Patent Application
20210024884
The present invention relates to the field of mammalian cells, and to the use of such cells as donor cells for implantations.
The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Sep. 21, 2020, is named 190045US01_SeqList.txt and is 24 kilobytes in size.
Universally transplantable tissues and/or cells are being researched on in hope for significant benefits such as reduction in graft rejection risk e.g. in the context of non-matching donor/recipient immunological profiles or of autoimmune conditions such as Type 1 diabetes mellitus (T1 D).
To limit the risk of draft rejection, auto-transplantation is an option whereby stem cells are extracted from a patient, expanded, differentiated and transplanted back into the same patient. However, this process is technically very difficult and expensive.
Tissue mismatch rejection is mediated by class I HLA (Human Leucocyte Antigen) peptide complexes and subsequent T-cell based tissue destruction. The depletion of class I HLA peptide complexes absolves the requirement for tissue matching for most cells.
There exist 6 class I HLA peptide complexes: highly polymorphic class I HLA peptide complexes HLA-A, HLA-B and HLA-C, and less polymorphic class I HLA peptide complexes HLA-E, -F, and -G.
Depletion of class I HLA peptide complexes can be achieved through either of two pathways:
1) By direct removal of all six highly polymorphic class I HLA alleles, or
2) By elimination of the beta 2 microglobulin (B2M) protein. B2M is necessary for the translocation of all HLA-I complexes to the cell surface. The absence of B2M protein renders the cell's surface devoid of all class I HLA peptide complexes.
While pan-class I HLA deficient cells are protected from mismatch rejection, they are susceptible to Natural Killer cell rejection (NK cells) due to the absence of class I HLA-E complexes. When present on the cell surface, class I HLA-E complexes deliver an inhibitory signal to NK cells. In absence of HLA-E complexes, the loss of this inhibitory signal results in lysis of the HLA deficient cell by NK cells.
Attempts to solve this issue of NK lysis rely on the expression of engineered variants of B2M protein fused to HLA-E protein (WO19032675). One approach (Gornalusse, et al. Nature Biotechnology 2017) is to pre-build a signal peptide (HLA class I leader peptide sequence) in the fusion protein in the form of a signal peptide/B2M/HLA-E trimer to increase stability and membrane expression of the complex. Most significant development programs use fusion constructs including a fused (or “pre-bound”) HLA-G derived signal peptide as HLA class I leader peptide.
An acknowledged issue in generating HLA-deficient cells (also named “universal donor” cells) is that they become silent to immune surveillance for viral infection or neoplastic transformation. There remains an associated risk that upon viral infection or malignant dedifferentiation, the cells are no longer subject to regular immune surveillance, and this triggers safety concerns.
There remains a need for improved safe universal donor cells.
Gornalusse G. et al (Nature Biotechnology 2017) disclose HLA-E expressing pluripotent stem cells.
WO2012145384 discloses B2M deficient cells.
U.S. Pat. No. 8,586,358B2 discloses HLA homozygous cells that are homozygous for a HLA haplotype.
US20040225112A1 discloses genes encoding single chain HLA-E proteins to prevent NK cell-mediated cytotoxicity.
Deuse et al (Nature Biotechnology, 2019) discloses knocked out B2M and CIITA and added CD47.
WO19032675 discloses an isolated genetically modified T-cell comprising sequences encoding a fusion protein comprising a B2M protein and HLA-E and/or HLA-G protein.
WO18005556 allegedly discloses cells comprising an MHC-E molecule.
Young et al. Cancer Gen. Therapy (2000), 7:240-246 discloses ganciclovir mediated cell killing using the Herpes Simplex Virus-Thymidine Kinase (HSV-TK) gene.
In one aspect the present invention provides a mammalian cell comprising a B2M/HLA-E gene, such as B2M/HLA-E*0101 and B2M/HLA-E*0103 genes, wherein said mammalian cell comprises no other expressible B2M genes. In an embodiment, said mammalian cell has knock-ins of at least 4 HSV-TK genes at distinct and known locations.
In another aspect the present invention provides a mammalian cell which has knock-ins of B2M/HLA-E genes, such as both B2M/HLA-E*0101 and B2M/HLA-E*0103 genes into an otherwise B2M and HLA-II deficient cell, for example CIITA deficient cell.
In another aspect the present invention provides a mammalian cell comprising a B2M/HLA-E gene wherein said mammalian cell comprises no other expressible B2M genes, is CIITA deficient and has knock-ins of 4 HSV-TK genes at distinct and known locations.
In another aspect the present invention provides a mammalian cell comprising B2M/HLA-E*0101 and B2M/HLA-E*0103 genes wherein said mammalian cell comprises no other expressible B2M genes, is CIITA deficient and has knock-ins of 4 HSV-TK genes at distinct and known locations.
In one aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
In one aspect, said mammalian cell is a human cell.
In a further aspect, said mammalian cell is a stem cell.
In one aspect, said mammalian cell is an embryonic stem cell. In another aspect, said mammalian cell is a pluripotent stem cell. In a yet another aspect, said mammalian cell is at a differentiated stage.
In an embodiment, the method of the present invention further comprises a step of knock-in of at least 4 HSV-TK genes at distinct and known locations.
In yet another aspect the present invention provides the use of a mammalian cell according to the invention for the prevention, treatment or cure of a chronic disease.
In one embodiment this chronic disease is selected from the group consisting of diabetes, type 1 diabetes, type 2 diabetes, dry macular degeneration, retinitis pigmentosa, neurological disease, Parkinson's disease, heart disease, chronic heart failure and chronic kidney disease.
The present invention provides improved universal donor cells. The cells of the present invention are more universal and safer for patients.
Allele:
The term “allele” as used herein means a variant of a given gene. For example, HLA-E 01:01 and HLA-E 01:03 are variants, also called alleles or isotypes, of the HLA-E gene.
B2M: The term “B2M” as used herein means beta2-microglobuline, i.e. β2 microglobulin. The term “B2M gene” designates the gene that encodes the B2M protein. The B2M protein is a subunit of all class I HLA proteins. The B2M protein is necessary for class I HLA proteins to translocate to the cell surface. In humans, the B2M gene is located on chromosome 15.
B2M Deficient Cell:
The term “B2M deficient cell” as used means a cell which has no functional B2M gene. Hence, the B2M gene may be entirely absent from the cell or it can be functionally defect, e.g. inactivated or damaged, such that it is not expressed or does not encode a functional B2M protein.
B2M/HLA-E Gene or Protein:
The term “B2M/HLA-E gene” as used herein is equivalent to “B2M/HLA-E fusion gene” and means a genetic fusion construct encoding a protein comprising a B2M part and a HLA-E part, which is equivalent to “B2M/HLA-E fusion protein”. As used herein, unless otherwise specified, the terms “B2M/HLA-E gene” and “B2M/HLA-E fusion protein” refer to any functional versions thereof, wherein the gene has the ability to express the corresponding fusion protein and wherein the expressed B2M/HLA-E fusion protein has the ability to translocate to the cell surface.
B2M/HLA-E*0101 Protein:
The term “B2M/HLA-E*0101 protein” as used herein means a fusion protein comprising a “B2M” part and a “HLA-E” part wherein the HLA-E part is of the 01:01 isotype, also called the 01:01 allele, i.e. a fusion comprising a B2M functional peptide and a HLA-E 01:01 functional peptide.
B2M/HLA-E*0101 Gene:
The term “B2M/HLA-E*0101 gene” as used herein means a genetic fusion construct encoding a B2M/HLA-E*0101 protein.
HLA/MHC:
The term “HLA” stands for Human Leucocyte Antigen. As used herein, HLA refers to the well-known HLA system responsible for the regulation of the immune system in mammalians. “HLA genes” encode for “HLA proteins” also called “MHC proteins”. “MHC” stands for “major histocompatibility complex”.
Functional “HLA proteins” (or “MHC proteins”) translocate to the cell-surface and induce an immune response as need be. In humans, the HLA genes are located on chromosome 6.
Class I HLAs proteins are heterodimers and comprise HLA-A, HLA-B and HLA-C proteins, which are highly polymorphic, and HLA-E, HLA-F and HLA-G proteins, which are less polymorphic. Class I HLA proteins are normally found on all nucleated cells' surface in humans.
The role of Class I HLA proteins is to present small peptides, herein called “endogenous peptides”, from inside the cell on the outer surface of the cell. In case of cell infection, the class I HLA peptides present to the outer cell surface a small peptide from the invader pathogen (e.g. a virus), which will be recognised as “non-self” (or “foreign” or “antigen”) and induce an immune response by destruction of the cells by the immune system. In absence of cell infection, the class I HLA peptides present to the outer cell surface an endogenous small peptide e.g. from HLA-E (HLA-E fragments) which will be recognised as “self” (or “self-antigen”) and will not induce an immune response.
Class II HLAs proteins are heterodimers and comprise HLA-DP, HLA-DM, HLA-DOA, HLA-DOB, HLA-DQ, and HLA-DR. Class II HLA proteins are normally found on professional antigen-presenting cells.
The role of Class II HLA proteins is to present antigens derived primarily from exogenous sources to the cell surface and initiate an antigen-specific immune response (via CD4(+) T-lymphocytes).
Cell Genotype:
A “gene A−/− cell” means a cell wherein both copies of gene A are non-functional, e.g. deleted or otherwise disrupted. A “gene A+/− cell” means a cell wherein one copy of gene A is functional, and the second copy is non-functional, e.g. is deleted or otherwise disrupted. A “gene A+ cell” means that the cell comprises only one copy of gene A and that said one copy of gene A is functional.
Cell Surface Phenotype:
As used herein the expression “cell surface phenotype of HLA-A/B/C−/− cells” refers to a cell surface with no HLA-A, HLA-B and HLA-C proteins.
As used herein the expression “cell surface phenotype of HLA-E*0101+ HLA-E*0103+ cells” refers to a cell surface comprising HLA-E*0101 proteins and HLA-E*0103 proteins as expressed from one copy of each HLA-E allele.
CIITA/CIITA Deficient:
The term CIITA stands for “class II, major histocompatibility complex, transactivator”. The term CIITA as used herein designates the “CIITA gene” or the “CIITA protein”, i.e. the protein encoded by the CIITA gene. The CIITA protein is a transcription factor involved in the transcription of all class II HLA peptides. In the human genome, the CIITA protein is located on chromosome 16.
The term “CIITA deficient” as used herein means “without a functional CIITA gene”. A “CIITA deficient cell” means a cell that does not express a functional CIITA protein, for example the cell's CIITA gene has been knocked-out or otherwise inactivated or express a non-functional protein. In a CIITA deficient cell, all HLA class II proteins are ablated.
Distinct and Known Locations:
The expression “at known location(s)” as used herein means “in a targeted locus”. The expression refers to a gene modification, such as insertion, deletion or disruption, in a specific targeted locus (location) on the genome, as opposed to random gene modification in a random location in the genome. In particular, in connection with knock-in, the expression “at distinct and known location(s)” means that a gene of interest is not inserted at a random location in the genome but is inserted in a locus that has been predetermined and specifically targeted. This provides the advantage of ensuring a consistent level of expression of the inserted gene and for example to target safe-harbour loci.
The expression “at distinct locations” as used herein means “at different loci on the genome”. The expression refers for example to more than one nucleic acid sequence insertion, where said 2 or more nucleic acid sequences are not inserted on the same locus on the genome, i.e. on the one same position on the genome. Rather, said 2 or more nucleic acid sequences are inserted at different loci on the genome. For example, if inserted on the same chromosome, the 2 or more sequences are separated from each other by a number of nucleotides after insertion. The expression “distinct locations” may include the same locus located on 2 chromosomes of a pair of chromosomes.
EF1a Mini, EF1a, UbC, PGK, CMV and CAG Promoters:
EF1a promoter stands for human elongation factor 1α promoter, UbC promoter stands for human Ubiquitin C promoter, PGK promoter stands for mouse phosphoglycerate kinase 1 promoter, CMV promoter stands for cytomegalovirus immediate-early promoter, CAG (or CAGG) promoter stands for chicken β-Actin promoter coupled with CMV early enhancer. These promoters are constitutive promoters that may be used to drive ectopic gene expression.
UCO and UCOE:
UCOE stands for ubiquitous chromatin opening element. UCO elements prevent silencing of promotors. A UCO element may be placed upstream of a promoter.
Heterozygous for HLA-E:
A cell comprising at least two different alleles for the HLA-E gene, such as comprising a HLA-E*0101 gene and a HLA*0103 gene, is heterozygous for HLA-E.
HSV-TK Genes:
The term “HSV-TK” as used herein stands for Herpes simplex virus (HSV) thymidine kinase (TK) and designates a suicide switch system. The HSV-TK gene encodes a TK enzyme. To trigger suicide of HSV-TK+ cells, ganciclovir is provided to the HSV-TK+ cells or to the organism hosting such cells, the TK enzyme phosphorylates ganciclovir into a toxic compound that inhibits the DNA polymerase and triggers death of HSV-TK+ cells.
Knock-in and Knock-Out:
The term “knock-in” as used herein refers to the insertion of a gene into a genome. With knock-in techniques, the gene insertion is targeted, which means that the gene is inserted into a specific locus, in a location on the genome that has been predefined and is specifically targeted, as opposed to a random gene insertion with other genetic engineering methods.
The term “knock-out” as used herein refers to the deletion or inactivation by disruption of a gene from a genome. To achieve the deletion or disruption of a given gene of interest, knock-out techniques usually require a genetic modification in a specifically targeted location on the genome.
Several knock-in and knock-out techniques exist and are well defined in the art.
Mammalian Cell:
The term “mammalian cell” as used herein means a cell originating from a mammalian living organism, such as a mammalian animal cell or a human cell. The mammalian cell may be at an undifferentiated stage, for example at a pluripotent or multipotent stage, or at a differentiated stage, such as a fully mature stage, or at an intermediate stage of differentiation.
Matching HLA Type:
The term “matching HLA” or “matching HLA type” as used herein means a HLA isotype that is sufficiently similar between a donor cell and a host organism to not induce rejection of the donor cell by the immune system. In mammalians, HLA proteins are unique to individuals. The immune system of a host organism will recognize the “non-matching” HLA proteins on the outer cell surface of a donor cell (e.g. a grafted cell or cells in a grafted organ) as “non-self” (or “invader”) and induce an immune response and rejection of the donor cell. If the HLA proteins of a donor cell are of same or sufficiently similar isotype to the HLA proteins of a host organism, i.e. of matching HLA type with the host organism, the immune system will recognize the donor cells as “self” and will not induce rejection of the donor cell.
Polymorphic:
The term “polymorphic” as used herein means that there exist different isotypes of a given gene within a given cell. The polymorphism in the HLA system allows for a more effective and adaptive immune response.
Protein, Peptide:
Unless otherwise specified, the terms “protein” and “peptide” refer to a functional version thereof.
Safe Harbour:
The term “safe harbour site” or “safe harbour locus” or “safe genomic harbour site” as used herein means a location on the genome that is constantly expressed, that does not get silenced for example due to epigenetic silencing or downregulation of the transcription activity. AAVS1 and hROSA16 are safe harbour sites examples in the human genome. “AAVS1” stands for adeno-associated virus integration site 1 and is located on human chromosome 19. “hROSA26” stands for “human version of Gt(ROSA)26S” or “human version of ROSA26” and is located on human chromosome 3. CLYBL and CCR5 are other possible safe-harbour sites, “CLYBL” stands for “Citrate lyse beta-like” and is located on human chromosome 13, “CCR5” stands for “C—C chemokine receptor type 5” and is located on human chromosome 5.
Universally Implantable Cell, Transplantable Cell, Implantable Cell or Universal Donor Cell:
The terms “universally transplantable/implantable cell” or “universal cell” or “universal donor cell” or “transplantable cell” or “immune-safe cell” or “stealth cell” or “immuno-stealth cell” or “implantable cell” as used herein all designate a cell that can be transplanted into a host organism without being recognized as non-self hence without being rejected by the immune system of the host organism. The cell usually originates from a donor organism that is different from the host organism. A purpose of the present invention is to provide cells that may be safely implanted into a broad variety of patients without being rejected.
Implantable Mammalian Cell and Mammalian Cell:
In the context of the method(s) of the invention, method claims and method embodiments, the term “mammalian cell” refers to a cell prior to completion of the genetic modification(s) of the invention, the term “implantable mammalian cell” refers to a cell comprising the genetic modification(s) of the invention.
illustrates a promoter driving expression of the gene construct.
illustrates a promoter driving expression of the gene construct.
In one aspect the present invention provides a mammalian cell comprising at least one B2M/HLA-E gene wherein said mammalian cell comprises no other expressible B2M genes.
In another aspect the present invention provides a mammalian cell comprising a B2M/HLA-E gene wherein said mammalian cell comprises no other expressible B2M genes and has knock-ins of at least 4 HSV-TK genes at distinct and known locations.
In an embodiment, said mammalian cell comprises B2M/HLA-E genes. In an embodiment, said cell comprises one type of B2M/HLA-E allele, i.e. one HLA-E variant in the B2M/HLA-E fusion. In an embodiment, the HLA-E variant in the B2M/HLA-E fusion(s) is the HLA-E*01:01 allele or is the HLA-E*01:03 allele.
In an embodiment, said mammalian cell comprises two different B2M/HLA-E alleles, i.e. said cell is heterozygous for the B2M/HLA-E gene. In an embodiment, the HLA-E variants in the B2M/HLA-E fusions are the HLA-E*01:01 allele and the HLA-E*01:03 allele.
In one aspect the present invention provides a mammalian cell comprising a B2M/HLA-E*0101 or B2M/HLA-E*0103 fusion gene wherein said mammalian cell comprises no other expressible B2M genes. In one aspect the present invention provides a mammalian cell comprising B2M/HLA-E*0101 and B2M/HLA-E*0103 genes wherein said mammalian cell comprises no other expressible B2M genes.
In the present invention, the B2M/HLA-E*0101 gene encodes a B2M/HLA-E*0101 protein.
In an embodiment, the B2M/HLA-E*0101 protein comprises a B2M protein, a HLA-E*0101 protein and a linker in between the B2M protein and the HLA-E*0101 protein. In an embodiment, the B2M part is located at the N-terminus and the HLA-E part is located at the C-terminus of the B2M/HLA-E*0101 fusion protein.
In an embodiment the B2M/HLA-E*0101 protein also comprises a signal peptide.
In an embodiment, the B2M/HLA-E*0101 protein comprises a signal peptide, a B2M protein, a HLA-E*0101 protein and a linker in between the B2M protein and the HLA-E*0101 protein. In an embodiment, the signal peptide is located at the N-terminus, is followed by the B2M protein and a linker, and the HLA-E protein is located at the C-terminus of the B2M/HLA-E*0101 fusion protein.
In an embodiment, the linker between the B2M protein and the HLA-E*0101 protein is a (G4S)4 linker.
In the present invention, the B2M/HLA-E*0103 gene encodes a B2M/HLA-E*0103 protein. The term “B2M/HLA-E*0103” as used herein is intended to mean a fusion between a beta 2 microglobulin (B2M) and a HLA-E*0103.
In an embodiment, the B2M/HLA-E*0103 protein comprises a B2M protein, a HLA-E*0103 peptide and a linker in between the B2M protein and the HLA-E*0103 peptide. In an embodiment, the B2M part is located at the N-terminus and the HLA-E part is located at the C-terminus of the B2M/HLA-E*0103 fusion protein.
In an embodiment the B2M/HLA-E*0103 protein also comprises a signal peptide.
In an embodiment, the B2M/HLA-E*0103 protein comprises a signal peptide, a B2M protein, a HLA-E*0103 protein and a linker in between the B2M protein and the HLA-E*0103 protein. In an embodiment, the signal peptide is located at the N-terminus, is followed by the B2M protein and a linker, and the HLA-E protein is located at the C-terminus of the B2M/HLA-E*0103 fusion protein.
In an embodiment, the linker between the B2M protein and the HLA-E*0103 is a (G4S)4 linker.
In a preferred embodiment, the B2M/HLA-E*0101 and/or the B2M/HLA-E*0103 fusion proteins retain the ability to further bind an endogenous peptide prior to translocation to the cell surface. That is made possible by the absence of a pre-bound HLA class I leader peptide sequence (such as VMAPRTLIL) as part of said fusion protein. In an embodiment, the B2M/HLA-E*0101 and/or the B2M/HLA-E*0103 fusion proteins do not comprise a pre-bound HLA class I leader peptide sequence.
In an embodiment, the HLA-E*0101 part of the B2M/HLA-E*0101 fusion protein comprises the amino acid sequence [SEQ ID NO:01]:
In an embodiment, the B2M part of the B2M/HLA-E*0101 fusion protein or of the B2M/HLA-E*0103 fusion protein comprises the amino acid sequence [SEQ ID NO:02]:
In an embodiment, the HLA-E*0103 part of the B2M/HLA-E*0103 fusion protein comprises the amino acid sequence [SEQ ID NO:03]:
In an embodiment, the B2M/HLA-E*0101 fusion protein comprising a (G4S)4 linker and a signal peptide comprises the amino acid sequence [SEQ ID NO:04]:
In an embodiment, the B2M/HLA-E*0103 fusion protein comprising a (G4S)4 linker and a signal peptide comprises the amino acid sequence [SEQ ID NO:05]:
In an embodiment, the B2M/HLA-E*0101 gene encoding for a B2M/HLA-E*0101 fusion protein with a (G4S)4 linker and a signal peptide comprises the nucleic acid sequence SEQ ID NO 06:
In an embodiment, the B2M/HLA-E*0103 gene encoding for a B2M/HLA-E*0103 fusion protein with a (G4S)4 linker and a signal peptide comprises the nucleic acid sequence SEQ ID NO 07:
In another aspect the present invention provides a mammalian cell which has knock-ins of both B2M/HLA-E*0101 and B2M/HLA-E*0103 genes into an otherwise B2M deficient cell.
In an embodiment, the B2M/HLA-E gene is inserted at the locus of the native B2M gene, on chromosome 5 in the case of a human cell. In an embodiment, a copy of the B2M/HLA*0101 gene and a copy of the B2M/HLA*0103 gene are inserted on the locus of each of the two copies of the native B2M gene of the cell, thereby inactivating the native B2M gene. An example is illustrated in
In an embodiment, the B2M/HLA gene does not comprise a sequence encoding a pre-bound HLA class I leader peptide, and the B2M/HLA protein does not comprise a pre-bound HLA class I leader peptide.
It has surprisingly been found that the use of both B2M/HLA-E*0101 and B2M/HLA-E*0103 gene fusion constructs which do not comprise a sequence encoding a pre-bound HLA class I leader peptide, into B2M-deficient cells generates the cell surface phenotype of HLA-A/B/C−/− HLA-E*0101+ HLA-E*0103+ cells with both a high and robust HLA-E density, maximum endogenous peptide binding diversity, optimal protection against NK cell mediated non-infected target cell lysis and enhanced recognition and optimal elimination by NK cells of target mammalian cells infected with virus or other pathogen.
The present invention advantageously allows to A) constitutively increase the density of HLA-E proteins on the donor cell surface to inhibit NK cell-mediated rejection of B2M deficient cells, B) retain normal immune surveillance functions of HLA-E via native endogenous peptide binding (resulting in a slight reduction of tolerogenic capacity), C) maximize the diversity of potential endogenous peptides bound to the HLA proteins through inclusion of multiple HLA-E isotypes, and D) mitigate the risk upon viral infection or malignant dedifferentiation that the cells are no longer subject to regular immune surveillance.
To provide increased HLA-E density and achieve advantage A) through a non-native promoter, two, rather than one, alleles of the B2M/HLA-E genes are inserted in the cell. To achieve advantage B), the inventors use a B2M/HLA-E gene encoding a B2M/HLA-E fusion protein that is devoid of pre-engineered, i.e. pre-bound HLA class I leader peptide, and in turn that utilizes native endogenous peptides processing and loading mechanisms. To achieve advantage C) both two major HLA-E alleles, HLA-E*0101 and HLA-E*0103 are utilized. The two encoded HLA-E*0101 and HLA-E*0103 proteins load and present different endogenous peptide subsets, thereby increasing both the likelihood that the HLA proteins will be adequately loaded with tolerogenic endogenous peptide under normal circumstances and with activating endogenous peptide during viral infection. To achieve advantage D) the inventors have introduced 4 copies of the HSV-TK gene serving as a robust switch which can swiftly kill the cells if so desired. The combination of several modifications holds potential for both substantially better cell retention and immune surveillance under conditions of infection.
Advantageously, the combination of normal endogenous peptide loading (by not using a pre-bound peptide) and multiple HLA-E isotypes allows for expanded immune surveillance of the cells for viral and/or bacterial infection while preserving a maximally tolerogenic phenotype. During infection, several peptides from viral or bacterial pathogens can displace the normal endogenous peptides from HLA-E. When HLA-E presents pathogen-derived peptides, it stimulates NK lysis of the infected cell; contrary to HLA-E with a pre-bound peptide which would indicate a “healthy state” to NK cells, would not stimulate NK lysis and thereby provide a tolerance function). This is an important safety feature achieved with the present invention.
In an embodiment, the mammalian cell of the present invention is HLA-II deficient. In an embodiment, the mammalian cell is CIITA deficient.
Any available and relevant gene editing technology (CRISPR, TALEN, ZFN, homing endonuclease, adenoviral recombination, etc.) may be used to modify cells such that both alleles of native B2M are knocked-out while simultaneously one or more copies each of B2M/HLA-E*0101 and B2M/HLA-E*0103 genes are knocked-in.
The knock-in of B2M/HLA-E genes, such as B2M/HLA-E*0101 and B2M/HLA-E*0103 genes, may be accomplished directly over the native B2M gene locus, over other loci, such as safe harbour loci, such as the AAVS1 safe harbour locus, or any combination thereof. Any available promoter may be used for these knock-in genes, for instance a promoter selected from the group consisting of EF1a mini, EF1a, UbC, PGK, CMV and CAG. According to the present invention, the desired increase in HLA-E density is obtained via bi-allelic HLA-E knock-ins controlled by constitutively active promoters. In a native cell, endogenous HLA-E promoters are controlled by promoter INF gamma response elements.
Similarly the HSV-TK genes may be knocked-in at desired locations, i.e. at targeted loci. Any available and relevant gene editing technologies may be used.
Cells of the present invention comprise at least 4 HSV-TK genes at distinct and known locations.
In the present invention, the HSV-TK genes serve as an inducible ‘suicide switch’ system to control survival of the engineered mammalian cell for example in a host organism. The concept of a suicide switch entails genomic introduction of a gene that renders the cell sensitive to an exogenous molecule, that can be administered when needed. The HSV-TK gene encodes a thymidine kinase that converts the common small molecule antiviral drug ganciclovir into a toxic substance within the HSV-TK expressing cell. A problem with such suicide genes is that they could in theory be inactivated or eliminated by spontaneous genomic deletion or promoter slicing, resulting in the loss of the intended control by ‘suicide switch’.
In an embodiment of the invention, HSV-TK suicide genes are placed in safe harbour loci in the genome. In an embodiment of the invention, the expression of HSV-TK is driven by a promoter with an upstream UCO element. In an embodiment of the invention, the expression of HSV-TK suicide genes is driven by a UbC promoter with an upstream UCO element.
In an embodiment of the present invention, four copies of the HSV-TK suicide gene are inserted in the genome of the cell.
In an embodiment of the present invention, the knock-ins of 4 HSV-TK genes, i.e. of 4 copies of the HSV-TK gene, are at distinct locations, i.e. at locations on the genome having some separation such as to provide a safe system which is not amenable to deteriorate due to genetic rearrangements or deletions. In an embodiment the 4 HSV-TK genes are knocked-in on the same chromosome and separated from each other by at least 10 Kbp, such as at least 100 Kbp, at least 1 Mbp or at least 20 Mbp. In another embodiment the 4 HSV-TK genes are knocked-in at locations on 4 different chromosomes. In another embodiment the 4 HSV-TK genes are knocked-in at locations on 3 different chromosomes. In another embodiment the 4 HSV-TK genes are knocked-in at locations on 2 different chromosomes, such as two HSV-TK copies on same location on each both chromosomes 3 and two HSV-TK copies on same location on both chromosomes 19 in a diploid cell. In another embodiment of the present invention 2 HSV-TK genes are knock-in at safe genomic harbour sites. In another embodiment one HSV-TK gene is knocked-in to disrupt and eliminate a B2M allele. In another embodiment one HSV-TK gene is knocked-in to eliminate a CIITA allele.
Patients safety is a very important parameter in cellular therapy.
Inserting 4 copies of TK suicide gene also advantageously increases safety to patients. It was surprisingly found that a cell with 4 copies of TK suicide gene is significantly more sensitive to ganciclovir treatment than a cell with 2 copies, achieving cellular death with lower amounts of ganciclovir.
Placing TK suicide genes at known, predefined locations, advantageously increases safety to patients compared to random integration into a cell genome. Compared to random integration, targeted integration decreases the risk of disruption of important genes or of important gene expression regulation. It also decreases the risk that the suicide genes randomly integrate into a region of suboptimal expression activity. thereby ensures an optimal TK expression level.
Placing TK suicide genes at distinct locations further increases patients' safety by limiting the risk that all TK suicide gene copies get silenced or downregulated at once in the event their insertion loci get exposed to gene silencing or transcription downregulation.
Placing TK suicide genes at safe harbor loci advantageously increases safety to patients. Safe harbor loci are regions of the genome that are constantly expressed. This approach decreases the risk of the suicide genes being involuntarily silenced or downregulated, thereby increases the chance of an optimal expression level of the suicide TK protein at all time and subsequently a controlled cell death when need be upon ganciclovir administration.
It results that placing 4 TK suicide gene copies at known and distinct locations, such as safe harbor loci, provide significantly improved safety for patients receiving cell therapy as per the present invention.
In an embodiment, at least 2 HSV-TK genes are knocked-in in a safe harbour site, such as the AAVS1 gene locus or the hROSA26 gene locus or the CLYBL gene locus. In an embodiment, 2 HSV-TK genes are knocked-in in a safe harbour site, such as the AAVS1 gene locus or the hROSA26 gene locus or the CLYBL gene locus, and 2 HSV-TK genes are knocked-in in the CIITA gene locus.
In another embodiment, 2 HSV-TK genes are knocked-in in a safe harbour site, and 2 HSV-TK genes are knocked-in in another safe harbour site, and the CIITA gene locus is knocked-out. In a more specific embodiment, 2 HSV-TK genes are knocked-in in the AAVS1 gene locus, and 2 HSV-TK genes are knocked-in in the CLYBL gene locus, and the CIITA gene is knocked-out.
In an embodiment, a B2M/HLA-E gene is knocked-in in the loci of the B2M gene, thereby inactivating the cell's native B2M gene. In an embodiment, a B2M/HLA-E*01:01 gene or a B2M/HLA-E*01:03 gene is knocked-in in the loci of the B2M gene, thereby inactivating the cell's native B2M gene. In an embodiment, a B2M/HLA-E*0101 gene is knocked-in in the locus of one copy of the B2M gene, a B2M/HLA-E*0103 gene is knocked-in in the locus of the other copy of the B2M gene, thereby inactivating the cell's native B2M gene. In an embodiment, 2 HSV-TK genes are knocked-in in the loci of the AAVS1 gene and 2 HSV-TK genes are knocked-in in the loci of the CIITA gene, thereby inactivating the cell's native CIITA gene. Inactivation of the cell's native CIITA gene leads to depletion in HLA-II proteins.
In an embodiment, a B2M/HLA-E*0101 gene is knocked-in in the locus of one copy of the B2M gene, a B2M/HLA-E*0103 gene is knocked-in in the locus of the other copy of the B2M gene, 2 copies of the HSV-TK gene are knocked-in in safe harbour loci such as the AAVS1 gene, and 2 HSV-TK genes are knocked-in in the loci of the CIITA gene.
In an embodiment, a B2M/HLA-E*0101 gene is knocked-in in the locus of one copy of the B2M gene, a B2M/HLA-E*0103 gene is knocked-in in the locus of the other copy of the B2M gene, 2 copies of the HSV-TK gene are knocked-in the AAVS1 gene loci, 2 HSV-TK genes are knocked-in in the CLYBL gene loci, and the CIITA gene is knocked-out, i.e. both copies of the CIITA gene are knocked-out.
The 4 HSV-TK genes are preferably expressed to an extent where each of them alone would kill said mammalian cell upon exposure to ganciclovir.
In an embodiment, the HSV-TK protein comprises the amino acid sequence SEQ ID NO: 08:
In an embodiment, the HSV-TK gene encoding a HSV-TK protein comprises the nucleic acid sequence SEQ ID NO 09:
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
The order of the steps may vary where it makes sense. For example, the genetic modification steps and the cell differentiation step(s) may occur in different orders, the knock-in of a B2M/HLA-E gene may occur prior to B2M gene inactivation, the differentiation step may take place prior to B2M/HLA-E gene and/or B2M gene inactivation.
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
whereby said implantable mammalian cell is obtained, is B2M deficient and expresses B2M/HLA-E*0101 and/or B2M/HLA-E*0103 proteins.
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
whereby said implantable mammalian cell is obtained.
In another aspect the present invention provides a method for making an implantable mammalian cell, comprising the steps of:
whereby said implantable mammalian cell is obtained.
It is envisioned that the mammalian cell that is subject to the genetic modifications as per the method of the invention may be at various stage of differentiation and may, as need be, be subject to further differentiation. For example, in case of a stem cell, a pluripotent cell or a cell at an early differentiation stage, this cell may be differentiated to a more advanced differentiation stage, a more mature cell type prior to implantation. The method of the invention might as well be applied to a functional cell type which does not require further differentiation prior to implantation.
In yet another embodiment the present invention provides the use of a mammalian cell according to the invention for the prevention, treatment or cure of a disease such as a chronic disease. It is envisioned that the mammalian cells and the methods of the present invention might be useful in the treatment of a wide range of chronic diseases. It is also envisioned that they might be useful in preventing chronic diseases as well as other diseases.
In an embodiment said disease is selected from the group consisting of diabetes, type 1 diabetes, type 2 diabetes, dry macular degeneration, retinitis pigmentosa, neurological disease, Parkinson's disease, heart disease, chronic heart failure and chronic kidney disease.
In an embodiment, the mammalian cell is an animal cell. In another embodiment, the mammalian cell is a human cell.
In an embodiment, the mammalian cell is an undifferentiated cell. In an embodiment, the mammalian cell is a stem cell, such as a human stem cell, a pluripotent cell, such as a pluripotent human cell or an iPS cell (induced pluripotent stem cell), such as a human iPS cell.
In an embodiment, the mammalian cell of the invention is an undifferentiated cell, such as stem cell, pluripotent cell or iPS cell, that is further differentiated into a functional cell type.
In another embodiment, the mammalian cell is a differentiated cell.
In an embodiment, the mammalian cell is a human differentiated cell derived from a stem cell, from a pluripotent cell or from an iPS cell of the invention.
In particular embodiments of the present invention, the mammalian cell is a differentiated cell selected from the below list.
Said differentiated cell may be derived from a stem cell, a pluripotential cell or an iPS cell of the invention according to one of the differentiation methods described in the publications referred to in the below list:
In an embodiment of the method of the invention, where a differentiation step applies, the mammalian cell is an undifferentiated cell, such as stem cell, pluripotent cell or iPS cell, and is differentiated into a cell selected from the above list.
In an embodiment of the method of the invention, the implantable mammalian cell is a differentiated cell selected from the above list.
Non-limiting embodiments of the invention include:
15. Mammalian cell according to any of the preceding embodiments, wherein said mammalian cell is selected from the group consisting of a neuron, a cardiomyocyte, retinal cell, a retinal pigment epithelium cell and a beta cell.
Description
An undifferentiated parental hESC (Human Embryonic Stem Cell) cell line (WT), a hESC cell line with 2 copies of the HSV-TK gene (2×HSV-TK), and a hESC cell line with 4 copies of the HSV-TK gene (4×HSV-TK) were plated on hFN (human fibronectin coating). The cells were seeded at 60.000 cells/well in 24 wells format dishes and cultured overnight in DEF-CS media. The cells were then cultured in DEF-CS media containing ganciclovir (GCV) at 5 different concentrations for 7 days: 0, 1, 12.5, 25, 50 or 100 □M. DEF-CS media containing ganciclovir was changed every day. The cells were passaged 1:2 in DEF-CS with ganciclovir, when they reached 90% confluency. After 7 days in culture the cells were stained with DAPI and images were captured. The result images are shown in
Cells having four copies of HSV-TK at distinct sites in the genome are more sensitive toward ganciclovir, than cells only having two copies of HSV-TK at distinct sites in the genome.
Human embryonic stem cells (SA121) are electroporated with a total of 500 ng TALEN® mRNA pair (ThermoFisher®, forward target sequence:
TTCTGTCACCAATCCTGT) against AAVS1 and 500 ng donor plasmid containing 300 bp homology arms flanking the TALEN® cut site in AAVS1, an HSV-TK cassette followed by a mCherry selection cassette. The cells are cultured for a week and the mCherry positive cells are bulk sorted using a FACS cell sorter. The cells are cultured for an additional week before they are electroporated with a total of 500 ng TALEN® mRNA pair (ThermoFisher®, forward target sequence:
GAAAGTCTTCTCCTCCAA) against CLYBL and 500 ng donor plasmid containing 300 bp homology arms flanking the TALEN® cut site in CLYBL, a HSV-TK cassette followed by a eGFP selection cassette. Cells are cultured for one week and the mCherry/eGFP double positive cells are bulk sorted using a FACS cell sorter. The cells are cultured for an additional week before they are electroporated with 100 ng Cre recombinase mRNA to excise the selection cassettes. The mCherry/eGFP double negative cells are single cell sorted into a 96 well plate using a FACS cell sorter and cultured in for two to four weeks. The cell clones are screened for targeted bi-allelic integration using PCR.
A clone containing four HSV-TK copies from the protocol above is electroporated with a total of 200 ng TALEN® mRNA pair (ThermoFisher®, forward target sequence: TCTCGCTCCGTGGCCTT, reverse target sequence: AGCCTCCAGGCCAGAAAG) against B2M and 200 ng donor plasmid containing 300 bp homology arms flanking the TALEN® cut site in B2M, a B2M-HLAIE01:01 fusion cassette followed by a mCherry selection cassette and 200 ng donor plasmid containing 300 bp homology arms flanking the TALEN® cut site in B2M, a B2M-HLAIE01:03 fusion cassette followed by a eGFP selection cassette. Cells are cultured for one week and the mCherry/eGFP double positive cells are bulk sorted using a FACS cell sorter. The cells are cultured for an additional week before they are electroporated with 100 ng Cre recombinase mRNA to excise the selection cassettes. The mCherry/eGFP double negative cells are single cell sorted into a 96 well plate using a FACS cell sorter and cultured in for two to four weeks. The cell clones are screened for targeted mono-allelic integration using PCR
All the electroporation's are done using the 10 uL Neon transfection kit according the manufactures instructions (ThermoFisher®#MPK1025, Puls voltage 1100V, Pulse width 20, Pulse no 2, 4e5 cells).
Cells are cultured in DEF-CS according to manufacturer's instructions (Takare®#Y30017).
| Number | Date | Country | Kind |
|---|---|---|---|
| 19182963.9 | Jun 2019 | EP | regional |
| 19218122.0 | Dec 2019 | EP | regional |
| 20170447.5 | Apr 2020 | EP | regional |
This application is a Continuation of International Application PCT/EP2020/067995, filed Jun. 26, 2020, which claims priority to European Patent Applications 19182963.9, filed Jun. 27, 2019, 19218122.0, filed Dec. 19, 2019, and 20170447.5, filed Apr. 20, 2020; the contents of which are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/EP2020/067995 | Jun 2020 | US |
| Child | 17069896 | US |
