril, enalapril, fosinopril, Lisinopril, moexipril, perindopril, quinapril, Ramipril, trandolapril), angiotensin II receptor blockers (e.g., candesartan, eprosartan, irbesartan, losartan, telmisartan, valsartan), angiotensin receptor neprilysin inhibitors (e.g., sacubitril/valsartan), beta blockers (e.g., acebutelol, atenolol, betaxolol, bisoprolol, metoprolol, nadolol, propranolol, sotalol), combined alpha and beta blockers (e.g., carvedilol, labetalol hydrochloride), calcium channel blockers (e.g., amlodipine, diltiazem, felodipine, nifedipine, nimodipine, nisoldipine, verapamil), cholesterol lowering medication (e.g., statins (e.g., atorvastatin, rosuvastatin), nicotinic acids (e.g., lovastatin), cholesterol absorption inhibitors (e.g., ezetimibe/simvastatin)), digitalis preparation (e.g., lanoxin), diuretics (e.g., amiloride, bumentanide, chlorothiazide, chlorthalidone, furosemide, hydro-chlorothiazide, indipamide, spironolactone), vasodilators (e.g., isosorbide dinitrate, nesiritide, hydralazine, nitrates, minoxidil), dual anti-platelet therapy (e.g., aspirin and a P2Y12 inhibitor), or a cardiac procedure (e.g., an angioplasty, artificial heart valve surgery, atherectomy, bypass surgery, cardiomyoplasty, heart transplant, minimally invasive heart surgery, radiofrequency ablation, stent procedure, or transmyocardial revascularization). The cloaked cell(s) administered could be cardiac muscle cells.

For use in treating infectious disease, the additional agent may be an antiviral compound (e.g., vidarabine, acyclovir, gancyclovir, valgancyclovir, nucleoside-analog reverse transcriptase inhibitor (NRTI) (e.g., AZT (Zidovudine), ddl (Didanosine), ddC (Zalcitabine), d4T (Stavudine), or 3TC (Lamivudine)), non-nucleoside reverse transcriptase inhibitor (NNRTI) (e.g., (nevirapine or delavirdine), protease inhibitor (saquinavir, ritonavir, indinavir, or nelfinavir), ribavirin, or interferon); an antibacterial compound; an antifungal compound; an antiparasitic compound. The cloaked cell(s) administered could be immune cells (e.g., cell that could assist in fighting the infectious disease, e.g., a cloaked T cell or B cell).

For use in treating diabetes, the additional agent may be insulin, a sulfonylurea (e.g., chlorpropamide, glipizide, glyburide, glimepiride), a biguanide (e.g., metformin), a meglitinide (e.g., repaglinide, nateglinide), a thiazolidinedione (e.g., rosiglitazone, pioglitazone), a DPP-4 inhibitor (sitagliptin, saxagliptin, linagliptin, alogliptin), an SGLT2 inhibitor (e.g., canagliflozin, dapagliflozin), an alpha-glucosidase inhibitor (e.g., acarbose, miglitol), a bile acid sequestrant (e.g., colesevelam), aspirin, or a dietary regimen. The cloaked cell(s) administered could be pancreatic beta cells, which can optionally be modified to express a transgene encoding insulin.

For use in treating hemophilia, the additional therapeutic agent may be a clotting factor, desmopressin, a clot-preserving medication (e.g., an anti-fibrinolytic, e.g., aprotinin, aminocaproic acid, fibrigongen, or tranexamic acid), a fibrin sealant, or physical therapy. The cloaked cell(s) administered could be liver sinusoidal cells or endothelial cells, which can optionally be modified to express a transgene encoding Factor VIII.

For treatment of a metabolic deficiency or disorder, the additional therapeutic agent may be a coenzyme (e.g., biotin, hydroxycobalamine, riboflavin, pyridoxine, folate, thiamin, ubichinone, tetrahydrobiopterine), a bone marrow transplant, an organ transplant (e.g., a liver, kidney, or heart transplant), hemodialysis, hemofiltration, exchange transfusion, peritoneal dialysis, medium-chain triacylglycerols, miglustat, enzyme supplementation therapy, or dietary restriction (e.g., low protein or phenylalanine-restricted diet for subjects with phenylketonuria), The cloaked cell(s) can be cells that carry a wild-type copy of the gene that is mutated in a subject with a metabolic disorder or cells that endogenously produce the enzyme that is deficient in subject with a metabolic disorder (e.g., a liver cell, kidney cell, heart cell, or any other cell that carries a wild-type copy of a gene that is mutated in a subject with a metabolic disorder or produces an enzyme that is deficient in a subject with a metabolic disorder).

For use in treating cancer, the additional agent may be a checkpoint inhibitor, a chemotherapeutic drug, a biologic drug, a non-drug therapy (e.g., radiation therapy, cryotherapy, hyperthermia, or surgical excision or tumor tissue), or an anti-cancer vaccine. The cloaked cell(s) could be an immune cell that could help fight the cancer (e.g., a macrophage, natural killer cell, dendritic cell, or T cell).

Checkpoint inhibitors can be broken down into at least 4 major categories: i) agents such as antibodies that block an inhibitory pathway directly on T cells or natural killer (NK) cells (e.g., PD-1 targeting antibodies such as nivolumab, pidilizumab/CT-011, and pembrolizumab, antibodies targeting TIM-3, and antibodies targeting LAG-3, 2B4, CD160, A2aR, BTLA, CGEN-15049, or KIR), ii) agents such as antibodies that activate stimulatory pathways directly on T cells or NK cells (e.g., antibodies targeting OX40, GITR, or 4-1 BB), iii) agents such as antibodies that block a suppressive pathway on immune cells or rely on antibody-dependent cellular cytotoxicity to deplete suppressive populations of immune cells (e.g., CTLA-4 targeting antibodies such as ipilimumab or tremelimumab, antibodies targeting VISTA, and antibodies targeting PD-L2 (e.g., a PDL2/Ig fusion protein such as AMP 224), Gr1, or Ly6G), and iv) agents such as antibodies or small molecules that block a suppressive pathway directly on cancer cells or that rely on antibody-dependent cellular cytotoxicity to enhance cytotoxicity to cancer cells (e.g., rituximab, antibodies or small molecules targeting PD-L1 (e.g., MPDL3280A/RG7446; MED14736; MSB0010718C; BMS 936559), and antibodies or small molecule inhibitors targeting B7-H3 (e.g., MGA271), B7-H4, Gal-9, or MUC1). In one embodiment, the inhibitor of checkpoint is an inhibitor (e.g., an inhibitory antibody or small molecule inhibitor) of HVEM, CD160, CHK 1, CHK2, B-7 family ligands, or a combination thereof. Such agents described herein can be designed and produced, e.g., by conventional methods known in the art (e.g., Templeton, Gene and Cell Therapy, 2015; Green and Sambrook, Molecular Cloning, 2012). In one embodiment, the inhibitor of checkpoint is an inhibitory antibody (e.g., a monospecific antibody such as a monoclonal antibody). The antibody may be, e.g., humanized or fully human. In other embodiments, the inhibitor of checkpoint is a fusion protein, e.g., an Fc-receptor fusion protein. In some embodiments, the inhibitor of checkpoint is an agent, such as an antibody, that interacts with a checkpoint protein. In other embodiments, the inhibitor of checkpoint is an agent, such as an antibody, that interacts with the ligand of a checkpoint protein.

Chemotherapeutic agents include alkylating agents, antimetabolites, folic acid analogs, pyrimidine analogs, purine analogs and related inhibitors, vinca alkaloids, epipodopyyllotoxins, antibiotics, L-asparaginase, topoisomerase inhibitors, interferons, platinum coordination complexes, anthracenedione substituted urea, methyl hydrazine derivatives, adrenocortical suppressant, adrenocorticosteroides, progestins, estrogens, antiestrogen, androgens, antiandrogen, and gonadotropin-releasing hormone analog. Also included is 5-fluorouracil (5-FU), leucovorin (LV), irenotecan, oxaliplatin, capecitabine, paclitaxel and doxetaxel. Non-limiting examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall; dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfomithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid; triaziquone; 2,2′,2″-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxoids, e.g., paclitaxel; chloranbucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum coordination complexes such as cisplatin, oxaliplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids such as retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above. Two or more chemotherapeutic agents can be used in a cocktail to be administered in combination with the cloaked cells described herein. Suitable dosing regimens of combination chemotherapies are known in the art.

Anti-cancer biologics include cytokines (e.g., interferon or an interleukin (e.g., IL-2)) used in cancer treatment. In other embodiments the biologic is an anti-angiogenic agent, such as an anti-VEGF agent, e.g., bevacizumab. In some embodiments the biologic is an immunoglobulin-based biologic, e.g., a monoclonal antibody (e.g., a humanized antibody, a fully human antibody, an Fc fusion protein or a functional fragment thereof) that agonizes a target to stimulate an anti-cancer response, or antagonizes an antigen important for cancer. Such agents include Rituximab; Daclizumab; Basiliximab; Palivizumab; Infliximab; Trastuzumab; Gemtuzumab ozogamicin; Alemtuzumab; Ibritumomab tiuxetan; Adalimumab; Omalizumab; Tositumomab-I-131; Efalizumab; Cetuximab; Bevacizumab; Natalizumab; Tocilizumab; Panitumumab; Ranibizumab; Eculizumab; Certolizumab pegol; Golimumab; Canakinumab; Ustekinumab; Ofatumumab; Denosumab; Motavizumab; Raxibacumab; Belimumab; Ipilimumab; Brentuximab Vedotin; Pertuzumab; Ado-trastuzumab emtansine; and Obinutuzumab. Also included are antibody-drug conjugates.

Kits

The invention also features a kit containing the cloaked cells described herein (e.g., cloaked cells expressing a set of the cloaking transgenes described herein (e.g., 1, 2, 3, 4, 5, 6, 7, or 8 of PD-L1, H2-M3, Cd47, Cd200, FasL, Ccl21 b, Mfge8, and Spi6), optionally further expressing one or more of the following transgenes: TGF-β, Cd73, Cd39, Lag3, Il1r2, Ackr2, Tnfrsf22, Tnfrs23, Tnfrsf10, Dad1,and IFNγR1 d39). In some embodiments, the cloaked cells are further modified to contain one or more systems for regulating cell division (e.g., an ALINK or EARC system), and/or a therapeutic agent (e.g., a transgene encoding a protein or antibody). The cloaked cells may be provided in a pharmaceutical composition. The kit may further include a syringe for administration of the cloaked cells or pharmaceutical composition and instructions for administering the cloaked cells or pharmaceutical composition for treating a disease or condition described herein.

Examples

The following examples are provided to further illustrate some embodiments of the present invention, but are not intended to limit the scope of the invention; it will be understood by their exemplary nature that other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.

Example 1: Materials and Methods

Construction of vectors that express target genes essential for allo-tolerance Plasmids containing the cDNA sequences of genes involved in allo-tolerance were obtained as follows:

PD-L1: Mount Sinai Hospital, clone #V102001

FasL: Mount Sinai Hospital, #75719

Cd47: Mount Sinai Hospital, #V75535

Cd200: GE Dharmacon, ID #17470

H2-M3: Mount Sinai Hospital, clone #8188

Ccl21: Mount Sinai Hospital, clone #V77120

Mfge8: Mount Sinai Hospital, clone #V72614

Spi6: Mount Sinai Hospital, clone #V8907

Expression vectors that contain these Genes of Interest (GOI), or the luciferase enzyme, were generated using the Gateway cloning system (Thermo Fisher). Cd47, Ccl21, Mfge8 and Spi6 cDNAs were acquired in a form that contained cDNA-flanking attB sites. For H2-M3, Cd200, FasL, and PD-L1, primers were designed to amplify the cDNA sequence, and add attB sites (FIG. 15(a)). Following PCR amplification, attB-containing cDNA was recombined into pDONR221 vectors (Thermo Fisher, #1256017) by the BP (recombination between attB and attP sites) reaction to create entry (pENTRY) clones (FIG. 15(b)). The BP reaction entails mixing the attB-flanked transgene cDNA with the pDONR221 plasmid in a 1 mL tube, along with buffers and the BP enzyme provided by Invitrogen, where the BP enzyme recombines the GOI into the docking site of the pDONR221 plasmid. Insertion of the transgene into the pDONR221 plasmid was verified by DNA sequencing (TCAG Sequencing Facility at the Centre for Applied Genomics, Toronto). pENTRY clones that contained the GOI were then recombined into destination vectors via the gateway LR (recombination between attL and attR sites) reaction (FIG. 15(c)). The LR reaction entails mixing the GOI-containing pDONR221 plasmid and the destination vector in a 1 mL tube, along with buffers and the LR enzyme provided by Invitrogen, where the LR enzyme recombines the GOI cassette from the pDONR221 plasmid into the docking site of the destination plasmid. Destination vectors, which were used for all transgene constructions, contain a CAGG promoter followed by a Gateway entry site, internal ribosomal entry site (IRES) and either a Puromycin resistance selectable marker or a green fluorescent protein (GFP) reporter. The entire cassette is flanked by transposable PB sites. Following LR recombination, the final destination vectors containing the GOI (FIG. 15(d)) were verified by restriction enzyme digestion.

ES Cell Culture, Transfection, Selection and Cloning

Mouse ES cells derived from the inbred C57BL/6N mouse strain (Gertsenstein 2010) were cultured in DMEM high glucose supplemented with 15% fetal bovine serum (FBS, tested for compatibility with ES cell cultures) and standard amounts of Sodium Pyruvate, non-essential amino acid (NEAA), Glutamax, Penicillin/Streptomycin, Beta-mercapto-ethanol and leukemia inhibitory factor (LIF) (Behringer et al 2014). Cells were cultured on a feeder layer of MitomycinC-inactivated Murine Embryonic Fibroblasts (MEFs). Cultures were kept in a standard cell culture incubator at 37° C. and 5% CO2.

Transfection was performed using JetPRIME reagent (Polyplus, catalog #14-07) per manufacturer protocol, and was done in three steps: 1) transfection with PD-L1-IRES-GFP destination vector only, 2) transfection with all the other transgenes carrying a Puromycin selectable marker, and 3) transfection with an eLuciferase-IRES-GFP transgene.

Step 1: Following transfection with PD-L1-IRES-GFP, cells were plated at low density so that after multiple rounds of proliferation 5-6 days later, individual cell clones—existing as cell aggregates (colonies)—were selected based on the intensity of GFP expression and then expanded as a clonal cell culture. The clone with the highest and most consistent GFP expression was chosen for the next step.

Step 2: 24 hours after transfection with transgenes containing a Puromycin selection marker, Puromycin was added to the culture media. On the third day, cells were plated at clonal density and Puromycin selection was continued until individual colonies were picked and expanded as clones. A large number of these clones were screened in vivo and the one capable of forming a teratoma in an allogeneic setting was designated “NT2”.

Step 3: NT2 was transfected with PB-CAG-eLuciferase-IRES-GFP as described above and plated at clonal density. GFP+ clones were picked and expanded. 10 clones with high levels of GFP expression were chosen for further studies.

Evaluation of Transgene Expression Levels

RNA was isolated from cultures grown on 30 mm culture plates, as well as from tumours grown in vivo. Cells were dissociated with Trypsin, centrifuged, and the supernatant removed. The cell pellet was immediately frozen on dry ice and stored at −80° C. Tumour tissues were dissected, immediately frozen on dry ice and stored at −80° C. RNA was isolated per standard protocols using Sigma GeneElute Total RNA Miniprep kit #RTN350. cDNA was obtained by reverse transcriptase reaction using the Qiagen Quantifast Reverse Transcriptase kit #205313. Quantitative PCR was performed using Sensifast mastermix from Bioline, #Bio-98020, gene specific primers and RNA at a 1:50 dilution. Samples were plated in 384 well plates using the Eppendorf epMotion 5070 robot and the quantitative PCR was performed on BioRad CFX384 Real-Time System C1000 Thermal cycler according to standard protocols. qPCR data was captured by BioRad CFX Manager 3.1 software and expression levels calculated with Microsoft Excel.

Teratoma Assay

Matrigel Matrix High Concentration (Corning cat #354248) was diluted 1:1 with cold DMEM media on ice. 5×10⁷cells were suspended into 500 uL of DMEM and equal volume of Matrigel. 100 ul 5×10 cells of the suspension was injected subcutaneously into each dorsal flank of B6N (isogenic) or FVB/N (allogeneic) mice. The resulting teratomas formed 2-4 weeks after injection. Teratoma size was measured using calipers, and the volume was calculated with the formula V=(L×W×H)/2. The tumours were allowed to grow to approximately 500 mm², a size that is well-tolerated and also well-suited for downstream experiments. All of the transgenes were delivered into cells that contain “Fail-safe system” (as described, for example, in WO 2016/141480, the entire contents of which are incorporated herein by reference. This genetic system allows for the complete inhibition of cell division with the administration of Ganciclovir (GCV). Once teratomas from the previously described experiments reached 500 mm², mice were injected into the peritoneal cavity with 50 mg/kg GCV every 2-3 days for 2-3 weeks. This treatment regimen resulted in an initial brief shrinkage of the tumours, followed by stabilization of tumour size at 400-500 mm²after 2-3 weeks of treatment. At the endpoint of the experiment, mice were sacrificed and tumours were dissected. A small portion of tissue was snap-frozen for RNA extraction while the rest was fixed in 4% paraformaldehyde.

Bioluminescence Imaging

Mice that developed teratomas derived from cells transfected with the eLuciferase transgene were injected with 30 mg/mL VivoGlo Luciferin at 100 uL/25 g body mass (Promega #P104C) 10 min before imaging. Animals were anaesthetized with Isoflurane and placed in an IVIS Lumina II imager (Caliper Life Sciences) driven by Living Image software. Exposure times were set between 5 seconds and 5 minutes depending on signal intensity.

Histology

Fixed tumours were embedded in paraffin, sectioned and stained with Hematoxylin/Eosin for histological analysis at the CMHD Pathology Core. Histology images were processed with NDPview2 software.

Example 2: Generation of Cloaked Cells

Transgenes encoding the genes in Table 1 were cloned into expression vectors and sequence verified both by polymerase chain reaction (PCR), restriction enzyme digestion and sequencing, all using standard methods know in the art.

A set of constructs containing transgenes Cd47, Cd200, FasL and H2-M3 (Set 1) were transfected into mouse embryonic stem cells derived from the inventors' C57BL/6 mouse ES line (C2). The presence of the transgenes was verified by PCR and expression of the expressed proteins was documented by immunohistochemistry (FIGS. 1A-D). A second set of constructs containing transgenes Ccl21, Mfge8, TGF-β and Spi6 (Set 2) were transfected into ES cells derived from FVB/N (ES line C2).

Similar methods were used to generate cloaked B16F10 melanoma cells, except that the media used DMEM containing 10% fetal bovine serum (FBS).

Example 3: Screening Process for Inhibition of T-Cell Activation

A modified in vitro Mixed Lymphocyte Reaction (MLR) assay was used to screen for the transgene combination resulting in the most efficient inhibition of T-cell activation. Cell lines transfected with Set 1 and Set 2 cloaking transgenes from Example 1 were used. Donor OT-I splenocytes were labeled with carboxyfluorescein succinimidyl ester CFSE and 60,000 cells were added to each well of the 96-well plate. ES or melanoma cells were mixed 10:1 with ova expressing cells. 10,000 of these were added to each well of splenocytes. IL-2 was added as a general activator and T-cell proliferation was measured by flow cytometry 3 days later (FIGS. 2A-2E). Cells were initially gated to include CD8+ cells only and all conditions were set up in 4 replicates.

The negative control (splenocytes only) resulted in a baseline 6.12% proliferation rate (FIG. 2A). Wildtype B16 melanoma (+10% ova expressing) cells resulted in distinct acceleration of proliferation to 17.1% (FIG. 2B), while cloaked cells reduced this proliferation to 9.51% (FIG. 2C). Similar results were obtained for wildtype (FIG. 2D) versus cloaked ES cells (FIG. 2E).

Example 4: Studies with WT and Cloaked Cancer Cells in Iso- and Allografted B16F10 Melanoma Cells

Since some of the candidate cloaking transgenes are intended to inhibit or modulate the initiation phase of the immune recognition cascade, the effect of these transgenes could be evaluated by the MLR alone as these events act on the maturation and physical migration of host APCs to local lymph nodes where they subsequently activate naïve T and B cells.

This called for an alternative assay that can screen a large number of transgene combinations in an in vivo allogeneic setting. Intraperitoneal and intravenous injection ES cells harboring a variety of transgene combinations was tried as an option. However, teratoma formation is dependent on the aggregation of a minimum number of ES cells (1×10⁵-5×10⁶depending on site of injection), rendering this option not compatible with such a screen. However, the murine melanoma cancer cell line B16F10 derived from C57BL/6 mice is not limited in such a way. Intravenous injection of less than 5×10³results in the efficient induction of a multitude of small cancer nodules in the lung. By limiting number of cells injected, one can anticipate that the cancer cells are trapped in the lung alveoli will form nodules derived from single or just a very small number of cells. By isolating and genotyping these nodules, the transgene can be identified.

Injection B16F10 melanoma cells into the blood-stream of C57BL/6 mice (isogenic graft control) resulted in the formation of cancer nodules in the lung (FIG. 3A, left panel). However, small melanoma nodules formed also in the lungs of the negative controls—wild type B16F10 melanoma grafted into allogeneic control FVB mice when observed at day 14 post injection. However, when the melanoma was allowed to grow for 24 days, the nodules regressed almost completely (FIG. 3A, right panel).

The above experiment was repeated, by injecting a mixture of cancer cells that expressed random combinations of the candidate cloaking genes, generated using the PiggyBac transposon system. Lung nodules developed in the allogeneic settings contained the successful combination(s) needed to protect the allograft from recognition and rejection (FIG. 3B, right panel). The same immune cloaked cells also gave rise to an accelerated development in the isogenic host (FIG. 3B, left panel).

Example 5: Non-Cloaked Embryonic Stem Cells do not Form Teratoma in Allogenic Settings

As shown in Table 4, it was verified that wild-type ESCs derived from C57BL/6 mice are not capable of forming teratomas in FVB/N mice. Likewise, we have also shown that wild-type ESCs derived from the FVB/N background are not capable of forming teratomas in C57BL/6 hosts. ES cell colonies were dissociated with Trypsin, washed once with DMEM without additives and resuspended in Matrigel HC at a concentration of about 50 million cells per milliliter. Recipient mice were anaesthetized and one hundred microliter injected subcutaneously in each flank area. Developing teratomas were followed for 12 weeks and verified by palpation and measurement of volume with caliper.

TABLE 4

Teratomas formed in FVB/N mice and C57BL/6 hosts injected

with wild-type ESCs derived from C57BL/6 mice or wild-

type ESCs derived from the FVB/N background

Donor ESCs
Recipient mouse
# injection sites
# teratomas

C57BL/6
C57BL/6
18
14

C57BL/6
FVB
22
0

FVB
FVB
8
8

FVB
C57BL/6
8
0

Example 6: Cloaked ES Cells can Proliferate in Isogenic Hosts and Allogenic Hosts

To verify the cloaking ability of the candidate transgenes, ESCs were transfected with the same transgenes while also adding a Luciferase transgene that can be detected by imaging. Briefly, ES cells were prepared as described above. The presence of viable cells were repeatedly measured by imaging. The images in FIG. 4 were taken on day 17 post injection.

In FIG. 4, the top panel shows the proliferation of immune cloaked cells in isogenic hosts, while the lower panel shows the proliferation of immune cloaked cells in allogeneic hosts.

In another experiment, cloaked ES cells from C57BL/6 mice that had high expression of the 8 immunomodulatory transgenes (clone NT2) were injected subcutaneously into different allogenic mouse strains (C3H, FVB/N, and CD1) with mismatched MHC alleles. Red arrows indicate the teratoma that formed (FIGS. 5A-5C).

Example 7: Mice with Cloaked Tissues are not Immune Compromised

Non-immune cloaked (wild type) ESCs were transplanted into mice carrying an existing immune cloaked tissue and the mouse was evaluated to determine if it could effectively reject a non-immune cloaked graft (FIG. 6). The same mice were imaged several times over a period of 15 days. As shown in the left panel of FIG. 6, in isogenic mouse controls, the graft was not rejected over time. With allogenic FVB mice, the left mouse in the right panel of FIG. 6 had a pre-existing immune cloaked graft (arrows). The middle mouse in the right panel of FIG. 6 had previously been grafted with C57BL/6 allogeneic ESCs but rejected the graft (while not being bound to a theory, the rejection may have been due to pre-formed antibodies against C57BL/6 cells). The mouse on the right in the right panel of FIG. 6 had never been grafted before. All three mice successfully rejected the non-immune cloaked graft. The mouse on the right rejected the graft slower, which may have been because it did not have any preformed antibodies against C57BL/6 cells.

A similar experiment was conducted where wild type embryonic stem cells were detected up to 9 days post injection into FVB/N mice with cloaked teratomas (FIG. 7). However, at day 12, no evidence of cells remaining could be detected. Control animals were C57BL/6 mice also carrying the cloaked tumors. The signal in these mice increased over the time-course of the experiment.

Example 8: Cloaked and Fail-Safe Embryonic Stem Cell Line

When a Fail-Safe C57BL/6 ES cell line (as described, for example, in WO/2016/141480) was co-transfected with 5 candidate cloaking transgenes (PD-L1, FasL, Cd47, Cd200 and H2-M3), none of these transgene lines resulted in teratomas in allograft settings. When the set of co-transfected genes was expanded by three additional candidate cloaking genes: Spi6, Ccl21 b and Mfge8, 38 clonal lines were generated. One of these lines, NT2, created teratomas in an allogeneic recipient (FVB). The expression levels of the cloaking genes in the 38 clonal lines, including the NT2 line (see arrows in FIGS. 8A-H), were measured using quantitative PCR (FIGS. 8A-H). Of the 38 clones, NT2 was the highest overexpression of Ccl21b (16,000×), FasL (25,000×), Cd200 (1700×), Cd47 (16×), Mfge8 (34×), Spi6 (600×) and H2-M3 (750×) compared to VVT ES cells. PD-L1, although not the highest level expresser among the clones, the 350× expression over ES cells was also a significant increase. The expression of these genes was also checked in the Project Grandiose dataset (www.stemformatics.org/project_grandiose) and found that Ccl21b, FasL, Cd200, PD-L1 and Spi6 expression is under the detection threshold, therefore, their relative-to-ES cells expression is very high. Based on this data these eight, highly activated genes could have a primary role in inducing immune tolerance of an allograft.

NT2 cells were injected into both C57BL/6 to create teratomas in an FVB allogenic setting (FIGS. 11A-11B) and an FVB iso C57131/6 isogenic setting. Allogenic teratomas (n=6) were steadily growing from day 12 to day 38. At the size of 500 mm², ganciclovir (GCV) treatment was started to remove the proliferative component of the tumors (FIGS. 12A-12B, upper panel (FIG. 12A) isogenic teratomas; bottom panel (FIG. 12B) allogenic teratomas)). Twenty days of treatment stopped the allograft growth. This experiment shows that: 1) Fail-safe and cloaked (NT2) cell-derived teratomas respond similarly to GCV treatment; they enter to dormancy after brief GCV exposure; 2) After GCV the teratomas remain stable. There is no sign of rejection of the dormant tissue; and 3). The dynamics of teratoma growth in FVB animals is different than in C57BL/6.

Cloaking transgenes expressed at a high level survive to form teratomas in an allogenic mouse. In our system, the cloaking transgenes are expressed under a very strong synthetic promoter, CAG (depicted in the schematic in FIG. 19). The CAG promoter is a combination of the cytomegalovirus early enhancer element, the splicer acceptor of the rabbit beta-globin gene, and also the promoter, first exon and first intron of the chicken beta-actin gene. We have performed extensive qPCR analysis on the level of transgene transcripts in many different ES cell clones, each of which has a different expression level of the transgenes. Only those ES clones that have the highest expression of cloaking transgenes survive in allogenic hosts.

As shown in FIG. 9, transcript expression level of the immunomodulatory genes relevant to the cloaking technology varied between ES cell clones. Concentric circles are depicted on a log 10 scale. The thick black line is 1×, the next outer ring is 10×, and then 100×. The innermost ring is 0.1×. All values are normalized to positive controls, which were activated leukocytes isolated from murine lymph organs that naturally express the immunomodulatory transgenes. The upper left panel shows wild-type ES cells with no transgenic modifications for reference—they express little or none of the relevant immunomodulatory transgenes. By contrast, clone NT2 and clone 15 (indicated by red squares), both with high expression of the genes, survived in allogenic hosts. All other clones shown in FIG. 9 did not survive in allogenic hosts.

The high expression of the cloaking transgenes is also depicted in FIG. 10. As shown in FIG. 10, all 8 cloaking transgenes in the NT2 cell line and NT2-derived teratoma had an expression level that was among the top 5% of all genes in the ES cell genome, with 5 of the cloaking transgenes having an expression level in the top 1% of all genes in the ES cell genome. The expression of these genes is much lower in VVT ES cells, as only one of the genes has an expression level among the top 5% of all genes in the genome.

Example 9: Cloaked ESCs Contribute to all Three Germ Layers in Allogenic Teratomas

It was next asked if immune cloaking would allow the full pluripotent developmental potential of ESCs to unfold in teratomas. Teratomas resulting from the injection of cloaked and uncloaked ESCs derived from C57BL/6 mice into isogenic and allogeneic hosts were analyzed by histopathology (hematoxylin and eosin staining). FIGS. 13A-13B (isogenic host neuronal, bone and columnar epithelium in upper panels (FIG. 13A); and allogenic host neuronal, bone, columnar epithelium and blood vessels in lower panels (FIG. 13B)) shows representative images obtained from both backgrounds, proving that the expression of the cloaking transgenes do not interfere with the normal developmental potential of these ES cells and the tumors are well vascularized. Both isogenic and allogenic tissues did not show any immune cell infiltration.

In another experiment, we tested if the cloaked ES cell were truly pluripotent by testing whether they could form cells from all three germ layers—endoderm, ectoderm, and mesoderm (FIGS. 14A-140). This was assayed by injecting between 10⁶and 10⁷cloaked ES cells subcutaneously into a mouse and allowing them to proliferate and differentiate into a tissue mass named a teratoma. The teratoma was then removed 3-4 weeks after ES cell injection, and tissue sections cut and stained with H&E. These sections were analyzed under the microscope for cell morphology to determine if all three germ layers were present.

We asked whether the 8 cloaking transgenes inserted into ES cells and expressed at high levels would disrupt their ability to form all three germ layers. They did not. FIGS. 14A-140 show the three germ layers (ec=ectoderm, shown in FIG. 14A; en=endoderm, shown in FIG. 14C; me=mesoderm, shown in FIG. 14B). FIG. 14D shows a blood vessel, which verifies that these tissues are well-vascularized.

Example 10: ES Cells that Express Cloaking Transgenes Produce the Proteins Encoded by the Transgenes

We confirmed the presence of the proteins encoded by the cloaking transgenes in NT2 ES cells (one of the clones with the highest expression) directly using fluorescent antibody-based microscopy (FIGS. 16A-16H). These data confirm that the proteins encoded by the transgenes are expressed in ES cells at easily detectable levels, which is expected based on the high levels of mRNA expression.

Example 11: ES Cells that Express High Levels of Cloaking Transgenes have Typical Morphology and Express Common ES Cell Markers

We analyzed cloaked ES cells to determine whether they expressed markers of ES cells and retained a normal ES cell morphology. Cloaked ES cells have the typical morphology observed with healthy and pluripotent ES cells (FIG. 17A) and also stain positively for alkaline phosphatase (FIG. 17B), which is characteristic of healthy and pluripotent ES cells. Furthermore, our cloaked ES cells stained positively for the transcription factor Oct4 (FIG. 18A) as well as SSEA (FIG. 18B) using fluorescent antibodies, both common markers of normal pluripotent ES cells. These data show that ES cells that express high levels of the 8 immunomodulatory cloaking transgenes appear as normal ES cells with respect to their morphology and expression of common ES cell markers. The insets show that staining for Oct4 and SSEA1 (lower left inset) colocalizes with ES cells (visualized using DAPI in upper right insets).

Example 12: IFNγR1 d39 Prevents Upregulation of MHCs in ES Cells

Activated T-cells secrete IFNγ, which binds to the IFNγR1/R2 complex expressed on many cell types, including tissues and cells derived from ES cells. IFNγ binding to the IFNγ receptor induces upregulation of HLA (MHC in mice) and HLA-related molecules on the cell surface, which increases the allogenicity of the allograft and the likelihood of immune rejection. Differences in HLA proteins (also called major antigens) between the donor and recipient are the primary cause of rejection in all allogenic transplants.

To evaluate whether disrupting IFNγ signaling prevents or reduces HLA upregulation, we transfected C57BL/6 ES cells with piggyback-integratable vectors containing a wild-type IFNγR1 or dominant negative IFNγR1 (IFNγR1 d39, which lacks 39 amino acids in the cytoplasmic tail) transgene. These transgenes were expressed under the control of a constitutive CAG promoter upstream of the transgene contained on the same piggyback-integrated cassette.

Wild type and transfected ES cells were then grown in culture and exposed to 100 ng/mL of IFNγ ligand for 24 hours. In wild-type ES and IFNγR1-transfected cells (left and middle panels of FIG. 20, respectively), IFNγ exposure resulted in increased expression of the H-2kb and H-2Db major histocompatibility surface molecules (MHC class I), but not in IFNγR1 d39 cells (right panel of FIG. 20). Exposure to PBS alone had no effect. MHC class I levels were detected by fluorescent antibody staining, and the expression level quantified by measuring the mean fluorescent intensity (MFI) by flow cytometry. These data show that overexpression of IFNγR1 d39 completely inhibits IFNγ-mediated upregulation of MHCs in ES cells, indicating that expression of IFNγR1 d39 in ES cells can be used to prevent activation of the immune system and reduce the likelihood of immune rejection. Therefore, IFNγR1 d39 is a useful immunosuppressive transgene that can be expressed by the cloaked cells described herein to reduce immune activation and transplant rejection.

Example 13: Administration of Cloaked Cells Expressing a VEGF Inhibitor to a Subject with Wet AMD

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with wet AMD to reduce vascularization of the eye or prevent or reduce disease progression. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked RPE cells or cloaked stem cells that have been differentiated into RPE cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG) and a VEGF inhibitor (e.g., VEGF-Trap, e.g., aflibercept) under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells may be administered to the patient, for example, by local administration to the eye (e.g., injection into the subretinal space), to treat wet AMD. Twenty five thousand to one hundred thousand cloaked cells (e.g., 25,000, 50,000, 75,000, or 100,000 cloaked cells) can be administered to each affected eye.

Following administration of the cloaked cells to a patient, a practitioner of skill in the art can monitor the expression of the VEGF inhibitor, and the patient's improvement in response to the therapy, by a variety of methods. For example, a physician can monitor the patient's vision and the vascularization of the eye using standard approaches. A finding that the patient's vision improves or does not worsen, or that vascularization of the eye decreases or does not worsen compared to measurements taken prior to administration of the cloaked cells indicates that the patient is responding favorably to the treatment. Subsequent doses can be determined and administered as needed.

Example 14: Administration of Cloaked Dopaminergic Neurons to a Subject with Parkinson's Disease (PD)

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with PD to reduce motor symptoms of PD (e.g., bradykinesia, tremors, or rigidity) or prevent or reduce disease progression. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., dopaminergic neurons that have been modified to express cloaking transgenes or cloaked stem cells that have been differentiated into dopaminergic neurons) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells may be administered to the patient, for example, by local administration to the central nervous system (e.g., stereotactic injection into the substantia nigra), to treat PD. Twenty five thousand to one hundred thousand cloaked cells (e.g., 25,000, 50,000, 75,000, or 100,000 cloaked cells) can be administered. The patient can optionally be administered an additional therapy for PD, such as a dopamine agonist.

Following administration of the cloaked cells to a patient, a practitioner of skill in the art can monitor the patient's improvement in response to the therapy by a variety of methods. For example, a physician can monitor the patient's movement using standard neurological tests. A finding that the patient's motor symptoms improve or do not worsen compared to measurements taken prior to administration of the cloaked cells indicates that the patient is responding favorably to the treatment. Subsequent doses can be determined and administered as needed.

Example 15: Administration of Cloaked Cardiac Muscle Cells to a Subject that has Suffered a Myocardial Infarction

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, who has recently suffered a myocardial infarction to improve cardiac function (e.g., to replace or dead or damaged cardiac muscle cells). To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked cardiac muscle cells or cloaked stem cells that have been differentiated into cardiac muscle cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells may be administered to the patient, for example, by local administration to the heart (e.g., injection into the cardiac muscle), to promote recovery after the myocardial infarction. The cells can be injected into the cardiac muscle as a monotherapy, or the cells can be delivered during the performance of a bypass surgery or another open heart surgical procedure. One million to five billion cloaked cardiac muscle cells (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, 3×10⁹, 4×10⁹, or 5×10⁹cloaked cells) can be administered.

Following administration of the cloaked cells to a patient, a practitioner of skill in the art can monitor the patient's improvement in response to the therapy by a variety of methods. For example, a physician can monitor the patient's cardiac function using standard approaches (e.g., EKG, echocardiogram, angiogram, stress test, or nuclear imaging). A finding that the patient's cardiac function improves or stabilizes compared to measurements taken prior to administration of the cloaked cells indicates that the patient is responding favorably to the treatment. Subsequent doses can be determined and administered as needed.

Example 16: Administration of Cloaked Cells Expressing a TNFα Inhibitor to a Subject with RA

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with rheumatoid arthritis to reduce join stiffness, swelling, or pain. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked articular fibroblasts or cloaked stem cells that have been differentiated into articular fibroblasts) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG) and a TNFα inhibitor (e.g., a TNFα inhibitory antibody, such as adalimumab) under the control of an inducible promoter (e.g., a tetracycline response element). The cloaked cells may be administered to the patient, for example, by local administration to a joint (e.g., injection into an arthritic joint, such as joint in the hand), to treat RA. One million to one hundred million cloaked articular fibroblasts expressing an anti-inflammatory biologic (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸cloaked articular fibroblasts) can be administered to each affected joint. When the patient experiences a flare up of RA symptoms, the patient can be treated with tetracycline or doxycycline to drive expression of the TNFα inhibitor. Tetracycline or doxycycline can be withdrawn when the patient's flare up has resolved.

Following administration of the cloaked cells and tetracycline or doxycycline to a patient, a practitioner of skill in the art can monitor the expression of the TNFα inhibitor, and the patient's improvement in response to the therapy, by a variety of methods. For example, a physician can monitor the patient's joint pain, swelling, and stiffness using standard approaches. A finding that the patient's joint pain, swelling, or stiffness is reduced compared to measurements taken prior to administration of the cloaked cells indicates that the patient is responding favorably to the treatment. Subsequent doses can be determined and administered as needed.

Example 17: Administration of Cloaked Cells Expressing Insulin to a Subject with Type 1 Diabetes

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with Type 1 diabetes to increase insulin levels. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked stem cells, cloaked pancreatic beta cells, or cloaked stem cells that have been differentiated into pancreatic beta cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG) and insulin under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells may be administered to the patient, for example, by subcutaneous injection (e.g., to create a cloaked subcutaneous tissue), to treat Type 1 diabetes. One million to three billion cloaked cells expressing insulin (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹cloaked cells) can be administered subcutaneously.

Example 18: Administration of Cloaked Cells Expressing Factor VIII to a Subject with Hemophilia

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with hemophilia to increase the levels of a blood clotting factor or reduce excessive bleeding or bruising. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked stem cells, cloaked endothelial cells, or cloaked stem cells that have been differentiated into endothelial cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG) and Factor VIII under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells may be administered to the patient, for example, by subcutaneous injection (e.g., to create a cloaked subcutaneous tissue), to treat hemophilia. One million to three billion cloaked cells expressing Factor VIII (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁶, 2×10⁶, or 3×10⁶cloaked cells) can be administered subcutaneously.

Example 19: Administration of Cloaked Cells Expressing Glucocerebrosidase to a Subject with Gaucher's Disease

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with Gaucher's disease to reduce the accumulation of glucocerebroside or to reduce symptoms of Gaucher's disease (e.g., fatigue, anemia, low blood platelet count, enlarged liver or spleen). To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked stem cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG) and glucocerebrosidase under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells may be administered to the patient, for example, by subcutaneous injection (e.g., to create a cloaked subcutaneous tissue), to treat Gaucher's disease. One million to three billion cloaked cells expressing glucocerebrosidase (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹cloaked cells) can be administered subcutaneously.

Following administration of the cloaked cells to a patient, a practitioner of skill in the art can monitor the expression of the patient's improvement in response to the therapy by a variety of methods. For example, a physician can monitor accumulation of glucocerebroside or symptoms of Gaucher's disease (e.g., fatigue, anemia, low blood platelet count, enlarged liver or spleen) using standard approaches. A finding of a reduction in the patient's accumulation of glucocerebroside or symptoms of Gaucher's disease compared to measurements taken prior to administration of the cloaked cells indicates that the patient is responding favorably to the treatment. Subsequent doses can be determined and administered as needed.

Example 20: Administration of Cloaked Cells to a Subject Receiving a Liver Transplant

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, who is receiving a liver transplant to reduce the risk of transplant rejection. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked stem cells, cloaked liver cells, or cloaked stem cells that have been differentiated into liver cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells may be administered to the patient, for example, by injection into the liver or near the site of the transplanted liver, to reduce the risk of transplant rejection. One million to one hundred billion cloaked cells (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, 3×10⁹, 4×10⁹, 5×10⁹, 6×10⁹, 7×10⁹, 8×10⁹, 9×10⁹, 1×10¹⁰, 2×10¹⁰, 3×10¹⁰, 4×10¹⁰, 5×10w, 6×10w, 7×10¹⁰, 8×10¹⁰, 9×10¹⁰, or 1×10¹¹cloaked cells) can be administered to or near the liver.

Following administration of the cloaked cells to a patient, a practitioner of skill in the art can monitor the expression of the patient's improvement in response to the therapy by a variety of methods. For example, a physician can monitor the patient for symptoms that predict transplant rejection using standard approaches. A finding of an equivalent outcome in transplant rejection as that observed in subjects administered immunosuppressive agent(s) indicates that the patient is responding favorably to the treatment. Subsequent doses can be determined and administered as needed.

Example 21: Administration of Cloaked and Fail Safe Cells Expressing Insulin to a Subject with Type 1 Diabetes

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with Type 1 diabetes to increase insulin levels. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked stem cells, cloaked pancreatic beta cells, or cloaked stem cells that have been differentiated into pancreatic beta cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG) and insulin under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells can also be modified to allow for control of their proliferation by linking the expression of a CDL with that of a DNA sequence encoding a negative selectable marker. For example, the cloaked cells can be modified to contain homozygous ALINKS (e.g., HSV-TK systems) in two CDL loci (e.g., Cdk1 and Top2A). The cloaked cells may be administered to the patient, for example, by subcutaneous injection (e.g., to create a cloaked subcutaneous tissue), to treat Type 1 diabetes. One million to three billion cloaked cells expressing insulin (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷, 4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹cloaked cells) can be administered subcutaneously.

A practitioner of skill in the art can also monitor the size of the cloaked subcutaneous tissue. If it appears that the cloaked subcutaneous tissue is becoming tumorigenic, the practitioner can administer ganciclovir to the subject to ablate the proliferating cloaked cells. Non-proliferating cloaked cells will not express the CDLs, and, therefore, will not be ablated by ganciclovir treatment.

Example 22: Administration of Cloaked and Fail Safe Cells Expressing Insulin to a Subject with Type 1 Diabetes

According to the methods disclosed herein, a physician of skill in the art can treat a patient, such as a human patient, with Type 1 diabetes to increase insulin levels. To this end, a physician of skill in the art can administer to the human patient cloaked cells (e.g., cloaked stem cells, cloaked pancreatic beta cells, or cloaked stem cells that have been differentiated into pancreatic beta cells) that express one or more (e.g., one, two, three, four, five, six, seven, or all eight) of PD-L1, HLA-G (H2-M3), Cd47, Cd200, FASLG (FasL), Ccl21 (Ccl21b), Mfge8, and Serpin B9 (Spi6) under the control of a constitutive promoter (e.g., CMV or CAG) and insulin under the control of a constitutive promoter (e.g., CMV or CAG). The cloaked cells can also be modified to allow for control of their proliferation by linking the expression of a CDL with that of a DNA sequence encoding an inducible activator system. For example, a dox-bridge can be inserted into two CDLs (e.g., Cdk1 and Top2A) to generate homozygous modifications in both CDLs in a cloaked cell, such that in the presence of an inducer (e.g., doxycycline) the dox-bridge permits CDL expression, thereby allowing cell division and proliferation. The cloaked cells may be administered to the patient, for example, by subcutaneous injection (e.g., to create a cloaked subcutaneous tissue), to treat Type 1 diabetes. One million to three billion cloaked cells expressing insulin (e.g., 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶, 6×10⁶, 7×10⁶, 8×10⁶, 9×10⁶, 1×10⁷, 2×10⁷, 3×10⁷,4×10⁷, 5×10⁷, 6×10⁷, 7×10⁷, 8×10⁷, 9×10⁷, or 1×10⁸, 2×10⁸, 3×10⁸, 4×10⁸, 5×10⁸, 6×10⁸, 7×10⁸, 8×10⁸, 9×10⁸, 1×10⁹, 2×10⁹, or 3×10⁹cloaked cells) can be administered subcutaneously.

Following administration of the cloaked cells to a patient, a practitioner of skill in the art can monitor the expression of the patient's improvement in response to the therapy by a variety of methods. For example, a physician can monitor insulin levels or symptoms of Type 1 diabetes (e.g., unintended weight loss, fatigue, or blurred vision) using standard approaches. A finding that the patient's insulin levels are increased or the symptoms of Type 1 diabetes are reduced compared to measurements taken prior to administration of the cloaked cells indicates that the patient is responding favorably to the treatment. Subsequent doses can be determined and administered as needed. If the practitioner determines that the subject needs a higher level of insulin, the practitioner can allow the cloaked cells to proliferate by treating the subject with doxycycline. Once the desired level of insulin is reached, treatment with doxycycline can be stopped and the cloaked cells will cease to proliferate.

TABLE 5

Predicted CDLs (ID refers to EntrezGene identification number; CS score refers to the CRISPR score average provided in Wang et al.,

2015; function refers to the known or predicted function the locus, of predictions being based on GO terms, as set forth in the

Gene Ontology Consortium website http://geneontology.org/; functional category refers to 4 categories of cell functions based on

the GO term-predicted function; CDL (basis) refers to information that the inventors used to predict that a gene is a CDL, predictions

being based on CS score, available gene knockout (KO) data, gene function, and experimental data provided in WO 2016 141480).

Name
ID
Name
ID
CS
Function
Functional
CDL

(mouse)
(mouse)
(human)
(human)
score
(GO term)
category
(basis)
Citation

Actr8
56249
ACTR8
93973
−1.88
chromatin
Cell cycle
CS score,

remodeling

function

Alg11
207958
ALG11
440138
−1.27
dolichol-
Cell cycle
CS score,

linked

oligosaccharide

function

biosynthetic process

Anapc11
66156
ANAPC11
51529
−2.68
protein ubiquitination
Cell cycle
CS score,

involved in ubiquitin-

function

dependent protein

catabolic process

Anapc2
99152
ANAPC2
29882
−2.88
mitotic cell cycle
Cell cycle
CS score,
Wirth K G, et al.

mouse
Genes Dev. 2004

K.O.,
Jan. 1; 18(1): 88-98

function

Anapc4
52206
ANAPC4
29945
−1.79
regulation of mitotic
Cell cycle
CS score,

metaphase/anaphase

function

transition

Anapc5
59008
ANAPC5
51433
−1.66
mitotic cell cycle
Cell cycle
CS score,

function

Aurka
20878
AURKA
6790
−2.26
meiotic spindle
Cell cycle
CS score,
Sasai K, et al.

organization

mouse
Oncogene. 2008 Jul.

K.O.,
3; 27(29): 4122-7

function

Banf1
23825
BANF1
8815
−2.14
mitotic cell cycle
Cell cycle
CS score,

function

Birc5
11799
BIRC5
332
−2.24
regulation of signal
Cell cycle
CS score,
Uren A G et al. Curr

transduction

mouse
Biol. 2000 Nov.

K.O.,
2; 10(21): 1319-28

function

Bub3
12237
BUB3
9184
−3.15
mitotic sister
Cell cycle
CS score,
Kalitsis F, et al.

chromatid

mouse
Genes Dev. 2000

segregation

K.O.,
Sep.

function
15; 14(18): 2277-82

Casc5
76464
CASC5
57082
−1.16
mitotic cell cycle
Cell cycle
CS score,
Overbeek P A, et al.

mouse
MGI Direct Data

K.O.,
Submission. 2011

function

Ccna2
12428
CCNA2
890
−1.59
regulation of cyclin-
Cell cycle
CS score,
Kalaszczynska I, et

dependent protein

mouse
al. Cell. 2009 Jul.

serine/threonine

K.O.,
23; 138(2): 352-65

kinase activity

function

Ccnh
66671
CCNH
902
−2.01
regulation of cyclin-
Cell cycle
CS score.

dependent protein

function

serine/threonine

kinase activity

Cdc123
98828
CDC123
8872
−2.45
cell cycle
Cell cycle
CS score,

function

Cdc16
69957
CDC16
8881
−3.58
cell division
Cell cycle
CS score.

function

Cdc20
107995
CDC20
99
−2.97
mitotic cell cycle
Cell cycle
CS score,
Li M, et al. Mol Cell

mouse
Biol. 2007

K.O.,
May; 27(9): 3481-8

function

Cdc23
52563
CDC23
8697
−2.28
mitotic cell cycle
Cell cycle
CS score,

function

Cdk1
12534
CDK1
983
−2.44
cell cycle
Cell cycle
CS score,
Diril M K, et al. Proc

mouse
Natl Acad Sci USA.

K.O.,
2012 Mar.

function
6; 109(10): 3826-31

Cenpa
12615
CENPA
1058
−1.87
cell cycle
Cell cycle
CS score,
Howman E V, et al.

mouse
Proc Natl Acad Sci

K.O.,
USA. 2000 Feb.

function
1; 97(3): 1148-53

Cenpm
66570
CENPM
79019
−2.53
mitotic cell cycle
Cell cycle
CS score,

function

Chek1
12649
CHEK1
1111
−1.67
protein
Cell cycle
CS score,
Takai H, et al.

phosphorylation

mouse
Genes Dev. 2000

K.O.,
Jun. 15; 14(12): 1439-

function
47

Chmp2a
68953
CHMP2A
27243
−2.40
vacuolar transport
Cell cycle
CS score,

function

Ckap5
75786
CKAP5
9793
−2.94
G2/M transition of
Cell cycle
CS score,
Barbarese E, et al.

mitotic cell cycle

mouse
PLoS One.

K.O.,
2013; 8(8): e69989

function

Cltc
67300
CLTC
1213
−1.75
intracellular protein
Cell cycle
CS score,

transport

function

Cops5
26754
COPS5
10987
−1.75
protein deneddylation
Cell cycle
CS score,
Tian L, et al.

mouse
Oncogene. 2010

K.O.,
Nov.

function
18; 29(46): 6125-37

Dctn2
69654
DCTN2
10540
−1.48
G2/M transition of
Cell cycle
CS score,

mitotic cell cycle

function

Dctn3
53598
DCTN3
11258
−1.77
G2/M transition of
Cell cycle
CS score,

mitotic cell cycle

function

Dhfr
13361
DHFR
1719
−2.84
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Dtl
76843
DTL
51514
2.69
protein
Cell cycle
CS score,
Liu C L, et al. J Biol

polyubiquitination

mouse
Chem. 2007 Jan.

K.O.,
12; 282(2): 1109-18

function

Dync1h1
13424
DYNC1H1
1778
−3.44
G2/M transition of
Cell cycle
CS score,
Harada A, et al. J

mitotic cell cycle

mouse
Cell Biol. 1998 Apr.

K.O.,
6; 141(1): 51-9

function

Ecd
70601
ECD
11319
−3.18
regulation of
Cell cycle
CS score,

glycolytic process

function

Ect2
13605
ECT2
1894
−1.80
cell morphogenesis
Cell cycle
CS score,
Hansen J, et al.

mouse
Proc Natl Acad Sci

K.O.,
USA. 2003 Aug.

function
19; 100(17): 9918-22

Ep300
328572
EP300
2033
−2.04
G2/M transition of
Cell cycle
CS score,
Yao T P, et al. Cell.

mitotic cell cycle

mouse
1998 May

K.O.,
1; 93(3): 361-72

function

Ercc3
13872
ERCC3
2071
−2.10
nucleotide-
Cell cycle
CS score,
Andressoo J O, et

excision repair

mouse
al. Mol Cell Biol.

K.O.,
2009

function
March; 29(5): 1276-90

Espl1
105988
ESPL1
9700
−3.24
proteolysis
Cell cycle
CS score,
Wirth K G et al. J

mouse
Cell Biol. 2006 Mar.

K.O.,
13; 172(6): 847-60

function

Fntb
110606
FNTB
2342
−2.42
phototransduction,
Cell cycle
CS score,
Mijimolle N, et al.

visible light

mouse
Cancer Cell. 2005

K.O.,
April; 7(4): 313-24

function

Gadd45gip1
102060
GADD45GIP1
90480
−1.81
organelle
Cell cycle
CS score,
Kwon M C, et al.

organization

mouse
EMBO J. 2008 Feb.

K.O.,
20; 27(4): 642-53

function

Gins1
69270
GINS1
9837
−1.84
mitotic cell cycle
Cell cycle
CS score,
Ueno M, et al. Mol

mouse
Cell Biol. 2005

K.O.,
December; 25(23): 10528-

function
32

Gnb2l1
14694
GNB2L1
10399
−2.84
osteoblast
Cell cycle
CS score,

differentiation

function

Gspt1
14852
GSPT1
2935
−1.77
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Haus1
225745
HAUS1
115106
−1.92
spindle assembly
Cell cycle
CS score,

function

Haus3
231123
HAUS3
79441
−1.38
mitotic nuclear
Cell cycle
CS score,

division

function

Haus5
71909
HAUS5
23354
−2.55
spindle assembly
Cell cycle
CS score,

function

Haus8
76478
HAUS8
93323
−1.73
mitotic nuclear
Cell cycle
CS score,

division

function

Hdac3
15183
HDAC3
8841
−2.12
histone deacetylation
Cell cycle
CS score,
Bhaskara S, et al.

mouse
Mol Cell. 2008 Apr.

K.O.,
11; 30(1): 61-72

function

Kif11
16551
KIF11
3832
−3.23
microtubule-
Cell cycle
CS score,
Castillo A, et al.

based movement

mouse
Biochem Biophys

K.O.,
Res Commun. 2007

function
Jun. 8; 357(3): 694-9

Kif23
71819
KIF23
9493
−1.59
microtubule-
Cell cycle
CS score,

based movement

function

Kpnb1
16211
KPNB1
3837
−3.19
nucleocytoplasmic
Cell cycle
CS score,
Miura K, et al.

transport

mouse
Biochem Biophys

K.O.,
Res Commun. 2006

function
Mar. 3; 341(1): 132-8

Mastl
67121
MASTL
84930
−2.36
protein
Cell cycle
CS score,
Alvarez-Fernandez

phosphorylation

mouse
M, et al. Proc Natl

K.O.,
Acad Sci USA.

function
2013 Oct.

22; 110(43): 17374-9

Mau2
74549
MAU2
23383
−2.71
mitotic cell cycle
Cell cycle
CS score,
Smith T G, et al.

mouse
Genesis. 2014

K.O.,
July; 52(7): 687-94

function

Mcm3
17215
MCM3
4172
−2.52
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Mcm4
17217
MCM4
4173
−1.87
G1/S transition of
Cell cycle
CS score,
Shima N, et al. Nat

mitotic cell cycle

mouse
Genet. 2007

K.O.,
January; 39(1): 93-8

function

Mcm7
17220
MCM7
4176
−2.39
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Mnat1
17420
MNAT1
4331
−1.22
regulation of cyclin-
Cell cycle
CS score,
Rossi D J. et al.

dependent protein

mouse
EMBO J. 2001 Jun.

serine/threonine

K.O.,
1; 20(11): 2844-56

kinase activity

function

Mybbp1a
18432
MYBBP1A
10514
−2.17
osteoblast
Cell cycle
CS score,
Mori S, et al. PLoS

differentiation

mouse
One.

K.O.,
2012; 7(10): e39723

function

Ncapd2
68298
NCAPD2
9918
−2.03
mitotic chromosome
Cell cycle
CS score,

condensation

function

Ncaph
215387
NCAPH
23397
−2.33
mitotic chromosome
Cell cycle
CS score,
Nishide K, et al.

condensation

mouse
PLoS Genet. 2014

K.O.,
December; 10(12):

function
e1004847

Ndc80
67052
NDC80
10403
−2.98
attachment of mitotic
Cell cycle
CS score,

spindle microtubules

function

to kinetochore

Nle1
217011
NLE1
54475
−1.88
somitogenesis
Cell cycle
CS score,
Hentges K E, et al.

mouse
Gene Exor

K.O.,
Patterns. 2006

function
August; 6(6): 653-65

Nsl1
381318
NSL1
25936
−1.90
mitotic cell cycle
Cell cycle
CS score,

function

Nudc
18221
NUDC
10726
−1.93
mitotic cell cycle
Cell cycle
CS score,

function

Nuf2
66977
NUF2
83540
−1.78
mitotic nuclear
Cell cycle
CS score,

division

function

Nup133
234865
NUP133
55746
−2.26
mitotic cell cycle
Cell cycle
CS score,
Garcia-Garcia M J,

mouse
et al. Proc Natl

K.O.,
Acad Sci USA.

function
2005 Apr.

26; 102(17): 5913-9

Nup160
59015
NUP160
23279
−2.64
mitotic cell cycle
Cell cycle
CS score,

function

Nup188
227699
NUP188
23511
−1.16
mitotic cell cycle
Cell cycle
CS score,

function

Nup214
227720
NUP214
8021
−2.70
mitotic cell cycle
Cell cycle
CS score,
van Deursen J, et

mouse
al. EMBO J. 1996

K.O.,
Oct. 15; 15(20): 5574-

function
83

n/a
n/a
NUP62
23636
−2.35
mitotic cell cycle
Cell cycle
CS score,

function

Nup85
445007
NUP85
79902
−2.47
mitotic cell cycle
Cell cycle
CS score,

function

Orc3
50793
ORC3
23595
−1.67
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Pafah1b1
18472
PAFAH1B1
5048
−2.34
G2/M transition of
Cell cycle
CS score,
Cahana A, et al.

mitotic cell cycle

mouse
Proc Natl Acad Sci

K.O.,
USA. 2001 May

function
22; 98(11): 6429-34

Pcid2
234069
PCID2
55795
−1.98
negative regulation of
Cell cycle
CS score,

apoptotic process

function

Pfas
237823
PFAS
5198
−2.58
purine nucleotide
Cell cycle
CS score,

biosynthetic process

function

Phb2
12034
PHB2
11331
−2.98
protein import into
Cell cycle
CS score,
Park S E, et al. Mol

nucleus,

mouse
Cell Biol. 2005

translocation

K.O.,
March; 25(5): 1989-99

function

Pkmyt1
268930
PKMYT1
9088
−1.93
regulation of cyclin-
Cell cycle
CS score,

dependent protein

function

serine/threonine

kinase activity

Plk1
18817
PLK1
5347
−2.83
protein
Cell cycle
CS score,
Lu L Y, et al. Mol

phosphorylation

mouse
Cell Biol. 2008

K.O.,
November; 28(22): 6870-

function
6

Pmf1
67037
PMF1
11243
−2.15
mitotic cell cycle
Cell cycle
CS score,

function

Pole2
18974
POLE2
5427
−3.08
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Ppat
231327
PPAT
5471
−2.15
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psma6
26443
PSMA6
5687
−3.51
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psma7
26444
PSMA7
5688
−2.91
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psmb1
19170
PSMB1
5689
−1.63
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psmb4
19172
PSMB4
5692
−2.91
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psmd12
66997
PSMD12
5718
−1.69
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psmd13
23997
PSMD13
5719
−1.57
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psmd14
59029
PSMD14
10213
−3.01
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Psmd7
17463
PSMD7
5713
−2.18
G1/S transition of
Cell cycle
CS score,
Soriano P, et al.

mitotic cell cycle

mouse
Genes Dev. 1987

K.O.,
June; 1(4): 366-75

function

Racgap1
26934
RACGAP1
29127
−1.94
mitotic spindle
Cell cycle
CS score,
Van de Putte T, et

assembly

mouse
al. Mech Dev. 2001

K.O.,
April; 102(1-2): 33-44

function

Rad21
19357
RAD21
5885
−2.12
mitotic cell cycle
Cell cycle
CS score,

function

Rae1
66679
RAE1
8480
−2.15
mitotic cell cycle
Cell cycle
CS score,
Babu J R. et al. J

mouse
Cell Biol. 2003 Feb.

K.O.,
3; 160(3): 341-53

function

Rcc1
100088
RCC1
1104
−2.91
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Rfc3
69263
RFC3
5983
−2.74
mitotic cell cycle
Cell cycle
CS score,

function

Rps27a
78294
RPS27A
6233
−2.74
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Rrm2
20135
RRM2
6241
−3.09
G1/S transition of
Cell cycle
CS score,

mitotic cell cycle

function

Sae1
56459
SAE1
10055
−2.08
cellular protein
Cell cycle
CS score,

modification process

function

Sec13
110379
SEC13
6396
−2.96
mitotic cell cycle
Cell cycle
CS score,

function

Smarcb1
20587
SMARCB1
6598
−1.98
chromatin
Cell cycle
CS score,
Guidi C J, et al. Mol

remodeling

mouse
Cell Biol. 2001 May

K.O.,
15; 21(10): 3598-603

function

Smc2
14211
SMC2
10592
−2.13
mitotic chromosome
Cell cycle
CS score,
Nishide K, et al.

condensation

mouse
PLoS Genet. 2014

K.O.,
December; 10(12): e10048

function
47

Smc4
70099
SMC2
10051
−1.47
chromosome
Cell cycle
CS score,

organization

function

Son
20658
SON
6651
−1.99
microtubule
Cell cycle
CS score,

cytoskeleton

function

organization

Spc24
67629
SPC24
147841
−2.83
mitotic cell cycle
Cell cycle
CS score,

function

Spc25
66442
SPC25
57405
−1.63
mitotic cell cycle
Cell cycle
CS score,

function

Terf2
21750
TERF2
7014
−2.17
telomere
Cell cycle
CS score,
Celli G B, et al. Nat

maintenance

mouse
Cell Biol. 2005

K.O.,
July; 7(7): 712-8

function

Tpx2
72119
TPX2
22974
−2.08
apoptotic process
Cell cycle
CS score,
Aguirre-Portoles C,

mouse
et al. Cancer Res.

K.O.,
2012 Mar.

function
15; 72(6): 1518-28

Tubg1
103733
TUBG1
7283
−2.08
microtubule
Cell cycle
CS score,
Yuba-Kubo A, et al.

nucleation

mouse
Dev Biol. 2005 Jun.

K.O.,
15; 282(2): 361-73

function

Tubgcp2
74237
TUBGCP2
10844
−2.78
microtubule
Cell cycle
CS score,

cytoskeleton

function

organization

Tubgcp5
233276
TUBGCP5
114791
−1.76
microtubule
Cell cycle
CS score,

cytoskeleton

function

organization

Tubgcp6
328580
TUBGCP6
85378
−1.52
microtubule
Cell cycle
CS score,

cytoskeleton

function

organization

Txnl4a
27366
TXNL4A
10907
−3.89
mitotic nuclear
Cell cycle
CS score,

division

function

Usp39
28035
USP39
10713
−2.85
spliceosomal
Cell cycle
CS score,

complex assembly

function

Wdr43
72515
WDR43
23160
−3.02
reproduction
Cell cycle
CS score,

function

Zfp830
66983
ZNF830
91603
−1.52
blastocyst growth
Cell cycle
CS score,
Houlard M, et al.

mouse
Cell Cycle. 2011

K.O.,
Jan. 1; 10(1): 108-17

function

Aatf
56321
AATF
26574
−1.46
cellular response to
DNA
CS score,
Thomas T, et al.

DNA damage
replication,
mouse
Dev Biol. 2000 Nov.

stimulus
DNA repair
K.O.,
15; 227(2): 324-42

function

Alyref
21681
ALYREF
10189
−1.92
regulation of DNA
DNA
CS score,

recombination
replication,
function

DNA repair

Brf2
66653
BRF2
55290
−2.30
DNA-
DNA
CS score,

templated transcription,
replication,
function

initiation
DNA repair

Cdc45
12544
CDC45
8318
−3.69
DNA replication
DNA
CS score,
Yoshida K, et al.

checkpoint
replication,
mouse
Mol Cell Biol. 2001

DNA repair
K.O.,
July; 21(14): 4598-603

function

Cdc6
23834
CDC6
990
−1.87
DNA replication
DNA
CS score,

initiation
replication,
function

DNA repair

Cdt1
67177
CDT1
81620
−2.74
DNA replication
DNA
CS score,

initiation
replication,
function

DNA repair

Cinp
67236
CINP
51550
−1.64
DNA replication
DNA
CS score,

replication,
function

DNA repair

Cirh1a
21771
CIRH1A
84916
−2.62
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Ddb1
13194
DDB1
1642
−2.14
nucleotide-
DNA
CS score,
Cang Y, et al. Cell.

excision repair, DNA
replication,
mouse
2006 Dec.

damage removal
DNA repair
K.O.,
1; 127(5): 929-40

function

Ercc2
13871
ERCC2
2068
−2.80
DNA duplex
DNA
CS score,
de Boer J, et al.

unwinding
replication,
mouse
Cancer Res. 1998

DNA repair
K.O.,
Jan. 1; 58(1): 89-94

function

Gabpb1
14391
GABPB1
2553
−1.74
transcription, DNA-
DNA
CS score,
Xue H H, et al. Mol

templated
replication,
mouse
Cell Biol. 2008

DNA repair
K.O.,
July; 28(13): 4300-9

function

Gtf2b
229906
GTF2B
2959
−2.76
regulation of
DNA
CS score,

transcription, DNA-
replication,
function

templated
DNA repair

Gtf2h4
14885
GTF2H4
2968
−1.93
nucleotide-
DNA
CS score,

excision repair, DNA
replication,
function

damage removal
DNA repair

Gtf3a
66596
GTF3A
2971
−2.25
regulation of
DNA
CS score,

transcription, DNA-
replication,
function

templated
DNA repair

Gtf3c1
233863
GTF3C1
2975
−2.45
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Gtf3c2
71752
GTF3C2
2976
−2.09
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Hinfp
102423
HINFP
25988
−2.35
DNA damage
DNA
CS score,
Xie R, et al. Proc

checkpoint
replication,
mouse
Natl Acad Sci USA.

DNA repair
K.O.,
2009 Jul. 9

function

n/a
n/a
HIST2H2AA3
8337
−1.71
DNA repair
DNA
CS score,

replication,
function

DNA repair

Ints3
229543
INTS3
65123
−3.14
DNA repair
DNA
CS score,

replication,
function

DNA repair

Kin
16588
KIN
22944
−1.99
DNA replication
DNA
CS score,

replication,
function

DNA repair

Mcm2
17216
MCM2
4171
−2.86
DNA replication
DNA
CS score,

initiation
replication,
function

DNA repair

Mcm6
17219
MCM6
4175
−1.55
DNA replication
DNA
CS score,

replication,
function

DNA repair

Mcrs1
51812
MCRS1
10445
−1.23
DNA repair
DNA
CS score,

replication,
function

DNA repair

Med11
66172
MED11
400569
−2.39
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Mtpap
67440
MTPAP
55149
−1.86
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Myc
17869
MYC
4609
−2.49
regulation of
DNA
CS score,
Trumpp A, et al.

transcription, DNA-
replication,
mouse
Nature. 2001 Dec.

templated
DNA repair
K.O.,
13; 414(6865): 768-

function
73

Ndnl2
66647
NDNL2
56160
−2.03
DNA repair
DNA
CS score,

replication,
function

DNA repair

Nol11
68979
NOL11
25926
−1.59
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Nol8
70930
NOL8
55035
−1.35
DNA replication
DNA
CS score,

replication,
function

DNA repair

Pcna
18538
PCNA
5111
−3.60
DNA replication
DNA
CS score,
Roa S, et al. Proc

replication,
mouse
Natl Acad Sci USA.

DNA repair
K.O.,
2008 Oct. 21;

function
105(42): 16248-53

Pola1
18968
POLA1
5422
−2.28
DNA-
DNA
CS score,

dependent DNA
replication,
function

replication
DNA repair

Pold2
18972
POLD2
5425
−2.51
DNA replication
DNA
CS score,

replication,
function

DNA repair

Pole
18973
POLE
5426
−2.90
DNA replication
DNA
CS score,

replication,
function

DNA repair

Polr1a
20019
POLR1A
25885
−2.62
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

n/a
n/a
POLR2J2
246721
−3.08
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Polr3a
218832
POLR3A
11128
−2.43
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Polr3c
74414
POLR3C
10623
−2.02
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Polr3h
78929
POLR3H
171568
−2.66
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Prmt1
15469
PRMT1
3276
−2.40
regulation of
DNA
CS score,
Pawlak M R, et al.

transcription, DNA-
replication,
mouse
Mol Cell Biol. 2000

templated
DNA repair
K.O.,
July; 20(13): 14859-69

function

Prmt5
27374
PRMT5
10419
−2.69
regulation of
DNA
CS score,
Tee W W, et al.

transcription, DNA-
replication,
mouse
Genes Dev. 2010

templated
DNA repair
K.O.,
Dec. 15; 24(24): 2772-7

function

Puf60
67959
PUF60
22827
−2.69
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Rad51
19361
RAD51
5888
−2.29
DNA repair
DNA
CS score,
Tsuzuki T, et al.

replication,
mouse
Proc Natl Acad Sci

DNA repair
K.O.,
USA. 1996 Jun.

function
25; 93(13): 6236-40

Rad51c
114714
RAD51C
5889
−1.62
DNA repair
DNA
CS score,
Smeenk G, et al.

replication,
mouse
Mutat Res. 2010 Jul.

DNA repair
K.O.,
7; 689(1-2): 50-58

function

Rbx1
56438
RBX1
9978
−2.19
DNA repair
DNA
CS score,
Tan M, et al. Proc

replication,
mouse
Natl Acad Sci USA.

DNA repair
K.O.,
2009 Apr.

function
14; 106(15): 6203-8

Rfc2
19718
RFC2
5982
−2.88
DNA-
DNA
CS score,

dependent DNA
replication,
function

replication
DNA repair

Rfc4
106344
RFC4
5984
−1.92
DNA-
DNA
CS score,

dependent DNA
replication,
function

replication
DNA repair

Rfc5
72151
RFC5
5985
−2.78
DNA-
DNA
CS score,

dependent DNA
replication,
function

replication
DNA repair

Rpa1
68275
RPA1
6117
−2.61
DNA replication
DNA
CS score,
Wang Y, et al. Nat

replication,
mouse
Genet. 2005

DNA repair
K.O.,
July; 37(7): 750-5

function

Rps3
27050
RPS3
6188
−2.75
DNA repair
DNA
CS score,

replication,
function

DNA repair

Rrm1
20133
RRM1
6240
−4.16
DNA replication
DNA
CS score,

replication,
function

DNA repair

Ruvbl1
56505
RUVBL1
8607
−3.26
DNA duplex
DNA
CS score,

unwinding
replication,
function

DNA repair

Ruvbl2
20174
RUVBL2
10856
−3.91
DNA repair
DNA
CS score,

replication,
function

DNA repair

Sap30bp
57230
SAP30BP
29115
−2.18
regulation of
DNA
CS score,

transcription, DNA-
replication,
function

templated
DNA repair

Smc1a
24061
SMC1A
8243
−2.76
DNA repair
DNA
CS score,

replication,
function

DNA repair

Smc3
13006
SMC3
9126
−3.22
DNA repair
DNA
CS score,
White J K, et al. Cell.

replication,
mouse
2013 Jul.

DNA repair
K.O.,
18; 154(2): 452-64

function

Snapc4
227644
SNAPC4
6621
−2.78
regulation of
DNA
CS score,

transcription, DNA-
replication,
function

templated
DNA repair

Snapc5
330959
SNAPC5
10302
−2.24
regulation of
DNA
CS score,

transcription, DNA-
replication,
function

templated
DNA repair

Snip1
76793
SNIP1
79753
−1.78
regulation of
DNA
CS score,

transcription, DNA-
replication,
function

templated
DNA repair

Srrt
83701
SRRT
51593
−2.18
transcription, DNA-
DNA
CS score,
Wilson M D, et al.

templated
replication,
mouse
Mol Cell Biol. 2008

DNA repair
K.O.,
March; 28(5): 1503-14

function

Ssrp1
20833
SSRP1
6749
−1.45
DNA replication
DNA
CS score,
Cao S, et al. 5

replication,
mouse
mouse embryos

DNA repair
K.O.,
Mol Cell Biol. 2003

function
August; 23(15): 5301-7

Taf10
24075
TAF10
6881
−1.38
DNA-templated
DNA
CS score,
Mohan W S Jr, et al.

transcription,
replication,
mouse
Mol Cell Biol. 2003

initiation
DNA repair
K.O.,
Jun. 23; (12): 4307-18

function

Taf1c
21341
TAF1C
9013
−1.80
chromatin silencing
DNA
CS score,

at rDNA
replication,
function

DNA repair

Taf6
21343
TAF6
6878
−1.84
DNA-
DNA
CS score,

templated
replication,
function

transcription,
DNA repair

initiation

Taf6l
67706
TAF6L
10629
−1.53
DNA-
DNA
CS score,

templated
replication,
function

transcription,
DNA repair

initiation

Ticrr
77011
TICRR
90381
−2.03
DNA replication
DNA
CS score,

replication,
function

DNA repair

Top1
21969
TOP1
7150
−2.02
DNA topical
DNA
CS score,
Morham S G, et al.

change
replication,
mouse
Mol Cell Biol. 1996

DNA repair
K.O.,
December; 16(12): 6804-9

function

Top2a
21973
TOP2A
7153
−1.50
DNA replication
DNA
CS score,

replication,
function

DNA repair

Trrap
100683
TRRAP
8295
−2.36
DNA repair
DNA
CS score,
Herceg Z et al. Nat

replication,
mouse
Genet. 2001

DNA repair
K.O.,
October; 29(2): 206-11

function

Zbtb11
271377
ZBTB11
27107
−2.34
transcription, DNA-
DNA
CS score,

templated
replication,
function

DNA repair

Actl6a
56456
ACTL6A
86
−2.33
neural retina
DNA
CS score,
Krasteva V, et al.

development
replication,
mouse
Blood. 2012 Dec.

DNA repair
K.O.,
6; 120(24): 4720-32

function

Atr
245000
ATR
545
−2.01
double-strand break
DNA
CS score,
de Klein A, et al.

repair via
replication,
mouse
Curr Biol. 2000 Apr.

homologous
DNA repair
K.O.,
20; 10(8): 479-82

recombination

function

Chd4
107932
CHD4
1108
−1.71
chromatin
DNA
CS score,

organization
replication,
function

DNA repair

Ciao1
26371
CIAO1
9391
−1.94
chromosome
DNA
CS score,

segregation
replication,
function

DNA repair

Ddx21
56200
DDX21
9188
−2.84
osteoblast
DNA
CS score,

differentiation
replication,
function

DNA repair

Dnaja3
83945
DNAJA3
9093
−2.19
mitochondrion
DNA
CS score,
Lo J F, et al. Mol

organization
replication,
mouse
Cell Biol. 2004

DNA repair
K.O.,
March; 24(6): 2226-36

function

Dnmt1
13433
DNMT1
1786
−1.97
methylation
DNA
CS score,
Lei H, et al.

replication,
mouse
Development. 1996

DNA repair
K.O.,
October; 122(10): 3195-

function
205

Gins2
272551
GINS2
51659
−3.32
double-strand break
DNA
CS score,

repair via break-
replication,
function

induced replication
DNA repair

Gtf2h3
209357
GTF2H3
2967
−1.84
nucleotide-
DNA
CS score,

excision repair
replication,
function

DNA repair

n/a
n/a
HIST2H2BF
440689
−1.70
chromatin
DNA
CS score,

organization
replication,
function

DNA repair

Mms22l
212377
MMS22L
253714
−1.38
double-strand break
DNA
CS score,

repair via
replication,
function

homologous
DNA repair

recombination

Mtor
56717
MTOR
2475
−1.98
double-strand break
DNA
CS score,
Murakami M, et al.

repair via
replication,
mouse
Mol Cell Biol. 2004

homologous
DNA repair
K.O.,
August; 24(15): 6710-8

recombination

function

Narfl
67563
NARFL
64428
−2.13
response hypoxia
DNA
CS score,
Song D, et al. J Biol

replication,
mouse
Chem. 2011 Mar. 2

DNA repair
K.O.,

function

Ndufa13
67184
NDUFA13
51079
−1.31
positive regulation of
DNA
CS score,
Huang G, et al. Mol

peptidase activity
replication,
mouse
Cell Biol. 2004

DNA repair
K.O.,
October; 24(19): 8447-56

function

Nol12
97961
NOL12
79159
−1.61
poly(A) RNA binding
DNA
CS score,

replication,
function

DNA repair

Nup107
103468
NUP107
57122
−1.30
transport
DNA
CS score,

replication,
function

DNA repair

Oraov1
72284
ORAOV1
220064
−2.26
biological_process
DNA
CS score,

replication,
function

DNA repair

Pam16
66449
PAM16
51025
−2.13
protein import into
DNA
CS score,

mitochondrial matrix
replication,
function

DNA repair

Pola2
18969
POLA2
23649
−2.84
protein import into
DNA
CS score,

nucleus,
replication,
function

translocation
DNA repair

Ppie
56031
PPIE
10450
−1.63
protein peptidyl-prolyl
DNA
CS score,

isomerization
replication,
function

DNA repair

Prpf19
28000
PRPF19
27339
−3.96
generation of
DNA
CS score,
Fortschegger K, et

catalytic spliceosome
replication,
mouse
al. Mol Cell Biol.

for first
DNA repair
K.O.,
2007

transesterification

function
April; 27(8): 3123-30

step

Psmc5
19184
PSMC5
5705
−2.57
ER-
DNA
CS score,

associated ubiquitin-
replication,
function

dependent protein
DNA repair

catabolic process

Rbbp5
213464
RBBP5
5929
−1.70
chromatin
DNA
CS score,

organization
replication,
function

DNA repair

Rbbp6
19647
RBBP6
5930
−1.78
in utero embryonic
DNA
CS score,
Li L, et al. Proc Natl

development
replication,
mouse
Acad Sci USA.

DNA repair
K.O.,
2007 May

function
8; 104(19): 7951-6

Rptor
74370
RPTOR
57521
−2.43
TOR signalling
DNA
CS score,
Guertin D A, et al.

replication,
mouse
Dev Cell. 2006

DNA repair
K.O.,
December; 11(6): 859-71

function

Rrn3
106298
RRN3
54700
−1.85
in utero embryonic
DNA
CS score,
Yuan X, et al. Mol

development
replication,
mouse
Cell. 2005 Jul.

DNA repair
K.O.,
1; 19(1): 77-87

function

Smg1
233789
SMG1
23049
−1.94
double-strand break
DNA
CS score,
Roberts T L, et al.

repair via
replication,
mouse
Proc Natl Acad Sci

homologous
DNA repair
K.O.,
USA. 2013 Jan.

recombination

function
22; 110(4): E285-94

Supt6
20926
SUPT6H
6830
−1.78
chromatin
DNA
CS score,
Dietrich J E, et al.

remodeling
replication,
mouse
EMBO Rep. 2015

DNA repair
K.O.,
August; 16(8): 1005-21

function

Tada2b
231151
TADA2B
93624
−1.23
chromatin
DNA
CS score,

organization
replication,
function

DNA repair

Tfip11
54723
TFIP11
24144
−2.19
spliceosomal
DNA
CS score,

complex disassembly
replication,
function

DNA repair

Tonsl
66914
TONSL
4796
−3.03
double-strand break
DNA
CS score,

repair via
replication,
function

homologous
DNA repair

recombination

Tpt1
22070
TPT1
7178
−2.05
calcium ion transport
DNA
CS score,
Susini L, et al. Cell

replication,
mouse
Death Differ. 2008

DNA repair
K.O.,
August; 15(8): 1211-20

function

Uba1
22201
UBA1
7317
−2.90
protein ubiquitination
DNA
CS score,

replication,
function

DNA repair

Vps25
28084
VPS25
84313
−2.31
protein targeting
DNA
CS score,

to vacuole involved
replication,
function

in ubiquitin-
DNA repair

dependent protein

catabolic process via

the multivesicular

body sorting pathway

Wbscr22
66138
WBSCR22
114049
−2.70
methylation
DNA
CS score,

replication,
function

DNA repair

Wdr5
140858
WDR5
11091
−1.99
skeletal system
DNA
CS score,

development
replication,
function

DNA repair

Xab2
67439
XAB2
56949
−2.86
generation of
DNA
CS score,
Yonemasu R, et al.

catalytic spliceosome
replication,
mouse
DNA Repair (Amst).

for first
DNA repair
K.O.,
2005 Apr.

transesterification

function
4; 4(4): 473-91

step

Zmat2
66492
ZMAT2
153527
−2.17
histidine-
DNA
CS score,

tRNA ligase
replication,
function

activity
DNA repair

Zfp335
329559
ZNF335
63925
−1.58
in utero embryonic
DNA
CS score,
Yang Y J, et al. Cell.

development
replication,
mouse
2012 Nov.

DNA repair
K.O.,
21; 151(5): 1097-112

function

Acly
104112
ACLY
47
−1.54
acetyl-CoA metabolic
Metabolism
CS score,
Beigneux A P, et al.

process

mouse
J Biol Chem. 2004

K.O.,
Mar.

function
5; 279(10): 9557-64

Adsl
11564
ADSL
158
−2.39
metabolic process
Metabolism
CS score,

function

Ahcy
269378
AHCY
191
−2.07
sulfur amino acid
Metabolism
CS score,

metabolic process

function

Arl2
56327
ARL2
402
−2.29
energy reserve
Metabolism
CS score,

metabolic process

function

Chka
12660
CHKA
1119
−1.64
lipid metabolic
Metabolism
CS score,
Wu G, et al. J Biol

process

mouse
Chem. 2008 Jan.

K.O.,
18; 283(3): 1456-62

function

Coasy
71743
COASY
80347
−1.82
vitamin metabolic
Metabolism
CS score,

process

function

Cox4i1
12857
COX4I1
1327
−2.00
generation of
Metabolism
CS score,

precursor

function

metabolites and

energy

n/a
n/a
COX7C
1350
−1.59
generation of
Metabolism
CS score,

precursor

function

metabolites and

energy

n/a
n/a
CTPS1
1503
−2.52
nucleobase-
Metabolism
CS score,

containing compound

function

metabolic process

Ddx10
77591
DDX10
1662
−2.02
metabolic process
Metabolism
CS score,

function

Ddx20
53975
DDX20
11218
−2.49
metabolic process
Metabolism
CS score,
Mouillet J F, et al.

mouse
Endocrinology.

K.O.,
2008

function
May; 149(5): 2168-75

Dhdds
67422
DHDDS
79947
−2.86
metabolic process
Metabolism
CS score,

function

Dhx30
72831
DHX30
22907
−1.93
metabolic process
Metabolism
CS score,

function

Dhx8
217207
DHX8
1659
−2.61
metabolic process
Metabolism
CS score,

function

Dhx9
13211
DHX9
1660
−1.73
metabolic process
Metabolism
CS score,
Lee C G, et al. Proc

mouse
Natl Acad Sci USA.

K.O.,
1998 Nov.

function
10; 95(23): 13709-13

Dlst
78920
DLST
1743
−1.93
metabolic process
Metabolism
CS score,

function

Dpagt1
13478
DPAGT1
1798
−2.80
UDP-N-
Metabolism
CS score,
Marek K W, et al.

acetylglucosamine

mouse
Glycobiology. 1999

metabolic process

K.O.,
November; 9(11): 1263-71

function

Gfpt1
14583
GFPT1
2673
−1.81
fructose 6-phosphate
Metabolism
CS score,

metabolic process

function

Gmps
229363
GMPS
8833
−1.80
Purine nucleobase
Metabolism
CS score,

metabolic process

function

Gpn1
74254
GPN1
11321
−1.79
metabolic process
Metabolism
CS score,

function

Gpn3
68080
GPN3
51184
−3.12
metabolic process
Metabolism
CS score,

function

Guk1
14923
GUK1
2987
−2.67
purine nucleotide
Metabolism
CS score,

metabolic process

function

Hsd17b10
15108
HSD17B10
3028
−1.84
lipid metabolic
Metabolism
CS score,

process

function

Lrr1
69706
LRR1
122769
−3.44
metabolic process
Metabolism
CS score,

function

Mtg2
52856
MTG2
26164
−2.04
metabolic process
Metabolism
CS score,

function

Myh9
17886
MYH9
4627
−1.70
metabolic process
Metabolism
CS score,
Matsushita T, et al.

mouse
Biochem Biophys

K.O.,
Res Commun. 2004

function
Dec.

24; 325(4): 1163-71

Nampt
59027
NAMPT
10135
−2.40
vitamin metabolic
Metabolism
CS score,
Revollo J R, et al.

process

mouse
Cell Metab. 2007

K.O.,
November; 6(5): 363-75

function

Ncbp1
433702
NCBP1
4686
−1.62
RNA metabolic
Metabolism
CS score,

process

function

Nfs1
18041
NFS1
9054
−2.40
metabolic process
Metabolism
CS score,

function

Ppcdc
66812
PPCDC
60490
−1.98
metabolic process
Metabolism
CS score,

function

Qrsl1
76563
QRSL1
55278
−1.67
metabolic process
Metabolism
CS score,

function

Rpp14
67053
RPP14
11102
−1.72
fatty acid metabolic
Metabolism
CS score,

process

function

Smarca4
20586
SMARCA4
6597
−1.89
metabolic process
Metabolism
CS score,
Bultman S, et al.

mouse
Mol Cell. 2000

K.O.,
December; 6(6): 1287-95

function

Snrnp200
320632
SNRNP200
23020
−2.50
metabolic process
Metabolism
CS score,

function

Srbd1
78586
SRBD1
55133
−2.35
nucleobase-
Metabolism
CS score,

containing compound

function

metabolic process

Srcap
100043597
SRCAP
10847
−1.43
metabolic process
Metabolism
CS score,

function

Ube2i
22196
UBE2I
7329
−2.55
metabolic process
Metabolism
CS score,
Nacerddine K, et al.

mouse
Dev Cell. 2005

K.O.,
December; 9(6): 769-79

function

Ube2m
22192
UBE2M
9040
−2.39
metabolic process
Metabolism
CS score,

function

Vcp
269523
VCP
7415
−2.85
metabolic process
Metabolism
CS score,
Muller J M, et al.

mouse
Biochem Biophys

K.O.,
Res Commun. 2007

function
Mar. 9; 354(2): 459-

465

Aamp
227290
AAMP
14
−2.37
angiogenesis
Metabolism
CS score,

function

Acin1
56215
ACIN1
22985
−1.53
positive regulation of
Metabolism
CS score,

defense response to

function

virus by host

Aco2
11429
ACO2
50
−2.08
tricarboxylic acid
Metabolism
CS score,

cycle

function

Adss
11566
ADSS
159
−2.46
purine nucleotide
Metabolism
CS score,

biosynthetic process

function

Alg2
56737
ALG2
85365
−2.29
biosynthetic process
Metabolism
CS score,

function

Ap2s1
232910
AP2S1
1175
−2.00
intracellular protein
Metabolism
CS score,

transport

function

Arcn1
213827
ARCN1
372
−1.91
intracellular protein
Metabolism
CS score,

transport

function

Armc7
276905
ARMC7
79637
−2.02
molecular_function
Metabolism
CS score,

function

Atp2a2
11938
ATP2A2
488
−3.01
calcium ion
Metabolism
CS score,
Andersson K B, et

transmembrane

mouse
al. Cell Calcium.

transport

K.O.,
2009

function
September; 46(3): 219-25

Atp5a1
11946
ATP5A1
498
−1.99
negative regulation of
Metabolism
CS score,

endothelial cell

function

proliferation

Atp5d
66043
ATP5D
513
−2.21
oxidative
Metabolism
CS score,

phosphorylation

function

Atp5o
28080
ATP5O
539
−1.17
ATP biosynthetic
Metabolism
CS score,

process

function

Atp6v0b
114143
ATP6V0B
533
−3.01
cellular iron ion
Metabolism
CS score,

homeostasis

function

Atp6v0c
11984
ATP6V0C
527
−3.84
cellular iron ion
Metabolism
CS score,
Sun-Wada G H, et

homeostasis

mouse
al. Dev Biol. 2000

K.O.,
Dec. 15; 228(2): 315-

function
25

Atp6v1a
11964
ATP6V1A
523
−3.58
proton transport
Metabolism
CS score,

function

Atp6v1b2
11966
ATP6V1B2
526
−2.94
cellular iron ion
Metabolism
CS score,

homeostasis

function

Atp6v1d
73834
ATP6V1D
51382
−2.58
transmembrane
Metabolism
CS score,

transport

function

Aurkaip1
66077
AURKAIP1
54998
−1.56
organelle
Metabolism
CS score,

organization

function

n/a
n/a
C1orf109
54955
−2.43
molecular_function
Metabolism
CS score,

function

n/a
n/a
C21orf59
56683
−2.77
cell projection
Metabolism
CS score,

morphogenesis

function

Ccdc84
382073
CCDC84
338657
−1.86
molecular_function
Metabolism
CS score,

function

Cct2
12461
CCT2
10576
−3.23
protein folding
Metabolism
CS score,

function

Cct3
12462
CCT3
7203
−3.31
protein folding
Metabolism
CS score,

function

Cct4
12464
CCT4
10575
−2.62
protein folding
Metabolism
CS score,

function

Cct5
12465
CCT5
22948
−2.84
protein folding
Metabolism
CS score,

function

Cct7
12468
CCT7
10574
−2.47
protein folding
Metabolism
CS score,

function

Cct8
12469
CCT8
10694
2.03
protein folding
Metabolism
CS score,

function

Cdipt
52858
CDIPT
10423
−2.53
phospholipid
Metabolism
CS score,

biosynthetic process

function

Cenpi
102920
CENPI
249
−1.81
centromere complex
Metabolism
CS score,

assembly

function

Chordc1
66917
CHORDC1
26973
−1.52
regulation of
Metabolism
CS score,
Ferretti R, et al. Dev

centrosome

mouse
Cell. 2010 Mar.

duplication

K.O.,
16; 18(3): 486-95

function

Coa5
76178
COA5
493753
−2.33
mitochondrion
Metabolism
CS score,

function

Cog4
102339
COG4
25839
−1.39
Golgi vesicle
Metabolism
CS score,

transport

function

Copa
12847
COPA
1314
−1.63
intracellular protein
Metabolism
CS score,

transport

function

Copb1
70349
COPB1
1315
−2.30
intracellular protein
Metabolism
CS score,

transport

function

Copb2
50797
COPB2
9276
−2.65
intracellular protein
Metabolism
CS score,

transport

function

Cope
59042
COPE
11316
−2.93
ER to Golgi vesicle-
Metabolism
CS score,

mediated transport

function

Copz1
56447
COPZ1
22818
−1.87
transport
Metabolism
CS score,

function

Coq4
227683
COQ4
51117
−1.29
ubiquinone
Metabolism
CS score,

biosynthetic process

function

Cox15
226139
COX15
1355
−2.14
mitochondrial
Metabolism
CS score,
Viscomi C, et al.

electron transport,

mouse
Cell Metab. 2011

cytochrome c

K.O.,
Jul. 6; 14(1): 80-90

to oxygen

function

Cox17
12856
COX17
10063
−1.97
copper ion transport
Metabolism
CS score,
Takahashi Y, et al.

mouse
Mol Cell Biol. 2002

K.O.,
November; 22(21): 7614-

function
21

Cse1l
110750
CSE1L
1434
−2.31
protein export from
Metabolism
CS score,
Bera T K, et al. Mol

nucleus

mouse
Cell Biol. 2001

K.O.,
October; 21(20): 7020-4

function

Csnk2b
13001
CSNK2B
1460
−1.94
regulation of protein
Metabolism
CS score,
Buchou T, et al. Mol

kinase activity

mouse
Cell Biol, 2003

K.O.,
February; 23(3): 908-15

function

Cycs
13063
CYCS
54205
−2.36
response to reactive
Metabolism
CS score,
Li K, et al. Cell.

oxygen species

mouse
2000 May

K.O.,
12; 101(4): 389-99

function

Dad1
13135
DAD1
1603
−2.21
protein glycosylation
Metabolism
CS score,
Brewster J L, et al.

mouse
Genesis. 2000

K.O.,
April; 26(4): 271-8

function

Dap3
65111
DAP3
7818
−1.70
apoptotic process
Metabolism
CS score,
Kim H R, et al.

mouse
FASEB J. 2007

K.O.,
January; 21(1): 188-96

function

Dctn5
59288
DCTN5
84516
−2.39
antigen processing
Metabolism
CS score,

and presentation of

function

exogenous peptide

antigen via MHC

class II

Ddost
13200
DDOST
1650
−2.38
protein N-linked
Metabolism
CS score,

glycosylation via

function

asparagine

Dgcr8
94223
DGCR8
54487
−2.10
gene expression
Metabolism
CS score,
Ouchi Y, et al. J

mouse
Neurosci. 2013 May

K.O.,
29; 33(22): 9408-19

function

Dhodh
56749
DHODH
1723
−2.57
de novo' pyrimidine
Metabolism
CS score,

nucleobase

function

biosynthetic process

Dnlz
52838
DNLZ
728489
−1.92
protein folding
Metabolism
CS score,

function

Dnm1l
74006
DNM1L
10059
3.25
mitochondrial fission
Metabolism
CS score,
Wakabayashi J, et

mouse
al. J Cell Biol. 2009

K.O.,
Sep. 21; 186(6): 805-

function
16

Dnm2
13430
DNM2
1785
−3.98
endocytosis
Metabolism
CS score,
Ferguson S M, et al.

mouse
Dev Cell. 2009

K.O.,
December; 17(6): 811-22

function

Dohh
102115
DOHH
83475
−1.76
peptidyl-
Metabolism
CS score,

lysine modification

function

to peptidyl-

hypusine

Dolk
227697
DOLK
22845
−2.38
dolichol-
Metabolism
CS score,

linked

function

oligosaccharide

biosynthetic process

Donson
60364
DONSON
29980
−2.30
multicellular
Metabolism
CS score,

organismal

function

development

Dph3
105638
DPH3
285381
−1.62
peptidyl-
Metabolism
CS score,
Liu S, et al. Mol Cell

diphthamide

mouse
Biol. 2006

biosynthetic process

K.O.,
May; 26(10): 3835-41

from peptidyl-

function

histidine

Dtymk
21915
DTYMK
1841
−3.54
phosphorylation
Metabolism
CS score,

function

Eif2b2
217715
EIF2B2
8892
−2.24
ovarian follicle
Metabolism
CS score,

development

function

Eif2s2
67204
EIF2S2
8894
−2.33
in utero embryonic
Metabolism
CS score,
Heaney J D, et al.

development

mouse
Hum Mol Genet.

K.O.,
2009 Apr.

function
15; 18(8): 1395-404

Emc1
230866
EMC1
23065
−1.34
protein folding in
Metabolism
CS score,

endoplasmic

function

reticulum

Emc7
73024
EMC7
56851
−2.27
biological_process
Metabolism
CS score,

function

Eno1
13806
ENO1
2023
−2.03
glycolytic process
Metabolism
CS score,
Couldrey C, et al.

mouse
Dev Dyn. 1998

K.O.,
June; 212(2): 284-92

function

Fam50a
108160
FAM50A
9130
−3.16
spermatogenesis
Metabolism
CS score,

function

Fam96b
68523
FAM96B
51647
−1.90
iron-sulfur cluster
Metabolism
CS score,

assembly

function

Fdps
110196
FDPS
2224
−2.41
isoprenoid
Metabolism
CS score,

biosynthetic process

function

Gapdh
14433
GAPDH
2597
−2.40
oxidation-
Metabolism
CS score,

reduction process

function

Gait
14450
GART
2618
−1.87
purine nucleobase
Metabolism
CS score,

biosynthetic process

function

Gemin4
276919
GEMIN4
50628
−1.56
spliceosomal snRNP
Metabolism
CS score,

assembly

function

Gemin5
216766
GEMIN5
25929
−2.51
spliceosomal snRNP
Metabolism
CS score,

assembly

function

Ggps1
14593
GGPS1
9453
−1.62
cholesterol
Metabolism
CS score,

biosynthetic process

function

Gmppb
331026
GMPPB
29925
−3.22
biosynthetic process
Metabolism
CS score,

function

Gnb1l
13972
GNB1L
54584
−1.93
G-protein coupled
Metabolism
CS score,

receptor signaling

function

pathway

n/a
n/a
GOLGA6L1
283767
−3.15

Metabolism
CS score,

function

Gosr2
56494
GOSR2
9570
−1.13
protein targeting to
Metabolism
CS score,

vacuole

function

Gpkow
209416
GPKOW
27238
−1.36
biological_process
Metabolism
CS score,

function

Gpn2
100210
GPN2
54707
−3.71
biological_process
Metabolism
CS score,

function

Gps1
209318
GPS1
2873
−2.11
inactivation of MAPK
Metabolism
CS score,

activity

function

Grpel1
17713
GRPEL1
80273
−2.61
protein folding
Metabolism
CS score,

function

Grwd1
101612
GRWD1
83743
−1.90
poly(A) RNA binding
Metabolism
CS score,

function

Hmgcr
15357
HMGCR
3156
−2.94
cholesterol
Metabolism
CS score,
Ohashi K. et al. J

biosynthetic process

mouse
Biol Chem. 2003

K.O.,
Oct.

function
31; 278(44): 42936-

41

Hmgcs1
208715
HMGCS1
3157
−2.41
liver development
Metabolism
CS score,

function

Hspa5
14828
HSPA5
3309
−3.86
platelet degranulation
Metabolism
CS score,
Luo S, et al. Mol

mouse
Cell Biol. 2006

K.O.,
August; 26(15): 5688-97

function

Hspa9
15526
HSPA9
3313
−3.55
protein folding
Metabolism
CS score,

function

Hspd1
15510
HSPD1
3329
−1.95
response to hypoxia
Metabolism
CS score,
Christensen J H, et

mouse
al. Cell Stress

K.O.,
Chaperones, 2010

function
November; 15(6): 851-63

Hspe1
15528
HSPE1
3336
−3.75
osteoblast
Metabolism
CS score,

differentiation

function

Hyou1
12282
HYOU1
10525
−2.06
response to ischemia
Metabolism
CS score,

function

Ipo13
230673
IPO13
9670
−2.84
intracellular protein
Metabolism
CS score,

transport

function

Iscu
66383
ISCU
23479
−2.40
cellular iron ion
Metabolism
CS score,

homeostasis

function

Itpk1
217837
ITPK1
3705
−1.55
phosphorylation
Metabolism
CS score,

function

Kansl2
69612
KANSL2
54934
−1.19
chromatin
Metabolism
CS score,

organization

function

Kansl3
226976
KANSL3
55683
−1.53
chromatin
Metabolism
CS score,

organization

function

Kri1
215194
KRI1
65095
−2.49
poly(A) RNA binding
Metabolism
CS score,

function

Lamtor2
83409
LAMTOR2
28956
−1.62
activation of MAPKK
Metabolism
CS score,
Teis D, et al. J Cell

activity

mouse
Biol. 2006 Dec.

K.O.,
18; 175(6): 861-8

function

Leng8
232798
LENG8
114823
−1.75
biological_process
Metabolism
CS score,

function

Ltv1
353258
LTV1
84946
−1.81
nucleoplasm
Metabolism
CS score,

function

Mak16
67920
MAK16
84549
−2.30
poly(A) RNA binding
Metabolism
CS score,

function

Mat2a
232087
MAT2A
4144
−2.34
S-adenosylmethionine
Metabolism
CS score,

biosynthetic process

function

Mcm3ap
54387
MCM3AP
8888
−1.58
immune system
Metabolism
CS score,
Yoshida M, et al.

process

mouse
Genes Cells. 2007

K.O.,
October; 12(10): 1205-13

function

Mdn1
100019
MDN1
23195
−1.68
protein complex
Metabolism
CS score,

assembly

function

n/a
n/a
MFAP1
4236
−1.94
biological_process
Metabolism
CS score,

function

Mmgt1
236792
MMGT1
93380
−1.55
magnesium ion
Metabolism
CS score,

transport

function

Mrpl16
94063
MRPL16
54948
−1.80
organelle
Metabolism
CS score,

organization

function

Mrpl17
27397
MRPL17
63875
−1.80
mitochondrial
Metabolism
CS score,

genome

function

maintenance

Mrpl33
66845
MRPL33
9553
−1.62
organelle
Metabolism
CS score,

organization

function

Mrpl38
60441
MRPL38
64978
−1.95
organelle
Metabolism
CS score,

organization

function

Mrpl39
27393
MRPL39
54148
−1.71
organelle
Metabolism
CS score,

organization

function

Mrpl45
67036
MRPL45
84311
−1.75
organelle
Metabolism
CS score,

organization

function

Mrpl46
67308
MRPL46
26589
−1.83
organelle
Metabolism
CS score,

organization

function

Mrpl53
68499
MRPL53
116540
−1.84
organelle
Metabolism
CS score,

organization

function

Mrps22
64655
MRPS22
56945
−1.32
organelle
Metabolism
CS score,

organization

function

Mrps25
64658
MRPS25
64432
−1.63
organelle
Metabolism
CS score,

organization

function

Mrps35
232536
MRPS35
60488
−1.60
organelle
Metabolism
CS score,

organization

function

Mrps5
77721
MRPS5
64969
−1.65
organelle
Metabolism
CS score,

organization

function

Mvd
192156
MVD
4597
−3.24
isoprenoid
Metabolism
CS score,

biosynthetic process

function

Mvk
17855
MVK
4598
−1.73
isoprenoid
Metabolism
CS score,

biosynthetic process

function

Naa25
231713
NAA25
80018
−2.40
peptide alpha-N-
Metabolism
CS score,

acetyltransferase

function

activity

Napa
108124
NAPA
8775
−2.31
intracellular protein
Metabolism
CS score,

transport

function

Nat10
98956
NAT10
55226
−2.16
biological_process
Metabolism
CS score,

function

Ndor1
78797
NDOR1
27158
−2.10
cell death
Metabolism
CS score,

function

Ndufab1
70316
NDUFAB1
4706
−1.83
fatty acid biosynthetic
Metabolism
CS score,

process

function

Nol10
217431
NOL10
79954
−1.79
poly(A) RNA binding
Metabolism
CS score,

function

Nop9
67842
NOP9
161424
−1.44
biological_process
Metabolism
CS score,

function

Nrde2
217827
NRDE2
55051
−2.69
biological_process
Metabolism
CS score,

function

Nsf
18195
NSF
4905
−2.76
intra-Golgi vesicle-
Metabolism
CS score,

mediated transport

function

Nubp1
26425
NUBP1
4682
−2.05
cellular iron ion
Metabolism
CS score,

homeostasis

function

Nudcd3
209586
NUDCD3
23386
−1.71
molecular_function
Metabolism
CS score,

function

Nup155
170762
NUP155
9631
−1.59
nucleocytoplasmic
Metabolism
CS score,
Zhang X, et al. Cell.

transport

mouse
2008 Dec.

K.O.,
12; 135(6): 1017-27

function

Nup93
71805
NUP93
9688
−2.11
protein import into
Metabolism
CS score,

nucleus

function

Nus1
52014
NUS1
116150
−1.94
angiogenesis
Metabolism
CS score,
Park E J, et al. Cell

mouse
Metab. 2014 Sep.

K.O.,
2; 20(3): 448-57

function

Nvl
67459
NVL
4931
−2.61
positive regulation of
Metabolism
CS score,

telomerase activity

function

Ogdh
18293
OGDH
4967
−2.98
tricarboxylic acid
Metabolism
CS score,

cycle

function

Osbp
76303
OSBP
5007
−2.06
lipid transport
Metabolism
CS score,

function

Pak1ip1
68083
PAK1IP1
55003
−2.28
cell proliferation
Metabolism
CS score,

function

Pfdn2
18637
PFDN2
5202
−1.32
protein folding
Metabolism
CS score,

function

Pgam1
18648
PGAM1
5223
−2.37
glycolytic process
Metabolism
CS score,

function

Pkm
18746
PKM
5315
−1.68
glycolytic process
Metabolism
CS score,
Lewis S E, et al.

mouse
1983:267-78.

K.O.,
Plenum Publ. Corp.

function

Pmpcb
73078
PMPCB
9512
−1.77
proteolysis
Metabolism
CS score,

function

Ppil2
66053
PPIL2
23759
−3.01
protein
Metabolism
CS score,

polyubiquitination

function

Ppp4c
56420
PPP4C
5531
−2.89
protein
Metabolism
CS score,
Toyo-oka K, et al. J

dephosphorylation

mouse
Cell Biol. 2008 Mar.

K.O.,
24; 180(6): 1133-47

function

Prelid1
66494
PRELID1
27166
−2.27
apoptotic process
Metabolism
CS score,

function

Prpf31
68988
PRPF31
26121
−3.20
spliceosomal tri-
Metabolism
CS score,
Bujakowska K, et al.

snRNP complex

mouse
Invest Ophthalmol

assembly

K.O.,
Vis Sci. 2009

function
December; 50(12): 5927-

33

Prpf6
68879
PRPF6
24148
−2.96
spliceosomal tri-
Metabolism
CS score,

snRNP complex

function

assembly

Psma1
26440
PSMA1
5682
−2.39
proteasomal
Metabolism
CS score,

ubiquitin-

function

independent protein

catabolic process

Psma2
19166
PSMA2
5683
−2.23
proteasomal
Metabolism
CS score,

ubiquitin-

function

independent protein

catabolic process

Psma3
19167
PSMA3
5684
−2.30
proteasomal
Metabolism
CS score,

ubiquitin-

function

independent protein

catabolic process

Psmb2
26445
PSMB2
5690
−2.12
proteasomal
Metabolism
CS score,

ubiquitin-

function

independent protein

catabolic process

Psmb3
26446
PSMB3
5691
−2.78
proteolysis involved
Metabolism
CS score,

in cellular protein

function

catabolic process

Psmb5
19173
PSMB5
5693
−1.67
proteasomal
Metabolism
CS score,

ubiquitin-

function

independent protein

catabolic process

Psmb6
19175
PSMB6
5694
−2.42
proteasomal
Metabolism
CS score,

ubiquitin-

function

independent protein

catabolic process

Psmb7
19177
PSMB7
5695
−2.69
proteasomal
Metabolism
CS score,

ubiquitin-

function

independent protein

catabolic process

Psmc2
19181
PSMC2
5701
−2.35
protein catabolic
Metabolism
CS score,

process

function

Psmc3
19182
PSMC3
5702
−2.76
ER-
Metabolism
CS score,
Sakao Y, et al.

associated ubiquitin-

mouse
Genomics. 2000 Jul.

dependent protein

K.O.,
1; 67(1): 1-7

catabolic process

function

Psmc4
23996
PSMC4
5704
−2.36
blastocyst
Metabolism
CS score,
Sakao Y, et al.

development

mouse
Genomics. 2000 Jul.

K.O.,
1; 67(1): 1-7

function

Psmd1
70247
PSMD1
5707
−1.88
regulation of protein
Metabolism
CS score,

catabolic process

function

Psmd2
21762
PSMD2
5708
−2.16
regulation of protein
Metabolism
CS score,

catabolic process

function

Psmd3
22123
PSMD3
5709
−2.10
regulation of protein
Metabolism
CS score,

catabolic process

function

Psmd4
19185
PSMD4
5710
−1.77
ubiquitin-
Metabolism
CS score,
Soriano P, et al.

dependent protein

mouse
Genes Dev. 1987

catabolic process

K.O.,
June; 1(4): 366-75

function

Psmd6
66413
PSMD6
9861
−2.27
proteasome-
Metabolism
CS score,

mediated ubiquitin-

function

dependent protein

catabolic process

Psmg3
66506
PSMG3
84262
−2.57
molecular_function
Metabolism
CS score,

function

Ptpmt1
66461
PTPMT1
114971
−2.89
protein
Metabolism
CS score,
Shen J, et al. Mol

dephosphorylation

mouse
Cell Biol. 2011

K.O.,
December; 31(24): 4902-

function
16

Ptpn23
104831
PTPN23
25930
−1.59
negative regulation of
Metabolism
CS score,
Gingras M C, et al.

epithelial cell

mouse
Int J Dev Biol.

migration

K.O.,
2009; 53(7): 1069-74

function

Rabggta
56187
RABGGTA
5875
−3.18
protein prenylation
Metabolism
CS score,

function

Rabggtb
19352
RABGGTB
5876
−2.44
protein
Metabolism
CS score,

geranylgeranylation

function

Rbm19
74111
RBM19
9904
−2.03
multicellular
Metabolism
CS score,
Zhang J, et al. BMC

organismal

mouse
Dev Biol.

development

K.O.,
2008; 8:115

function

Rfk
54391
RFK
55312
−1.56
riboflavin biosynthetic
Metabolism
CS score,
Yazdanpanah B, et

process

mouse
al. Nature. 2009

K.O.,
Aug.

function
27; 460(7259): 1159-63

Rheb
19744
RHEB
6009
−1.38
signal transduction
Metabolism
CS score,
Zou J, et al. Dev

mouse
Cell. 2011 Jan.

K.O.,
18; 20(1): 97-108

function

Riok1
71340
RIOK1
83732
−1.27
protein
Metabolism
CS score,

phosphorylation

function

Rpn1
103963
RPN1
6184
−2.13
protein glycosylation
Metabolism
CS score,

function

Rtfdc1
66404
RTFDC1
51507
−2.09
biological_process
Metabolism
CS score,

function

Sacm1l
83493
SACM1L
22908
−1.80
protein
Metabolism
CS score,

dephosphorylation

function

Samm50
68653
SAMM50
25813
−1.62
protein targeting to
Metabolism
CS score,

mitochondrion

function

Sco2
100126824
SCO2
9997
−1.60
eye development
Metabolism
CS score,
Yang H, et al. Hum

mouse
Mol Genet. 2010

K.O.,
Jan. 1; 19(1): 170-80

function

Sdha
66945
SDHA
6389
−2.20
tricarboxylic acid
Metabolism
CS score,

cycle

function

Sdhb
67680
SDHB
6390
−2.33
tricarboxylic acid
Metabolism
CS score,

cycle

function

Sec61a1
53421
SEC61A1
29927
−2.42
protein transport
Metabolism
CS score,

function

Slc20a1
20515
SLC20A1
6574
−2.38
sodium ion transport
Metabolism
CS score,
Festing M H, et al.

mouse
Genesis. 2009

K.O.,
December; 47(12): 858-63

function

Slc7a6os
66432
SLC7A6OS
84138
−2.30
hematopoietic
Metabolism
CS score,

progenitor cell

function

differentiation

Smn1
20595
SMN1
6606
−1.58
spliceosomal
Metabolism
CS score,
Hsieh-Li H M, et al.

complex assembly

mouse
Nat Genet. 2000

K.O.,
Janunary; 24(1): 66-70

function

Smu1
74255
SMU1
55234
−3.65
molecular_function
Metabolism
CS score,

function

Snrpd1
20641
SNRPD1
6632
−2.79
spliceosomal
Metabolism
CS score,

complex assembly

function

Snrpd3
67332
SNRPD3
6634
−3.62
spliceosomal
Metabolism
CS score,

complex assembly

function

Snrpe
20643
SNRPE
6635
−2.74
spliceosomal
Metabolism
CS score,

complex assembly

function

Spata5
57815
SPATA5
166378
−1.50
multicellular
Metabolism
CS score,

organismal

function

development

Spata5l1
214616
SPATA5L1
79029
−2.70
molecular_function
Metabolism
CS score,

function

Tango6
272538
TANGO6
79613
−2.29
integral component of
Metabolism
CS score,

membrane

function

n/a
n/a
TBC1D3B
414059
−1.67
positive regulation of
Metabolism
CS score,

GTPase activity

function

n/a
n/a
TBC1D3C
414060
−2.01
positive regulation of
Metabolism
CS score,

GTPase activity

function

Tbcb
66411
TBCB
1155
−1.97
nervous system
Metabolism
CS score,

development

function

Tbcc
72726
TBCC
6903
−3.02
cell morphogenesis
Metabolism
CS score,

function

Tbcd
108903
TBCD
6904
−1.82
microtubule
Metabolism
CS score,

cytoskeleton

function

organization

Tcp1
21454
TCP1
6950
−2.34
protein folding
Metabolism
CS score,

function

Telo2
71718
TELO2
9894
−2.34
regulation of TOR
Metabolism
CS score,
Takai H, et al. Cell.

signaling

mouse
2007 Dec.

K.O.,
28; 131(7): 1248-59

function

Tex10
269536
TEX10
54881
−1.26
integral component of
Metabolism
CS score,

membrane

function

mouse

Tfrc
22042
TFRC
7037
−3.40
cellular iron ion
Metabolism
CS score,
Levy J E, et al. Nat

homeostasis

mouse
Genet. 1999

K.O.,
April; 21(4): 396-9

function

Timm10
30059
TIMM10
26519
−1.99
protein targeting to
Metabolism
CS score,

mitochondrion

function

Timm13
30055
TIMM13
26517
−1.62
protein targeting to
Metabolism
CS score,

mitochondrion

function

Timm23
53600
TIMM23
100287932
−2.00
protein targeting to
Metabolism
CS score,
Ahting U, et al.

mitochondrion

mouse
Biochim Biophys

K.O.,
Acta. 2009

function
May; 1787(5): 371-6

Timm44
21856
TIMM44
10469
−1.73
protein import into
Metabolism
CS score,

mitochondrial matrix

function

Tmx2
66958
TMX2
51075
−2.29
biological_process
Metabolism
CS score,

function

Tnpo3
320938
TNPO3
23534
−1.82
splicing factor protein
Metabolism
CS score,

import into nucleus

function

Trmt112
67674
TRMT112
51504
−3.70
peptidyl-glutamine
Metabolism
CS score,

methylation

function

Trnau1ap
71787
TRNAU1AP
54952
−1.40
selenocysteine
Metabolism
CS score,

incorporation

function

Ttc1
66827
TTC1
7265
−1.74
protein folding
Metabolism
CS score,

function

Ttc27
74196
TTC27
55622
−2.54
biological_process
Metabolism
CS score,

function

Tti1
75425
TTI1
9675
−2.91
regulation of TOR
Metabolism
CS score,

signaling

function

Tti2
234138
TTI2
80185
−1.94
molecular_function
Metabolism
CS score,

function

n/a
n/a
TUBB
203068
−3.40
microtubule-
Metabolism
CS score,

based process

function

Txn2
56551
TXN2
25828
−1.41
sulfate assimilation
Metabolism
CS score,
Nonn L, et al. Mol

mouse
Cell Biol. 2003

K.O.,
February; 23(3): 916-22

function

Uqcrc1
22273
UQCRC1
7384
−1.29
oxidative
Metabolism
CS score,

phosphorylation

function

Uqcrh
66576
UQCRH
7388
−1.28
oxidative
Metabolism
CS score,

phosphorylation

function

Urb2
382038
URB2
9816
−2.25
molecular_function
Metabolism
CS score,

function

Vmp1
75909
VMP1
81671
−1.75
exocytosis
Metabolism
CS score,

function

n/a
n/a
VPS28
51160
−3.06
protein targeting
Metabolism
CS score,

to vacuole involved

function

in ubiquitin-

dependent

protein catabolic

process via the

multivesicular body

sorting pathway

Vps29
56433
VPS29
51699
−2.05
intracellular protein
Metabolism
CS score,

transport

function

Vps52
224705
VPS52
6293
−1.85
ectodermal cell
Metabolism
CS score,
Sugimoto M, et al.

differentiation

mouse
Cell Rep. 2012 Nov.

K.O.,
29; 2(5): 1363-74

function

Wars2
70560
WARS2
10352
−1.16
vasculogenesis
Metabolism
CS score,

function

Wdr7
104082
WDR7
23335
−1.47
hematopoietic
Metabolism
CS score,

progenitor cell

function

differentiation

Wdr70
545085
WDR70
55100
−1.69
enzyme binding
Metabolism
CS score,

function

Wdr74
107071
WDR74
54663
−2.84
blastocyst formation
Metabolism
CS score,

function

Wdr77
70465
WDR77
79084
−2.19
spliceosomal snRNP
Metabolism
CS score,
Zhou L, et al. J Mol

assembly

mouse
Endocrinol. 2006

K.O.,
October; 37(2): 283-300

function

Yae1d1
67008
YAE1D1
57002
−1.71
molecular_function
Metabolism
CS score,

function

Yrdc
230734
YRDC
79693
−2.33
negative regulation of
Metabolism
CS score,

transport

function

Znhit2
29805
ZNHIT2
741
−2.70
metal ion binding
Metabolism
CS score,

function

Aars
234734
AARS
16
−2.48
alanyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Bms1
213895
BMS1
9790
−1.36
ribosome assembly
RNA
CS score,

tran-
function

scription,

protein

translation

Bud31
231889
BUD31
8896
−2.46
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Bysl
53414
BYSL
705
−2.24
maturation of SSU-
RNA
CS score,
Aoki R, et al. FEBS

rRNA from tricistronic
tran-
mouse
Lett. 2006 Nov.

rRNA transcript
scription,
K.O.,
13; 580(26): 6062-8

(SSU-rRNA, 5.8S
protein
function

rRNA, LSU-rRNA)
translation

Cars
27267
CARS
833
−2.45
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Cdc5l
71702
CDC5L
988
−2.09
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Cdc73
214498
CDC73
79577
−2.58
negative regulation of
RNA
CS score,
Wang P, et al. Mol

transcription from
tran-
mouse
Cell Biol. 2008

RNA polymerase II
scription,
K.O.,
May; 28(9): 2930-40

promoter
protein
function

translation

Cebpz
12607
CEBPZ
10153
−2.11
transcription from
RNA
CS score,

RNA polymerase II
tran-
function

promoter
scription,

protein

translation

Clasrp
53609
CLASRP
11129
−1.30
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Clp1
98985
CLP1
10978
−3.47
mRNA splicing, via
RNA
CS score,
Hanada T, et al.

spliceosome
tran-
mouse
Nature. 2013 Mar.

scription,
K.O.,
28; 495(7442): 474-

protein
function
80

translation

Cox5b
12859
COX5B
1329
−1.50
transcription initiation
RNA
CS score,

from RNA
tran-
function

polymerase II
scription,

promoter
protein

translation

Cpsf1
94230
CPSF1
29894
−2.58
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Cpsf2
51786
CPSF2
53981
−2.55
mRNA
RNA
CS score,

polyadenylation
tran-
function

scription,

protein

translation

Cpsf3l
71957
CPSF3L
54973
−2.09
snRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Dars
226414
DARS
1615
−2.90
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Dbr1
83703
DBR1
51163
−3.75
RNA splicing, via
RNA
CS score,

transesterification
tran-
function

reactions
scription,

protein

translation

Ddx18
66942
DDX18
8886
−2.33
RNA secondary
RNA
CS score,

structure unwinding
tran-
function

scription,

protein

translation

Ddx23
74351
DDX23
9416
−3.01
RNA secondary
RNA
CS score,

structure unwinding
tran-
function

scription,

protein

translation

Ddx24
27225
DDX24
57062
−1.40
RNA secondary
RNA
CS score,

structure unwinding
tran-
function

scription,

protein

translation

Ddx41
72935
DDX41
51428
−1.74
RNA secondary
RNA
CS score,

structure unwinding
tran-
function

scription,

protein

translation

Ddx46
212880
DDX46
9879
−2.79
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Ddx47
67755
DDX47
51202
−2.20
RNA secondary
RNA
CS score,

structure unwinding
tran-
function

scription,

protein

translation

Ddx49
234374
DDX49
54555
−3.20
RNA secondary
RNA
CS score,

structure unwinding
tran-
function

scription,

protein

translation

Ddx54
71990
DDX54
79039
−2.94
RNA secondary
RNA
CS score,

structure unwinding
tran-
function

scription,

protein

translation

Ddx56
52513
DDX56
54606
−2.85
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Dgcr14
27886
DGCR14
8220
−1.76
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Dhx15
13204
DHX15
1665
−2.58
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Dhx16
69192
DHX16
8449
−1.35
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Dhx38
64340
DHX38
9785
−1.76
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Diexf
215193
DIEXF
27042
−2.03
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Dimt1
66254
DIMT1
27292
−1.87
rRNA methylation
RNA
CS score,

tran-
function

scription,

protein

translation

Dis3
72662
DIS3
22894
−1.77
mRNA catabolic
RNA
CS score,

process
tran-
function

scription,

protein

translation

Dkc1
245474
DKC1
1736
−2.37
box H/ACA snoRNA
RNA
CS score,
He J, et al.

3′-end processing
tran-
mouse
Oncogene. 2002

scription,
K.O.,
Oct. 31; 21(50): 7740-

protein
function
4

translation

Dnajc17
69408
DNAJC17
55192
−2.25
negative regulation of
RNA
CS score,
Amendola E, et al.

transcription from
tran-
mouse
Endocrinology.

RNA polymerase II
scription,
K.O.,
2010

promoter
protein
function
April; 151(4): 1948-58

translation

Ears2
67417
EARS2
124454
−1.91
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Ebna1bp2
69072
EBNA1BP2
10969
−1.52
ribosome biogenesis
RNA
CS score,

tran-
function

scription,

protein

translation

Eef1a1
13627
EEF1A1
1915
−3.11
translational
RNA
CS score,

elongation
tran-
function

scription,

protein

translation

Eef1g
67160
EEF1G
1937
−1.42
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Eef2
13629
EEF2
1938
−3.53
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Eftud2
20624
EFTUD2
9343
−3.79
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Eif1ad
69860
EIF1AD
84285
−2.26
translational initiation
RNA
CS score,

tran-
function

scription,

protein

translation

Eif2b1
209354
EIF2B1
1967
−2.23
regulation of
RNA
CS score,

translational initiation
tran-
function

scription,

protein

translation

Eif2b3
108067
EIF2B3
8891
−3.00
translational initiation
RNA
CS score,

tran-
function

scription,

protein

translation

Eif2s1
13665
EIF2S1
1965
−3.93
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Eif3c
56347
EIF3C
8663
−2.59
formation of
RNA
CS score,

translation
tran-
function

preinitiation complex
scription,

protein

translation

n/a
n/a
EIF3CL
728689
−2.71
formation of
RNA
CS score,

translation
tran-
function

preinitiation complex
scription,

protein

translation

Eif3d
55944
EIF3D
8664
−3.23
formation of
RNA
CS score,

translation
tran-
function

preinitiation complex
scription,

protein

translation

Eif3f
66085
EIF3F
8665
−1.44
formation of
RNA
CS score,

translation
tran-
function

preinitiation complex
scription,

protein

translation

Eif3g
53356
EIF3G
8666
−3.10
translational initiation
RNA
CS score,

tran-
function

scription,

protein

translation

Eif3i
54709
EIFI
8668
−2.24
formation of
RNA
CS score,

translation
tran-
function

preinitiation complex
scription,

protein

translation

Eif3l
223691
EIF3L
51386
−1.28
translational initiation
RNA
CS score,

tran-
function

scription,

protein

translation

Eif4a1
13681
EIF4A1
1973
−1.97
translational initiation
RNA
CS score,

tran-
function

scription,

protein

translation

Eif4a3
192170
EIF4A3
9775
−4.32
RNA splicing
RNA
CS score,

tran-
function

scription,

protein

translation

Eif4g1
208643
EIF4G1
1981
−1.79
nuclear-
RNA
CS score,

transcribed
tran-
function

mRNA catabolic
scription,

process, nonsense-
protein

mediated decay
translation

Eif5b
226982
EIF5B
9669
−2.93
translational initiation
RNA
CS score,

tran-
function

scription,

protein

translation

Eif6
16418
EIF6
3692
−2.75
mature ribosome
RNA
CS score,
Gandin V, et al.

assembly
tran-
mouse
Nature, 2008 Oct.

scription,
K.O.,
2; 455(7213): 684-8

protein
function

translation

Elac2
68626
ELAC2
60528
−2.06
tRNA 3′-trailer
RNA
CS score,

cleavage,
tran-
function

endonucleolytic
scription,

protein

translation

Ell
13716
ELL
8178
−2.23
transcription
RNA
CS score,
Mitani K, et al.

elongation from RNA
tran-
mouse
Biochem Biophys

polymerase II
scription,
K.O.,
Res Commun. 2000

promoter
protein
function
Dec. 20; 279(2): 563-

translation

7

Etf1
225363
ETF1
2107
−2.44
translational
RNA
CS score,

termination
tran-
function

scription,

protein

translation

Exosc2
227715
EXOSC2
23404
−1.66
exonucleolytic
RNA
CS score,

trimming to generate
tran-
function

mature 3′-end of 5.8S
scription,

rRNA from tricistronic
protein

rRNA transcript
translation

(SSU-rRNA, 5.8S

rRNA, LSU-rRNA)

Exosc4
109075
EXOSC4
54512
−3.21
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Exosc5
27998
EXOSC5
56915
−2.09
rRNA catabolic
RNA
CS score,

process
tran-
function

scription,

protein

translation

n/a
n/a
EXOSC6
118460
−3.20
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Exosc7
66446
EXOSC7
23016
−2.17
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Exosc8
69639
EXOSC8
11340
−2.08
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Fars2
69955
FARS2
10667
−1.90
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Farsa
66590
FARSA
2193
−3.30
phenylalanyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Farsb
23874
FARSB
10056
−2.49
phenylalanyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Fau
14109
FAU
2197
−2.64
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Fip1l1
66899
FIP1L1
81608
−1.93
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Ftsj3
56095
FTSJ3
117246
−1.50
rRNA methylation
RNA
CS score,

tran-
function

scription,

protein

translation

Gle1
74412
GLE1
2733
−1.89
mRNA export from
RNA
CS score,

nucleus
tran-
function

scription,

protein

translation

Gnl3l
237107
GNL3L
54552
−1.35
ribosome biogenesis
RNA
CS score,

tran-
function

scription,

protein

translation

Gtf2e1
74197
GTF2E1
2960
−1.22
transcriptional open
RNA
CS score,

complex formation at
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Gtpbp4
69237
GTPBP4
23560
−2.25
ribosome biogenesis
RNA
CS score,

tran-
function

scription,

protein

translation

Hars
15115
HARS
3035
−3.49
histidyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Hars2
70791
HARS2
23438
−1.92
histidyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Heatr1
217995
HEATR1
55127
−2.58
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Hnrnpc
15381
HNRNPC
3183
−1.95
mRNA splicing, via
RNA
CS score,
Williamson D J, et

spliceosome
tran-
mouse
al. Mol Cell Biol.

scription,
K.O.,
2000

protein
function
June; 20(11): 4094-

translation

105

Hnrnpk
15387
HNRNPK
3190
−2.39
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Hnrnpl
15388
HNRNPL
3191
−1.88
mRNA processing
RNA
CS score,
Gaudreau M C, et al.

tran-
mouse
J Immunol. 2012

scription,
K.O.,
Jun. 1; 188(11): 5377-

protein
function
88

translation

Hnrnpu
51810
HNRNPU
3192
−2.44
mRNA splicing, via
RNA
CS score,
Roshon M J, et al.

spliceosome
tran-
mouse
Transgenic Res.

scription,
K.O.,
2005 April; 14(2): 179-

protein
function
92

translation

Iars
105148
IARS
3376
−3.87
isoleucyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Iars2
381314
IARS2
55699
−2.83
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Imp3
102462
IMP3
55272
−3.46
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Imp4
27993
IMP4
92856
−2.01
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Ints1
68510
INTS1
26173
−1.93
snRNA processing
RNA
CS score,
Nakayama M, et al.

tran-
mouse
FASEB J. 2006

scription,
K.O.,
August; 20(10): 1718-20

protein
function

translation

Ints4
101861
INTS4
92105
−1.75
snRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Ints5
109077
INTS5
80789
−2.10
snRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Ints8
72656
INTS8
55656
−1.35
snRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Ints9
210925
INTS9
55756
−2.26
snRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Isg20l2
229504
ISG20L2
81875
−2.27
ribosome biogenesis
RNA
CS score,

tran-
function

scription,

protein

translation

Kars
85305
KARS
3735
−2.76
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

n/a
n/a
KIAA0391
9692
−1.56
tRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Lars
107045
LARS
51520
−1.83
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Lars2
102436
LARS2
23395
−1.60
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Las1l
76130
LAS1L
81887
−2.12
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Lrpprc
72416
LRPPRC
10128
−1.39
negative regulation
RNA
CS score,
Ruzzenente B, et al.

of mitochondrial RNA
tran-
mouse
EMBO J. 2012 Jan.

catabolic process
scription,
K.O.,
18; 31(2): 143-56

protein
function

translation

Lsm2
27756
LSM2
57819
−2.96
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Lsm3
67678
LSM3
27258
−1.66
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Lsm7
66094
LSM7
51690
−1.96
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Magoh
17149
MAGOH
4116
−1.78
nuclear-
RNA
CS score,
Silver D L, et al. Nat

transcribed
tran-
mouse
Neurosci. 2010

mRNA catabolic
scription,
K.O.,
May; 13(5): 551-8

process, nonsence-
protein
function

dependent decay
translation

Mars
216443
MARS
4141
−3.24
methionyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Mars2
212679
MARS2
92935
−2.31
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Med17
234959
MED17
9440
−1.78
regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Med20
56771
MED20
9477
−2.00
regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Med22
20933
MED22
6837
−1.86
regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Med27
68975
MED27
9442
−1.48
regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Med30
69790
MED30
90390
−2.21
regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

Med8
80509
MED8
112950
−1.64
regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Mepce
231803
MEPCE
56257
−2.08
negative regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Mettl16
67493
METTL16
79066
−2.10
rRNA base
RNA
CS score,

methylation
tran-
function

scription,

protein

translation

Mphosph10
67973
MPHOSPH10
10199
−1.85
RNA splicing, via
RNA
CS score,

transesterification
tran-
function

reactions
scription,

protein

translation

Mrpl10
107732
MRPL10
124995
−1.38
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl12
56282
MRPL12
6182
−1.56
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl21
353242
MRPL21
219927
−1.91
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl28
68611
MRPL28
10573
−1.50
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl3
94062
MRPL3
11222
−1.58
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl34
94065
MRPL34
64981
−1.66
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl4
66163
MRPL4
51073
−2.41
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl41
107733
MRPL41
64975
−2.15
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrpl51
66493
MRPL51
51258
−1.40
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps14
64659
MRPS14
63931
−1.82
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps15
66407
MRPS15
64960
−1.28
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps16
66242
MRPS16
51021
−2.29
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps18a
68565
MRPS18A
55168
−1.55
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps2
118451
MRPS2
51116
−1.59
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps21
66292
MRPS21
54460
−1.51
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps24
64660
MRPS24
64951
−1.71
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Mrps6
121022
MRPS6
64968
−1.65
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Nars
70223
NARS
4677
−3.31
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Nars2
244141
NARS2
79731
−1.32
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Ncbp2
68092
NCBP2
22916
−3.00
mRNA cis splicing,
RNA
CS score,

via spliceosome
tran-
function

scription,

protein

translation

Nedd8
18002
NEDD8
4738
−2.45
regulation of
RNA
CS score,

transcription form
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Ngdn
68966
NGDN
25983
−2.35
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Nhp2
52530
NHP2
55651
−1.74
rRNA pseudouridine
RNA
CS score,

synthesis
tran-
function

scription,

protein

translation

Nip7
66164
NIP7
51388
−2.03
ribosome assembly
RNA
CS score,

tran-
function

scription,

protein

translation

Noc2l
57741
NOC2L
26155
−2.34
negative regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Noc4l
100608
NOC4L
79050
−2.11
ribosome biogenesis
RNA
CS score,

tran-
function

scription,

protein

translation

Nol6
230082
NOL6
65083
−2.28
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Nol9
74035
NOL9
79707
−2.20
cleavage in ITS2
RNA
CS score,

between 5.8S rRNA
tran-
function

and LSU-rRNA of
scription,

tricistronic rRNA
protein

transcript (SSU-
translation

rRNA, 5.8S rRNA,

LSU-rRNA)

Nop16
28126
NOP16
51491
−2.10
ribosomal large
RNA
CS score,

subunit biogenesis
tran-
function

scription,

protein

translation

Nop2
110109
NOP2
4839
−2.14
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Nop58
55989
NOP58
51602
−2.54
rRNA modification
RNA
CS score,

tran-
function

scription,

protein

translation

Nsa2
59050
NSA2
10412
−1.78
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Nudt21
68219
NUDT21
11051
−2.36
mRNA
RNA
CS score,

polyadenylation
tran-
function

scription,

protein

translation

Osgep
66246
OSGEP
55644
−1.98
tRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Pabpn1
54196
PABPN1
8106
−1.92
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Pdcd11
18572
PDCD11
22984
−1.47
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Pes1
64934
PES1
23481
−2.92
maturation of LSU-
RNA
CS score,
Lerch-Gaggl A, et

rRNA from tricistronic
tran-
mouse
al. J Biol Chem.

rRNA transcript
scription,
K.O.,
2002 Nov.

(SSU-rRNA, 5.8S
protein
function
22; 277(47): 45347-

rRNA, LSU-rRNA)
translation

55

Phb
18673
PHB
5245
−2.26
regulation of
RNA
CS score,
He B, et al.

transcription from
tran-
mouse
Endocrinology.

RNA polymerase II
scription,
K.O.,
2011

promoter
protein
function
March; 152(3): 1047-56

translation

Phf5a
68479
PHF5A
84844
−3.52
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Pnn
18949
PNN
5411
−1.34
mRNA splicing, via
RNA
CS score,
Joo J H, et al. Dev

spliceosome
tran-
mouse
Dyn. 2007

scription,
K.O.,
August; 236(8): 2147-58

protein
function

translation

Polr1b
20017
POLR1B
84172
−3.23
transcription from
RNA
CS score,
Chen H, et al.

RNA polymerase I
tran-
mouse
Biochem Biophys

promoter
scription,
K.O.,
Res Commun. 2008

protein
function
Jan. 25; 365(4): 636-

translation

42

Polr1c
20016
POLR1C
9533
−2.79
transcription from
RNA
CS score,

RNA polymerase I
tran-
function

promoter
scription,

protein

translation

Polr2a
20020
POLR2A
5430
−3.15
transcription from
RNA
CS score,

RNA polymerase II
tran-
function

promoter
scription,

protein

translation

Polr2b
231329
POLR2B
5431
−3.09
transcription from
RNA
CS score,

RNA polymerase II
tran-
function

promoter
scription,

protein

translation

Polr2c
20021
POLR2C
5432
−3.15
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Polr2d
69241
POLR2D
5433
−2.23
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

deadenylation-
protein

dependent decay
translation

Polr2f
69833
POLR2F
5435
−2.31
transcription from
RNA
CS score,

RNA polymerase I
tran-
function

promoter
scription,

protein

translation

Polr2g
67710
POLR2G
5436
−2.78
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

exonucleolytic
protein

translation

Polr2h
245841
POLR2H
5437
−1.83
transcription from
RNA
CS score,

RNA polymerase I
tran-
function

promoter
scription,

protein

translation

Polr2i
69920
POLR2I
5438
−2.92
maintenance of
RNA
CS score,

transcriptional fidelity
tran-
function

during DNA-
scription,

templated
protein

transcription
translation

elongation from RNA

polymerase II

promoter

Polr2j
20022
POLR2J
5439
−3.31
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Polr21
66491
POLR2L
5441
−3.55
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Polr3e
26939
POLR3E
55718
−2.33
transcription from
RNA
CS score,

RNA polymerase III
tran-
function

promoter
scription,

protein

translation

Pop1
67724
POP1
10940
−1.79
tRNA 5′-leader
RNA
CS score,

removal
tran-
function

scription,

protein

translation

Pop4
66161
POP4
10775
−1.87
RNA phosphodiester
RNA
CS score,

bond hydrolysis
tran-
function

scription,

protein

translation

Ppa1
67895
PPA1
5464
−1.63
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Ppan
235036
PPAN
56342
−1.62
ribosomal large
RNA
CS score,

subunit assembly
tran-
function

scription,

protein

translation

Ppp2ca
19052
PPP2CA
5515
−3.01
nuclear-
RNA
CS score,
Gu P, et al.

transcribed mRNA
tran-
mouse
Genesis. 2012

catabolic process,
scription,
K.O.,
May; 50(5): 429-36

nonsense-
protein
function

mediated decay
translation

Prim1
19075
PRIM1
5557
−2.07
DNA replication,
RNA
CS score,

synthesis of RNA
tran-
function

primer
scription,

protein

translation

Prpf38b
66921
PRPF38B
55119
−2.68
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Prpf4
70052
PRPF4
9128
−2.24
RNA splicing
RNA
CS score,

tran-
function

scription,

protein

translation

Prpf8
192159
PRPF8
10594
−3.43
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Ptcd1
71799
PTCD1
26024
−1.77
tRNA 3′-end
RNA
CS score,

processing
tran-
function

scription,

protein

translation

Pwp2
110816
PWP2
5822
−2.52
ribosomal small
RNA
CS score,

subunit assembly
tran-
function

scription,

protein

translation

Qars
97541
QARS
5859
−3.35
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Ran
19384
RAN
5901
−3.09
ribosomal large
RNA
CS score,

subunit export from
tran-
function

nucleus
scription,

protein

translation

Rars
104458
RARS
5917
−2.30
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Rars2
109093
RARS2
57038
−1.93
arginyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Rbm25
67039
RBM25
58517
−2.15
regulation of
RNA
CS score,

alternative mRNA
tran-
function

splicing, via
scription,

spliceosome
protein

translation

Rbm8a
60365
RBM8A
9939
−2.97
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rbmx
19655
RBMX
27316
−1.95
regulation of
RNA
CS score,

alternative mRNA
tran-
function

splicing, via
scription,

spliceosome
protein

translation

Rcl1
59028
RCL1
10171
−2.08
endonucleolytic
RNA
CS score,

cleavage of
tran-
function

tricistronic rRNA
scription,

transcript (SSU-
protein

rRNA, 5.8S rRNA,
translation

LSU-rRNA)

Rngtt
24018
RNGTT
8732
−2.90
transcription from
RNA
CS score,

RNA polymerase II
tran-
function

promoter
scription,

protein

translation

Rnmt
67897
RNMT
8731
−1.45
7-methylguanosine
RNA
CS score,

mRNA capping
tran-
function

scription,

protein

translation

Rnpc3
67225
RNPC3
55599
−1.95
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Rpap1
68925
RPAP1
26015
−2.58
transcription from
RNA
CS score,

RNA polymerase II
tran-
function

promoter
scription,

protein

translation

Rpl10
110954
RPL10
6134
−3.76
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl10a
19896
RPL10A
4736
−2.15
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl11
67025
RPL11
6135
−2.99
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl12
269261
RPL12
6136
−2.64
ribosomal large
RNA
CS score,

subunit assembly
tran-
function

scription,

protein

translation

Rpl13
270106
RPL13
6137
−3.28
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl14
67115
RPL14
9045
−2.92
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl15
66480
RPL15
6138
−3.50
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl18
19899
RPL18
6141
−3.72
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl18a
76808
RPL18A
6142
−3.37
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl23
65019
RPL23
9349
−3.02
translation
RNA
CS score,

tran-
function

scription,

protein

translation

n/a
n/a
RPL23A
6147
−4.25
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl24
68193
RPL24
6152
−2.55
ribosomal large
RNA
CS score,
Oliver E R, et al.

subunit assembly
tran-
mouse
Development. 2004

scription,
K.O.,
August; 131(16): 3907-

protein
function
20

translation

Rpl26
19941
RPL26
6154
−2.88
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl27
19942
RPL27
6155
−2.25
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rp127a
26451
RPL27A
6157
−2.87
translation
RNA
CS score,
Terzian T, et al. J

tran-
mouse
Pathol. 2011

scription,
K.O.,
August; 224(4): 540-52

protein
function

translation

Rpl3
27367
RPL3
6122
−3.27
ribosomal large
RNA
CS score,

subunit assembly
tran-
function

scription,

protein

translation

Rpl30
19946
RPL30
6156
−2.53
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl31
114641
RPL31
6160
−1.92
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl32
19951
RPL32
6161
−3.70
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

n/a
n/a
RPL34
6164
−2.37
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl35
66489
RPL35
11224
−2.25
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl35a
57808
RPL35A
6165
−3.20
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl36
54217
RPL36
25873
−3.44
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl37
67281
RPL37
6167
−3.02
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl37a
19981
RPL37A
6168
−2.62
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl38
67671
RPL38
6169
−2.57
translation
RNA
CS score,
MORGAN W C, et

tran-
mouse
al. J Hered. 1950

scription,
K.O.,
August; 41(8): 208-15

protein
function

translation

Rpl4
67891
RPL4
6124
−2.67
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl5
100503670
RPL5
6125
−3.20
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl6
19988
RPL6
6128
−3.07
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl7
19989
RPL7
6129
−2.15
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpl7a
27176
RPL7A
6130
−3.45
ribosome biogenesis
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl7l1
66229
RPL7L1
285855
−1.86
maturation of LSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA, transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Rpl8
26961
RPL8
6132
−4.00
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpl9
20005
RPL9
6133
−3.57
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rplp0
11837
RPLP0
6175
−2.61
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rpp21
67676
RPP21
79897
−2.96
tRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Rpp30
54364
RPP30
10556
−1.79
tRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Rps10
67097
RPS10
6204
−2.88
ribosomal small
RNA
CS score,

subunit assembly
tran-
function

scription,

protein

translation

Rps11
27207
RPS11
6205
−2.93
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps12
20042
RPS12
6206
−3.33
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rps13
68052
RPS13
6207
−3.13
translation
RNA
CS score,

tran-
function

scription,

protein

translation

n/a
n/a
RPS14
6208
−3.18
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps15
20054
RPS15
6209
−3.20
ribosomal small
RNA
CS score,

subunit assembly
tran-
function

scription,

protein

translation

Rps15a
267019
RPS15A
6210
−3.18
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps16
20055
RPS16
6217
−2.35
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps17
20068
RPS17
6218
−2.69
ribosomal small
RNA
CS score,

subunit assembly
tran-
function

scription,

protein

translation

Rps19
20085
RPS19
6223
−3.49
translation
RNA
CS score,
Matsson H, et al.

tran-
mouse
Mol Cell Biol. 2004

scription,
K.O.,
May; 24(9): 4032-7

protein
function

translation

Rps2
16898
RPS2
6187
−2.50
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps21
66481
RPS21
6227
−1.84
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rps23
66475
RP523
6228
−2.86
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps25
75617
RPS25
6230
−2.38
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

n/a
n/a
RPS3A
6189
−3.72
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps4x
20102
RPS4X
6191
−3.04
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps5
20103
RPS5
6193
−2.61
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps6
20104
RPS6
6194
−3.31
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rps7
20115
RPS7
6201
−2.97
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rps8
20116
RPS8
6202
−3.44
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Rps9
76846
RPS9
6203
−3.16
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Rpsa
16785
RPSA
3921
−3.06
ribosomal small
RNA
CS score,
Han J, et al. MGI

subunit assembly
tran-
mouse
Direct Data

scription,
K.O.,
Submission. 2008

protein
function

translation

Rsl24d1
225215
RSL24D1
51187
−2.76
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Sars
20226
SARS
6301
−2.67
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Sars2
71984
SARS2
54938
−2.25
seryl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Sart1
20227
SART1
9092
−2.13
maturation of 5S
RNA
CS score,

rRNA
tran-
function

scription,

protein

translation

Sart3
53890
SART3
9733
−1.88
RNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Sdad1
231452
SDAD1
55153
−1.96
ribosomal large
RNA
CS score,

subunit export from
tran-
function

nucleus
scription,

protein

translation

Sf1
22668
SF1
7536
−3.04
mRNA splicing, via
RNA
CS score,
Shitashige M, et al.

spliceosome
tran-
mouse
Cancer Sci. 2007

scription,
K.O.,
December; 98(12): 1862-7

protein
function

translation

Sf3a1
67465
SF3A1
10291
−3.18
mRNA 3′-splice site
RNA
CS score,

recognition
tran-
function

scription,

protein

translation

Sf3a2
20222
SF3A2
8175
−2.66
mRNA 3′-splice site
RNA
CS score,

recognition
tran-
function

scription,

protein

translation

Sf3a3
75062
SF3A3
10946
−2.26
mRNA splicing, via
RNA
CS score,

transesterification
tran-
function

reactions
scription,

protein

translation

Sf3b2
319322
SF3B2
10992
−2.51
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Sf3b3
101943
SF3B3
23450
−4.13
RNA splicing, via
RNA
CS score,

transesterification
tran-
function

reactions
scription,

protein

translation

Sf3b4
107701
SF3B4
10262
−2.60
RNA splicing, via
RNA
CS score,

transesterification
tran-
function

reactions
scription,

protein

translation

Sfpq
71514
SFPQ
6421
−2.27
negative regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Sin3a
20466
SIN3A
25942
−1.74
negative regulation of
RNA
CS score,
Dannenberg J H, et

transcription from
tran-
mouse
al. Genes Dev.

RNA polymerase II
scription,
K.O.,
2005 Jul.

promoter
protein
function
1; 19(13): 581-95

translation

Smg5
229512
SMG5
23381
−2.35
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Smg6
103677
SMG6
23293
−1.18
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

nonsense-
protein

mediated decay
translation

Snrnp25
78372
SNRNP25
79622
−2.43
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Snrnp27
66618
SNRNP27
11017
−1.36
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Snrpd2
107686
SNRPD2
6633
−2.47
RNA splicing
RNA
CS score,

tran-
function

scription,

protein

translation

Snrpf
69878
SNRPF
6636
−3.58
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Srrm1
51796
SRRM1
10250
−1.81
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Srsf1
110809
SRSF1
6426
−2.75
mRNA 5′-splice site
RNA
CS score,
Xu X, et al. Cell.

recognition
tran-
mouse
2005 Jan.

scription,
K.O.,
14; 120(1): 59-72

protein
function

translation

Srsf2
20382
SRSF2
6427
−3.66
regulation of
RNA
CS score,
Ding J H, et al.

alternative mRNA
tran-
mouse
EMBO J. 2004 Feb.

splicing, via
scription,
K.O.,
25; 23(4): 885-96

spliceosome
protein
function

translation

Srsf3
20383
SRSF3
6428
−2.28
mRNA splicing, via
RNA
CS score,
Jumaa H et al. Curr

spliceosome
tran-
mouse
Biol. 1999 Aug.

scription,
K.O.,
26; 9(16): 399-902

protein
function

translation

Srsf7
225027
SRSF7
6432
−2.06
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Ssu72
68991
SSU72
29101
−2.57
mRNA
RNA
CS score,

polyadenylation
tran-
function

scription,

protein

translation

Sugp1
70616
SUGP1
57794
−1.36
RNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Tars
110960
TARS
6897
−2.53
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Tars2
71807
TARS2
80222
−1.91
threonyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Tbl3
213773
TBL3
10607
−2.41
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Thoc2
331401
THOC2
57187
−2.52
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Thoc5
107829
THOC5
8563
−1.57
mRNA processing
RNA
CS score,
Mancini A, et al.

tran-
mouse
BMC Biol 2010; 8:1

scription,
K.O.,

protein
function

translation

Thoc7
66231
THOC7
80145
−2.23
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Timeless
21853
TIMELESS
8914
−2.27
negative regulation
RNA
CS score,
Gotter A L, et al. Nat

of transcription from
tran-
mouse
Neurosci. 2000

RNA polymerase II
scription,
K.O.,
August; 3(8): 755-6

promoter
protein
function

translation

Tsen2
381802
TSEN2
80746
−1.41
tRNA-type intron
RNA
CS score,

splice site recognition
tran-
function

and cleavage
scription,

protein

translation

Tsr1
104662
TSR1
55720
−1.76
ribosome biogenesis
RNA
CS score,

tran-
function

scription,

protein

translation

Tsr2
69499
TSR2
90121
−2.82
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Tufm
233870
TUFM
7284
−1.92
translational
RNA
CS score,

elongation
tran-
function

scription,

protein

translation

Tut1
70044
TUT1
64852
−2.65
mRNA
RNA
CS score,

polyadenylation
tran-
function

scription,

protein

translation

Twistnb
28071
TWISTNB
221830
−2.17
transcription from
RNA
CS score,

RNA polymerase I
tran-
function

promoter
scription,

protein

translation

U2af1
108121
U2AF1
7307
−2.41
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

U2af2
22185
U2AF2
11338
−2.80
mRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Uba52
22186
UBA52
7311
−2.54
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Ub15
66177
UBL5
59286
−2.56
mRNA splicing, via
RNA
CS score,

spliceosome
tran-
function

scription,

protein

translation

Upf1
19704
UPF1
5976
−2.63
nuclear-
RNA
CS score,
Medghalchi S M, et

transcribed mRNA
tran-
mouse
al. Hum Mol Genet.

catabolic process,
scription,
K.O.,
2001 Jan.

nonsense-
protein
function
15; 10(2): 99-105

mediated decay
translation

Upf2
326622
UPF2
26019
−2.16
nuclear-
RNA
CS score,
Weischenfeldt J, et

transcribed mRNA
tran-
mouse
al. Genes Dev.

catabolic process,
scription,
K.O.,
2008 May

nonsense-
protein
function
15; 22(10): 1381-96

mediated decay
translation

Utp15
105372
UTP15
84135
−1.65
maturation of SSU-
RNA
CS score,

RNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Utp20
70683
UTP20
27340
−2.28
endonucleolytic
RNA
CS score,

cleavage in ITS1 to
tran-
function

separate SSU-rRNA
scription,

from 5.8S rRNA and
protein

LSU-rRNA from
translation

tricistronic rRNA

transcript (SSU-

rRNA, 5.8S rRNA,

LSU-rRNA)

Utp23
78581
U1P23
84294
−2.54
rRNA processing
RNA
CS score,

tran-
function

scription,

protein

translation

Utp3
65961
UTP3
57050
−1.58
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Utp6
216987
UTP6
55813
−1.99
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Vars
22321
VARS
7407
−3.35
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Wars
22375
WARS
7453
−2.22
tryptophanyl-tRNA
RNA
CS score,

aminoacylation
tran-
function

scription,

protein

translation

Wdr12
57750
WDR12
55759
−2.16
maturation of LSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Wdr3
269470
WDR3
10885
−2.65
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Wdr33
74320
WDR33
55339
−2.63
mRNA
RNA
CS score,

polyadenylation
tran-
function

scription,

protein

translation

Wdr36
225348
WDR36
134430
−2.04
rRNA processing
RNA
CS score,
Gallenberger M, et

tran-
mouse
al. Hum Mol Genet.

scription,
K.O.,
2011 Feb.

protein
function
1; 20(3): 422-35

translation

Wdr46
57315
WDR46
9277
−2.41
maturation of SSU-
RNA
CS score,

rRNA from tricistronic
tran-
function

rRNA transcript
scription,

(SSU-rRNA, 5.8S
protein

rRNA, LSU-rRNA)
translation

Wdr61
66317
WDR61
80349
−2.63
nuclear-
RNA
CS score,

transcribed mRNA
tran-
function

catabolic process,
scription,

exonucleolytic,
protein

3′-5′
translation

Wdr75
73674
WDR75
84128
−2.12
regulation of
RNA
CS score,

transcription from
tran-
function

RNA polymerase II
scription,

promoter
protein

translation

Xpo1
103573
XPO1
7514
−3.50
ribosomal large
RNA
CS score,

subunit export from
tran-
function

nucleus
scription,

protein

translation

Yars
107271
YARS
8565
−2.78
tRNA aminoacylation
RNA
CS score,

for protein translation
tran-
function

scription,

protein

translation

Yars2
70120
YARS2
51067
−2.40
translation
RNA
CS score,

tran-
function

scription,

protein

translation

Ythdc1
231386
YTHDC1
91746
−2.35
mRNA splice site
RNA
CS score,

selection
tran-
function

scription,

protein

translation

Zbtb8os
67106
ZBTB8OS
339487
−2.54
tRNA splicing, via
RNA
CS score,

endonucleolytic
tran-
function

cleavage and ligation
scription,

protein

translation

Zc3h3
223642
ZC3H3
23144
−1.22
mRNA
RNA
CS score,

polyadenylation
tran-
function

scription,

protein

translation

Although the disclosure has been described with reference to certain specific embodiments, various modifications thereof will be apparent to those skilled in the art. Any examples provided herein are included solely for the purpose of illustrating the disclosure and are not intended to limit the disclosure in any way. Any drawings provided herein are solely for the purpose of illustrating various aspects of the disclosure and are not intended to be drawn to scale or to limit the disclosure in any way. The scope of the claims appended hereto should not be limited by the preferred embodiments set forth in the above description, but should be given the broadest interpretation consistent with the present specification as a whole. The disclosures of all prior art recited herein are incorporated herein by reference in their entirety.

	Number	Date	Country
	62666626	May 2018	US
	62518151	Jun 2017	US

ALLOGRAFT TOLERANCE WITHOUT THE NEED FOR SYSTEMIC IMMUNE SUPPRESSION

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