Patent Application
20230279352
The disclosure relates to methods, cells, and compositions for preparing cell populations and compositions for adoptive cell therapy. In particular, provided herein are methods for expansion and proliferation of primary immune cells including T cell populations.
Engineered adoptive cellular therapies have been transformative for patients with hematological malignancies in recent years with the first approval for a chimeric antigen receptor (CAR)-based therapy by the FDA in 2017 (Larson & Maus, Nat Rev Cancer 21, 145-161 (2021); Yu, et al., Nature Reviews Drug Discovery 19, 583-584 (2020)). Since 2017, the number of clinical trials investigating adoptive cell therapies such as CAR-T cells, CAR-Natural Killer (NK) and CAR-NKT cells, T cell receptor (TCR)-T cells, tumor infiltrating lymphocytes (TILs), tumor-specific antigen-targeting T cells, and other cellular therapies has grown rapidly. More recently, the first CAR-macrophages (CAR-M) have entered the clinic for the treatment of solid tumors (Mukhopadhyay, Nat Methods 17, 561 (2020); Klichinsky, et al., Nat Biotechnol., 8, 947-953 (2020); Villanueva, Nature Reviews Drug Discovery 19, 308 (2020); ClinicalTrials.gov Identifier: NCT04660929)).
While there is much potential for cellular therapies to be curative for patients, a number of factors limit the widespread development and administration of these drugs. Most cellular therapies are currently produced in an autologous fashion and are associated with variable cell product quality, cytokine release syndrome and other toxicities, extended manufacturing times, high costs, and a limited period in which these therapies may be genetically modified to enhance their efficacy (Larson & Maus, Nat Rev Cancer 21, 145-161 (2021)).
The majority of cellular therapies currently being tested in the clinic utilize CAR-T or CAR-NK cells, as these subsets of immune cells demonstrate potent cytotoxicity. Mature primary human T cells that are used for these therapies are found in the blood and secondary lymphoid organs of humans where they act to protect individuals against infectious diseases and cancer. T cells are comprised of αβ (“classic” T cells) and γδ subsets. αβ T cells consist of CD4+ helper T cells and CD8+ cytotoxic T cells. CD4+ T cells can be further subdivided into TH1 cells, TH2 cells, TH9 cells, TH17 cells, TFH cells, and regulatory T cells. Many αβ T cell subsets exhibit potent cytotoxic function which has been harnessed for the development of cellular therapies.
Similarly, mature primary human NK cells that can be used for cellular therapies are found in the blood, secondary lymphoid organs, liver, and mucosal associated lymphoid tissues, sites that NK cells patrol for the presence of pathogens or transformed cells (Jianhua, et al., Trends in Immunology 34, 573-582 (2013). Like T cells, NK cells demonstrate potent cytotoxic function and are of interest for the development of cellular therapies.
However, primary human immune cells, such as T cells and NK cells, also possess a finite potential for proliferation in vitro and in vivo, limiting their ability to be used for the generation of widespread off-the-shelf cellular therapies. Further, this limited proliferative capacity of mature primary human immune cells impairs their ability to be genetically edited to mitigate cytokine release syndrome and other potential cellular-therapy-associated toxicities, to overcome tumor microenvironment-associated challenges, and to prevent the rejection of allogeneic cellular therapy products in patients.
Patient-derived leukemic cell lines have been studied for decades in cell culture, where their transformed status confers a long-term proliferative capacity that enables their use in a variety of cellular assays. This in turn has facilitated the development of numerous therapies. These cells, however, generally lack the potent cytotoxic function of mature primary human T and NK cells, as they are often immature or derived from dysfunctional T cell clones. The transformed nature of these cells can be mapped on to a collection of mutations that are also frequently found in patients with T cell acute lymphoblastic leukemia. Furthermore, mature T cells from non-human primates can be transformed by herpes viruses through pathways that converge on some of the same mechanisms involved in the transformation of primary human T cells in patients (Biesinger, et al., Proc Natl Acad Sci USA 89, 3116-3119 (1992); Weber, et al., Proc Natl Acad Sci USA 90, 11049-11053 (1993); Fickenscher H, Fleckenstein B., Philos Trans R Soc Lond B Biol Sci. 356(1408):545-67 (2001); Tsygankov, J Cell Physiol. 203(2):305-18 (2005).
While previous studies suggest that primary human T cells may be immortalized through the over-expression of factors such as telomerase-reverse transcriptase (TERT) (Barsov, Methods Mol Biol. 511, 143-58 (2009); Rufer, et al., Blood 98, 597-603 (2001); Hooijberg, et al., J Immunol. 165, 4239-45 (2000)) and human T cell leukemia virus type 1 or human T cell leukemia virus type 2 (HTLV-1/HTLV-2) transcriptional trans-activator protein Tax (Akagi, et. al., Oncogene 14, 2071-2080 (1997); Grassmann, et al., Proc Natl Acad Sci USA 86, 3351-3355 (1989); Ren, et al., J Biol. Chem. 287, 34683-34693 (2012), or by viruses such as Herpesvirus saimiri (Biesinger, et al., Proc Natl Acad Sci USA 89, 3116-3119 (1992); Weber, et al., Proc Natl Acad Sci USA 90, 11049-11053 (1993)) and HTLV-1/HTLV-2, these approaches are not highly reproducible and can result in reprogramming of modified or infected cells. In addition, cells whose proliferative longevity has been enhanced through the overexpression of TERT still require the use of feeder cells or extensive exogenous stimulation through their T cell receptors to drive proliferation (Rufer, et al., Blood 98, 597-603 (2001); Hooijberg, et al., J Immunol. 165, 4239-45 (2000)). The use of allogeneic feeder cells and extensive repeat stimulation is undesirable when establishing a bank of mature primary human T or NK cells as these methodologies are challenging to scale and may ultimately drive the cells to a dysfunctional state. Further, the use of infectious agents with the ability to transform mature primary human T or NK cells limits the use of these cells in the development of cellular therapies as patients are often immunocompromised.
In light of these challenges, there is a significant need to establish alternative methods by which to extend the proliferative longevity of primary human immune cells to enable large-scale manufacturing of allogeneic cytotoxic cells. The disclosure describes methods and cells that address this unmet need.
The disclosure herein provides a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: (a) introducing one or more genetic edits to primary immune cells; and (b) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS).
The disclosure herein also provides a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: (a) inhibiting the expression of one or more endogenous regulatory factors in the primary immune cells, wherein the endogenous regulatory factor is cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), or S-methyl-5′-thioadenosine phosphorylase (MTAP); (b) inhibiting the expression of one or more endogenous immune related genes in the primary immune cells, wherein the endogenous immune related gene is beta-2 microglobulin (B2M), and/or T-cell receptor α constant (TRAC); and (c) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS).
The disclosure herein further provides a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: (a) inhibiting the expression of one or more endogenous regulatory factors in the primary immune cells, wherein the endogenous regulatory factor is cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), or S-methyl-5′-thioadenosine phosphorylase (MTAP); (b) inhibiting the expression of one or more endogenous immune related genes in the primary immune cells, wherein the endogenous immune related gene is beta-2 microglobulin (B2M), and/or T-cell receptor α constant (TRAC); and (c) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS).
The disclosure herein provides a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: (a) inhibiting expression of one or more endogenous regulatory factors in the primary immune cells, wherein endogenous regulatory factor is cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), or S-methyl-5′-thioadenosine phosphorylase (MTAP); and (b) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS).
The disclosure herein also provides an engineered immune cell population produced according to the described methods. The disclosure herein further provides a pharmaceutical composition comprising the aforementioned engineered immune cell population and a pharmaceutically acceptable carrier. The disclosure herein further provides a method of treating a cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the aforementioned pharmaceutical composition.
The disclosure herein provides an engineered T cell that does not express cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), S-methyl-5′-thioadenosine phosphorylase (MTAP), beta-2 microglobulin (B2M), and/or T-cell receptor a constant (TRAC).
The disclosure herein provides an engineered T cell expressing a transgene encoding a B-cell lymphoma-extra large (Bcl-XL), wherein the engineered T cell does not express cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), S-methyl-5′-thioadenosine phosphorylase (MTAP), and/or phosphatase and tensin homolog (PTEN).
The disclosure relates to methods, cells, and compositions for preparing cell populations and compositions for adoptive cell therapy. In particular, provided herein are methods for expansion and proliferation of primary immune cells including T cell populations.
As utilized in accordance with the present disclosure, unless otherwise indicated, all technical and scientific terms shall be understood to have the same meaning as commonly understood by one of ordinary skill in the art. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.
As used herein, the terms “comprise” and “include” and variations thereof (e.g., “comprises,” “comprising,” “includes,” and “including”) will be understood to indicate the inclusion of a stated component, feature, element, or step or group of components, features, elements or steps but not the exclusion of any other component, feature, element, or step or group of components, features, elements, or steps. Any of the terms “comprising,” “consisting essentially of,” and “consisting of” may be replaced with either of the other two terms, while retaining their ordinary meanings.
As used herein, the singular forms “a,” “an” and “the” include plural referents unless the context clearly indicates otherwise.
Percentages disclosed herein can vary in amount by ±10, 20, or 30% from values disclosed and remain within the scope of the contemplated disclosure.
Unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values herein that are expressed as ranges can assume any specific value or sub-range within the stated ranges in different aspects of the disclosure, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.
As used herein, ranges and amounts can be expressed as “about” a particular value or range. The term “about” also includes the exact amount. For example, “about 5%” means “about 5%” and also “5%.” The term “about” can also refer to ±10% of a given value or range of values. Therefore, about 5% also means 4.5%-5.5%, for example. Unless otherwise clear from context, all numerical values provided herein are modified by the term “about.”
As used herein, the terms “or” and “and/or” can describe multiple components in combination or exclusive of one another. For example, “x, y, and/or z” can refer to “x” alone, “y” alone, “z” alone, “x, y, and z,” “(x and y) or z,” “x or (y and z),” or “x or y or z.” Resistant to replicative senescence (RRS) refers to primary immune cells that are resistant to replicative senescence (RS) that leads to a finite number of population doublings. As a result, the population of primary immune cells described herein advantageously have extended proliferative capacity.
In one aspect the disclosure herein provides a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: i) introduction of one or more genetic edits into the primary immune cells; and ii) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS).
In one aspect the disclosure herein provides a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: i) introducing a transgene encoding B-cell lymphoma-extra large (Bcl-xL) into the primary immune cells; ii) inhibiting the expression of one or more endogenous regulatory factors selected from cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and S-methyl-5′-thioadenosine phosphorylase (MTAP) in the primary immune cells; and iii) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS). In some aspects, the method comprises inhibiting the expression of one or more endogenous immune related genes in the primary immune cells. In certain aspects, the endogenous immune related gene is beta-2 microglobulin (B2M), or T-cell receptor α constant (TRAC). In some aspects, the method comprises inhibiting the expression of CD38.
In one aspect the disclosure herein provides a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: i) inhibiting the expression of one or more endogenous regulatory factors selected from cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and S-methyl-5′-thioadenosine phosphorylase (MTAP) in primary immune cells; and ii) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS). In some aspects, the method comprises inhibiting the expression of one or more endogenous immune related genes in the primary immune cells. In certain aspects, the endogenous immune related gene is beta-2 microglobulin (B2M), or T-cell receptor α constant (TRAC). In some aspects, the method comprises inhibiting the expression of CD38.
A genetic edit refers to a change to the genetic material of the primary immune cell. A genetic edit includes genetic material to be added, removed, or altered. In particular aspects, genetic edits comprise introducing a transgene into the primary immune cells and/or inhibiting the expression of a gene in the primary immune cell. In particular aspects, introducing one or more genetic edits comprise introducing one or more transgenes encoding an anti-apoptotic factor or a virally-derived factor into the primary immune cells.
The term “Primary immune cell(s)” can refer to any cell(s) involved in a primary immune response such as T cells, B-cells and NK cells, neutrophils, and monocytes/macrophages/dendritic cells. In some aspects, primary immune cells can comprise total T cells, CD4-positive T cells, CD8-positive T cells, regulatory T cells, gamma-delta T cells, mucosal associated invariant T (MAIT) T cells, natural killer (NK) cells, or natural killer T (NKT) cells.
The term “transgene” refers to any nucleic acid sequence that is introduced into the cell by experimental manipulations. A transgene may be an “endogenous DNA sequence” or a “heterologous DNA sequence.” The transgene may be isolated and obtained in suitable quantity using one or more methods that are well known in the art. These methods and others useful for isolating a transgene are set forth, for example, in Sambrook et al. (supra) and in Berger and Kimmel (Methods in Enzymology: Guide to Molecular Cloning Techniques, vol. 152, Academic Press, Inc., San Diego, Calif. (1987)).
The transgene can be incorporated into a “transgene construct” that comprises the gene of interest along with other regulatory DNA sequences needed either for temporal, or cell specific, or enhanced expression of the transgenes of interest.
The transgene may be introduced into the cells by any suitable method or technique known in the art. In particular aspects, the transgene is introduced using a plasmid-based DNA transposon, lentivirus platform, or site-specific integration via CRISPR. The transgene expression in the cell can be constitutive or inducible.
In particular aspects, the transgene encodes an anti-apoptotic factor. An “anti-apoptotic factor” refers to a protein or an oligonucleotide (which may be an oligonucleotide encoding for a protein or a silencing nucleotide) which acts to prevent apoptosis of a cell, in particular a cell experiencing stress, a cell received signal to undergo apoptosis or a cell undergoing abnormal cell proliferation. In particular aspects, the anti-apoptotic factor is B-cell lymphoma-extra large (Bcl-xL) or B-cell lymphoma 2 (Bcl-2).
In particular aspects, the transgene encodes a virally-derived factor. A “virally-derived factor” refers to both naturally-occurring viral peptides, polypeptides, or proteins, as well as peptides, polypeptides, or proteins displaying a degree of sequence identity and/or similarity to a viral protein and/or maintaining one or more structural, mechanistic, or antigenic qualities of the viral protein. In particular aspects, the virally-derived factor is from Saimiriine gammaherpesvirus 2 StpA All, Herpesvirus saimiri StpC, Herpesvirus saimiri Tip, or a modified Herpesvirus ateles-Epstein-Barr virus Tio-LMP1.
In other aspects, the transgene encodes a protein relating to activating signals in the cell.
In some aspects, methods of the disclosure further include inhibiting the expression of one or more endogenous regulatory factors in the primary immune cells such that the activity of the endogenous regulatory factor is eliminated or reduced. As used herein a “regulatory factor” refers to a gene that encodes a protein involved in regulating the cell cycle arrest, cell death, or signal suppression. The endogenous regulatory factor may be down regulated or blocked by any suitable method or technique known in the art. Known methods for down regulation of gene expression or decreasing the activity of a factor include, but are not limited to, CRISPR/Cas (including cytosine and adenine base editors), microRNA, shRNA, RNAi, TALENs, zinc finger nucleases, meganucleases, neutralizing antibodies, small molecule inhibitors, chemical inhibitors blocking downstream signaling pathways, and the like. The inhibition of the endogenous regulatory factor can be complete inhibition, partial inhibition, down regulation of gene expression or decreasing the activity of a factor. In some aspects, endogenous regulatory factor activity or gene expression is reduced by between 1%-100% (i.e., 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, 100%). A regulatory factor includes a gene that encodes a protein involved in regulating the cell cycle arrest, cell death or signal suppression. In particular aspects, the one or more endogenous regulatory factors are cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and/or S-methyl-5′-thioadenosine phosphorylase (MTAP). In particular aspects, the one or more endogenous regulatory factors are RB Transcriptional Corepressor 1 (RB1), TP53, Autophagy and Beclin 1 Regulator 1 (AMBRA1), Neurofibromatosis type 1 (NF1), Tyrosine-protein phosphatase non-receptor type 2 (PTPN2), or Suppressor of Cytokine Signaling 1 (SOCS1).
The term “endogenous” refers to developing or originating within a cell, a tissue, or an organism or part of a cell, a tissue or an organism.
In some aspects, methods of the disclosure further include inhibiting the expression of one or more endogenous immune related genes in the primary immune cells such that the activity of the immune related genes is eliminated or reduced. As used herein an “immune related gene” refers to a gene that encodes a protein involved in effecting an immune response. In certain aspects, the immune related gene encodes a protein that is involved in host-versus-graft (HvG) and graft-versus-host (GvH) allogeneic immune responses. The immune related gene may be down regulated or blocked by any suitable method or technique known in the art. Known methods for down regulation of gene expression or decreasing the activity of an immune related gene include, but are not limited to, CRISPR/Cas (including cytosine and adenine base editors), microRNA, shRNA, RNAi, TALENs, zinc finger nucleases, meganucleases, neutralizing antibodies, small molecule inhibitors, chemical inhibitors blocking downstream signaling pathways, and the like. The inhibition of the endogenous immune related gene can be complete inhibition, partial inhibition, down regulation of gene expression or decreasing the activity of a factor. In some aspects, endogenous immune related gene activity or gene expression is reduced by between 1%-100% (i.e., 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, 100%). An immune related gene includes a gene that encodes a protein involved in effecting an immune response. An immune related gene can encode a protein that is involved in host-versus-graft (HvG) and graft-versus-host (GvH) allogeneic immune responses. In particular aspects, the one or more endogenous immune related genes are beta-2 microglobulin (B2M), or T-cell receptor α constant (TRAC). In particular aspects, the one or more endogenous immune related genes are genes of the major histocompatibility complex (MHC), human leukocyte antigen class I genes (e.g. HLA-A, HLA-B, HLA-C), human leukocyte antigen class II genes (HLA-DR, HLA-DQ, and HLA-DP), T cell receptors (e.g. αβ T cell receptor), interleukin 1 (IL-1), interleukin 2 (IL-2), interleukin 4 (IL-4), interleukin 6 (IL-6), interleukin 10 (IL-10), interleukin 23 (IL-23), interferon-γ (IFNγ), CCL2, CCL3, CCL4, CCL5, CXCL2, CXCL9-11, CCL17, CCL27, programmed death-1 (PD-1), TIM3, or TIGIT.
In further aspects, the methods disclosed herein include inhibiting the expression of cluster of differentiation 38 (CD38) in the primary immune cells such that the activity of CD38 is eliminated or reduced. CD38 may be down regulated or blocked by any suitable method or technique known in the art. Known methods for down regulation of gene expression or decreasing the activity of CD38 include, but are not limited to, CRISPR/Cas (including cytosine and adenine base editors), microRNA, shRNA, RNAi, TALENs, zinc finger nucleases, meganucleases, neutralizing antibodies, small molecule inhibitors, chemical inhibitors blocking downstream signaling pathways, and the like. In some aspects, CD38 activity or gene expression is reduced by between 1%-100% (i.e., 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, 100%).
In further aspects, the methods disclosed herein include inhibiting the expression of phosphatase and tensin homolog (PTEN) in the primary immune cells such that the activity of PTEN is eliminated or reduced. PTEN may be down regulated or blocked by any suitable method or technique known in the art. Known methods for down regulation of gene expression or decreasing the activity of PTEN include, but are not limited to, CRISPR/Cas (including cytosine and adenine base editors), microRNA, shRNA, RNAi, TALENs, zinc finger nucleases, meganucleases, neutralizing antibodies, small molecule inhibitors, chemical inhibitors blocking downstream signaling pathways, and the like. In some aspects, PTEN activity or gene expression is reduced by between 1%-100% (i.e., 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, 100%).
The term “TREX” refers to a “T cell that is Renewably EXpandable” using e.g., the techniques and genetic modifications provided herein. More specifically, TREX cells refer to cells with decreased or ablated expression of some or all of cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B CDKN2B, and S-methyl-5′-thioadenosine phosphorylase (MTAP).
In some aspects, inhibiting the expression of one or more endogenous regulatory factors occurs after introduction of the one or more transgene into the cells. In some aspects, primary immune cells in which one or more transgene has been introduced are cultured for at least 2 days, at least 5 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 16 days, at least 17 days, at least 18 days, at least 19 days, at least 20 days before inhibition of one or more endogenous regulatory factor is performed. In further aspects, inhibiting the expression of PTEN occurs after introduction of the one or more transgenes into the cells. In some aspects, the method comprises the following sequential steps i) introducing one or more transgenes into the immune cells and then culturing the cells for at least 2 days, 5 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 16 days, at least 17 days, at least 18 days, at least 19 days, at least 20 days; ii) inhibiting one or more endogenous regulatory factor culturing the cell for at least 2 days, 5 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 16 days, at least 17 days, at least 18 days, at least 19 days, at least 20 days; and iii) inhibiting PTEN expression.
Primary immune cells are cultured under conditions appropriate for promoting proliferation and expansion. In vitro expansion using the culture step activates and induces proliferation of the primary immune cells to yield an expanded population comprising primary immune cells sufficient in numbers for use in therapy.
The methods disclosed herein are performed ex vivo meaning that the methods take place outside an organism. Treatment of immune cells ex vivo means exposing cells to certain biological molecules in vitro preferably under sterile conditions. In some cases, ex vivo methods additionally include culturing immune cells that have been isolated from a human prior to administration back into the same or different human subject.
The primary immune cells including the expanded populations, and/or the engineered T cells of this disclosure can comprise total T cells, CD4-positive T cells, CD8-positive T cells, regulatory T cells, gamma-delta T cells, mucosal associated invariant T (MAIT) T cells, natural killer (NK) cells, or natural killer T (NKT) cells. T cells are broadly divided into cells expressing CD4 on their surface (also referred to as CD4-positive cells) and cells expressing CD8 on their surface (also referred to as CD8-positive cells). T cells appropriate for use according to the methods provided herein are mononuclear lymphocytes derived from bone marrow (BM), peripheral blood (PB), or cord blood (CB) of a human donor. These cells could be collected directly from BM, PB, or CB or after mobilization or stimulation via administration of growth factors and/or cytokines such as granulocyte-colony stimulating factor (G-CSF) or granulocyte-macrophage colony-stimulating factor (GM-CSF) to allogeneic or autologous donors. Those skilled in the art would appreciate that there are many established protocols for isolating peripheral blood mononuclear cells (PBMC) from peripheral blood. Isolation of PBMC can be aided by density-gradient separation protocols, usually employing a density-gradient centrifugation technique using Ficoll®-Hypaque or Histopaque® for separating lymphocytes from other elements in the blood. Preferably, PBMC isolation is performed under sterile conditions. Isolation of PBMC can also use negative selection kits. Alternatively, cell elutriation methods may be employed to separate mononuclear cell populations. In some aspects, the primary immune cells are human.
In some cases, methods of this disclosure further include introducing a genetically engineered or chimeric antigen receptor into activated T cells, wherein the method thereby generates an expanded population comprising of T cells expressing the genetically engineered or chimeric antigen receptor. Chimeric antigen receptors (CARs), also known as chimeric T cell receptors, artificial T cell receptors, and chimeric immunoreceptors, are engineered receptors, which graft specificity onto an immune effector cell. In general, a chimeric antigen receptor is a transmembrane protein having a target-antigen binding domain that is fused via a spacer and a transmembrane domain to a signaling endodomain. When the CAR binds its target antigen, an activating signal is transmitted to the T cell. In one embodiment, a polynucleotide that encodes a chimeric antigen receptor is introduced to the primary cells. In one embodiment, a nucleic acid vector encoding the chimeric antigen receptor or genetically engineered receptor is introduced into the T cells whereby the T cells express the chimeric antigen receptor. In some aspects, the CAR binds glypican 3 (GPC3), human epidermal growth factor receptor 2 ((HER2); also known as Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2)), B-cell maturation antigen (BCMA). In certain aspects, the CAR can bind any target for use in immunotherapy.
CAR construct design: CAR constructs of the present disclosure can have several components, many of which can be selected based upon a desired or refined function of the resultant CAR construct. In addition to an antigen binding domain, CAR constructs can have a spacer domain, a hinge domain, a signal peptide domain, a transmembrane domain, and one or more costimulatory domains. Selection of one component over another (i.e., selection of a specific co-stimulatory domain from one receptor versus a co-stimulatory domain from a different receptor) can influence clinical efficacy and safety profiles.
Antigen binding domain: Antigen binding domains contemplated herein can include antibodies or one or more antigen-binding fragments thereof. In an embodiment, a CAR construct targets GPC3. In an embodiment, a CAR construct targets BCMA. In an embodiment, a CAR construct targets HER2. In an embodiment, a CAR construct targets any molecule useful in an immunotherapy. In certain aspects, the antigen binding domain comprises a single chain variable fragment (scFv) containing light and heavy chain variable regions from one or more antibodies specific for GPC3, BCMA, or HER2 that are either directly linked together or linked together via a flexible linker (e.g., a repeat of G4S having 1, 2, 3 or more repeats).
Spacer domain: A CAR construct can have a spacer domain to provide conformational freedom to facilitate binding to the target antigen on the target cell. The optimal length of a spacer domain may depend on the proximity of the binding epitope to the target cell surface. For example, proximal epitopes can require longer spacers and distal epitopes can require shorter ones. Besides promoting binding of the CAR to the target antigen, achieving an optimal distance between a CAR cell and a cancer cell may also help to sterically occlude large inhibitory molecules from the immunological synapse formed between the CAR cell and the target cancer cell. A CAR can have a long spacer, an intermediate spacer, or a shorter spacer. Long spacers can include a CH2CH3 domain (˜220 amino acids) of immunoglobulin G1 (IgG1) or IgG4 (either native or with modifications common in therapeutic antibodies, such as a S228P mutation), whereas the CH3 region can be used on its own to construct an intermediate spacer (˜120 amino acids). Shorter spacers can be derived from segments (<60 amino acids) of CD28, CD8α, CD3 or CD4. Short spacers can also be derived from the hinge regions of IgG molecules. These hinge regions may be derived from any IgG isotype and may or may not contain mutations common in therapeutic antibodies such as the S228P mutation mentioned above.
Hinge domain: A CAR can also have a hinge domain. The flexible hinge domain is a short peptide fragment that provides conformational freedom to facilitate binding to the target antigen on the tumor cell. It may be used alone or in conjunction with a spacer sequence. The terms “hinge” and “spacer” are often used interchangeably—for example, IgG4 sequences can be considered both “hinge” and “spacer” sequences (i.e., hinge/spacer sequences).
Signal peptide: A CAR construct can further include a sequence comprising a signal peptide. Signal peptides function to prompt a cell to translocate the CAR to the cellular membrane. Examples include an IgG1 heavy chain signal polypeptide, Ig kappa or lambda light chain signal peptides, granulocyte-macrophage colony stimulating factor receptor 2 (GM-CSFR2 or CSFR2) signal peptide, a CD8a signal polypeptide, or a CD33 signal peptide.
Transmembrane domain: A CAR construct can further include a sequence comprising a transmembrane domain. The transmembrane domain can include a hydrophobic a helix that spans the cell membrane. The properties of the transmembrane domain have not been as meticulously studied as other aspects of CAR constructs, but they can potentially affect CAR expression and association with endogenous membrane proteins. Transmembrane domains can be derived, for example, from CD4, CD8α, or CD28.
Costimulatory domain: A CAR construct can further include one or more sequences that form a co-stimulatory domain. A co-stimulatory domain is a domain capable of potentiating or modulating the response of immune effector cells. Co-stimulatory domains can include sequences, for example, from one or more of CD3zeta (or CD3z), CD28, 4-1BB, OX-40, ICOS, CD27, GITR, CD2, IL-2R13 and MyD88/CD40. The choice of co-stimulatory domain influences the phenotype and metabolic signature of CAR cells. For example, CD28 co-stimulation yields a potent, yet short-lived, effector-like phenotype, with high levels of cytolytic capacity, interleukin-2 (IL-2) secretion, and glycolysis. By contrast, T cells modified with CARs bearing 4-1BB costimulatory domains tend to expand and persist longer in vivo, have increased oxidative metabolism, are less prone to exhaustion, and have an increased capacity to generate central memory T cells.
In particular aspects, the methods disclosed herein compromise early stimulation of the primary immune cells to ensure the cells are in cycle prior to introduction of the one or more genetic edits to the cells. In other aspects, the methods disclosed herein compromise late stimulation of the primary immune cells (also referred to as “restimulation”). Once the primary immune cells have exited cell cycle, the cells are restimulated causing the cells to re-enter into cell cycle (i.e., proliferation).
In particular aspects, the methods disclosed herein further comprise stimulating the primary immune cells before the introduction of the one or more genetic edits to the primary immune cells. In particular aspects, the primary immune cells are stimulated before at least 1 day, at least 2 days, at least 5 days, at least 10 days, at least 15 days, at least 20 days, or at least 30 days before the introduction of the one or more genetic edits to the primary immune cell. Thus, in particular aspects, provided herein is a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: i) stimulating the primary immune cells; ii) introducing one or more genetic edits into the primary immune cells; iii) culturing the primary immune cells in a culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS).
In particular aspects, the methods disclosed herein further comprise stimulating the primary immune cells following the introduction of the one or more genetic edits to the primary immune cells. In particular aspects, the primary immune cells are stimulated after at least 1 day, at least 2 days, at least 5 days, at least 10 days, at least 15 days, at least 20 days, or at least 30 days following the introduction of the one or more genetic edits to the primary immune cell. Thus, in particular aspects, provided herein is a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: i) introducing one or more genetic edits into the primary immune cells; ii) culturing the primary immune cells in a culture medium; iii) stimulating the primary immune cells; and iv) culturing the primary immune cells in the culture medium; wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS). In further aspects, the primary immune cells are re-stimulated at least one time, at least two times, at least three time, at least four times, or at least five times. Thus, in particular aspects, provided herein is a method of generating a population of primary immune cells resistant to replicative senescence (RRS), comprising: i) introducing one or more genetic edits into the primary immune cells; ii) culturing the primary immune cells in a culture medium; iii) stimulating the primary immune cells; iv) culturing the primary immune cells in the culture medium; v) re-stimulating the primary immune cells; and vi) culturing the primary immune cells in the culture medium wherein the culturing induces proliferation of the primary immune cells to yield a population of primary immune cells resistant to replicative senescence (RRS). Any suitable stimulus known in the art can be used stimulate the immune cells.
In particular aspects, the primary immune cells undergo at least about a 50-fold expansion, at least about a 500-fold expansion, at least about a 5000-fold expansion, at least about a 250,000-fold expansion, at least about a 500,000-fold expansion, at least about a 106 fold expansion, at least about a 107 fold expansion, at least about a 108 fold expansion, at least about a 109 fold expansion, or at least about a 1010 fold expansion during culturing. In particular aspects, the population of expanded primary immune cells is resistant to replicative senescence. Furthermore, these cells are not functionally exhausted following long-term expansion and can be directed to carry out cytotoxic function through engagement of their TCRs by a T cell engager antibody or through engagement of a chimeric antigen receptor (CAR), (or through a natural or genetically-introduced TCR).
In particular aspects, the primary immune cells are cultured in a culture medium that includes supportive cytokine(s) but does not include a primary immune cell stimulus. In particular aspects, the primary immune cells undergo expansion during culturing in the absence of feeder cells or stimulation through CD3 and/or their antigen receptor. The ability of the disclosed methods to generate immune cells in the absence of extensive T cell re-stimulation or feeder cells advantageously eliminates the issues of scaling up the methods and producing dysfunctional populations of immune cells.
The methods disclosed herein advantageously provide populations of expanded primary immune cells including human CD8+ T cells, human CD4+ T cells, human regulatory T cells human gamma-delta T cells, or human natural killer T cells that have the ability to proliferate for substantial periods of time in the absence of re-stimulation through their T cell receptors (TCRs), expanding millions of fold in long-term culture. In particular aspects, the population of primary immune cells are cultured for at least 20 days, at least 30 days, at least 40 days, at least 50 days, at least 60 days, at least 70 days, at least 80 days, at least 90 days, at least 100 days, at least 150 days, at least 200 days, at least 300 days, or at least 400 days.
In further aspects provided herein is an engineered T cell expressing a transgene encoding a B-cell lymphoma-extra large (Bcl-xL) that does not express cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and/or S-methyl-5′-thioadenosine phosphorylase (MTAP).
In further aspects provided herein is an engineered T cell that does not express cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and/or S-methyl-5′-thioadenosine phosphorylase (MTAP).
In further aspects provided herein is an engineered T cell expressing a transgene encoding a B-cell lymphoma-extra large (Bcl-XL) that does not express cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), S-methyl-5′-thioadenosine phosphorylase (MTAP) and/or phosphatase and tensin homolog (PTEN).
In certain aspects, the engineered T cell as disclosed herein does not express of one or more endogenous immune related genes in the primary immune cells. In some aspects, the endogenous immune related gene is beta-2 microglobulin (B2M), or T-cell receptor α constant (TRAC).
In certain aspects, the engineered T cell as disclosed herein does not express cluster of differentiation 38 (CD38).
In further aspects the disclosure herein provides an engineered T cell that does not express cyclin-dependent kinase inhibitor 2A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), S-methyl-5′-thioadenosine phosphorylase (MTAP), beta-2 microglobulin (B2M), T-cell receptor α constant (TRAC), cluster of differentiation 38 (CD38), and/or phosphatase and tensin homolog (PTEN).
In certain aspects, the engineered T cell as disclosed comprises a polynucleotide that encodes a chimeric antigen receptor (CAR). In some aspects, the CAR binds glypican 3 (GPC3), B-cell maturation antigen (BCMA), or human epidermal growth factor receptor 2 ((HER2); also known as Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2)).
In certain aspects, the engineered T cell as disclosed herein is a CD8+ T cell, a CD4+ T cell, a gamma delta T cell, a mucosal associated invariant T (MAIT) T cell, a natural killer (NK) cell, a natural killer T (NKT) cell, or a combination thereof.
In some aspects, the engineered T cell is resistant to replicative senescence (RRS). In some aspects, the engineered T cell is a CD8+ T cell. In some aspects, the engineered T cell is a CD4+ T cell. In some aspects, the engineered T cell is human.
Expanded T cell populations disclosed herein are useful for cellular immunotherapies including, without limitation, T cell therapy, adoptive cell therapy (ACT), and CAR T cell therapy.
Expanded populations of T cells populations disclosed herein are useful for treating or preventing various disorders such as a cancer (e.g., a blood malignancy such as lymphoma or leukemia or solid tumors such as melanoma or kidney cancer), autoimmune diseases or an infectious disease such as HIV.
The terms “treatment” or “treat,” as used herein, refer to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include subjects having cancer as well as those prone to having cancer or those in cancer is to be prevented. In some aspects, the methods, compositions, and combinations disclosed herein can be used for the treatment of cancer. In other aspects, those in need of treatment include subjects having a tumor as well as those prone to have a tumor or those in which a tumor is to be prevented. In certain aspects, the methods, compositions, and combinations disclosed herein can be used for the treatment of tumors. In other aspects, treatment of a tumor includes inhibiting tumor growth, promoting tumor reduction, or both inhibiting tumor growth and promoting tumor reduction.
In some cases, T cells obtained according to a method provided herein can be administered as a pharmaceutical composition comprising a therapeutically effective amount of T cells as a therapeutic agent (i.e., for therapeutic applications).
The terms “pharmaceutical composition” or “therapeutic composition,” as used herein, refer to a compound or composition capable of inducing a desired therapeutic effect when properly administered to a subject. In some aspects, the disclosure provides a pharmaceutical composition comprising a pharmaceutically acceptable carrier and a therapeutically effective amount of at least one immune cell of the disclosure.
The terms “pharmaceutically acceptable carrier” or “physiologically acceptable carrier,” as used herein, refer to one or more formulation materials suitable for accomplishing or enhancing the delivery of one or more immune cells of the disclosure.
The term “subject” is intended to include human and non-human animals, particularly mammals. In certain aspects, the subject is a human patient.
The terms “administration” or “administering,” as used herein, refer to providing, contacting, and/or delivering a compound or compounds by any appropriate route to achieve the desired effect. Administration may include, but is not limited to, oral, sublingual, parenteral (e.g., intravenous, subcutaneous, intracutaneous, intramuscular, intraarticular, intraarterial, intrasynovial, intrasternal, intrathecal, intralesional, or intracranial injection), transdermal, topical, buccal, rectal, vaginal, nasal, ophthalmic, via inhalation, and implants.
Without limiting the disclosure, a number of aspects of the disclosure are described herein for purpose of illustration.
The Examples that follow are illustrative of specific aspects of the disclosure, and various uses thereof. They are set forth for explanatory purposes only and should not be construed as limiting the scope of the disclosure in any way.
Transposon frequency was assessed in T cell subsets over a period of 66-137 days using flow cytometry. Total primary human T cells were isolated from the blood of healthy donors, activated for 72 hours with Dynabeads (Human T-Activator CD3/CD28) and then transfected with plasmids containing transposons encoding anti-apoptotic factors, virally-derived factors, mutant cytokine receptors, mutant signaling molecules, and/or mutant cell cycle regulatory molecules in addition to a fluorescent reporter. mRNA encoding a transposase was simultaneously transfected into cells to enable chromosomal integration of the transposable elements. In total, 52 transposon constructs were tested across various screens. Four to 8 days after transfection, cells were assessed for baseline transposon incorporation using flow cytometry. Cells were periodically restimulated with Dynabeads to drive them through proliferation and transposon enrichment was assessed using flow cytometry. Molecules that enhance the survival of expanding T cells would be expected to enrich over their starting frequency within the total T cell pool as demonstrated in the CD8+ and CD4+ T cells. (
While cells expressing transgenes encoding endogenous anti-apoptotic factors (Bcl-2 and Bcl-xL) or virally-derived factors (StpA All, StpC and Tip, and a modified Tio-LMP1) demonstrated an enhanced ability to survive in long-term culture with repeated stimulation through their TCRs relative to untransfected control cells in the same wells, these cells did not exhibit a large, sustained boost in their proliferative capacities. These data suggest that additional edits may be required to confer the desired phenotype of a TREX cell.
Patient-derived leukemic cell lines have been used for years in laboratories to conduct a variety of cellular assays. The transformed nature of these cells can be mapped on to a collection of mutations that are also frequently found in patients with T cell acute lymphoblastic leukemia (T-ALL) (Table 1). Mutations in T-ALL patients can be broken down into several large classes that each presumably contribute to the phenotype and generation of T-ALL cells: gain of activating signals, loss of signal suppressors, loss of cell cycle arrest regulators, as well as modification of pleiotropic factors such as transcription factors, epigenetic regulators, and other cellular machinery.
As stated above, it was hypothesized that in addition to providing a survival factor such as Bcl-XL, it may be necessary to modify T cell expression of a collection of the aforementioned genes in order to recreate the desired phenotype (Table 1). Therefore, total CD8+ T cells were isolated from the blood of healthy donors, activated using αCD3/αCD28 Dynabeads, and 72 hours later a transgene encoding Bcl-XL was inserted into the collective pool of purified CD8+ T cells. These cells were then expanded for a period of 17 days prior to reactivation using αCD3/αCD28 Dynabeads and subsequent ablation of expression of factors identified from leukemic T cell lines and patients with T-ALL. Increased proliferative capacity is one of the primary characteristics that was to be engineered into TREX cells, therefore, effects of ablating expression of molecules from the “Cell Cycle ARREST” bin: cyclin-dependent kinase inhibitor 2A (CDKN2A) and CDKN2B were tested in these cells (
Bcl-xL-edited, Bcl-xL and CDKN2A/CDKN2B-edited, and TREX+Bcl-xL cells were maintained in culture for nearly 100 days without additional stimulation through their TCRs and total fold expansion of each population was assessed (
While TREX+Bcl-xL cells demonstrated a substantially enhanced proliferative capacity relative to control CD8+ T cells from the same donor, further experiments were conducted to test whether these edits could confer a similar phenotype in other donors and whether it was possible to further enhance the TREX+Bcl-xL phenotype by ablating expression of signal suppressors that are frequently mutated in patients with T-ALL (Table 1). The phosphatase and tensin homolog (PTEN) locus demonstrates frequent loss-of-function mutations in patient-derived leukemic cell lines and patients with T-ALL and is known to negatively regulate cell cycle progression (Table 1). TREX+Bcl-xL cells were generated as above from two different donors (40A30 and 40B30) and expression of PTEN was ablated in one of these TREX+Bcl-xL lines (40B32) approximately 2 weeks after “triplex” editing (
While TREX+Bcl-xL cells with intact PTEN expression expanded dramatically in the absence of additional TCR stimulation, their proliferation ultimately slowed relative to TREX+Bcl-xL cells deficient in PTEN expression (
Primary T cells are dependent on cytokines such as IL-2 for survival and proliferation in vitro and in vivo, however, some leukemic cell lines grow independently of IL-2. TREX+Bcl-xL cells and PTEN-deficient TREX+Bcl-xL cells were generated in media containing IL-2. It was investigated whether these cells still resemble normal primary human T cells in regards to cytokine dependence by tracking cell proliferation and survival across a range of IL-2 concentrations over a period of 6 days in culture (
It was also tested whether TREX+Bcl-xL cells and PTEN-deficient TREX+Bcl-xL cells maintain phenotypes similar to normal T cells after modification and extended in vitro culture or whether these conditions drive TREX+Bcl-xL cells to an exhausted phenotype (
Chemokine receptors are important for trafficking of immune cells to sites of inflammation. Therefore, TREX+Bcl-xL cells, PTEN-deficient TREX+Bcl-xL cells, restimulated TREX+Bcl-xL cells, and restimulated PTEN-deficient TREX+Bcl-xL cells were analyzed for expression of the chemokine receptors CCR2, CCR5, CCR6, CCR7, CXCR3, and CXCR5 using flow cytometry (
Having established that TREX+Bcl-xL lines resemble normal primary human T cells, it was determined whether TREX+Bcl-xL cells maintain potent cytotoxic function after long-term culture and expansion. A T cell engager was used in the presence of target tumor cells and the impedance-based xCELLigence platform to quantify TREX+Bcl-xL cell cytotoxic function (
In order to develop TREX+Bcl-xL cells into a potential cellular therapy these cells must be capable of expressing a targeting molecule such as a chimeric antigen receptor (CAR) to direct their cytotoxic function. The three TREX+Bcl-xL cell lines generated as described above were transduced with a lentivirus encoding a CAR that recognizes glypican 3 (GPC3). Surface expression of the GPC3 CAR was subsequently measured using flow cytometry (
CAR-directed cytotoxic function of TREX+Bcl-xL cells was assessed by performing impedance-based xCELLigence assays using target tumor cells with varying degrees of antigen expression: OE21 (antigen-negative), HuH-7 (antigen-intermediate), and Hep3B (antigen-high) (
These data confirm that TREX+Bcl-xL and PTEN-deficient TREX+Bcl-xL cells are capable of expressing a CAR and carrying out CAR-directed cytotoxic function in an antigen-dependent manner even after significant in vitro expansion.
Cytokine cues can be used to modulate activity and expansion of human and murine T cells (Zhang et al., Science Translational Medicine, 22 Dec. 2021, Vol 13, Issue 625; Aspuria et al., Science Translational Medicine, 22 Dec. 2021, Vol 13, Issue 625) therefore TREX cells were assessed for their capacity to respond to different human cytokines in vivo. Briefly, primary human CD8+ T cells or 278-day old TREX cells were labeled with a luciferase reporter and 3E6 luciferase-expressing cells were infused into NSG mice with or without supplementation with a recombinant human IL-2 fusion protein. Mice were imaged using an IVIS Optical Imaging system to detect luciferase-expressing T cells (
GPC3 targeting CAR-TREX+Bcl-xL cells were assessed for their capacity to respond to different human cytokines in vivo. NSG, hIL-2 NOG, or hIL-15 NOG mice were inoculated with GPC3 expressing Hep3B tumor cells. Once tumors were established, mice were left untreated or were treated with 10E6 GPC3 targeting CAR-TREX+Bcl-xL cells. CAR-TREX+Bcl-xL cells were 121 days at the time of infusion. Mice were sacrificed 8 days after CAR-TREX+Bcl-xL cell infusion and bodyweights were measured (
The capacity of GPC3 targeting CAR-TREX cells to control solid tumors was determined. Hep3B tumors were established in NSG mice and then 92 day old purified CAR-TREX cells (
While the REX edits confer enhanced proliferation of the TREX cell product, additional editing at the B2M and CD38 loci was performed to delay rejection of the TREX cell product by a patient's immune system. B2M is a protein of 119 amino acids that is encoded by a gene on chromosome 15 in humans. It is also a component of major histocompatibility class (MHC) I molecules and also associates with non-classical, MHC I like molecules such as CD1, MR1, the neonatal Fc receptor, and Qa-1. Though it is located outside of the MHC locus, B2M is required for the successful expression of classical and non-classical MHC I molecules on the surfaces of nucleated cells. By eliminating B2M expression in TREX cells using CRISPR/Cas9, the cells will be shielded from patient CD8+ T cells. Additionally, ablation of B2M expression and consequently MHC-I expression by the TREX cell product will sensitize it to rejection by patient NK cells. Knockout of B2M was carried out simultaneously with knock in of a targeting a CAR (e.g. GPC3, HER2, BCMA) in the TREX cell product.
NK cells express high levels of CD38 and are depleted in certain cancer patients, e.g., multiple myeloma patients, receiving anti-CD38 monoclonal antibodies such as daratumumab and isatuximab. In order to prolong the persistence of this allogeneic cell population in patients, CD38 was knocked out of TREX cells using CRISPR/Cas9 and daratumumab or isatuximab can be co-administered with TREX cells (see
As an allogeneic CD8+ T cell population, TREX cells are expected to be capable of targeting the HLA-mismatched patient's healthy cells through their TCRs, resulting in GvHD. In order to prevent the development of this pathology, the TREX cell population was edited at the T Cell Receptor Alpha Constant (TRAC) locus, which encodes the TCR a chain. CRISPR/Cas9 editing of TRAC leads to loss of expression of the TCR a chain, which in turn prevents surface expression of the TCR by TREX cells.
A BCMA targeting CAR was expressed in TREX cells (i.e., cells lacking CDKN2A/CDKN2B/MTAP) (
Assessment of anti-BCMA-TREX cells indicates that these cells are likely to control BCMA-expressing tumors similarly to primary anti-BCMA-CAR-T cells while exhibiting a potentially improved safety profile in the form of diminished cytokine release and potentially reduced risk of CRS (
Anti-BCMA-TREX cells (82 days in culture) or anti-BCMA-CAR-T cells were cultured with BCMA-expressing tumor cells. Supernatants were collected 72 hours after initiation of co-culture and assessed for levels of IFN-γ using MSD kits (
Anti-BCMA-TREX cells (112 days in culture) were assessed for their ability to persist in a serial kill assay with or without IL-2 support. Briefly, anti-BCMA-TREX cells or anti-BCMA-CAR-T cells were serially cultured with BCMA-expressing JJN3 cells at an effector:target cell ratio of 1:1. Tumor cell control (% cytolysis), effector cell numbers, and effector cytokine secretion was measured after each round of co-culture and graphed (
A HER2 targeting CAR was expressed in TREX cells or Primary T cells (
Requirements for overexpression of Bcl-xL and the various REX target genes to confer the REX phenotype were assessed in isolated CD8+ T cells from two donors (denoted as G and H). Briefly, CD8+ T cells were negatively selected and then activated with αCD3/αCD28 Dynabeads for 3 days. Bcl-xL was introduced into some cells while other cells were cultured and various combinations of the REX target genes were knocked out using CRISPR/Cas9 (
TREX cells and γδ TREX cells were examined for ablation of expression of the REX target genes by Western Blot analysis (
Bcl-xL overexpressing TREX cells and donor-matched unedited control CD8+ T cells were cultured over time. RNAseq analysis was performed on cell pellets generated at various points and gene signatures were assessed in Bcl-xL TREX cells and control cells; as expected, TREX cells showed enrichment in gene signatures associated with cell cycle such as E2F target genes and G2M checkpoint target genes (
TREX cells and were cultured with varying amounts of IL-2 for a period of 12-14 days. Cell expansion was tracked and graphed over this time (
REX edits reproducibly confer an enhanced resistance to replicative senescence in CD8+ T cells. The capacity of ablation of expression of the REX target genes (CDKN2A, CDKN2B, and MTAP) to enhance CD4+ T cell resistance to replicative senescence was determined. CD4+ T cells were isolated from three healthy donors, stimulated using αCD3/αCD28 Dynabeads and then edited at these loci. Proliferation of CD4+ TREX cells and donor-matched unedited CD4+ T cell controls was tracked over time and graphed. (
γδ T cells are another cytotoxic subset of T cells. The ability of REX edits to confer a TREX cell phenotype in γδ T cells was investigated using γδ T cells from eight different donors (
Having established that γδ TREX cell lines demonstrate enhanced resistance to replicative senescence, it was determined whether γδ TREX cells maintain potent cytotoxic function after long-term culture and expansion. A T cell engager was used in the presence of target tumor cells and the impedance-based xCELLigence platform to quantify γδ TREX cell cytotoxic function (
γδ T cells are typically comprised of multiple subsets including Vδ1, Vδ2, Vδ3, and Vδ5, among others (Lawand et al., Front. Immunol., 30 Jun. 2017). In humans the Vδ1 and Vδ2 make up the majority of γδ T cells with Vδ2 cells being found primarily in the blood and VM cells being found in tissues.
γδ TREX cells, γδ CAR-TREX cells, and donor-matched, unedited γδ T cells were stained and analyzed for expression of Vδ1 and Vδ2 (
γδ TREX cells were next investigated for their ability take instruction from a tumor-targeting moiety such as a BCMA-targeting CAR (
REX edits enhance T cell resistance to replicative senescence, however it was unclear whether they would support an NKREX cell phenotype. Therefore, NK cells were isolated from three different donors and cultured in media containing IL-2 or a combination of IL-2 and IL-15. NK cells were then edited at the REX loci using CRISPR/Cas9 and proliferation of NKREX and donor-matched unedited NK cells was monitored over time (
Given the enhancement in resistance to replicative senescence, it was important to determine whether NKREX cells maintained their dependence on cytokine support. NKREX cells were generated in media containing IL-2 or a combination of IL-2 and IL-15. NKREX cell dependency on these cytokines was determined in an experiment in which cytokines were withdrawn from the growth media and NKREX cell numbers were monitored for a period of 37 days. NKREX cells failed to proliferate following cytokine withdrawal and these cells demonstrated a rapid drop off in cell viability and viable cell diameter, reinforcing their dependency on cytokine support despite editing of the REX genes (
NKREX cells were transduced to express a BCMA-targeting CAR to determine whether these cells were capable of stably expressing a tumor-targeting CAR (
While NKREX cells could be expanded in culture for long periods of time, it was unclear: 1) whether their cytotoxic potential was maintained following sustained proliferation; and 2) whether they could take direction a tumor-targeting CAR. Therefore, CAR-NKREX cells were generated from two different NKREX lines (
TREX cells have been modified to increase their resistance to replicative senescence. However, these cells have displayed hallmarks of normal T cells. In order to better understand the ability to control TREX cells, their susceptibility to standard T cell depleting agents and chemotherapies was determined relative to unedited total T cells that were activated to enter cell cycle (
As an allogenic cell product, TREX cells are modified at the B2M locus, increasing their susceptibility to NK cell mediated depletion. These cells can be further modified at the CD38 locus to limit their depletion by anti-CD38 antibodies. TREX cell lines and CD38KOB2MKO TREX cell lines were generated using CRISPR/Cas9. TREX cells and CD38KOB2MKO TREX cells were co-cultured with PBMCs isolated from healthy donors. TREX cells did not exhibit a drop in number when co-cultured with PBMCs while CD38KOB2MKO TREX cells were susceptible to NK cell mediated lysis as expected (
This application claims priority to U.S. Provisional Application No. 63/236,443, filed Aug. 24, 2021, the disclosure of which is incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63236443 | Aug 2021 | US |
