WO2022167798A1 - Molecule - Google Patents
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- WO2022167798A1 WO2022167798A1 PCT/GB2022/050280 GB2022050280W WO2022167798A1 WO 2022167798 A1 WO2022167798 A1 WO 2022167798A1 GB 2022050280 W GB2022050280 W GB 2022050280W WO 2022167798 A1 WO2022167798 A1 WO 2022167798A1
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- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2510/00—Genetically modified cells
Definitions
- the present invention relates a molecule capable of down-regulating the expression of Fas at the cell surface.
- Adoptive immunotherapy of cancer involves the ex vivo generation of cancer-antigen specific cells and their administration.
- Adoptively transferred immune effector cells also activate existing adaptive and innate immune cells within the tumour once they activate and start causing inflammation.
- the native specificity of immune effector cells can be exploited in adoptive immunotherapy – for example during the generation of melanoma specific T-cells from expansion of tumour infiltrating lymphocytes in tumour resections. Otherwise a specificity can be grafted onto a T-cell using genetic engineering.
- CARs chimeric antigen receptors
- TCRs transgenic T-cell receptors
- Adoptive immunotherapy has been successful in treating a number of lymphoid malignancies, such as B-cell Acute Lymphoblastic Leukaemia (B-ALL), Diffuse Large B-cell Lymphoma (DLBCL) and Multiple Myeloma (MM). Avoiding Fas/Fas-L mediated killing of immune effector cells
- B-ALL B-cell Acute Lymphoblastic Leukaemia
- DLBCL Diffuse Large B-cell Lymphoma
- MM Multiple Myeloma
- TME tumour microenvironment
- the TME is immunosuppressive and can inhibit the persistence and survival of immune cells in cancer immunotherapies, such as CAR T cell therapy.
- Immunosuppressive mechanisms employed by the TME include e.g., upregulating immune checkpoint signals such as PDL-1 and/or CTLA-4 and secretion of cytokines such as IL-6 and/or TGF-beta.
- the immunosuppressive TME also upregulates death ligands such as Fas ligand (FasL). FasL induces apoptosis of immune cells that express death receptors for Fas, such as tumour-infiltrating lymphocytes (TILs).
- TILs tumour-infiltrating lymphocytes
- CAR-T cells themselves also upregulate death receptors and their ligands upon activation and transduction of the CAR construct, triggering activation-induced death (AICD) and further exacerbating the problem of CAR-T cell persistence in the TME.
- AICD activation-induced death
- FasL is not only expressed by activated T cells bit is also upregulated by exposure to IFN ⁇ that is produced by activated T cells.
- third generation CARs which have two co-stimulatory endodomains, seem to be particularly susceptible to AICD as a result of increased FasL expression (Xu et al., 2017, Hum Vaccin Immunother. 13(7):1548-1555, Benmebarek et al., 2019, In J Mol Sci.20(6): 1283).
- Fas signals via non-apoptotic cascades and it has been shown that when naive and memory T cells are mixed prior to adoptive transfer, na ⁇ ve T cells undergo precocious differentiation which limits their anti-tumour efficacy. This effect is mediated by non-apoptotic, AKT-driven Fas signalling on memory CD8 T cells.
- Fas binding to FasL triggers receptor trimerization and recruitment of Fas-associated death domain (FADD) via homotypic interactions of their death domains (DDs).
- FADD then recruits procaspase-8 to the activated receptor and the resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation, which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis.
- FasL has been reported to be expressed by many cancers including melanomas, lung carcinomas, hepatocellular carcinomas, esophageal carcinomas and colon carcinomas.
- Tumour endothelial cells which line blood vessels and control blood and nutrient flow and trafficking of leukocytes, have been shown to express FasL, whereas normal vasculature do not.
- FasL is expressed by myeloid-derived suppressor cells (MDSC). MDSC are a heterogenous populations of cells that expand during cancer, chronic inflammation, autoimmune and infectious diseases, and dampen down the immune response thereby promoting tumour growth. FasL is also reportedly expressed by cancer-associated fibroblasts (CAFs) and CD4+CD25+ regulatory T cells. FasL is also expressed by T cells themselves and has been shown to be further upregulated in CAR-Ts, meaning a) CAR T cells are susceptible to fratricide, but also b) CAR-T cells can kill Fas-expressing tumour cells by virtue of the Fas-FasL interaction.
- CAFs cancer-associated fibroblasts
- FasL is also expressed by T cells themselves and has been shown to be further upregulated in CAR-Ts, meaning a) CAR T cells are susceptible to fratricide, but also b) CAR-T cells can kill Fas-expressing tumour cells by virtue of the Fas-FasL interaction.
- an antibody blockade has previously been described as a way of preventing T-cell apoptosis, using anti-Fas antibodies (Gargell et al (2016) Mol. Ther. 24: 1135-1149) or anti-FasL antibodies (Motz et al (2014) Nat. Med. 20:607-615).
- Other groups have used genetic modification to knock-down or knock out Fas expression, for example using siRNA (Dotti et al (2005) Blood 105:4677-4684) or CRISPR/Cas9 (Ren et al (2017) Oncotarget 8:17002-17011).
- a disadvantage of the dominant negative Fas receptor approach is that dominant negative Fas competes with endogenous Fas for incorporation into a trimeric structure, so high expression levels are needed to reduce or block Fas-mediated signalling.
- dominant negative Fas receptors ligate and sequester FasL within the cell, preventing FasL mediated killing of target cells by CAR-T cells. There is thus a need for mechanisms to prevent FASL-induced death and improve the effectiveness of engineered immune effector cells to persist and survive in the TME which are not associated with the disadvantages mentioned above.
- FIGURES Annotated sequence for an example of a bicistronic construct co- expressing an anti-Fas KDEL with FasL: Anti-Fas-KDEL–2A–FasL
- Figure 2 Schematic diagram showing Fas/FasL-mediated induction of apoptosis. Expression of a dominant negative Fas receptor with a truncated Death Domain (Fas ⁇ DD) which does not bind FADD competes with endogenous Fas for binding FasL blocking or reducing apoptosis.
- Figure 3 Schematic diagram illustrating the intracellular retention of Fas using an anti-Fas-KDEL molecule.
- the Fas receptor is synthesised at the rough endoplasmic reticulum (ER) and transported to the plasma membrane via the Golgi apparatus.
- the anti-Fas-KDEL polypeptide binds to the extracellular domain on Fas and consequently Fas is retained at the ER via the KDEL receptor recognising the KDEL sequence. Fas molecules that are trafficked to the Golgi apparatus (to eventually be transported to the plasma membrane) are trafficked back to the ER by retrograde transport via the KDEL receptor recognising the KDEL sequence.
- Figure 4 Fas staining histograms of PBMCs and SupT1 cells transduced with the Fas binder-KDEL polypeptide demonstrating decreased staining of Fas when transduced with the Fas binder-KDEL polypeptide.
- Figure 5 Two independent PBMC donors and SupT1 cells that were either non- transduced (NT) or transduced to express a Fas binder-KDEL polypeptide, were either untreated or treated with MEGA FasL (100 ng/mL) for 48 hours, at which point cells were analysed by flow cytometry.
- NT non- transduced
- MEGA FasL 100 ng/mL
- the raw flow cytometry plots are shown in (A), with the percentage of surviving BFP positive PBMCs and SupT1s made relative to untreated conditions shown in (B).
- Figure 6 Two independent PBMC donors that were either non-transduced (NT) or transduced to express a Fas binder-KDEL polypeptide, were co-cultured with NT SupT1 cells or FasL-expressing SupT1 cells at a 1:2 PBMC:SupT1 ratio for 48 hours, at which point cells were analysed by flow cytometry.
- Raw flow cytometry plots are shown in (A) with PBMCs identified from SupT1 cells through dual expression of CD2 and CD3.
- the present invention provides a molecule which comprises i) a binding domain which binds to a FAS extracellular domain and ii) a retention domain that intracellularly retains FAS within the endoplasmic reticulum or Golgi apparatus.
- the binding domain may comprise a native FAS ligand (FASL), single chain variable fragment (scFv), a single domain antibody (sdAb), a Fab antigen binding domain (Fab) or a monoclonal antibody.
- FSL native FAS ligand
- scFv single chain variable fragment
- sdAb single domain antibody
- Fab Fab antigen binding domain
- a single domain antibody may, for example, be derived from an artificial VHH fragment or a camelid antibody.
- the retention domain may be C-terminal to the binding domain.
- the retention domain may comprise a sequence selected from the group consisting of: NPX’Y, YX’X’Z, [DE]X’X’X'L[LI], DX’X’LL, DP[FW], FX’DX’F, NPF, LZX’Z[DE], LLDLL, PWDLW, KDEL, HDEL, KKX’X’ or KX’KX’X’; wherein X’ is any amino acid and Z’ is an amino acid with a bulky hydrophobic side chain.
- the retention domain may, for example, comprises a sequence shown in Tables 1 to 5.
- the present invention provides a nucleic acid sequence encoding a molecule according to any of the preceding claims wherein the nucleic acid sequence encodes molecule according to the first aspect of the invention.
- the present invention provides a nucleic acid construct comprising a first nucleic acid sequence which encodes at least one polypeptide of interest (POI) and a second nucleic acid sequence according to the second aspect of the invention.
- the first and second nucleic acid sequences may be separated by a third nucleic acid sequence encoding a coexpression peptide.
- the present invention provides a kit of nucleic acid sequences comprising: (a) a first nucleic acid sequence which encodes at least one POI, and (b) a second nucleic acid sequence which encodes a molecule according to the first aspect of the invention.
- the present invention provides a vector comprising the nucleic acid sequence according to the second aspect of the invention or a nucleic acid construct according to the third aspect of the invention.
- the POI may be, for example, a chimeric antigen receptor or a T-cell receptor, such that when the vector is used to transduce a target cell, the target cell co-expresses a molecule according to the first aspect of the invention and a chimeric antigen receptor or T-cell receptor.
- the present invention provides a kit of vectors comprising: (i) a first vector comprising a nucleic acid encoding at least one POI; and (ii) a second vector comprising a nucleic acid which encodes a molecule according to the first aspect of the invention.
- the present invention provides a cell expressing a molecule according to the first aspect of the invention. The cell may also express at least one POI.
- the present invention provides a pharmaceutical composition which comprises a plurality of cells according to the seventh aspect of the invention.
- the present invention provides a pharmaceutical composition according to the eighth aspect of the invention for use in treating and/or preventing a disease.
- the present invention provides a method for treating and/or preventing a disease, which comprises the step of administering a pharmaceutical composition according to the eight aspect of the invention to a subject in need thereof.
- the method may comprise the following steps: (i) isolation of a cell containing sample; (ii) transduction or transfection of the cell with a nucleic acid sequence according to the second aspect of the invention; a nucleic acid construct according to the thris aspect of the invention, a vector according to the fourth aspect of the invention, or a kit of vectors according to the fifth aspect of the invention; and (iii) administering the cells from (ii) to a subject.
- the cell may be autologous or allogenic.
- the present invention provides a use of a pharmaceutical composition according to paragraph 16 in the manufacture of a medicament for the treatment and/or prevention of a disease.
- the disease may be cancer.
- the present invention provides a method for making a cell according to the seventh aspect of the invention, which comprises the step of introducing: a nucleic acid sequence according to the second aspect of the invention; a nucleic acid construct according to the thris aspect of the invention, a vector according to the fourth aspect of the invention, or a kit of vectors according to the fifth aspect of the invention into the cell ex vivo.
- the cell may be from a sample isolated from a subject.
- the molecule of the invention provides a novel mechanism by which to block FasL- Fas pathway within the TME.
- the molecule of the present invention is very efficient at low cell expression levels. Secondly, the molecule does not ligate and sequester FasL, allowing for FasL mediated killing of target cells. This is particularly evident when the molecule is co-expressed with for example, a Chimeric Antigen Receptor (CAR) because the approach overcomes FAS-included CAR T cell apoptosis and improves CAR-T cell infiltration via tumour vasculature and persistence within the TME.
- CAR Chimeric Antigen Receptor
- a method for selecting for cells transduced to express a nucleic acid sequence of interest which comprises the following steps: (a) transducing a population of cells with a vector co-expressing (i) the NOI and (ii) a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; (b) exposing the cells from (a) to FasL such that untransduced cells are eliminated by apoptosis. 2.
- FasL is soluble FasL, FasL bound to a solid substrate, or FasL expressed on the surface of a cell. 3.
- a method which comprises the following steps: (a) transducing a population of cells with a vector co-expressing (i) the NOI, (ii) the nucleic acid sequence encoding the molecule which comprises a Fas-binding domain linked to an intracellular retention signal and (iii) a nucleic acid sequence encoding FasL; (b) culturing the cells, thereby self-selecting for cells transduced with the vector. 6.
- a method which comprises the following steps: (a) co-transducing a population of cells with: a first vector co-expressing (i) a CAR or TCR; and (ii) the nucleic acid sequence encoding the molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and a second vector expressing FasL (b) culturing the cells, thereby selecting for cells transduced with the first vector, together with cells co-transduced with the first and second vector. 7.
- the second vector also comprises a nucleic acid sequence encoding a cytokine.
- the mutant FasL has reduced susceptibility to metalloprotease cleavage.
- the mutant FasL comprises a deletion of amino acid residues 126-135, or a deletion of amino acid residues 126- 145, with reference to the sequence shown as SEQ ID No.7.
- the cell expresses FasL which comprises a signalling domain and/or a costimulatory domain. 12.
- CAR chimeric antigen receptor
- TCR transgenic T cell receptor
- NOI encodes: (i) a TCR or CD3-binding domain linked to an intracellular retention signal; (ii) a gRNA molecule comprising a targeting domain that is complementary with a target domain in a TCR gene; or (iii) an siRNA complementary with a target domain in a TCR gene.
- a cell engineered to express (a) nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and (b) FasL 17.
- a cell according to paragraph 16 which also expresses (c) a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) and/or a nucleic acid sequence of interest (NOI) which inhibits expression of endogenous T-cell receptor (TCR).
- a cell according to paragraph 17 which expresses a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR), wherein the CAR or TCR-expressing nucleic acid is introduced into the FAS gene, knocking-out FAS gene expression.
- a nucleic acid construct for expression in a cell which comprises: a nucleic acid sequence encoding a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) and/or a nucleic acid sequence of interest (NOI) which inhibits expression of endogenous T-cell receptor (TCR); a nucleic acid sequence encoding FasL; and a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal.
- CAR chimeric antigen receptor
- TCR transgenic T cell receptor
- NOI nucleic acid sequence of interest
- a kit of vectors which comprises: (a) a first vector which comprises: a nucleic acid sequence encoding a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) and/or a nucleic acid sequence of interest (NOI) which inhibits expression of endogenous T-cell receptor (TCR); and a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and (b) a second vector which comprises a nucleic acid sequence encoding FasL.
- a first vector which comprises: a nucleic acid sequence encoding a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) and/or a nucleic acid sequence of interest (NOI) which inhibits expression of endogenous T-cell receptor (TCR); and a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and (b)
- a cell according to paragraph 42 which also expresses a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) 29.
- a method for making a cell according to any of paragraphs 16 to 23, 27 or 28 which comprises the step of introducing into a cell ex vivo: a nucleic acid construct according to paragraph 24, a vector according to paragraph 25, or a kit of vectors according to paragraph 26.
- a pharmaceutical composition which comprises plurality of cells selected by a method according to any of paragraphs 1 to 15 or a plurality of cells according to any of any of paragraphs 16 to 23, 27 or 28.
- a method for treating cancer which comprises the step of administering a pharmaceutical composition according to paragraph 30 to a subject. 32.
- a method for treating cancer in a subject which comprises cancer cells negative for CAR or TCR target antigen which comprises the step of administering a plurality of cells according to any of paragraphs 16 to 23, 27 or 28 to the subject, such that target-antigen negative cancer cells are killed by FasL binding to Fas on the cancer cells. 35.
- a method for depleting alloreactive immune cells from a population of immune cells which comprises the step of contacting the population of immune cells with a plurality of cells according to any of paragraphs any of paragraphs 16 to 23, 27 or 28 in vitro.
- 36. A method for preventing graft versus host disease in a subject, which comprises the step of administering a plurality of cells selected by a method according to any of paragraphs 1 to 25, to the subject.
- 37. An allogeneic or autologous transplant which has been depleted of untransduced cells by a method according to any of paragraphs 1 to 15. 38.
- a method for preventing graft rejection in a subject which comprises the step of administering a plurality of cells according to any of any of paragraphs 16 to 23, 27 or 28, to the subject.
- the present invention provides a molecule which comprises a Fas-binding domain linked to an intracellular retention signal. When this molecule is expressed in a cell, it binds newly synthesised Fas and retains it in an intracellular compartment or complex, down-regulating the cell surface expression of Fas.
- the Fas receptor also known as Fas, FasR, CD95, tumour necrosis factor receptor superfamily member 6
- Fas receptor also known as Fas, FasR, CD95, tumour necrosis factor receptor superfamily member 6
- Fas receptor is a type 1 transmembrane glycoprotein receptor which is localized on the surface of various cells including lymphocytes and hepatocytes.
- Fas receptor triggers a signal transduction pathway leading to apoptosis and expression of Fas can be increased by activation of lymphocytes as well as by cytokines such as IFN ⁇ and TNF.
- cytokines such as IFN ⁇ and TNF.
- FasL/CD95L ligand FasL
- Both Fas and FasL are members of the TNF-R superfamily, all of which contain one to five extracellular cysteine rich domains (CRDs), and in their cytoplasmic tail, a death domain (DD), which are 80-100 residue long motifs.
- Fas binding to FasL triggers receptor trimerization and recruits a protein called Fas- associated death domain (FADD) via homotypic interactions of their death domains (DDs).
- FADD then recruits procaspase-8 to the activated receptor and the resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation, which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis (see Figure 2).
- FasL has been reported to be expressed by many cancers themselves such as melanomas, lung carcinomas, hepatocellular carcinomas, esophageal carcinomas and colon carcinomas.
- FasL is expressed by myeloid-derived suppressor cells (MDSC). MDSC are a heterogenous populations of cells that expand during cancer, chronic inflammation, autoimmune and infectious diseases, and dampen down the immune response thereby promoting tumour growth. FasL is also reportedly expressed by cancer-associated fibroblasts (CAFs) and CD4+CD25+ regulatory T cells. FasL is also expressed by T cells themselves and has been shown to be further upregulated in CAR-Ts, meaning CAR T cells themselves are susceptible to fratricide.
- CAFs cancer-associated fibroblasts
- FasL is also expressed by T cells themselves and has been shown to be further upregulated in CAR-Ts, meaning CAR T cells themselves are susceptible to fratricide.
- FasL is not only expressed by activated T cells but is also upregulated by exposure to IFN ⁇ that is produced by activated T cells.
- T cells that are constantly activated die through a mechanism called activation-induced cell death (AICD), and the Fas-FasL pathway has been characterised as the cause of this.
- AICD activation-induced cell death
- third generation CAR-T cells are more susceptible to AICD as a result of increased FasL expression.
- sequence of human Fas is available from Uniprot (Accession No. P25445) and shown below as sequence ID No. 1. In this sequence, residues 26-173 form the extracellular domain (SEQ ID No.
- SEQ ID No.1 human Fas
- MLGIWTLLPLVLTSVARLSSKSVNAQVTDINSKGLELRKTVTTVETQNLEGLHHDGQ FCHKPCPPGERKARDCTVNGDEPDCVPCQEGKEYTDKAHFSSKCRRCRLCDEGH GLEVEINCTRTQNTKCRCKPNFFCNSTVCEHCDPCTKCEHGIIKECTLTSNTKCKEE GSRSNLGWLCLLLLPIPLIVWVKRKEVQKTCRKHRKENQGSHESPTLNPETVAINLS DVDLSKYITTIAGVMTLSQVKGFVRKNGVNEAKIDEIKNDNVQDTAEQKVQLLRNWH QLHGKKEAYDTLIKDLKKANLCTLAEKIQTIILKDITSDSENSNFRNEIQSLV SEQ ID No.2 (Fas extracellular domain) QVTDINSKGLELRKTVTTVETQNLEGLHHDGQFCHKPCPPGERKARDCTVNGDEPD CVPCQEGKEYTDKA
- the cell of the present invention comprises a nucleic acid sequence which inhibits Fas expression in the cell.
- the nucleic acid sequence encodes a molecule comprising Fas-binding domain linked to an intracellular retention signal FAS-KDEL
- the present invention provides a molecule which comprises a Fas-binding domain linked to an intracellular retention signal.
- the molecule may comprise i) a binding domain which binds to a FAS extracellular domain and ii) a retention domain that intracellularly retains FAS within the endoplasmic reticulum or Golgi apparatus.
- the retention domain may be C-terminal to the binding domain.
- FAS BINDING DOMAIN The Fas-binding domain may be a protein or polypeptide chain which is capable of binding to Fas.
- the Fas-binding domain may comprises an antibody, an antibody fragment or antigen binding fragment, a single-chain variable fragment (scFv), a domain antibody (dAb), a Fab antigen binding domain (Fab), a single domain antibody (sdAb), a VHH/nanobody, a nanobody, an affibody, a fibronectin artificial antibody scaffold, an anticalin, an affilin, a DARPin, a VNAR, an iBody, an affimer, a fynomer, an abdurin/ nanoantibody, a centyrin, an alphabody or a nanofitin which binds to Fas.
- scFv single-chain variable fragment
- dAb domain antibody
- Fab Fab antigen binding domain
- sdAb single domain antibody
- the Fas-binding domain may be or comprise a domain antibody (dAb) or a single-chain variable fragment (scFv).
- dAb domain antibody
- scFv single-chain variable fragment
- a single domain antibody may, for example, be derived from an artificial VHH fragment or a camelid antibody
- the Fas-binding domain may bind the extracellular domain of Fas.
- the target- binding domain may bind the sequence shown as SEQ ID No.2. Apoptosis is induced when FasL binds to the Fas receptor.
- An anti-Fas retaining polypeptide which binds to the extracellular domain of Fas has the additional advantage that, in addition to downregulating the expression of Fas at the cell surface, it also directly blocks the interaction of FasL to Fas for any residual Fas expressed at the cell surface inhibiting the induction of apoptosis.
- Numerous Fas-binding antibodies are known in the art.
- WO2010/102792 describes the anti-Fas antibody F45D9.
- the VH and VL domains from this antibody are shown below as SEQ ID No.5 and 6 respectively.
- the Fas-binding domain of the molecule of the present invention may comprise an antibody or fragment thereof which binds Fas, such as an scFv comprising the VH and VL sequences shown as SEQ ID No.5 and 6.
- the Fas-binding domain may comprise all or part of Fas ligand (FasL), the natural ligand for FAS.
- Human FasL has the sequence shown as SEQ ID No.7.
- the Fas-binding domain may comprise all of FasL or a portion thereof.
- the Fas- binding domain may comprise FasL, FasL extracellular domain (shown below as SEQ ID No.
- a variant FasL extracellular domain may have 80%, 85%, 90%, 95% or 99% identity with the sequence shown as SEQ ID No. 8, provided that the variant sequence retains the capacity to bind Fas.
- FasL is a type II transmembrane protein, so the C-terminus is extracellular.
- the molecule of the present invention may comprise a signal sequence on the N- terminus, followed by the FasL ectodomain, then an intrcellular retention sequence (such as a KDEL-containing sequence) on the C-terminus.
- an intrcellular retention sequence such as a KDEL-containing sequence
- Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion. This delivery process is carried out based on sequence information contain in the protein itself. Proteins synthesised in the rough endoplasmic reticulum (ER) of eukaryotic cells use the exocytic pathway for transport to their final destinations. Proteins lacking special sorting signals are vectorially transported from the ER via the Golgi and the trans- Golgi network (TGN) to the plasma membrane. Other proteins have targeting signals for incorporation into specific organelles of the exocytic pathway, such as endosomes and lysosomes.
- ER endoplasmic reticulum
- TGN trans- Golgi network
- Lysosomes are acidic organelles in which endogenous and internalised macromolecules are degraded by luminal hydrolases. Endogenous macromolecules reach the lysosome by being sorted in the TGN from which they are transported to endosomes and then lysosomes.
- the targeting signals used by a cell to sort proteins to the correct intracellular location may be exploited by the present invention.
- the signals may be broadly classed into the following types: i) endocytosis signals ii) Golgi retention signals iii) TGN recycling signals iv) ER retention signals v) lysosomal sorting signals
- the intracellular retention signal may direct the transmembrane protein away from the secretory pathway during translocation from the ER.
- the intracellular retention signal may direct the transmembrane protein to an intracellular compartment or complex.
- the intracellular retention signal may direct the transmembrane protein to a membrane-bound intracellular compartment.
- the intracellular retention signal may direct the protein to a lysosomal, endosomal or Golgi compartment (trans-Golgi Network, ‘TGN’).
- TGN Trans-Golgi Network
- Lysosomes are cellular organelles that contain acid hydrolase enzymes that break down waste materials and cellular debris. The membrane around a lysosome allows the digestive enzymes to work at the pH they require. Lysosomes fuse with autophagic vacuoles (phagosomes) and dispense their enzymes into the autophagic vacuoles, digesting their contents.
- An endosome is a membrane-bounded compartment inside eukaryotic cells.
- the Golgi apparatus is part of the cellular endomembrane system, the Golgi apparatus packages proteins inside the cell before they are sent to their destination; it is particularly important in the processing of proteins for secretion.
- sorting signals include those from the transferrin receptor and the asialoglycoprotein receptor.
- endocytosis signals include those from the transferrin receptor and the asialoglycoprotein receptor.
- signals which cause TGN-endosome recycling include those form proteins such as the CI- and CD-MPRs, sortilin, the LDL-receptor related proteins LRP3 and LRP10 and ⁇ -secretase, GGA1-3, LIMP-II, NCP1, mucolipn-1, sialin, GLUT8 and invariant chain.
- TGN retention signals include those from the following proteins which are localized to the TGN: the prohormone processing enzymes furin, PC7, CPD and PAM; the glycoprotein E of herpes virus 3 and TGN38.
- ER retention signals include C-terminal signals such as KDEL (SEQ ID No.9), KKXX (SEQ ID No.10) or KXKXX (SEQ ID No.11) and the RXR(R) (SEQ ID No.12) motif of potassium channels.
- Known ER proteins include the adenovirus E19 protein and ERGIC53.
- lysosomal sorting signals include those found in lysosomal membrane proteins, such as LAMP-1 and LAMP-2, CD63, CD68, endolyn, DC-LAMP, cystinosin, sugar phosphate exchanger 2 and acid phosphatase.
- the molecule of the present invention comprises a Fas-binding domain coupled to an intracellular retention signal. Intracellular retention signals are well known in the art (see, for example, Bonifacino & Traub; Annu. Rev. Biochem.; 2003; 72; 395-447).
- intracellular retention signal refers to an amino acid sequence which directs or maintains the protein in which it is encompassed to a cellular compartment other than that to which it would be directed in the absence of the intracellular retention signal.
- the intracellular retention signal directs or maintains nascent Fas to a cellular compartment other than the cell surface membrane.
- the intracellular retention signal may be any protein or protein domain which is a resident of a given intracellular compartment. This means that said protein or domain is in majority, located in a given compartment. At least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% of said protein or domain is located in said compartment in a cell.
- compartment refers to a given subdomain of cell.
- a compartment may be an organelle (such as endoplasmic reticulum, Golgi apparatus, endosome, lysosome) or an element of an organelle (such as multi-vesicular bodies of endosomes, cis-medial-or trans- cisternae of the Golgi apparatus etc.) or the plasma membrane or sub-domains of the plasma membrane (such as apical, basolateral, axonal domains) or micro domains such as focal adhesions or tight junctions.
- intracellular compartment refers to a compartment within a cell.
- endogenous Fas may be retained within the cell or within a specific intracellular compartment by the interaction with the Fas binding domain of the molecule of the invention which binding domain is coupled to an intracellular retention signal.
- the intracellular retention signal may direct the protein to a Golgi (trans-Golgi Network, “TGN”), endosomal or lysosomal compartment.
- the intracellular retention signal may be selected from the following group: a Golgi retention sequence; a trans-Golgi network (TGN) recycling signal; an endoplasmic reticulum (ER) retention sequence; a proteasome localization sequence or a lysosomal sorting signal.
- the intracellular retention signal may be a protein or domain which is resident in the Golgi.
- the Golgi retention domain may be selected from the group comprising: Giantin (GolgB1, GenBank Accession number NM+004487.3), TGN38/46, Menkes receptor and Golgi enzymes such as ManII ( ⁇ -1,3-1,6 mannosidase, Genbank accession number NM_008549), Sialyl Transferase ( ⁇ - galactosamide ⁇ 2,6-sialytransferae 1, NM_003032), GalT ( ⁇ -1,4- galactosyltransferase 1, NM_001497) adenoviral E19, HLA invariant chain or fragments thereof comprising the localisation domains.
- the Golgi retention sequence comprises an amino acid sequence selected from: SEKDEL (SEQ ID NO: 13), KDEL (SEQ ID NO: 9), KKXX (SEQ ID NO: 10), KXKXX (SEQ ID NO: 11), a tail of adenoviral E19 protein comprising the sequence KYKSRRSFIDEKKMP (SEQ ID NO: 14), a fragment of HLA invariant chain comprising the sequence MHRRRSRSCR (SEQ ID NO: 15), KXD/E (SEQ ID NO: 16) or a YQRL (SEQ ID NO: 17) or variants thereof which retain the ability to function as Golgi retention sequences, wherein X is any amino acid.
- the intracellular retention sequence may comprise a SEKDEL (SEQ ID NO: 13) or KDEL (SEQ ID NO: 9) sequence.
- the KDEL sequence in the Fas-retaining molecules described in the Examples of the present application has the sequence DPAEPSEKDEL (SEQ ID No. 18).
- the KDEL receptor binds protein in the ER-Golgi intermediate compartment, or in the early Golgi and returns them to the ER. Proteins only leave the ER after the KDEL sequence has been cleaved off. Thus the protein resident in the ER will remain in the ER as long as it contains a KDEL sequence. This is illustrated schematically in Figure 3.
- the intracellular retention sequence may be located at the C-terminus of the molecule.
- the molecule of the invention is encoded by a nucleic acid sequence which is part of a bicistronic (or multi-cistronic) nucleic acid construct
- the intracellular retention sequence encoding sequence is not located immediately upstream/5’ of a sequence encoding a self-cleaving peptide (such as a 2A or 2A-like peptide).
- KKX’X’ and KX’KX’X’ signals are retrieval signals which can be placed on the cytoplasmic side of a type I membrane protein. Sequence requirements of these signals are provided in detail by Teasdale & Jackson (Annu. Rev. Cell Dev. Biol.; 12; 27 (1996)).
- the retention signal may be a KKXX (SEQ ID NO: 10) motif.
- the KKXX domain may be located that the C terminus of the protein.
- KKXX is responsible for retrieval of ER membrane proteins from the cis end of the Golgi apparatus by retrograde transport, via interaction with the coat protein (COPI) complex.
- the intracellular retention signal may be from the adenovirus E19 protein.
- the intracellular retention signal may be from the protein E3/19K, which is also known as E3gp 19 kDa; E19 or GP19K.
- the intracellular retention signal may comprise the full cytosolic tail of E3/19K; or the last 6 amino acids of this tail.
- the retention signal may be a tail of adenoviral E19 protein comprising the sequence KYKSRRSFIDEKKMP (SEQ ID NO: 14).
- the retention signal may be a tail of adenoviral E19 protein comprising the sequence: DEKKMP (SEQ ID No.19).
- An ER retention signal may selected from the group comprising: an isoform of the invariant chain which resides in the ER (Ii33), Ribophorin I, Ribophorin II, SEC61 or cytochrome b5 or fragments thereof comprising the localisation domains.
- An example of an ER localisation domain is the ER localisation of Ribophorin II, Genbank accession BC060556.1.
- the intracellular retention signal may be a tyrosine-based sorting signal, a dileucine- based sorting signal, an acidic cluster signal, a lysosomal avoidance signal, an NPFX’(1,2)D-Type signal, a KDEL, a KKX’X’ or a KX’KX’X’ signal (wherein X’ is any amino acid).
- Tyrosine-based sorting signals mediate rapid internalization of transmembrane proteins from the plasma membrane and the targeting of proteins to lysosomes (Bonifacino & Traub; supra).
- NPX’Y and YX’X’Z’ consensus motifs Two types of tyrosine-based sorting signals are represented by the NPX’Y and YX’X’Z’ consensus motifs (wherein Z’ is an amino acid with a bulky hydrophobic side chain).
- NPX’Y signals mediate rapid internalization of type I transmembrane proteins, they occur in families such as members of the LDL receptor, integrin ⁇ , and ⁇ -amyloid precursor protein families. Examples of NPX’Y signals are provided in Table 1. Table 1 – NPX’Y signals Numbers in parentheses indicate motifs that are present in more than one copy within the same protein. The signals in this and other tables should be considered examples. Key residues are indicated in bold type.
- Tm transmembrane
- LDL low density lipoprotein
- LRP LDL receptor related protein 1
- APP 13-amyloid precursor protein
- APLP APP-like protein 1.
- YX’X’Z’-type signals are found in endocytic receptors such as the transferrin receptor and the asialoglycoprotein receptor, intracellular sorting receptors such as the CI- and CD-MPRs, lysosomal membrane proteins such as LAMP-1 and LAMP-2, and TGN proteins such as TGN38 and furin, as well as in proteins localized to specialized endosomal-lysosomal organelles such as antigen-processing compartments (e.g., HLA-DM) and cytotoxic granules (e.g., GMP-17).
- the YX’X’Z’-type signals are involved in the rapid internalization of proteins from the plasma membrane.
- YX’X’Z’-type signals are provided in Table 2.
- Table 2 - YX’X’Z’-type signals Protein Species Sequence Dileucine-based sorting signals ([DE]X’X’X’LL[LI]) play critical roles in the sorting of many type I, type II, and multispanning transmembrane proteins. Dileucine-based sorting signals are involved in rapid internalization and lysosomal degradation of transmembrane proteins and the targeting of proteins to the late endosomal- lysosomal compartments.
- Transmembrane proteins that contain constitutively active forms of this signal are mainly localised to the late endosomes and lysosomes.
- Examples of [DE]X’X’X’LL[LI] sorting signals are provided in Table 3.
- DX’X’LL signals constitute a distinct type of dileucine-based sorting signals. These signals are present in several transmembrane receptors and other proteins that cycle between the TGN and endosomes, such as the CI- and CD-MPRs, sortilin, the LDL- receptor-related proteins LRP3 and LRP10, and ⁇ -secretase. Examples of DX’X’LL sorting signals are provided in Table 4. Table 4 - DX’X’LL sorting signals Protein Species Sequence
- Another family of sorting motifs is provided by clusters of acidic residues containing sites for phosphorylation by CKII. This type of motif is often found in transmembrane proteins that are localized to the TGN at steady state, including the prohormone- processing enzymes furin, PC6B, PC7, CPD, and PAM, and the glycoprotein E of herpes virus 3. Examples of acidic cluster signals are provided in Table 5.
- the intracellular retention signal may be selected from the group of: NPX’Y, YX’X’Z, [DE]X’X’X'L[LI], DX’X’LL, DP[FW], FX’DX’F, NPF, LZX’Z[DE], LLDLL, PWDLW, KDEL, HDEL, KKX’X’ or KX’KX’X’; wherein X’ is any amino acid and Z’ is an amino acid with a bulky hydrophobic side chain.
- the intracellular retention signal may be any sequence shown in Tables 1 to 5.
- the intracellular retention signal may comprise the Tyrosinase-related protein (TYRP)-1 intracellular retention signal.
- the intracellular retention signal may comprise the TYRP-1 intracellular domain.
- the intracellular retention signal may comprise the sequence NQPLLTD (SEQ ID No.20) or a variant thereof.
- TYRP1 is a well-characterized melansomal protein which is retained in the melanosome (a specialized lysosome) at >99% efficiency.
- TYRP1 is a 537 amino acid transmembrane protein with a lumenal domain (1-477aa), a transmembrane domain (478-501), and a cytoplasmic domain (502-537).
- a di-leucine signal residing on the cytoplasmic domain causes retention of the protein. This di-leucine signal has the sequence shown as SEQ ID No.20 (NQPLLTD).
- the molecule of the invention may comprise a linker to connect the Fas-binding domain to the intracellular retention signal.
- the linker may, for example, be a peptide linker. Numerous suitable peptide linker sequence are known in the art and/or could be readily designed by a skilled person. Flexible polypeptide linkers composed of glycine and serine are commonly used to connect separate domains of engineered multidomain proteins. Such a linker may, for example, comprise repeats of the sequence (GGGGS)n (SEQ ID NO: 21) or, in which n is an integer of, e.g., about 1 to about 8.
- the linker may comprise the sequence GGGGSGGGGS (SEQ ID NO: 22) or SGGGSGGGSGGGS (SEQ ID NO: 23).
- the anti-Fas KDEL molecule having the amino acid sequence shown in Figure 1 has a linker with the sequence shown as SED ID No.23.
- the peptide linker used in the molecule of the invention may have a length of about 5 to about 40; about 10 to about 30; or about 10 to about 20 amino acids.
- SIGNAL PEPTIDE The molecule of the invention may comprise a signal peptide so that when it is expressed inside a cell, the nascent protein is directed to the endoplasmic reticulum.
- the signal peptide may, for example, be an IL-2 signal peptide, a kappa leader sequence, a CD8 leader sequence or a peptide with essentially equivalent activity.
- the construct shown in Figure 1 encodes an anti-Fas KDEL molecule with an Ig Kappa leader sequence having the following sequence MGWSCIILFLVATATGVHS (SEQ ID No.24).
- the molecule of the present invention may have the sequence shown as SEQ ID No.
- SEQ ID No. 25 which is made up of an mIg Kappa Leader sequence (signal peptide), the light chain from the anti-Fas antibody F45D9 (shown above as SEQ ID No.6), a GS linker, the heavy chain from the anti-Fas antibody F45D9 (shown above as SEQ ID No. 5) and the intracellular retention sequence shown above as SEQ ID No.18.
- SEQ ID No.25 (anti-Fas-KDEL) MGWSCIILFLVATATGVHSDIQMTQSPSSLSASVGDRVTITCRASQGIRRWLAWYQQ KPEKAPKSLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNSYP YTFGQGTKLEIKRSGGGGSGGGGSGGGGSQVQLQQWGAGLLKPSETLSLICAVYG GSFSTYYWTWIRQPPGKGLEWIGEINHRGTTNYSPSLKSRVTISVDTSKNHISLNLTS VTAADTALYYCARGLLWIGEGDYGLDVWGQGTTVTVSSDPAEPSEKDEL
- CAR chimeric antigen receptor
- TCR engineered T-cell receptor
- CAR A classical chimeric antigen receptor (CAR) is a chimeric type I trans-membrane protein which connects an extracellular antigen-recognizing domain (binder) to an intracellular signalling domain (endodomain).
- the binder is typically a single-chain variable fragment (scFv) derived from a monoclonal antibody (mAb), but it can be based on other formats which comprise an antibody-like antigen binding site.
- scFv single-chain variable fragment
- mAb monoclonal antibody
- a spacer domain may be used to isolate the binder from the membrane and to allow it a suitable orientation.
- a common spacer domain used is the Fc of IgG1. More compact spacers can suffice e.g. the stalk from CD8 ⁇ and even just the IgG1 hinge alone, depending on the antigen.
- a trans-membrane domain anchors the protein in the cell membrane and connects the spacer to the endodomain.
- Early CAR designs had endodomains derived from the intracellular parts of either the ⁇ chain of the Fc ⁇ R1 or CD3 ⁇ . Consequently, these first generation receptors transmitted immunological signal 1, which was sufficient to trigger T-cell killing of cognate target cells but failed to fully activate the T-cell to proliferate and survive.
- compound endodomains have been constructed: fusion of the intracellular part of a T-cell co-stimulatory molecule to that of CD3 ⁇ results in second generation receptors which can transmit an activating and co-stimulatory signal simultaneously after antigen recognition.
- the co-stimulatory domain most commonly used is that of CD28.
- Some receptors have also been described which include TNF receptor family endodomains, such as the closely related OX40 and 41BB which transmit survival signals.
- Even more potent third generation CARs have now been described which have endodomains capable of transmitting activation, proliferation and survival signals. When the CAR binds the target-antigen, this results in the transmission of an activating signal to the T-cell it is expressed on. Thus the CAR directs the specificity and cytotoxicity of the T cell towards tumour cells expressing the targeted antigen.
- CARs typically therefore comprise: (i) an antigen-binding domain; (ii) a spacer; (iii) a transmembrane domain; and (iii) an intracellular domain which comprises or associates with a signalling domain.
- a CAR may have the general structure: Antigen binding domain – spacer domain - transmembrane domain - intracellular signaling domain (endodomain).
- ANTIGEN BINDING DOMAIN The antigen binding domain is the portion of the CAR which recognizes antigen.
- the antigen-binding domain comprises: a single-chain variable fragment (scFv) derived from a monoclonal.
- CARs have also been produced with domain antibody (dAb), VHH or Fab-based antigen binding domains.
- a CAR may comprise a ligand for the target antigen.
- B-cell maturation antigen (BCMA)-binding CARs have been described which have an antigen binding domain based on the ligand a proliferation inducing ligand (APRIL).
- SPACER Classical CARs comprise a spacer sequence to connect the antigen-binding domain with the transmembrane domain and spatially separate the antigen-binding domain from the endodomain. A flexible spacer allows the antigen-binding domain to orient in different directions to facilitate binding.
- transmembrane domain is the portion of the CAR which spans the membrane.
- the transmembrane domain may be any protein structure which is thermodynamically stable in a membrane. This is typically an alpha helix comprising of several hydrophobic residues.
- the transmembrane domain of any transmembrane protein can be used to supply the transmembrane portion of the CAR.
- the presence and span of a transmembrane domain of a protein can be determined by those skilled in the art using the TMHMM algorithm (http://www.cbs.dtu.dk/services/TMHMM-2.0/). Alternatively, an artificially designed TM domain may be used.
- ENDODOMAIN The endodomain is the signal-transmission portion of the CAR. It may be part of or associate with the intracellular domain of the CAR. After antigen recognition, receptors cluster, native CD45 and CD148 are excluded from the synapse and a signal is transmitted to the cell. The most commonly used endodomain component is that of CD3-zeta which contains 3 ITAMs. This transmits an activation signal to the T cell after antigen is bound.
- CD3-zeta may not provide a fully competent activation signal and additional co-stimulatory signalling may be needed.
- Co-stimulatory signals promote T-cell proliferation and survival.
- co-stimulatory signals include those that belong the Ig family (CD28, ICOS) and the TNF family (OX40, 41BB, CD27, GITR etc).
- chimeric CD28 and OX40 can be used with CD3-Zeta to transmit a proliferative / survival signal, or all three can be used together.
- the endodomain may comprise: (i) an ITAM-containing endodomain, such as the endodomain from CD3 zeta; and/or (ii) a co-stimulatory domain, such as the endodomain from CD28 or ICOS; and/or (iii) a domain which transmits a survival signal, for example a TNF receptor family endodomain such as OX-40, 4-1BB, CD27 or GITR.
- ITAM-containing endodomain such as the endodomain from CD3 zeta
- a co-stimulatory domain such as the endodomain from CD28 or ICOS
- a domain which transmits a survival signal for example a TNF receptor family endodomain such as OX-40, 4-1BB, CD27 or GITR.
- the CAR of the present invention may therefore comprise an antigen-binding component comprising an antigen-binding domain and a transmembrane domain; which is capable of interacting with a separate intracellular signalling component comprising a signalling domain.
- the vector of the invention may express a CAR signalling system comprising such an antigen-binding component and intracellular signalling component.
- the CAR may comprise a signal peptide so that when it is expressed inside a cell, the nascent protein is directed to the endoplasmic reticulum and subsequently to the cell surface, where it is expressed.
- the signal peptide may be at the amino terminus of the molecule.
- target antigen is an entity which is specifically recognised and bound by the antigen-binding domain of a CAR.
- the target antigen may be an antigen present on a cancer cell, for example a tumour- associated antigen.
- tumour associated antigens are known, as shown in the following Table 6.
- the CAR may be capable of binding such a TAA.
- Table 6 TRANSGENIC T-CELL RECEPTOR
- TCR T-cell receptor
- MHC major histocompatibility complex
- the TCR In humans, in 95% of T cells the TCR consists of an alpha ( ⁇ ) chain and a beta ( ⁇ ) chain (encoded by TRA and TRB, respectively), whereas in 5% of T cells the TCR consists of gamma and delta ( ⁇ / ⁇ ) chains (encoded by TRG and TRD, respectively).
- TCR engages with antigenic peptide and MHC (peptide/MHC)
- the T lymphocyte is activated through signal transduction.
- antigens recognized by the TCR can include the entire array of potential intracellular proteins, which are processed and delivered to the cell surface as a peptide/MHC complex. It is possible to engineer cells to express heterologous (i.e.
- non-native TCR molecules by artificially introducing the TRA and TRB genes; or TRG and TRD genes into the cell using vector.
- the genes for engineered TCRs may be reintroduced into autologous T cells and transferred back into patients for T cell adoptive therapies.
- Such ‘heterologous’ TCRs may also be referred to herein as ‘transgenic TCRs’.
- NUCLEIC ACID SEQUENCE The present invention provides a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal.
- polynucleotide “nucleotide”, and “nucleic acid” are intended to be synonymous with each other.
- nucleic acids according to the invention may comprise DNA or RNA. They may be single-stranded or double-stranded. They may also be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to oligonucleotides are known in the art.
- polynucleotides may be modified by any method available in the art. Such modifications may be carried out in order to enhance the in vivo activity or life span of polynucleotides of interest.
- variant “homologue” or “derivative” in relation to a nucleotide sequence include any substitution of, variation of, modification of, replacement of, deletion of or addition of one (or more) nucleic acid from or to the sequence.
- the present invention also provides a nucleic acid construct comprising a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and a nucleic acid encoding a polypeptide of interest (POI).
- POI polypeptide of interest
- the POI may, for example, be a CAR or transgenic TCR.
- the nucleic acids may be in either order in the construct. Nucleic acids encoding two or more polypeptides may be separated by a co- expression site enabling co-expression of two polypeptides as separate entities. It may be a sequence encoding a cleavage site, such that the nucleic acid construct produces both polypeptides, joined by a cleavage site(s).
- the cleavage site may be self-cleaving, such that when the polypeptide is produced, it is immediately cleaved into individual peptides without the need for any external cleavage activity.
- the cleavage site may be any sequence which enables the two polypeptides to become separated.
- the term “cleavage” is used herein for convenience, but the cleavage site may cause the peptides to separate into individual entities by a mechanism other than classical cleavage.
- FMDV Foot-and-Mouth disease virus
- various models have been proposed for to account for the “cleavage” activity: proteolysis by a host-cell proteinase, autoproteolysis or a translational effect (Donnelly et al (2001) J. Gen. Virol. 82:1027-1041).
- the exact mechanism of such “cleavage” is not important for the purposes of the present invention, as long as the cleavage site, when positioned between nucleic acid sequences which encode proteins, causes the proteins to be expressed as separate entities.
- the cleavage site may, for example be a furin cleavage site, a Tobacco Etch Virus (TEV) cleavage site or encode a self-cleaving peptide.
- TSV Tobacco Etch Virus
- a ‘self-cleaving peptide’ refers to a peptide which functions such that when the polypeptide comprising the proteins and the self-cleaving peptide is produced, it is immediately “cleaved” or separated into distinct and discrete first and second polypeptides without the need for any external cleavage activity.
- the self-cleaving peptide may be a 2A self-cleaving peptide from an aphtho- or a cardiovirus.
- the primary 2A/2B cleavage of the aptho- and cardioviruses is mediated by 2A “cleaving” at its own C-terminus.
- apthoviruses such as foot-and-mouth disease viruses (FMDV) and equine rhinitis A virus
- the 2A region is a short section of about 18 amino acids, which, together with the N-terminal residue of protein 2B (a conserved proline residue) represents an autonomous element capable of mediating “cleavage” at its own C-terminus (Donelly et al (2001) as above).
- the present invention also provides a vector, or kit of vectors, which comprises one or more nucleic acid sequence(s) or nucleic acid construct(s) according to the invention.
- Such a vector may be used to introduce the nucleic acid sequence(s) into a host cell so that it expresses a molecule which comprises a Fas-binding domain linked to an intracellular retention signal and optionally a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR).
- the vector may, for example, be a plasmid or a viral vector, such as a retroviral vector or a lentiviral vector, or a transposon based vector or synthetic mRNA.
- the vector may be capable of transfecting or transducing an immune effector cell, such as a T cell or a NK cell.
- kits of nucleic acid sequences comprising: (a) a first nucleic acid sequence which encodes a molecule which comprises a Fas- binding domain linked to an intracellular retention signal, and (b) a second nucleic acid sequence which encodes a POI.
- the POI may, for example, be a CAR or engineered TCR
- kit of vectors comprising: (a) a first vector comprising a first nucleic acid sequence which encodes a molecule which comprises a Fas-binding domain linked to an intracellular retention signal, and (b) a second vector comprising a second nucleic acid sequence which encodes a POI.
- the present invention provides a cell which comprises a molecule of the first aspect of the invention.
- the cell may comprise a nucleic acid sequence, a nucleic acid construct or a vector of the present invention.
- the present invention provides a cell engineered to express (a) a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and (b) FasL
- the cell may be a tumour-infiltrating lymphocyte (TIL).
- Tumour-infiltrating lymphocytes are white blood cells that have left the bloodstream and migrated towards a tumour.
- tumour-infiltrating immune cells consist of both mononuclear and polymorphonuclear immune cells, (i.e., T cells, B cells, natural killer cells, macrophages, neutrophils, dendritic cells, mast cells, eosinophils, basophils, etc.) in variable proportions.
- T cells, B cells natural killer cells, macrophages, neutrophils, dendritic cells, mast cells, eosinophils, basophils, etc.
- adoptive T cell transfer therapy tumour-infiltrating lymphocytes are removed from a patient’s tumour, expanded ex vivo, and then given back to the patient to help the immune system kill the cancer cells.
- the immunosuppressive tumour microenvironment upregulates death ligands such as Fas ligand (FasL).
- FasL induces apoptosis of immune cells that express death receptors for Fas, such as tumour-infiltrating lymphocytes (TILs).
- TILs tumour-infiltrating lymphocytes
- the cell of the present invention has an in-built resistance to FasL-mediated apoptosis so an enhanced capacity to survive and persist in the hostile tumour microenvironment.
- the cell may be an effector immune cell.
- the cell may be a cytolytic immune cell such as a T cell or an NK cell.
- T cells or T lymphocytes are a type of lymphocyte that play a central role in cell- mediated immunity. They can be distinguished from other lymphocytes, such as B cells and natural killer cells (NK cells), by the presence of a T-cell receptor (TCR) on the cell surface.
- TCR T-cell receptor
- Helper T helper cells assist other white blood cells in immunologic processes, including maturation of B cells into plasma cells and memory B cells, and activation of cytotoxic T cells and macrophages.
- TH cells express CD4 on their surface.
- TH cells become activated when they are presented with peptide antigens by MHC class II molecules on the surface of antigen presenting cells (APCs).
- APCs antigen presenting cells
- These cells can differentiate into one of several subtypes, including TH1, TH2, TH3, TH17, Th9, or TFH, which secrete different cytokines to facilitate different types of immune responses.
- Cytolytic T cells destroy virally infected cells and tumor cells, and are also implicated in transplant rejection.
- CTLs express the CD8 at their surface. These cells recognize their targets by binding to antigen associated with MHC class I, which is present on the surface of all nucleated cells.
- MHC class I MHC class I
- IL-10 adenosine and other molecules secreted by regulatory T cells, the CD8+ cells can be inactivated to an anergic state, which prevent autoimmune diseases such as experimental autoimmune encephalomyelitis.
- Memory T cells are a subset of antigen-specific T cells that persist long-term after an infection has resolved.
- Memory T cells comprise three subtypes: central memory T cells (TCM cells) and two types of effector memory T cells (TEM cells and TEMRA cells). Memory cells may be either CD4+ or CD8+. Memory T cells typically express the cell surface protein CD45RO. Regulatory T cells (Treg cells), formerly known as suppressor T cells, are crucial for the maintenance of immunological tolerance. Their major role is to shut down T cell- mediated immunity toward the end of an immune reaction and to suppress auto- reactive T cells that escaped the process of negative selection in the thymus.
- Treg cells Two major classes of CD4+ Treg cells have been described — naturally occurring Treg cells and adaptive Treg cells.
- Naturally occurring Treg cells also known as CD4+CD25+FoxP3+ Treg cells
- Naturally occurring Treg cells arise in the thymus and have been linked to interactions between developing T cells with both myeloid (CD11c+) and plasmacytoid (CD123+) dendritic cells that have been activated with TSLP.
- Naturally occurring Treg cells can be distinguished from other T cells by the presence of an intracellular molecule called FoxP3. Mutations of the FOXP3 gene can prevent regulatory T cell development, causing the fatal autoimmune disease IPEX.
- Adaptive Treg cells also known as Tr1 cells or Th3 cells
- the cell may be a tumour infiltrating lymphocyte (TIL) as described above.
- TIL tumour infiltrating lymphocyte
- the cell may be a T-cell expended from a TIL isolated from a subject having cancer.
- the cell may be a Natural Killer cell (or NK cell).
- NK cells form part of the innate immune system. NK cells provide rapid responses to innate signals from virally infected cells in an MHC independent manner NK cells (belonging to the group of innate lymphoid cells) are defined as large granular lymphocytes (LGL) and constitute the third kind of cells differentiated from the common lymphoid progenitor generating B and T lymphocytes.
- LGL large granular lymphocytes
- NK cells are known to differentiate and mature in the bone marrow, lymph node, spleen, tonsils and thymus where they then enter into the circulation.
- the cells of the invention may be any of the cell types mentioned above.
- Cells according to the invention may either be created ex vivo either from a patient’s own peripheral blood (1st party), or in the setting of a haematopoietic stem cell transplant from donor peripheral blood (2nd party), or peripheral blood from an unconnected donor (3rd party).
- cells may be derived from ex vivo differentiation of inducible progenitor cells or embryonic progenitor cells to, for example, T or NK cells.
- chimeric polypeptide-expressing cells are generated by introducing DNA or RNA coding for the chimeric polypeptide by one of many means including transduction with a viral vector, transfection with DNA or RNA.
- the cell of the invention may be an ex vivo cell from a subject.
- the cell may be from a peripheral blood mononuclear cell (PBMC) sample.
- PBMC peripheral blood mononuclear cell
- the cells may be activated and/or expanded prior to being transduced with nucleic acid encoding the molecules providing the chimeric polypeptide according to the first aspect of the invention, for example by treatment with an anti-CD3 monoclonal antibody.
- the cell of the invention may be made by: (i) isolation of a cell-containing sample from a subject or other sources listed above; and (ii) transduction or transfection of the cells with one or more a nucleic acid sequence(s), nucleic acid construct(s) or vector(s) of the invention.
- the cells may then by purified, for example, selected on the basis of expression of one or more heterologous nucleic acid sequences.
- the effector immune cell is capable of recognising and killing a target immune cell.
- the target immune cell may be a cytolytic immune cell such as a T-cell or NK cell as defined above.
- the invention also provides a method for making a cell of the invention which comprises the step of introducing into a cell a nucleic acid sequence, a nucleic acid construct, a vector, or a kit of vectors according to the invention.
- the cell may be made by transduction.
- the cell may be screened, post-transduction by a method according to the second aspect of the invention.
- PHARMACEUTICAL COMPOSITION The present invention also relates to a pharmaceutical composition containing a plurality of cells according to the invention.
- the pharmaceutical composition may additionally comprise a pharmaceutically acceptable carrier, diluent or excipient.
- the pharmaceutical composition may optionally comprise one or more further pharmaceutically active polypeptides and/or compounds.
- the present invention provides a method for treating a disease which comprises the step of administering the cells of the present invention (for example in a pharmaceutical composition as described above) to a subject.
- a method for treating a disease relates to the therapeutic use of the cells of the present invention.
- the cells may be administered to a subject having an existing disease or condition in order to lessen, reduce or improve at least one symptom associated with the disease and/or to slow down, reduce or block the progression of the disease.
- the method for preventing a disease relates to the prophylactic use of the cells of the present invention.
- Such cells may be administered to a subject who has not yet contracted the disease and/or who is not showing any symptoms of the disease to prevent or impair the cause of the disease or to reduce or prevent development of at least one symptom associated with the disease.
- the subject may have a predisposition for, or be thought to be at risk of developing, the disease.
- the method may involve the steps of: (i) isolating a cell-containing sample; (ii) transducing or transfecting such cells with a nucleic acid sequence or vector provided by the present invention; (iii) administering the cells from (ii) to a subject.
- the cell-containing sample may be isolated from a subject or from other sources, as described above.
- the present invention provides a cell of the present invention for use in treating and/or preventing a disease.
- the invention also relates to the use of a cell of the present invention in the manufacture of a medicament for the treatment of a disease.
- the disease to be treated by the methods of the present invention may be a cancerous disease, such as bladder cancer, breast cancer, colon cancer, endometrial cancer, kidney cancer (renal cell), leukaemia, lung cancer, melanoma, non-Hodgkin lymphoma, pancreatic cancer, prostate cancer and thyroid cancer.
- the disease may be Multiple Myeloma (MM), B-cell Acute Lymphoblastic Leukaemia (B-ALL), Chronic Lymphocytic Leukaemia (CLL), Neuroblastoma, T-cell acute Lymphoblastic Leukaema (T-ALL) or diffuse large B-cell lymphoma (DLBCL).
- MM Multiple Myeloma
- B-ALL B-cell Acute Lymphoblastic Leukaemia
- CLL Chronic Lymphocytic Leukaemia
- Neuroblastoma T-cell acute Lymphoblastic Leukaema
- T-ALL T-cell acute Lymphoblastic Leukaema
- DLBCL diffuse large B-cell lymphoma
- the disease may be a plasma cell disorder such as plasmacytoma, plasma cell leukemia, multiple myeloma, macroglobulinemia,amyloidosis, Waldenstrom's macroglobulinemia, solitary bone plasmacytoma, extramedullary plasmacytoma, osteosclerotic myeloma, heavy chain diseases, monoclonal gammopathy of undetermined significance or smoldering multiple myeloma.
- plasmacytoma plasma cell leukemia, multiple myeloma, macroglobulinemia,amyloidosis, Waldenstrom's macroglobulinemia, solitary bone plasmacytoma, extramedullary plasmacytoma, osteosclerotic myeloma, heavy chain diseases, monoclonal gammopathy of undetermined significance or smoldering multiple myeloma.
- Example 1 Expression of an anti-Fas KDEL molecule reduces cell-surface expression of Fas Peripheral blood mononuclear cells (PBMCs) and SupT1 cells were either left untransduced or transduced with a construct expressing the anti-Fas KDEL molecule having the sequence shown as SEQ ID No. 25, together with BFP as a marker for transduction. Three days after transduction the cells were incubated with either a PE- conjugated anti-Fas antibody or a PE-conjugated isotype control and consequently Fas staining was analysed by flow cytometry, with the results shown in Figure 4.
- Example 2 Expression of an anti-Fas KDEL molecule protects a cell from FasL- mediated apoptosis PBMCs and SupT1 cells transduced as described for Example 4 were either left untreated or treated with MEGA FasL (100 ng/mL) for 48 hours, at which point cells were analysed by flow cytometry and the results are shown in Figure 5.
- PBMCs and SupT1s transduced with the Fas binder-KDEL polypeptide show almost 100% survival following exposure to MEGA FasL, whereas non-transduced PBMCs and SupT1 cells are completely killed following exposure to the ligand.
- the experiment above was repeated but this time cells were co-cultured with NT SupT1 cells or FasL-expressing SupT1 cells. Cells were co-cultured at a 1:2 PBMC:SupT1 ratio for 48 hours, at which point cells were analysed by flow cytometry. The results are shown in Figure 6.
Abstract
The present invention provides a molecule which comprises a Fas-binding domain linked to an intracellular retention signal. When expressed in a cell, the molecule inhibits Fas expression at the cell surface and therefore Fas:FasL-mediated apoptosis.
Description
MOLECULE FIELD OF THE INVENTION The present invention relates a molecule capable of down-regulating the expression of Fas at the cell surface. BACKGROUND TO THE INVENTION Adoptive immunotherapy of cancer involves the ex vivo generation of cancer-antigen specific cells and their administration. Adoptively transferred immune effector cells also activate existing adaptive and innate immune cells within the tumour once they activate and start causing inflammation. The native specificity of immune effector cells can be exploited in adoptive immunotherapy – for example during the generation of melanoma specific T-cells from expansion of tumour infiltrating lymphocytes in tumour resections. Otherwise a specificity can be grafted onto a T-cell using genetic engineering. Two common methods for achieving this are using chimeric antigen receptors (CARs) or transgenic T-cell receptors (TCRs). Adoptive immunotherapy has been successful in treating a number of lymphoid malignancies, such as B-cell Acute Lymphoblastic Leukaemia (B-ALL), Diffuse Large B-cell Lymphoma (DLBCL) and Multiple Myeloma (MM). Avoiding Fas/Fas-L mediated killing of immune effector cells The tumour microenvironment (TME) provides tumour cells with essential signals for survival, growth and immune resistance. The TME is immunosuppressive and can inhibit the persistence and survival of immune cells in cancer immunotherapies, such as CAR T cell therapy. Immunosuppressive mechanisms employed by the TME include e.g., upregulating immune checkpoint signals such as PDL-1 and/or CTLA-4 and secretion of cytokines such as IL-6 and/or TGF-beta. The immunosuppressive TME also upregulates death ligands such as Fas ligand (FasL). FasL induces apoptosis of immune cells that express death receptors for Fas, such as tumour-infiltrating lymphocytes (TILs).
CAR-T cells themselves also upregulate death receptors and their ligands upon activation and transduction of the CAR construct, triggering activation-induced death (AICD) and further exacerbating the problem of CAR-T cell persistence in the TME. Moreover, FasL is not only expressed by activated T cells bit is also upregulated by exposure to IFNγ that is produced by activated T cells. Notably, third generation CARs, which have two co-stimulatory endodomains, seem to be particularly susceptible to AICD as a result of increased FasL expression (Xu et al., 2017, Hum Vaccin Immunother. 13(7):1548-1555, Benmebarek et al., 2019, In J Mol Sci.20(6): 1283). In addition to inducing apoptosis, Fas signals via non-apoptotic cascades and it has been shown that when naive and memory T cells are mixed prior to adoptive transfer, naïve T cells undergo precocious differentiation which limits their anti-tumour efficacy. This effect is mediated by non-apoptotic, AKT-driven Fas signalling on memory CD8 T cells. The interaction of Fas with its ligand Fas triggers a signal transduction pathway leading to apoptosis (see Figure 2). Fas binding to FasL triggers receptor trimerization and recruitment of Fas-associated death domain (FADD) via homotypic interactions of their death domains (DDs). In turn, FADD then recruits procaspase-8 to the activated receptor and the resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation, which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. FasL has been reported to be expressed by many cancers including melanomas, lung carcinomas, hepatocellular carcinomas, esophageal carcinomas and colon carcinomas. Tumour endothelial cells, which line blood vessels and control blood and nutrient flow and trafficking of leukocytes, have been shown to express FasL, whereas normal vasculature do not. FasL is expressed by myeloid-derived suppressor cells (MDSC). MDSC are a heterogenous populations of cells that expand during cancer, chronic inflammation, autoimmune and infectious diseases, and dampen down the immune response thereby promoting tumour growth. FasL is also reportedly expressed by cancer-associated fibroblasts (CAFs) and CD4+CD25+ regulatory T cells.
FasL is also expressed by T cells themselves and has been shown to be further upregulated in CAR-Ts, meaning a) CAR T cells are susceptible to fratricide, but also b) CAR-T cells can kill Fas-expressing tumour cells by virtue of the Fas-FasL interaction. The use of an antibody blockade has previously been described as a way of preventing T-cell apoptosis, using anti-Fas antibodies (Gargell et al (2016) Mol. Ther. 24: 1135-1149) or anti-FasL antibodies (Motz et al (2014) Nat. Med. 20:607-615). However, the approach with also block FasL expressed on T cells, blocking FasL mediated killing giving inferior cancer cytotoxicity). Other groups have used genetic modification to knock-down or knock out Fas expression, for example using siRNA (Dotti et al (2005) Blood 105:4677-4684) or CRISPR/Cas9 (Ren et al (2017) Oncotarget 8:17002-17011). However, difficulties have arisen with knock out/down efficiency and with manufacturing i.e. scale up for clinical use. Yamamoto et al (J. Clin. Invest (2019) 129:1551-1565) describe two dominant negative versions of Fas receptor, designed to prevent recruitment of FADD by either: (i) truncation of the majority of the intracellular death domain; or (ii) substitution of an asparagine for an isoleucine residue at position 46 of the death domain. In a murine study, it is reported that T cells co-engineered with a dominant negative Fas receptor and a CAR show enhanced persistence following adoptive cell transfer, resulting in enhanced anti-tumour activity. A disadvantage of the dominant negative Fas receptor approach is that dominant negative Fas competes with endogenous Fas for incorporation into a trimeric structure, so high expression levels are needed to reduce or block Fas-mediated signalling. Secondly, dominant negative Fas receptors ligate and sequester FasL within the cell, preventing FasL mediated killing of target cells by CAR-T cells. There is thus a need for mechanisms to prevent FASL-induced death and improve the effectiveness of engineered immune effector cells to persist and survive in the TME which are not associated with the disadvantages mentioned above.
DESCRIPTION OF THE FIGURES Figure 1 - Annotated sequence for an example of a bicistronic construct co- expressing an anti-Fas KDEL with FasL: Anti-Fas-KDEL–2A–FasL Figure 2 - Schematic diagram showing Fas/FasL-mediated induction of apoptosis. Expression of a dominant negative Fas receptor with a truncated Death Domain (Fas ΔDD) which does not bind FADD competes with endogenous Fas for binding FasL blocking or reducing apoptosis. Figure 3 - Schematic diagram illustrating the intracellular retention of Fas using an anti-Fas-KDEL molecule. (A) The Fas receptor is synthesised at the rough endoplasmic reticulum (ER) and transported to the plasma membrane via the Golgi apparatus. (B) The anti-Fas-KDEL polypeptide binds to the extracellular domain on Fas and consequently Fas is retained at the ER via the KDEL receptor recognising the KDEL sequence. Fas molecules that are trafficked to the Golgi apparatus (to eventually be transported to the plasma membrane) are trafficked back to the ER by retrograde transport via the KDEL receptor recognising the KDEL sequence. Figure 4 - Fas staining histograms of PBMCs and SupT1 cells transduced with the Fas binder-KDEL polypeptide demonstrating decreased staining of Fas when transduced with the Fas binder-KDEL polypeptide. Figure 5 - Two independent PBMC donors and SupT1 cells that were either non- transduced (NT) or transduced to express a Fas binder-KDEL polypeptide, were either untreated or treated with MEGA FasL (100 ng/mL) for 48 hours, at which point cells were analysed by flow cytometry. The raw flow cytometry plots are shown in (A), with the percentage of surviving BFP positive PBMCs and SupT1s made relative to untreated conditions shown in (B). Figure 6 - Two independent PBMC donors that were either non-transduced (NT) or transduced to express a Fas binder-KDEL polypeptide, were co-cultured with NT SupT1 cells or FasL-expressing SupT1 cells at a 1:2 PBMC:SupT1 ratio for 48 hours, at which point cells were analysed by flow cytometry. Raw flow cytometry plots are shown in (A) with PBMCs identified from SupT1 cells through dual expression of CD2 and CD3. The percentage of surviving BFP positive PBMCs made relative to NT SupT1 cells are shown in (B).
SUMMARY OF ASPECTS OF THE INVENTION The present inventors have developed a molecule capable of reducing or preventing Fas expression at the cell surface which may be used in such a method. Thus, in a first aspect, the present invention provides a molecule which comprises i) a binding domain which binds to a FAS extracellular domain and ii) a retention domain that intracellularly retains FAS within the endoplasmic reticulum or Golgi apparatus. The binding domain may comprise a native FAS ligand (FASL), single chain variable fragment (scFv), a single domain antibody (sdAb), a Fab antigen binding domain (Fab) or a monoclonal antibody. A single domain antibody may, for example, be derived from an artificial VHH fragment or a camelid antibody. The retention domain may be C-terminal to the binding domain. The retention domain may comprise a sequence selected from the group consisting of: NPX’Y, YX’X’Z, [DE]X’X’X'L[LI], DX’X’LL, DP[FW], FX’DX’F, NPF, LZX’Z[DE], LLDLL, PWDLW, KDEL, HDEL, KKX’X’ or KX’KX’X’; wherein X’ is any amino acid and Z’ is an amino acid with a bulky hydrophobic side chain. The retention domain may, for example, comprises a sequence shown in Tables 1 to 5. In a second aspect, the present invention provides a nucleic acid sequence encoding a molecule according to any of the preceding claims wherein the nucleic acid sequence encodes molecule according to the first aspect of the invention. In a third aspect, the present invention provides a nucleic acid construct comprising a first nucleic acid sequence which encodes at least one polypeptide of interest (POI) and a second nucleic acid sequence according to the second aspect of the invention. The first and second nucleic acid sequences may be separated by a third nucleic acid sequence encoding a coexpression peptide. In a fourth aspect, the present invention provides a kit of nucleic acid sequences comprising: (a) a first nucleic acid sequence which encodes at least one POI, and
(b) a second nucleic acid sequence which encodes a molecule according to the first aspect of the invention. In a fifth aspect, the present invention provides a vector comprising the nucleic acid sequence according to the second aspect of the invention or a nucleic acid construct according to the third aspect of the invention. The POI may be, for example, a chimeric antigen receptor or a T-cell receptor, such that when the vector is used to transduce a target cell, the target cell co-expresses a molecule according to the first aspect of the invention and a chimeric antigen receptor or T-cell receptor. In a sixth aspect, the present invention provides a kit of vectors comprising: (i) a first vector comprising a nucleic acid encoding at least one POI; and (ii) a second vector comprising a nucleic acid which encodes a molecule according to the first aspect of the invention. In a seventh aspect, the present invention provides a cell expressing a molecule according to the first aspect of the invention. The cell may also express at least one POI. In an eighth aspect, the present invention provides a pharmaceutical composition which comprises a plurality of cells according to the seventh aspect of the invention. In a ninth aspect, the present invention provides a pharmaceutical composition according to the eighth aspect of the invention for use in treating and/or preventing a disease. In a tenth aspect, the present invention provides a method for treating and/or preventing a disease, which comprises the step of administering a pharmaceutical composition according to the eight aspect of the invention to a subject in need thereof. The method may comprise the following steps: (i) isolation of a cell containing sample; (ii) transduction or transfection of the cell with a nucleic acid sequence according to the second aspect of the invention; a nucleic acid construct according to the thris
aspect of the invention, a vector according to the fourth aspect of the invention, or a kit of vectors according to the fifth aspect of the invention; and (iii) administering the cells from (ii) to a subject. The cell may be autologous or allogenic. In an eleventh aspect, the present invention provides a use of a pharmaceutical composition according to paragraph 16 in the manufacture of a medicament for the treatment and/or prevention of a disease. The disease may be cancer. In a twelfth aspect, the present invention provides a method for making a cell according to the seventh aspect of the invention, which comprises the step of introducing: a nucleic acid sequence according to the second aspect of the invention; a nucleic acid construct according to the thris aspect of the invention, a vector according to the fourth aspect of the invention, or a kit of vectors according to the fifth aspect of the invention into the cell ex vivo. The cell may be from a sample isolated from a subject. The molecule of the invention provides a novel mechanism by which to block FasL- Fas pathway within the TME. This approach has two advantages: firstly, by not competing with endogenous Fas for incorporation into a trimeric structure, the molecule of the present invention is very efficient at low cell expression levels. Secondly, the molecule does not ligate and sequester FasL, allowing for FasL mediated killing of target cells. This is particularly evident when the molecule is co-expressed with for example, a Chimeric Antigen Receptor (CAR) because the approach overcomes FAS-included CAR T cell apoptosis and improves CAR-T cell infiltration via tumour vasculature and persistence within the TME. FURTHER ASPECTS OF THE INVENTION Further aspects of the invention are summarised in the following numbered paragraphs:
1. A method for selecting for cells transduced to express a nucleic acid sequence of interest (NOI), which comprises the following steps: (a) transducing a population of cells with a vector co-expressing (i) the NOI and (ii) a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; (b) exposing the cells from (a) to FasL such that untransduced cells are eliminated by apoptosis. 2. A method according to paragraph 2, in step (b), FasL is soluble FasL, FasL bound to a solid substrate, or FasL expressed on the surface of a cell. 3. A method according to paragraph 1 or 2, wherein hexameric FasL is used in step (b). 4. A method according to any preceding paragraph, which comprises the following steps: (a) transducing a population of cells with a plurality of vectors, one of which co-expresses the NOI and the nucleic acid sequence encoding the molecule which comprises a Fas-binding domain linked to an intracellular retention signal; (b) exposing the cells from (a) to FasL thereby selecting cells transduced with the vector expressing the NOI or cells transduced with a combination of vectors including the vector expressing the NOI. 5. A method according to any of paragraphs 1 to 3, which comprises the following steps: (a) transducing a population of cells with a vector co-expressing (i) the NOI, (ii) the nucleic acid sequence encoding the molecule which comprises a Fas-binding domain linked to an intracellular retention signal and (iii) a nucleic acid sequence encoding FasL; (b) culturing the cells, thereby self-selecting for cells transduced with the vector. 6. A method according to any of paragraphs 1 to 3, which comprises the following steps: (a) co-transducing a population of cells with:
a first vector co-expressing (i) a CAR or TCR; and (ii) the nucleic acid sequence encoding the molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and a second vector expressing FasL (b) culturing the cells, thereby selecting for cells transduced with the first vector, together with cells co-transduced with the first and second vector. 7. A method according to paragraph 6, wherein the second vector also comprises a nucleic acid sequence encoding a cytokine. 8. A method according to any of paragraphs 5 to 7, wherein the cell expresses mutant FasL with reduced susceptibility to cleavage. 9. A method according to paragraph 8, wherein the mutant FasL has reduced susceptibility to metalloprotease cleavage. 10. A method according to paragraph 9, wherein the mutant FasL comprises a deletion of amino acid residues 126-135, or a deletion of amino acid residues 126- 145, with reference to the sequence shown as SEQ ID No.7. 11. A method according to any of paragraphs 5 to 7, wherein the cell expresses FasL which comprises a signalling domain and/or a costimulatory domain. 12. A method according to paragraph 11, wherein the cell expresses one of the following: FasL-CD3z; FasL-CD28; FasL-41BB, FasL-CD28z; FasL-41BBz. 13. A method according to any preceding paragraph, wherein the NOI encodes a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR). 14. A method according to any of paragraphs 1 to 19, wherein the NOI inhibits expression of endogenous T-cell receptor (TCR). 15. A method according to paragraph 14, wherein the NOI encodes: (i) a TCR or CD3-binding domain linked to an intracellular retention signal; (ii) a gRNA molecule comprising a targeting domain that is complementary with a target domain in a TCR gene; or (iii) an siRNA complementary with a target domain in a TCR gene.
16. A cell engineered to express (a) nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and (b) FasL 17. A cell according to paragraph 16, which also expresses (c) a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) and/or a nucleic acid sequence of interest (NOI) which inhibits expression of endogenous T-cell receptor (TCR). 18. A cell according to paragraph 17, which expresses a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR), wherein the CAR or TCR-expressing nucleic acid is introduced into the FAS gene, knocking-out FAS gene expression. 19. A cell according to paragraphs 16 or 17 wherein the FasL is mutant FasL with reduced susceptibility to cleavage or FasL which comprises a signalling domain and/or a costimulatory domain. 20. A cell according to any of paragraphs 16 to 19 which co-expresses β2- microglibulin (β2m) linked to a signalling domain and/or a costimulatory domain. 21. A cell according to paragraph 20, which expresses one of the following: β2m- CD3z; β2m-CD28; β2m-41BB. 22. A cell according to any of paragraphs 15 to 21, which is engineered to be resistant to one or more calcineurin inhibitors. 23. A cell according to paragraph 22, which expresses: calcineurin A comprising mutations T351E and L354A; calcineurin A comprising mutations V314R and Y341F; or calcineurin B comprising mutation L124T and K-125-LA-Ins. 24. A nucleic acid construct for expression in a cell which comprises: a nucleic acid sequence encoding a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) and/or a nucleic acid sequence of interest (NOI) which inhibits expression of endogenous T-cell receptor (TCR); a nucleic acid sequence encoding FasL; and
a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal. 25. A vector which comprises a nucleic acid construct according to paragraph 24. 26. A kit of vectors which comprises: (a) a first vector which comprises: a nucleic acid sequence encoding a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) and/or a nucleic acid sequence of interest (NOI) which inhibits expression of endogenous T-cell receptor (TCR); and a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and (b) a second vector which comprises a nucleic acid sequence encoding FasL. 27. A cell transduced or transfected with a vector according to claim 25 or a fit of vestors according to claim 26. 28. A cell according to paragraph 42 which also expresses a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR) 29. A method for making a cell according to any of paragraphs 16 to 23, 27 or 28 which comprises the step of introducing into a cell ex vivo: a nucleic acid construct according to paragraph 24, a vector according to paragraph 25, or a kit of vectors according to paragraph 26. 30. A pharmaceutical composition which comprises plurality of cells selected by a method according to any of paragraphs 1 to 15 or a plurality of cells according to any of any of paragraphs 16 to 23, 27 or 28. 31. A method for treating cancer which comprises the step of administering a pharmaceutical composition according to paragraph 30 to a subject. 32. The use of a plurality of cells selected by a method according to any of paragraphs 1 to 15 or a plurality of cells according to any of paragraphs 16 to 23, 27 or 28 in the manufacture of a medicament for the treatment of cancer.
33. A pharmaceutical composition according to paragraph 32 for use in a method for treating cancer. 34. A method for treating cancer in a subject which comprises cancer cells negative for CAR or TCR target antigen, which comprises the step of administering a plurality of cells according to any of paragraphs 16 to 23, 27 or 28 to the subject, such that target-antigen negative cancer cells are killed by FasL binding to Fas on the cancer cells. 35. A method for depleting alloreactive immune cells from a population of immune cells, which comprises the step of contacting the population of immune cells with a plurality of cells according to any of paragraphs any of paragraphs 16 to 23, 27 or 28 in vitro. 36. A method for preventing graft versus host disease in a subject, which comprises the step of administering a plurality of cells selected by a method according to any of paragraphs 1 to 25, to the subject. 37. An allogeneic or autologous transplant which has been depleted of untransduced cells by a method according to any of paragraphs 1 to 15. 38. A method for preventing graft rejection in a subject, which comprises the step of administering a plurality of cells according to any of any of paragraphs 16 to 23, 27 or 28, to the subject. DETAILED DESCRIPTION FAS The present invention provides a molecule which comprises a Fas-binding domain linked to an intracellular retention signal. When this molecule is expressed in a cell, it binds newly synthesised Fas and retains it in an intracellular compartment or complex, down-regulating the cell surface expression of Fas. The Fas receptor (also known as Fas, FasR, CD95, tumour necrosis factor receptor superfamily member 6) is a type 1 transmembrane glycoprotein receptor which is localized on the surface of various cells including lymphocytes and hepatocytes. The
Fas receptor triggers a signal transduction pathway leading to apoptosis and expression of Fas can be increased by activation of lymphocytes as well as by cytokines such as IFNγ and TNF. The interaction of Fas with its ligand FasL (FasL/CD95L) regulates numerous physiological and pathological processes that are mediated through programmed cell death. Both Fas and FasL are members of the TNF-R superfamily, all of which contain one to five extracellular cysteine rich domains (CRDs), and in their cytoplasmic tail, a death domain (DD), which are 80-100 residue long motifs. Fas binding to FasL triggers receptor trimerization and recruits a protein called Fas- associated death domain (FADD) via homotypic interactions of their death domains (DDs). In turn, FADD then recruits procaspase-8 to the activated receptor and the resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation, which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis (see Figure 2). FasL has been reported to be expressed by many cancers themselves such as melanomas, lung carcinomas, hepatocellular carcinomas, esophageal carcinomas and colon carcinomas. Tumour endothelial cells, which line blood vessels and control blood and nutrient flow and trafficking of leukocytes, have been shown to express FasL, whereas normal vasculature do not. FasL is expressed by myeloid-derived suppressor cells (MDSC). MDSC are a heterogenous populations of cells that expand during cancer, chronic inflammation, autoimmune and infectious diseases, and dampen down the immune response thereby promoting tumour growth. FasL is also reportedly expressed by cancer-associated fibroblasts (CAFs) and CD4+CD25+ regulatory T cells. FasL is also expressed by T cells themselves and has been shown to be further upregulated in CAR-Ts, meaning CAR T cells themselves are susceptible to fratricide. FasL is not only expressed by activated T cells but is also upregulated by exposure to IFNγ that is produced by activated T cells. As a mechanism of T-cell homeostasis, T cells that are constantly activated die through a mechanism called activation-induced cell death (AICD), and the Fas-FasL pathway has been characterised as the cause of this. Despite improved cytolytic
activity and cytokine production, third generation CAR-T cells are more susceptible to AICD as a result of increased FasL expression. The sequence of human Fas is available from Uniprot (Accession No. P25445) and shown below as sequence ID No. 1. In this sequence, residues 26-173 form the extracellular domain (SEQ ID No. 2); residues 174-190 form the transmembrane domain (SEQ ID No.3); and residues 191-335 form the cytoplasmic domain (SEQ ID No.4). In SEQ ID No.4, the portion of sequence that is deleted in the truncated Fas described in the Examples (FasΔDD) is underlined. SEQ ID No.1 (human Fas) MLGIWTLLPLVLTSVARLSSKSVNAQVTDINSKGLELRKTVTTVETQNLEGLHHDGQ FCHKPCPPGERKARDCTVNGDEPDCVPCQEGKEYTDKAHFSSKCRRCRLCDEGH GLEVEINCTRTQNTKCRCKPNFFCNSTVCEHCDPCTKCEHGIIKECTLTSNTKCKEE GSRSNLGWLCLLLLPIPLIVWVKRKEVQKTCRKHRKENQGSHESPTLNPETVAINLS DVDLSKYITTIAGVMTLSQVKGFVRKNGVNEAKIDEIKNDNVQDTAEQKVQLLRNWH QLHGKKEAYDTLIKDLKKANLCTLAEKIQTIILKDITSDSENSNFRNEIQSLV SEQ ID No.2 (Fas extracellular domain) QVTDINSKGLELRKTVTTVETQNLEGLHHDGQFCHKPCPPGERKARDCTVNGDEPD CVPCQEGKEYTDKAHFSSKCRRCRLCDEGHGLEVEINCTRTQNTKCRCKPNFFCN STVCEHCDPCTKCEHGIIKECTLTSNTKCKEEGSRSN SEQ ID No.3 (Fas TM domain) LGWLCLLLLPIPLIVWV SEQ ID No.4 (Fas cytoplasmic domain) KRKEVQKTCRKHRKENQGSHESPTLNPETVAINLSDVDLSKYITTIAGVMTLSQVKG FVRKNGVNEAKIDEIKNDNVQDTAEQKVQLLRNWHQLHGKKEAYDTLIKDLKKANLC TLAEKIQTIILKDITDSENSNFRNEIQSLV INHIBITION OF FAS EXPRESSION In the cell of the present invention, Fas expression at the cell surface is inhibited, reduced or blocked.
The cell of the present invention comprises a nucleic acid sequence which inhibits Fas expression in the cell. The nucleic acid sequence encodes a molecule comprising Fas-binding domain linked to an intracellular retention signal FAS-KDEL The present invention provides a molecule which comprises a Fas-binding domain linked to an intracellular retention signal. The molecule may comprise i) a binding domain which binds to a FAS extracellular domain and ii) a retention domain that intracellularly retains FAS within the endoplasmic reticulum or Golgi apparatus. The retention domain may be C-terminal to the binding domain. FAS BINDING DOMAIN The Fas-binding domain may be a protein or polypeptide chain which is capable of binding to Fas. The Fas-binding domain may comprises an antibody, an antibody fragment or antigen binding fragment, a single-chain variable fragment (scFv), a domain antibody (dAb), a Fab antigen binding domain (Fab), a single domain antibody (sdAb), a VHH/nanobody, a nanobody, an affibody, a fibronectin artificial antibody scaffold, an anticalin, an affilin, a DARPin, a VNAR, an iBody, an affimer, a fynomer, an abdurin/ nanoantibody, a centyrin, an alphabody or a nanofitin which binds to Fas. In particular, the Fas-binding domain may be or comprise a domain antibody (dAb) or a single-chain variable fragment (scFv). A single domain antibody may, for example, be derived from an artificial VHH fragment or a camelid antibody The Fas-binding domain may bind the extracellular domain of Fas. The target- binding domain may bind the sequence shown as SEQ ID No.2.
Apoptosis is induced when FasL binds to the Fas receptor. An anti-Fas retaining polypeptide which binds to the extracellular domain of Fas has the additional advantage that, in addition to downregulating the expression of Fas at the cell surface, it also directly blocks the interaction of FasL to Fas for any residual Fas expressed at the cell surface inhibiting the induction of apoptosis. Numerous Fas-binding antibodies are known in the art. For example, WO2010/102792 describes the anti-Fas antibody F45D9. The VH and VL domains from this antibody are shown below as SEQ ID No.5 and 6 respectively. VH domain from anti-Fas antibody (SEQ ID No.5) QVQLQQWGAGLLKPSETLSLICAVYGGSFSTYYWTWIRQPPGKGLEWIGEINHRGT TNYSPSLKSRVTISVDTSKNHISLNLTSVTAADTALYYCARGLLWIGEGDYGLDVWG QGTTVTVSS VL domain from anti-Fas antibody (SEQ ID No.6) DIQMTQSPSSLSASVGDRVTITCRASQGIRRWLAWYQQKPEKAPKSLIYAASSLQSG VPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNSYPYTFGQGTKLEIKR A construct sequence which comprises the sequence of an anti-Fas KDEL having an F45D9 scFv Fas-binding domain is shown in Figure 1. In this construct, the Fas- KDEL is co-expressed with FasL. The Fas-binding domain of the molecule of the present invention may comprise an antibody or fragment thereof which binds Fas, such as an scFv comprising the VH and VL sequences shown as SEQ ID No.5 and 6. Alternatively, the Fas-binding domain may comprise all or part of Fas ligand (FasL), the natural ligand for FAS. Human FasL has the sequence shown as SEQ ID No.7. The Fas-binding domain may comprise all of FasL or a portion thereof. The Fas- binding domain may comprise FasL, FasL extracellular domain (shown below as SEQ ID No. 8) or a variant or truncated portion thereof which retains the capacity to bind Fas. SEQ ID No.7 (human FasL) MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPPLP PPPPPPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKELA
ELRESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGI VLLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLVM MEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGLY KL SEQ ID No.8 (FasL extracellular domain) ALVGLGLGMFQLFHLQKELAELRESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHL TGKSNSRSMPLEWEDTYGIVLLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNL PLSHKVYMRNSKYPQDLVMMEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYV NVSELSLVNFEESQTFFGLYKL The molecule of the invention may comprise the Fas-binding site of the FasL extracellular domain. A variant FasL extracellular domain may have 80%, 85%, 90%, 95% or 99% identity with the sequence shown as SEQ ID No. 8, provided that the variant sequence retains the capacity to bind Fas. FasL is a type II transmembrane protein, so the C-terminus is extracellular. The molecule of the present invention may comprise a signal sequence on the N- terminus, followed by the FasL ectodomain, then an intrcellular retention sequence (such as a KDEL-containing sequence) on the C-terminus. INTRACELLULAR RETENTION SIGNAL Protein targeting or protein sorting is the biological mechanism by which proteins are transported to the appropriate destinations in the cell or transported out of the cell. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion. This delivery process is carried out based on sequence information contain in the protein itself. Proteins synthesised in the rough endoplasmic reticulum (ER) of eukaryotic cells use the exocytic pathway for transport to their final destinations. Proteins lacking special sorting signals are vectorially transported from the ER via the Golgi and the trans- Golgi network (TGN) to the plasma membrane. Other proteins have targeting signals for incorporation into specific organelles of the exocytic pathway, such as endosomes and lysosomes.
Lysosomes are acidic organelles in which endogenous and internalised macromolecules are degraded by luminal hydrolases. Endogenous macromolecules reach the lysosome by being sorted in the TGN from which they are transported to endosomes and then lysosomes. The targeting signals used by a cell to sort proteins to the correct intracellular location may be exploited by the present invention. The signals may be broadly classed into the following types: i) endocytosis signals ii) Golgi retention signals iii) TGN recycling signals iv) ER retention signals v) lysosomal sorting signals The intracellular retention signal may direct the transmembrane protein away from the secretory pathway during translocation from the ER. The intracellular retention signal may direct the transmembrane protein to an intracellular compartment or complex. The intracellular retention signal may direct the transmembrane protein to a membrane-bound intracellular compartment. For example, the intracellular retention signal may direct the protein to a lysosomal, endosomal or Golgi compartment (trans-Golgi Network, ‘TGN’). Within a normal cell, proteins arising from biogenesis or the endocytic pathway are sorted into the appropriate intracellular compartment following a sequential set of sorting decisions. At the plasma membrane, proteins can either remain at the cell surface or be internalised into endosomes. At the TGN, the choice is between going to the plasma membrane or being diverted to endosomes. In endosomes, proteins can either recycle to the plasma membrane or go to lysosomes. These decisions are governed by sorting signals on the proteins themselves. Lysosomes are cellular organelles that contain acid hydrolase enzymes that break down waste materials and cellular debris. The membrane around a lysosome allows the digestive enzymes to work at the pH they require. Lysosomes fuse with
autophagic vacuoles (phagosomes) and dispense their enzymes into the autophagic vacuoles, digesting their contents. An endosome is a membrane-bounded compartment inside eukaryotic cells. It is a compartment of the endocytic membrane transport pathway from the plasma membrane to the lysosome and provides an environment for material to be sorted before it reaches the degradative lysosome. Endosomes may be classified as early endosomes, late endosomes, or recycling endosomes depending on the time it takes for endocytosed material to reach them. The intracellular retention signal used in the present invention may direct the protein to a late endosomal compartment. The Golgi apparatus is part of the cellular endomembrane system, the Golgi apparatus packages proteins inside the cell before they are sent to their destination; it is particularly important in the processing of proteins for secretion. There is a considerable body of knowledge which has arisen from studies investigating the sorting signals present in known proteins, and the effect of altering their sequence and/or position within the molecule (Bonifacino and Traub (2003) Ann. Rev. Biochem. 72:395-447; Braulke and Bonifacino (2009) Biochimica and Biophysica Acta 1793:605-614; Griffith (2001) Current Biology 11:R226-R228; Mellman and Nelson (2008) Nat Rev Mol Cell Biol. 9:833-845; Dell’Angelica and Payne (2001) Cell 106:395-398; Schafer et al (1995) EMBO J. 14:2424-2435; Trejo (2005) Mol. Pharmacol. 67:1388-1390). Numerous studies have shown that it is possible to insert one or more sorting signals into a protein of interest in order to alter the intracellular location of a protein of interest (Pelham (2000) Meth. Enzymol. 327:279-283). Examples of endocytosis signals include those from the transferrin receptor and the asialoglycoprotein receptor. Examples of signals which cause TGN-endosome recycling include those form proteins such as the CI- and CD-MPRs, sortilin, the LDL-receptor related proteins LRP3 and LRP10 and β-secretase, GGA1-3, LIMP-II, NCP1, mucolipn-1, sialin, GLUT8 and invariant chain.
Examples of TGN retention signals include those from the following proteins which are localized to the TGN: the prohormone processing enzymes furin, PC7, CPD and PAM; the glycoprotein E of herpes virus 3 and TGN38. Examples of ER retention signals include C-terminal signals such as KDEL (SEQ ID No.9), KKXX (SEQ ID No.10) or KXKXX (SEQ ID No.11) and the RXR(R) (SEQ ID No.12) motif of potassium channels. Known ER proteins include the adenovirus E19 protein and ERGIC53. Examples of lysosomal sorting signals include those found in lysosomal membrane proteins, such as LAMP-1 and LAMP-2, CD63, CD68, endolyn, DC-LAMP, cystinosin, sugar phosphate exchanger 2 and acid phosphatase. The molecule of the present invention comprises a Fas-binding domain coupled to an intracellular retention signal. Intracellular retention signals are well known in the art (see, for example, Bonifacino & Traub; Annu. Rev. Biochem.; 2003; 72; 395-447). The term, “intracellular retention signal” refers to an amino acid sequence which directs or maintains the protein in which it is encompassed to a cellular compartment other than that to which it would be directed in the absence of the intracellular retention signal. In this case, the intracellular retention signal directs or maintains nascent Fas to a cellular compartment other than the cell surface membrane. The intracellular retention signal may be any protein or protein domain which is a resident of a given intracellular compartment. This means that said protein or domain is in majority, located in a given compartment. At least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% of said protein or domain is located in said compartment in a cell. The intracellular retention signal prevents the molecule of the present invention and any Fas molecule to which is it bound being translocated to the plasma membrane. As used herein “compartment” or “subcellular compartment” refers to a given subdomain of cell. A compartment may be an organelle (such as endoplasmic reticulum, Golgi apparatus, endosome, lysosome) or an element of an organelle (such as multi-vesicular bodies of endosomes, cis-medial-or trans- cisternae of the Golgi apparatus etc.) or the plasma membrane or sub-domains of the plasma membrane (such as apical, basolateral, axonal domains) or micro domains such as focal adhesions or tight junctions.
An “intracellular compartment” refers to a compartment within a cell. According to the present invention, endogenous Fas may be retained within the cell or within a specific intracellular compartment by the interaction with the Fas binding domain of the molecule of the invention which binding domain is coupled to an intracellular retention signal. The intracellular retention signal may direct the protein to a Golgi (trans-Golgi Network, “TGN”), endosomal or lysosomal compartment. The intracellular retention signal may be selected from the following group: a Golgi retention sequence; a trans-Golgi network (TGN) recycling signal; an endoplasmic reticulum (ER) retention sequence; a proteasome localization sequence or a lysosomal sorting signal. The intracellular retention signal may be a protein or domain which is resident in the Golgi. Suitably, the Golgi retention domain may be selected from the group comprising: Giantin (GolgB1, GenBank Accession number NM+004487.3), TGN38/46, Menkes receptor and Golgi enzymes such as ManII (α-1,3-1,6 mannosidase, Genbank accession number NM_008549), Sialyl Transferase (β- galactosamide α2,6-sialytransferae 1, NM_003032), GalT (β-1,4- galactosyltransferase 1, NM_001497) adenoviral E19, HLA invariant chain or fragments thereof comprising the localisation domains. The Golgi retention sequence comprises an amino acid sequence selected from: SEKDEL (SEQ ID NO: 13), KDEL (SEQ ID NO: 9), KKXX (SEQ ID NO: 10), KXKXX (SEQ ID NO: 11), a tail of adenoviral E19 protein comprising the sequence KYKSRRSFIDEKKMP (SEQ ID NO: 14), a fragment of HLA invariant chain comprising the sequence MHRRRSRSCR (SEQ ID NO: 15), KXD/E (SEQ ID NO: 16) or a YQRL (SEQ ID NO: 17) or variants thereof which retain the ability to function as Golgi retention sequences, wherein X is any amino acid. As mentioned above, the intracellular retention sequence may comprise a SEKDEL (SEQ ID NO: 13) or KDEL (SEQ ID NO: 9) sequence. For example, the KDEL sequence in the Fas-retaining molecules described in the Examples of the present application has the sequence DPAEPSEKDEL (SEQ ID No. 18). The KDEL receptor
binds protein in the ER-Golgi intermediate compartment, or in the early Golgi and returns them to the ER. Proteins only leave the ER after the KDEL sequence has been cleaved off. Thus the protein resident in the ER will remain in the ER as long as it contains a KDEL sequence. This is illustrated schematically in Figure 3. The intracellular retention sequence may be located at the C-terminus of the molecule. Where the molecule of the invention is encoded by a nucleic acid sequence which is part of a bicistronic (or multi-cistronic) nucleic acid construct, it is preferable if the intracellular retention sequence encoding sequence is not located immediately upstream/5’ of a sequence encoding a self-cleaving peptide (such as a 2A or 2A-like peptide). KKX’X’ and KX’KX’X’ signals are retrieval signals which can be placed on the cytoplasmic side of a type I membrane protein. Sequence requirements of these signals are provided in detail by Teasdale & Jackson (Annu. Rev. Cell Dev. Biol.; 12; 27 (1996)). The retention signal may be a KKXX (SEQ ID NO: 10) motif. The KKXX domain may be located that the C terminus of the protein. KKXX is responsible for retrieval of ER membrane proteins from the cis end of the Golgi apparatus by retrograde transport, via interaction with the coat protein (COPI) complex. The intracellular retention signal may be from the adenovirus E19 protein. The intracellular retention signal may be from the protein E3/19K, which is also known as E3gp 19 kDa; E19 or GP19K. The intracellular retention signal may comprise the full cytosolic tail of E3/19K; or the last 6 amino acids of this tail. Suitably, the retention signal may be a tail of adenoviral E19 protein comprising the sequence KYKSRRSFIDEKKMP (SEQ ID NO: 14). The retention signal may be a tail of adenoviral E19 protein comprising the sequence: DEKKMP (SEQ ID No.19). An ER retention signal may selected from the group comprising: an isoform of the invariant chain which resides in the ER (Ii33), Ribophorin I, Ribophorin II, SEC61 or cytochrome b5 or fragments thereof comprising the localisation domains. An example of an ER localisation domain is the ER localisation of Ribophorin II, Genbank accession BC060556.1.
The intracellular retention signal may be a tyrosine-based sorting signal, a dileucine- based sorting signal, an acidic cluster signal, a lysosomal avoidance signal, an NPFX’(1,2)D-Type signal, a KDEL, a KKX’X’ or a KX’KX’X’ signal (wherein X’ is any amino acid). Tyrosine-based sorting signals mediate rapid internalization of transmembrane proteins from the plasma membrane and the targeting of proteins to lysosomes (Bonifacino & Traub; supra). Two types of tyrosine-based sorting signals are represented by the NPX’Y and YX’X’Z’ consensus motifs (wherein Z’ is an amino acid with a bulky hydrophobic side chain). NPX’Y signals mediate rapid internalization of type I transmembrane proteins, they occur in families such as members of the LDL receptor, integrin β, and β-amyloid precursor protein families. Examples of NPX’Y signals are provided in Table 1. Table 1 – NPX’Y signals
Numbers in parentheses indicate motifs that are present in more than one copy within the same protein. The signals in this and other tables should be considered examples. Key residues are indicated in bold type. Numbers of amino acids before (i.e., amino-terminal) and after (i.e., carboxy-terminal) the signals are indicated. Abbreviations: Tm, transmembrane; LDL, low density lipoprotein; LRP1, LDL receptor related protein 1; APP, 13-amyloid precursor protein; APLP1, APP-like protein 1. YX’X’Z’-type signals are found in endocytic receptors such as the transferrin receptor and the asialoglycoprotein receptor, intracellular sorting receptors such as the CI- and CD-MPRs, lysosomal membrane proteins such as LAMP-1 and LAMP-2, and TGN proteins such as TGN38 and furin, as well as in proteins localized to specialized endosomal-lysosomal organelles such as antigen-processing compartments (e.g., HLA-DM) and cytotoxic granules (e.g., GMP-17). The YX’X’Z’-type signals are involved in the rapid internalization of proteins from the plasma membrane. However, their function is not limited to endocytosis, since the same motifs have been implicated in the targeting of transmembrane proteins to lysosomes and lysosome- related organelles. Examples of YX’X’Z’-type signals are provided in Table 2. Table 2 - YX’X’Z’-type signals Protein Species Sequence
Dileucine-based sorting signals ([DE]X’X’X’LL[LI]) play critical roles in the sorting of many type I, type II, and multispanning transmembrane proteins. Dileucine-based sorting signals are involved in rapid internalization and lysosomal degradation of transmembrane proteins and the targeting of proteins to the late endosomal- lysosomal compartments. Transmembrane proteins that contain constitutively active forms of this signal are mainly localised to the late endosomes and lysosomes. Examples of [DE]X’X’X’LL[LI] sorting signals are provided in Table 3. Table 3 - [DE]X’X’X’LL[LI] sorting signals
DX’X’LL signals constitute a distinct type of dileucine-based sorting signals. These signals are present in several transmembrane receptors and other proteins that cycle between the TGN and endosomes, such as the CI- and CD-MPRs, sortilin, the LDL- receptor-related proteins LRP3 and LRP10, and β-secretase. Examples of DX’X’LL sorting signals are provided in Table 4. Table 4 - DX’X’LL sorting signals Protein Species Sequence
Another family of sorting motifs is provided by clusters of acidic residues containing sites for phosphorylation by CKII. This type of motif is often found in transmembrane proteins that are localized to the TGN at steady state, including the prohormone- processing enzymes furin, PC6B, PC7, CPD, and PAM, and the glycoprotein E of herpes virus 3. Examples of acidic cluster signals are provided in Table 5.
Table 5 – Acidic cluster sorting signals Protein Species Sequence
The intracellular retention signal may be selected from the group of: NPX’Y, YX’X’Z, [DE]X’X’X'L[LI], DX’X’LL, DP[FW], FX’DX’F, NPF, LZX’Z[DE], LLDLL, PWDLW, KDEL, HDEL, KKX’X’ or KX’KX’X’; wherein X’ is any amino acid and Z’ is an amino acid with a bulky hydrophobic side chain. The intracellular retention signal may be any sequence shown in Tables 1 to 5. The intracellular retention signal may comprise the Tyrosinase-related protein (TYRP)-1 intracellular retention signal. The intracellular retention signal may comprise the TYRP-1 intracellular domain. The intracellular retention signal may comprise the sequence NQPLLTD (SEQ ID No.20) or a variant thereof. TYRP1 is a well-characterized melansomal protein which is retained in the melanosome (a specialized lysosome) at >99% efficiency. TYRP1 is a 537 amino acid transmembrane protein with a lumenal domain (1-477aa), a transmembrane domain (478-501), and a cytoplasmic domain (502-537). A di-leucine signal residing
on the cytoplasmic domain causes retention of the protein. This di-leucine signal has the sequence shown as SEQ ID No.20 (NQPLLTD). LINKER The molecule of the invention may comprise a linker to connect the Fas-binding domain to the intracellular retention signal. The linker may, for example, be a peptide linker. Numerous suitable peptide linker sequence are known in the art and/or could be readily designed by a skilled person. Flexible polypeptide linkers composed of glycine and serine are commonly used to connect separate domains of engineered multidomain proteins. Such a linker may, for example, comprise repeats of the sequence (GGGGS)n (SEQ ID NO: 21) or, in which n is an integer of, e.g., about 1 to about 8. The linker may comprise the sequence GGGGSGGGGS (SEQ ID NO: 22) or SGGGSGGGSGGGS (SEQ ID NO: 23). The anti-Fas KDEL molecule having the amino acid sequence shown in Figure 1 has a linker with the sequence shown as SED ID No.23. The peptide linker used in the molecule of the invention may have a length of about 5 to about 40; about 10 to about 30; or about 10 to about 20 amino acids. SIGNAL PEPTIDE The molecule of the invention may comprise a signal peptide so that when it is expressed inside a cell, the nascent protein is directed to the endoplasmic reticulum. The signal peptide may, for example, be an IL-2 signal peptide, a kappa leader sequence, a CD8 leader sequence or a peptide with essentially equivalent activity. The construct shown in Figure 1 encodes an anti-Fas KDEL molecule with an Ig Kappa leader sequence having the following sequence MGWSCIILFLVATATGVHS (SEQ ID No.24). The molecule of the present invention may have the sequence shown as SEQ ID No. 25 which is made up of an mIg Kappa Leader sequence (signal peptide), the light chain from the anti-Fas antibody F45D9 (shown above as SEQ ID No.6), a GS linker, the heavy chain from the anti-Fas antibody F45D9 (shown above as SEQ ID No. 5) and the intracellular retention sequence shown above as SEQ ID No.18.
SEQ ID No.25 (anti-Fas-KDEL) MGWSCIILFLVATATGVHSDIQMTQSPSSLSASVGDRVTITCRASQGIRRWLAWYQQ KPEKAPKSLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNSYP YTFGQGTKLEIKRSGGGGSGGGGSGGGGSQVQLQQWGAGLLKPSETLSLICAVYG GSFSTYYWTWIRQPPGKGLEWIGEINHRGTTNYSPSLKSRVTISVDTSKNHISLNLTS VTAADTALYYCARGLLWIGEGDYGLDVWGQGTTVTVSSDPAEPSEKDEL The molecule of the invention may be co-expressed with a chimeric antigen receptor (CAR) or an engineered T-cell receptor (TCR). CAR A classical chimeric antigen receptor (CAR) is a chimeric type I trans-membrane protein which connects an extracellular antigen-recognizing domain (binder) to an intracellular signalling domain (endodomain). The binder is typically a single-chain variable fragment (scFv) derived from a monoclonal antibody (mAb), but it can be based on other formats which comprise an antibody-like antigen binding site. A spacer domain may be used to isolate the binder from the membrane and to allow it a suitable orientation. A common spacer domain used is the Fc of IgG1. More compact spacers can suffice e.g. the stalk from CD8α and even just the IgG1 hinge alone, depending on the antigen. A trans-membrane domain anchors the protein in the cell membrane and connects the spacer to the endodomain. Early CAR designs had endodomains derived from the intracellular parts of either the γ chain of the FcεR1 or CD3ζ. Consequently, these first generation receptors transmitted immunological signal 1, which was sufficient to trigger T-cell killing of cognate target cells but failed to fully activate the T-cell to proliferate and survive. To overcome this limitation, compound endodomains have been constructed: fusion of the intracellular part of a T-cell co-stimulatory molecule to that of CD3ζ results in second generation receptors which can transmit an activating and co-stimulatory signal simultaneously after antigen recognition. The co-stimulatory domain most commonly used is that of CD28. This supplies the most potent co-stimulatory signal - namely immunological signal 2, which triggers T-cell proliferation. Some receptors have also been described which include TNF receptor family endodomains, such as the closely related OX40 and 41BB which transmit survival signals. Even more potent
third generation CARs have now been described which have endodomains capable of transmitting activation, proliferation and survival signals. When the CAR binds the target-antigen, this results in the transmission of an activating signal to the T-cell it is expressed on. Thus the CAR directs the specificity and cytotoxicity of the T cell towards tumour cells expressing the targeted antigen. CARs typically therefore comprise: (i) an antigen-binding domain; (ii) a spacer; (iii) a transmembrane domain; and (iii) an intracellular domain which comprises or associates with a signalling domain. A CAR may have the general structure: Antigen binding domain – spacer domain - transmembrane domain - intracellular signaling domain (endodomain). ANTIGEN BINDING DOMAIN The antigen binding domain is the portion of the CAR which recognizes antigen. In a classical CAR, the antigen-binding domain comprises: a single-chain variable fragment (scFv) derived from a monoclonal. CARs have also been produced with domain antibody (dAb), VHH or Fab-based antigen binding domains. Alternatively a CAR may comprise a ligand for the target antigen. For example, B-cell maturation antigen (BCMA)-binding CARs have been described which have an antigen binding domain based on the ligand a proliferation inducing ligand (APRIL). SPACER Classical CARs comprise a spacer sequence to connect the antigen-binding domain with the transmembrane domain and spatially separate the antigen-binding domain from the endodomain. A flexible spacer allows the antigen-binding domain to orient in different directions to facilitate binding. A variety of sequences are commonly used as spacers for CAR, for example, an IgG1 Fc region, an IgG1 hinge, or a human CD8 stalk.
TRANSMEMBRANE DOMAIN The transmembrane domain is the portion of the CAR which spans the membrane. The transmembrane domain may be any protein structure which is thermodynamically stable in a membrane. This is typically an alpha helix comprising of several hydrophobic residues. The transmembrane domain of any transmembrane protein can be used to supply the transmembrane portion of the CAR. The presence and span of a transmembrane domain of a protein can be determined by those skilled in the art using the TMHMM algorithm (http://www.cbs.dtu.dk/services/TMHMM-2.0/). Alternatively, an artificially designed TM domain may be used. ENDODOMAIN The endodomain is the signal-transmission portion of the CAR. It may be part of or associate with the intracellular domain of the CAR. After antigen recognition, receptors cluster, native CD45 and CD148 are excluded from the synapse and a signal is transmitted to the cell. The most commonly used endodomain component is that of CD3-zeta which contains 3 ITAMs. This transmits an activation signal to the T cell after antigen is bound. CD3-zeta may not provide a fully competent activation signal and additional co-stimulatory signalling may be needed. Co-stimulatory signals promote T-cell proliferation and survival. There are two main types of co-stimulatory signals: those that belong the Ig family (CD28, ICOS) and the TNF family (OX40, 41BB, CD27, GITR etc). For example, chimeric CD28 and OX40 can be used with CD3-Zeta to transmit a proliferative / survival signal, or all three can be used together. The endodomain may comprise: (i) an ITAM-containing endodomain, such as the endodomain from CD3 zeta; and/or (ii) a co-stimulatory domain, such as the endodomain from CD28 or ICOS; and/or (iii) a domain which transmits a survival signal, for example a TNF receptor family endodomain such as OX-40, 4-1BB, CD27 or GITR. A number of systems have been described in which the antigen recognition portion is on a separate molecule from the signal transmission portion, such as those described in WO015/150771; WO2016/124930 and WO2016/030691. The CAR of the present invention may therefore comprise an antigen-binding component comprising an antigen-binding domain and a transmembrane domain; which is capable of interacting
with a separate intracellular signalling component comprising a signalling domain. The vector of the invention may express a CAR signalling system comprising such an antigen-binding component and intracellular signalling component. The CAR may comprise a signal peptide so that when it is expressed inside a cell, the nascent protein is directed to the endoplasmic reticulum and subsequently to the cell surface, where it is expressed. The signal peptide may be at the amino terminus of the molecule. TARGET ANTIGEN A ‘target antigen’ is an entity which is specifically recognised and bound by the antigen-binding domain of a CAR. The target antigen may be an antigen present on a cancer cell, for example a tumour- associated antigen. Various tumour associated antigens (TAA) are known, as shown in the following Table 6. The CAR may be capable of binding such a TAA. Table 6
TRANSGENIC T-CELL RECEPTOR
The T-cell receptor (TCR) is a molecule found on the surface of T cells which is responsible for recognizing fragments of antigen as peptides bound to major histocompatibility complex (MHC) molecules. The TCR is a heterodimer composed of two different protein chains. In humans, in 95% of T cells the TCR consists of an alpha (α) chain and a beta (β) chain (encoded by TRA and TRB, respectively), whereas in 5% of T cells the TCR consists of gamma and delta (γ/δ) chains (encoded by TRG and TRD, respectively). When the TCR engages with antigenic peptide and MHC (peptide/MHC), the T lymphocyte is activated through signal transduction. In contrast to conventional antibody-directed target antigens, antigens recognized by the TCR can include the entire array of potential intracellular proteins, which are processed and delivered to the cell surface as a peptide/MHC complex. It is possible to engineer cells to express heterologous (i.e. non-native) TCR molecules by artificially introducing the TRA and TRB genes; or TRG and TRD genes into the cell using vector. For example the genes for engineered TCRs may be reintroduced into autologous T cells and transferred back into patients for T cell adoptive therapies. Such ‘heterologous’ TCRs may also be referred to herein as ‘transgenic TCRs’. NUCLEIC ACID SEQUENCE The present invention provides a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal. As used herein, the terms “polynucleotide”, “nucleotide”, and “nucleic acid” are intended to be synonymous with each other. It will be understood by a skilled person that numerous different polynucleotides and nucleic acids can encode the same polypeptide as a result of the degeneracy of the genetic code. In addition, it is to be understood that skilled persons may, using routine techniques, make nucleotide substitutions that do not affect the polypeptide sequence encoded by the polynucleotides described here to reflect the codon usage of any particular host organism in which the polypeptides are to be expressed.
Nucleic acids according to the invention may comprise DNA or RNA. They may be single-stranded or double-stranded. They may also be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to oligonucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones, addition of acridine or polylysine chains at the 3' and/or 5' ends of the molecule. For the purposes of the use as described herein, it is to be understood that the polynucleotides may be modified by any method available in the art. Such modifications may be carried out in order to enhance the in vivo activity or life span of polynucleotides of interest. The terms “variant”, “homologue” or “derivative” in relation to a nucleotide sequence include any substitution of, variation of, modification of, replacement of, deletion of or addition of one (or more) nucleic acid from or to the sequence. NUCLEIC ACID CONSTRUCT The present invention also provides a nucleic acid construct comprising a nucleic acid sequence encoding a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and a nucleic acid encoding a polypeptide of interest (POI). The POI may, for example, be a CAR or transgenic TCR. The nucleic acids may be in either order in the construct. Nucleic acids encoding two or more polypeptides may be separated by a co- expression site enabling co-expression of two polypeptides as separate entities. It may be a sequence encoding a cleavage site, such that the nucleic acid construct produces both polypeptides, joined by a cleavage site(s). The cleavage site may be self-cleaving, such that when the polypeptide is produced, it is immediately cleaved into individual peptides without the need for any external cleavage activity. The cleavage site may be any sequence which enables the two polypeptides to become separated.
The term “cleavage” is used herein for convenience, but the cleavage site may cause the peptides to separate into individual entities by a mechanism other than classical cleavage. For example, for the Foot-and-Mouth disease virus (FMDV) 2A self- cleaving peptide (see below), various models have been proposed for to account for the “cleavage” activity: proteolysis by a host-cell proteinase, autoproteolysis or a translational effect (Donnelly et al (2001) J. Gen. Virol. 82:1027-1041). The exact mechanism of such “cleavage” is not important for the purposes of the present invention, as long as the cleavage site, when positioned between nucleic acid sequences which encode proteins, causes the proteins to be expressed as separate entities. The cleavage site may, for example be a furin cleavage site, a Tobacco Etch Virus (TEV) cleavage site or encode a self-cleaving peptide. A ‘self-cleaving peptide’ refers to a peptide which functions such that when the polypeptide comprising the proteins and the self-cleaving peptide is produced, it is immediately “cleaved” or separated into distinct and discrete first and second polypeptides without the need for any external cleavage activity. The self-cleaving peptide may be a 2A self-cleaving peptide from an aphtho- or a cardiovirus. The primary 2A/2B cleavage of the aptho- and cardioviruses is mediated by 2A “cleaving” at its own C-terminus. In apthoviruses, such as foot-and-mouth disease viruses (FMDV) and equine rhinitis A virus, the 2A region is a short section of about 18 amino acids, which, together with the N-terminal residue of protein 2B (a conserved proline residue) represents an autonomous element capable of mediating “cleavage” at its own C-terminus (Donelly et al (2001) as above). “2A-like” sequences have been found in picornaviruses other than aptho- or cardioviruses, ‘picornavirus-like’ insect viruses, type C rotaviruses and repeated sequences within Trypanosoma spp and a bacterial sequence (Donnelly et al (2001) as above). The cleavage site may comprise the 2A-like sequence shown as SEQ ID No.26 (RAEGRGSLLTCGDVEENPGP). VECTOR
The present invention also provides a vector, or kit of vectors, which comprises one or more nucleic acid sequence(s) or nucleic acid construct(s) according to the invention. Such a vector may be used to introduce the nucleic acid sequence(s) into a host cell so that it expresses a molecule which comprises a Fas-binding domain linked to an intracellular retention signal and optionally a chimeric antigen receptor (CAR) or a transgenic T cell receptor (TCR). The vector may, for example, be a plasmid or a viral vector, such as a retroviral vector or a lentiviral vector, or a transposon based vector or synthetic mRNA. The vector may be capable of transfecting or transducing an immune effector cell, such as a T cell or a NK cell. KIT OF NUCLEIC ACID SEQUENCES/VECTORS There is also provided a kit of nucleic acid sequences comprising: (a) a first nucleic acid sequence which encodes a molecule which comprises a Fas- binding domain linked to an intracellular retention signal, and (b) a second nucleic acid sequence which encodes a POI. The POI may, for example, be a CAR or engineered TCR The present invention also provides a kit of vectors comprising: (a) a first vector comprising a first nucleic acid sequence which encodes a molecule which comprises a Fas-binding domain linked to an intracellular retention signal, and (b) a second vector comprising a second nucleic acid sequence which encodes a POI. CELL The present invention provides a cell which comprises a molecule of the first aspect of the invention. The cell may comprise a nucleic acid sequence, a nucleic acid construct or a vector of the present invention.
The present invention provides a cell engineered to express (a) a molecule which comprises a Fas-binding domain linked to an intracellular retention signal; and (b) FasL The cell may be a tumour-infiltrating lymphocyte (TIL). Tumour-infiltrating lymphocytes are white blood cells that have left the bloodstream and migrated towards a tumour. They include T cells and B cells and are part of the larger category of ‘tumour-infiltrating immune cells’ which consist of both mononuclear and polymorphonuclear immune cells, (i.e., T cells, B cells, natural killer cells, macrophages, neutrophils, dendritic cells, mast cells, eosinophils, basophils, etc.) in variable proportions. In Adoptive T cell transfer therapy, tumour-infiltrating lymphocytes are removed from a patient’s tumour, expanded ex vivo, and then given back to the patient to help the immune system kill the cancer cells. As mentioned above, the immunosuppressive tumour microenvironment upregulates death ligands such as Fas ligand (FasL). FasL induces apoptosis of immune cells that express death receptors for Fas, such as tumour-infiltrating lymphocytes (TILs). The cell of the present invention has an in-built resistance to FasL-mediated apoptosis so an enhanced capacity to survive and persist in the hostile tumour microenvironment. The cell may be an effector immune cell. The cell may be a cytolytic immune cell such as a T cell or an NK cell. T cells or T lymphocytes are a type of lymphocyte that play a central role in cell- mediated immunity. They can be distinguished from other lymphocytes, such as B cells and natural killer cells (NK cells), by the presence of a T-cell receptor (TCR) on the cell surface. There are various types of T cell, as summarised below. Helper T helper cells (TH cells) assist other white blood cells in immunologic processes, including maturation of B cells into plasma cells and memory B cells, and activation of cytotoxic T cells and macrophages. TH cells express CD4 on their surface. TH cells become activated when they are presented with peptide antigens by MHC class II molecules on the surface of antigen presenting cells (APCs). These cells can differentiate into one of several subtypes, including TH1, TH2, TH3, TH17, Th9, or TFH, which secrete different cytokines to facilitate different types of immune responses.
Cytolytic T cells (TC cells, or CTLs) destroy virally infected cells and tumor cells, and are also implicated in transplant rejection. CTLs express the CD8 at their surface. These cells recognize their targets by binding to antigen associated with MHC class I, which is present on the surface of all nucleated cells. Through IL-10, adenosine and other molecules secreted by regulatory T cells, the CD8+ cells can be inactivated to an anergic state, which prevent autoimmune diseases such as experimental autoimmune encephalomyelitis. Memory T cells are a subset of antigen-specific T cells that persist long-term after an infection has resolved. They quickly expand to large numbers of effector T cells upon re-exposure to their cognate antigen, thus providing the immune system with "memory" against past infections. Memory T cells comprise three subtypes: central memory T cells (TCM cells) and two types of effector memory T cells (TEM cells and TEMRA cells). Memory cells may be either CD4+ or CD8+. Memory T cells typically express the cell surface protein CD45RO. Regulatory T cells (Treg cells), formerly known as suppressor T cells, are crucial for the maintenance of immunological tolerance. Their major role is to shut down T cell- mediated immunity toward the end of an immune reaction and to suppress auto- reactive T cells that escaped the process of negative selection in the thymus. Two major classes of CD4+ Treg cells have been described — naturally occurring Treg cells and adaptive Treg cells. Naturally occurring Treg cells (also known as CD4+CD25+FoxP3+ Treg cells) arise in the thymus and have been linked to interactions between developing T cells with both myeloid (CD11c+) and plasmacytoid (CD123+) dendritic cells that have been activated with TSLP. Naturally occurring Treg cells can be distinguished from other T cells by the presence of an intracellular molecule called FoxP3. Mutations of the FOXP3 gene can prevent regulatory T cell development, causing the fatal autoimmune disease IPEX. Adaptive Treg cells (also known as Tr1 cells or Th3 cells) may originate during a normal immune response.
The cell may be a tumour infiltrating lymphocyte (TIL) as described above. The cell may be a T-cell expended from a TIL isolated from a subject having cancer. The cell may be a Natural Killer cell (or NK cell). NK cells form part of the innate immune system. NK cells provide rapid responses to innate signals from virally infected cells in an MHC independent manner NK cells (belonging to the group of innate lymphoid cells) are defined as large granular lymphocytes (LGL) and constitute the third kind of cells differentiated from the common lymphoid progenitor generating B and T lymphocytes. NK cells are known to differentiate and mature in the bone marrow, lymph node, spleen, tonsils and thymus where they then enter into the circulation. The cells of the invention may be any of the cell types mentioned above. Cells according to the invention may either be created ex vivo either from a patient’s own peripheral blood (1st party), or in the setting of a haematopoietic stem cell transplant from donor peripheral blood (2nd party), or peripheral blood from an unconnected donor (3rd party). Alternatively, cells may be derived from ex vivo differentiation of inducible progenitor cells or embryonic progenitor cells to, for example, T or NK cells. Alternatively, an immortalized T-cell line which retains its lytic function and could act as a therapeutic may be used. In all these embodiments, chimeric polypeptide-expressing cells are generated by introducing DNA or RNA coding for the chimeric polypeptide by one of many means including transduction with a viral vector, transfection with DNA or RNA. The cell of the invention may be an ex vivo cell from a subject. The cell may be from a peripheral blood mononuclear cell (PBMC) sample. The cells may be activated and/or expanded prior to being transduced with nucleic acid encoding the molecules providing the chimeric polypeptide according to the first aspect of the invention, for example by treatment with an anti-CD3 monoclonal antibody. The cell of the invention may be made by:
(i) isolation of a cell-containing sample from a subject or other sources listed above; and (ii) transduction or transfection of the cells with one or more a nucleic acid sequence(s), nucleic acid construct(s) or vector(s) of the invention. The cells may then by purified, for example, selected on the basis of expression of one or more heterologous nucleic acid sequences. The effector immune cell is capable of recognising and killing a target immune cell. The target immune cell may be a cytolytic immune cell such as a T-cell or NK cell as defined above. The invention also provides a method for making a cell of the invention which comprises the step of introducing into a cell a nucleic acid sequence, a nucleic acid construct, a vector, or a kit of vectors according to the invention. The cell may be made by transduction. The cell may be screened, post-transduction by a method according to the second aspect of the invention. PHARMACEUTICAL COMPOSITION The present invention also relates to a pharmaceutical composition containing a plurality of cells according to the invention. The pharmaceutical composition may additionally comprise a pharmaceutically acceptable carrier, diluent or excipient. The pharmaceutical composition may optionally comprise one or more further pharmaceutically active polypeptides and/or compounds. Such a formulation may, for example, be in a form suitable for intravenous infusion. METHOD OF TREATMENT The present invention provides a method for treating a disease which comprises the step of administering the cells of the present invention (for example in a pharmaceutical composition as described above) to a subject. A method for treating a disease relates to the therapeutic use of the cells of the present invention. Herein the cells may be administered to a subject having an
existing disease or condition in order to lessen, reduce or improve at least one symptom associated with the disease and/or to slow down, reduce or block the progression of the disease. The method for preventing a disease relates to the prophylactic use of the cells of the present invention. Herein such cells may be administered to a subject who has not yet contracted the disease and/or who is not showing any symptoms of the disease to prevent or impair the cause of the disease or to reduce or prevent development of at least one symptom associated with the disease. The subject may have a predisposition for, or be thought to be at risk of developing, the disease. The method may involve the steps of: (i) isolating a cell-containing sample; (ii) transducing or transfecting such cells with a nucleic acid sequence or vector provided by the present invention; (iii) administering the cells from (ii) to a subject. The cell-containing sample may be isolated from a subject or from other sources, as described above. The present invention provides a cell of the present invention for use in treating and/or preventing a disease. The invention also relates to the use of a cell of the present invention in the manufacture of a medicament for the treatment of a disease. The disease to be treated by the methods of the present invention may be a cancerous disease, such as bladder cancer, breast cancer, colon cancer, endometrial cancer, kidney cancer (renal cell), leukaemia, lung cancer, melanoma, non-Hodgkin lymphoma, pancreatic cancer, prostate cancer and thyroid cancer. The disease may be Multiple Myeloma (MM), B-cell Acute Lymphoblastic Leukaemia (B-ALL), Chronic Lymphocytic Leukaemia (CLL), Neuroblastoma, T-cell acute Lymphoblastic Leukaema (T-ALL) or diffuse large B-cell lymphoma (DLBCL). The disease may be a plasma cell disorder such as plasmacytoma, plasma cell leukemia, multiple myeloma, macroglobulinemia,amyloidosis, Waldenstrom's
macroglobulinemia, solitary bone plasmacytoma, extramedullary plasmacytoma, osteosclerotic myeloma, heavy chain diseases, monoclonal gammopathy of undetermined significance or smoldering multiple myeloma. The invention will now be further described by way of Examples, which are meant to serve to assist one of ordinary skill in the art in carrying out the invention and are not intended in any way to limit the scope of the invention. EXAMPLES Example 1 - Expression of an anti-Fas KDEL molecule reduces cell-surface expression of Fas Peripheral blood mononuclear cells (PBMCs) and SupT1 cells were either left untransduced or transduced with a construct expressing the anti-Fas KDEL molecule having the sequence shown as SEQ ID No. 25, together with BFP as a marker for transduction. Three days after transduction the cells were incubated with either a PE- conjugated anti-Fas antibody or a PE-conjugated isotype control and consequently Fas staining was analysed by flow cytometry, with the results shown in Figure 4. For both PBMCs and SupT1 cells, decreased staining of Fas was observed when transduced with the Fas binder-KDEL polypeptide. Example 2 - Expression of an anti-Fas KDEL molecule protects a cell from FasL- mediated apoptosis PBMCs and SupT1 cells transduced as described for Example 4 were either left untreated or treated with MEGA FasL (100 ng/mL) for 48 hours, at which point cells were analysed by flow cytometry and the results are shown in Figure 5. PBMCs and SupT1s transduced with the Fas binder-KDEL polypeptide show almost 100% survival following exposure to MEGA FasL, whereas non-transduced PBMCs and SupT1 cells are completely killed following exposure to the ligand. In order to investigate the effect of exposure of the cells to FasL expressed on a cell surface rather than soluble FasL, the experiment above was repeated but this time cells were co-cultured with NT SupT1 cells or FasL-expressing SupT1 cells. Cells were co-cultured at a 1:2 PBMC:SupT1 ratio for 48 hours, at which point cells were analysed by flow cytometry. The results are shown in Figure 6. Again, PBMCs and
SupT1s transduced with the Fas binder-KDEL polypeptide show almost 100% survival following co-culture with FasL-expressing target cells, whereas non- transduced PBMCs and SupT1 cells are virtually undetectable following 48 hours of co-culture. All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the following claims.
Claims
CLAIMS 1. A molecule which comprises i) a binding domain which binds to a FAS extracellular domain and ii) a retention domain that intracellularly retains FAS within the endoplasmic reticulum or Golgi apparatus.
2. A molecule according to claim 1, wherein the binding domain comprises part of FAS ligand (FASL), a single chain variable fragment (scFv), a single domain antibody (sdAb), a Fab antigen binding domain (Fab) or a monoclonal antibody.
3. A molecule according to claim 2, wherein the single domain antibody is derived from an artificial VHH fragment or a camelid antibody.
4. A molecule according to claim 1, wherein the retention domain is C-terminal to the binding domain.
5. A molecule according to any preceding claim, wherein the retention domain comprises a sequence selected from the group consisting of: NPX’Y, YX’X’Z, [DE]X’X’X'L[LI], DX’X’LL, DP[FW], FX’DX’F, NPF, LZX’Z[DE], LLDLL, PWDLW, KDEL, HDEL, KKX’X’ or KX’KX’X’; wherein X’ is any amino acid and Z’ is an amino acid with a bulky hydrophobic side chain.
6. A molecule according to any preceding claim, wherein the retention domain comprises any sequence shown in Tables 1 to 5.
7. A nucleic acid sequence encoding a molecule according to any preceding claim.
8. A nucleic acid construct comprising a first nucleic acid sequence according to claim 7 and a second nucleic acid sequence which encodes a polypeptide of interest (POI).
9. A nucleic acid construct according to claim 8 wherein the first and second nucleic acid sequences are separated by a third nucleic acid sequence encoding a coexpression sequence enabling expression of the molecule and POI as separate polypeptides.
10. A kit of nucleic acid sequences comprising: (a) a first nucleic acid sequence according to claim 7, and (b) a second nucleic acid which encodes a POI.
11. A vector comprising a nucleic acid sequence according to claim 7 or a nucleic acid construct according to claim 8 or 9.
12. A kit of vectors comprising: (i) a first vector comprising a nucleic acid according to claim 7; and (ii) a second vector comprising a nucleic acid encoding a POI.
13. A cell expressing a molecule according to any of claims 1 to 6.
14. A cell according to claim 13 which also expresses and a POI.
15. A nucleic acid construct according to claim 8 or 9; a kit of nucleic acid sequences according to claim 10; a vector according to claim 11; a kit of vectors according to claim 12 or a cell according to claim 14 wherein the POI is a chimeric antigen receptor (CAR) or an engineered T-cell receptor (TCR).
16. A pharmaceutical composition which comprises a plurality of cells according to claim 13 or 14.
17. A pharmaceutical composition according to claim 16 for use in treating and/or preventing a disease.
18. A method for treating and/or preventing a disease, which comprises the step of administering a pharmaceutical composition according to claim 16 to a subject in need thereof.
19. A method according to claim 18, which comprises the following steps: (i) isolation of a cell containing sample; (ii) transduction or transfection of a cell from the sample with a nucleic acid sequence according to claim 7; a nucleic acid construct according to claim 8 or 9; a kit of nucleic acid sequences according to claim 10; a vector according to claim 11; a kit of vectors according to claim 12; and (iii) administering the cells from (ii) to a subject.
20. A method according to claim 19 wherein the cell is autologous.
21. A method according to claim 19 wherein the cell is allogenic.
22. The use of a cell according to claim 13 or 14 in the manufacture of a pharmaceutical composition for the treatment and/or prevention of a disease.
23. The pharmaceutical composition for use according to claim 17, the method according to any of claims 18 to 21, or the use according to claim 22 wherein the disease is cancer.
24. A method for making a cell according to claim 13 or 14, which comprises the step of introducing: a nucleic acid sequence according to claim 7; a nucleic acid construct according to claim 8 or 9; a kit of nucleic acid sequences according to claim 10; a vector according to claim 11; a kit of vectors according to claim 12, into the cell ex vivo.
25. A method according to claim 24, wherein the cell is from a sample isolated from a subject.
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