Polypeptide systems
The novel polypeptide system with a CAR and EAR enhances CAR-T cell persistence and shielding, addressing cancer escape issues and improving therapeutic efficacy in B cell leukemia and lymphoma treatments.
Patent Information
- Application Number
- PCT/CN2025/089553
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2024-09-06
- Filing Date
- 2025-04-17
- Publication Date
- 2025-10-23
AI Technical Summary
Existing CAR-T cell therapies for treating B cell leukemia and lymphoma show suboptimal efficacy due to cancer escape issues, with patients relapsing despite treatment with CD19-negative disease.
A novel polypeptide system comprising a chimeric antigen receptor (CAR) and additional polypeptides, including an engineered armor receptor (EAR), enhances cell persistence and shielding, improving therapeutic efficacy by reducing cancer escape.
The system improves CAR-T cell function in hostile environments, enhancing persistence and expansion, and providing strong cell shielding, thereby improving overall therapeutic efficacy.
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Figure PCTCN2025089553-FTAPPB-I100003
Abstract
Description
POLYPEPTIDE SYSTEMSFIELD OF THE INVENTION
[0001] The present disclosure relates to the fields of immunology, cell biology and molecular biology. More specifically, the disclosure relates to multiple polypeptides, cells expression such polypeptides and therapeutic uses thereof.BACKGROUND
[0002] Chimeric antigen receptor (CAR) T cells have shown remarkable response rates in patients with specific B cell leukemia or lymphoma subtypes and encouraging results have also been observed in patients with multiple myeloma. However, effector cells expressing single CAR may not show optimum efficacy. It was found that one patient administrated with a CD19 CAR product relapsed with CD19-negative disease after treatment. There is still a need for alternative CAR treatment approaches that address the cancer escape issue. BRIEF SUMMARY
[0003] The present disclosure provides a novel system comprising a CAR and one or more additional polypeptides for cell therapy. Compared to the traditional CAR-T cell therapies, this system reduces cancer escape, enhances cell persistence and expansion, and / or provides strong cell shielding, enabling the cells expressing which to better function in the hostile environment, further improving their overall efficacy.
[0004] In a first aspect, the disclosure provides a polypeptide system, comprising a first chimeric antigen receptor (CAR) and one or more additional polypeptides. In one aspect, the first CAR comprises, from its N (amino) to C (carboxy) terminus in order, a first extracellular antigen-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 31, a first transmembrane domain and a first intracellular signaling domain. In one aspect, the first extracellular antigen-binding domain is capable of binding CD19. In one aspect, the first CAR comprises, from its N to C terminus in order, a first extracellular CD20-binding domain, a first spacer of CD28 hinge, a first transmembrane domain and a first intracellular signaling domain. In one aspect, the additional polypeptide is a second CAR or a polypeptide of an engineered armor receptor (EAR) .
[0005] A second aspect of the disclosure provides a polypeptide system, comprising a polypeptide of a first EAR and a polypeptide of a second EAR, wherein the first EAR is capable of binding Fas ligand, the second EAR is capable of binding TGFβ.
[0006] The disclosure further provides a polynucleotide system encoding the polypeptide system as defined herein before, a vector system comprising one or more vectors comprising the polynucleotide system as defined herein before, a cell comprising the polynucleotide system, the vector system, or the polypeptide system as defined herein before, and a method of treating a disease in a subject, comprising administering a therapeutically effective amount of the cell as defined herein before to the subject.BRIEF DESCRIPTION OF THE DRAWINGS
[0007] Figure. 1 shows the association constant (Ka) , association rate (Kon) and dissociation rate (Koff) of FMC63-scFv, CD19 scFv-1, CD19 scFv-2 and CD19 scFv-3.
[0008] Figure. 2 shows the binding affinity to CD19 protein of CD19 CAR-W and CD19 CAR-1 to 12 on T cells.
[0009] Figure. 3 relates to the tonic signaling of CD19 CAR-W and CD19 CAR-1 to 12.
[0010] In Figure. 4A to 4C, the activities of CD19 CARs comprising spacer S-3 are shown. Figure. 4A shows the degree of CD19 expression of different target cells. The killing efficiency of the CARs is shown in Figure. 4B. Fig 4C shows the CD69 expression on T cells induced by CARs.
[0011] Figure. 5A to 5D relate to the T cell activation and expansion post target cell stimulation. Figure. 5A, 5B, and 5C show the IFN-γ, TNF-a, and IL-2 secreted by T cell transduced with CARs. Figure. 5D shows the proliferation of T cell 7 days after the initial simulation.
[0012] Figure. 6 shows the CAR-T cell killing of Raji-CD19Lo target cells at day 3 of co-culture assay (E: T=1: 1, 1: 2, 1: 8) .
[0013] Figure. 7A shows the degree of CD20 expression of different target cells. Figure. 7B depicts the result of an activation assay in Jurkat cells.
[0014] Figure. 8A to 8C show the percentage of CD25, CD69 and Ki67 positive populations in primary T cells after stimulated by either CD20KO, CD20lo or CD20WT Raji cells for 48 hours.
[0015] Figure. 9A to 9B show the IFN-γ and IL-2 secreted by T cell transduced with CARs, stimulated by different target cell lines.
[0016] Figure. 10 shows the killing score of T cells on different target cell lines after 24 hours.
[0017] Figure. 11 shows the growth of T cells without further stimulation in the presence of supplemented 100 IU / mL IL-2.
[0018] Figure. 12A shows the EGFR+ T cell expansion, T cell viability and EGFR+ T cell enrichment with 100 IU / mL supplemented IL-2. Figure 12B shows the EGFR+ T cell expansion, T cell viability and EGFR+T cell enrichment in absence of exogenous stimulation or cytokines. Figure 12C shows the EGFR+ T cell expansion, T cell viability and EGFR+ T cell enrichment with 50 ng / mL trimeric FasL stimulation in the presence of supplemented 100 IU / mL IL-2.
[0019] Figure. 13 shows the T cell expansion post 50 ng / mL trimeric FasL stimulation.
[0020] Figure. 14 shows the EGFR+ T cell expansion post non-IL-2 starvation.
[0021] Figure. 15A shows the transduction efficiency and surface level of CD19 CAR at day 7 after lentivirus transduction. Figure. 15B shows the CAR-T cell killing of K562 tumor cells at day 1 of co-culture assay (E: T=1: 1) . Figure. 15C shows the CAR-T cell killing of Raji-CD19Lo, Raji-CD20Lo, Raji-WT target cells at day 1 of co-culture assay (E: T=1: 1) .
[0022] Figure. 16 shows the CAR-T cell killing of Raji-WT target cells at day 1 of co-culture assay (E: T=1: 2) .
[0023] Figure. 17 shows the T cell expansion and viability with 100 IU / mL supplemented IL-2 or in the absence of cytokines.
[0024] Figure. 18A shows the T cell expansion and viability with 50 ng / mL trimeric FasL stimulation in the presence of supplemented 100 IU / mL IL-2. Figure. 18B shows the CAR-T cell killing of Raji-FasLOE target cells at day 1, 3, 7 of co-culture assay (E: T=1: 1, 1: 2, 1: 4) .
[0025] Figure. 19A shows the CAR-T cell killing of Raji-WT target cells at day 3 of co-culture assay (E: T=1: 2) in the absence / presence of 20 ng / mL TGFβ1 treatment. Figure. 19B shows the T cell and CAR-T cell expansion at day 7 co-cultured with Raji-WT target cells (E: T=1: 2) in the absence / presence of 20 ng / mL TGFβ1 treatment.
[0026] Figure. 20 shows the CAR-T cell killing of Raji-CD58KO target cells at day 1 of co-culture assay (E: T=1: 2, 1: 4, 1: 8) .
[0027] Figure. 21 shows the T cell expansion and viability with repetitive 50 ng / mL trimeric FasL stimulation in the presence of 20 ng / mL TGFβ1 treatment at day 0 and day 3.
[0028] Figure. 22 shows the T cell expansion and viability with repetitive 50 ng / mL trimeric FasL stimulation in the presence of 20 ng / mL TGFβ1 treatment at day 0 and day 3.
[0029] Figure. 23 shows the CAR-T cell efficacy in an in vivo xenograft model of Raji-WT tumor cells.
[0030] Figure. 24 shows the CAR-T cell efficacy in an in vivo xenograft model of Raji-CD19KO tumor cells.
[0031] Figure. 25 shows the CAR-T cell efficacy in an in vivo xenograft model of Raji-WT tumor cells.DETAILED DESCRIPTIONI. Definitions
[0032] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains.
[0033] The term “a” and “an” refers to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “apolypeptide” means one polypeptide or more than one polypeptide.
[0034] The term “about” used in combination with a numerical value is intended to encompass the numerical values in a range from a lower limit less than the specified numerical value by 5%to an upper limit greater than the specified numerical value by 5%.
[0035] The terms “comprising” , “comprises” and “comprised of” as used herein are synonymous with “including” , “includes” or “containing” , “contains” , and are inclusive or open-ended and do not exclude additional, non-recited members, elements or method steps. The terms “comprising” , “comprises” and “comprised of” also include the term “consisting of” .
[0036] The terms “first” , “second” and “third” used in combination with substances are intended to confer distinguishable names to similar substances, e.g. a first CAR and a second CAR. A system comprising the second substance may or may not comprise the first substance.
[0037] The term "antibody" herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g. bispecific antibodies) , intact antibodies and antibody fragments so long as they exhibit the desired antigen-binding activity.
[0038] The "antibody fragment" refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen. Examples of antibody fragments include but are not limited to Fv, Fab, Fab', Fab’ -SH, F (ab') 2, diabodies, linear antibodies, single-chain antibody molecules (e.g. scFv and scFab) , single-domain antibodies, and multispecific antibodies formed from antibody fragments.
[0039] A “Single-chain Fv” or “scFv” is an antibody fragment of the variable regions of the light (VL) and heavy chain (VH) , connected with a short linker peptide of about ten to 25 amino acids. The linker is usually flexible and can either connect the N-terminus of the VH with the C-terminus of the VL, or vice versa. This protein retains the specificity of the original antibody, despite removal of the constant regions and the introduction of the linker.
[0040] The term "antigen binding domain" refers to the part of an antibody that comprises the area which binds to and is complementary to part or all of an antigen. An antigen binding domain may be provided by, for example, one or more antibody variable domains (also called antibody variable regions) . In preferred aspects, an antigen binding domain comprises an antibody light chain variable domain (VL) and an antibody heavy chain variable domain (VH) . The term “CD19-VH” and “CD19-VL” refer to a VH and a VL in a CD19-binding domain, respectively. The term “CD20-VH” and “CD20-VL” refer to a VH and a VL in a CD20-binding domain, respectively.
[0041] The term “variable region” or “variable domain” refers to the domain of an antibody heavy or light chain that is involved in binding the antibody to antigen. The variable domains of the heavy chain and light chain (VH and VL, respectively) of a native antibody generally have similar structures, with each domain comprising four conserved framework regions (FRs) and complementarity determining regions (CDRs) . A single VH or VL domain may be sufficient to confer antigen-binding specificity. Furthermore, antibodies that bind a particular antigen may be isolated using a VH or VL domain from an antibody that binds the antigen to screen a library of complementary VL or VH domains, respectively. As used herein in connection with variable region sequences, "Kabat numbering" refers to the numbering system set forth by Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD (1991) .
[0042] The terms “complementarity determining region” and “CDR” are known to refer to non-contiguous sequences of amino acids within antibody variable regions, which confer antigen specificity and / or binding affinity. In general, there are three CDRs in each heavy chain variable region (HCDR1, HCDR2, HCDR3) and three CDRs in each light chain variable region (LCDR1, LCDR2, LCDR3) . “Framework regions” and “FR” refer to the non-CDR portions of the variable regions of the heavy and light chains. Table 1, below, lists exemplary position boundaries of HCDR1, HCDR2, HCDR3, LCDR1, LCDR2 and LCDR3 as identified by Kabat, Chothia, AbM, IMGT and Contact schemes, respectively. Unless otherwise indicated, the amino acid sequences of CDRs shown in the present disclosure are determined according to Kabat et al. Table 1. the CDR regions according to various numbering systems
[0043] The term “specifically binds” or “bind” , which can be used interchangeably, as used herein means the ability of a protein, under specific binding conditions, to bind to a target protein such that its affinity or avidity is at least 5 times as great, but optionally at least 10, 20, 30, 40, 50, 100, 250 or 500 times as great, or even at least 1000 times as great as the average affinity or avidity of the same protein to a collection of random peptides or polypeptides of sufficient statistical size. A specifically binding protein need not bind exclusively to a single target molecule but may specifically bind to a non-target molecule due to similarity in structural conformation between the target and non-target (e.g., paralogs or orthologs) . One skilled artisan recognizes that specific binding to a molecule having the same function in a different species of animal or to a non-target molecule having a substantially similar epitope as the target molecule is possible and does not detract from the specificity of binding which is determined relative to a statistically valid collection of unique non-targets. Thus, a polypeptide may specifically bind to more than one distinct species of target molecule due to cross-reactivity.
[0044] The term “epitope” refers to the moieties of an antigen that specifically interact with an antibody. Such moieties, referred to herein as epitopic determinants, typically comprise, or are part of, elements such as amino acid side chains or sugar side chains. An epitopic determinant can be defined, e.g. by methods known in the art, e.g. by crystallography or by hydrogen-deuterium exchange. At least one or some of the moieties on the antibody molecule that specifically interact with an epitopic determinant are typically located in a CDR (s) . Typically, an epitope has a specific three-dimensional structural characteristic and / or a specific charge characteristic. Some epitopes are linear epitopes while others are conformational epitopes.
[0045] “Percent (%) amino acid sequence identity” and “homology” with respect to a peptide, polypeptide or antibody sequence are defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific peptide or polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or MEGALIGNTM (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
[0046] The term “chimeric antigen receptor” or alternatively a “CAR” refers to an engineered protein including an extracellular portion comprising an antigen-binding domain (e.g. an scFv) linked to a spacer sequence, a transmembrane domain and an intracellular signaling domains (optionally containing co-stimulatory signaling domain (s)) .
[0047] The term “engineered armor receptor” or alternatively a “EAR” used herein refers to an engineered protein that is capable of (i) binding a suppressive ligand so that the negative signal is neutralized, and / or (ii) conferring a positive signal (e.g. activating signal or stimulatory signal) as a receptor when present on a surface of a cell. The EAR includes various types of molecules in the art, such as chimeric activation receptor or dominant negative receptor (DNR) . The chimeric activation receptor is capable of transmitting a positive signal; while the DNR is a protein which acts antagonistically to the wild-type receptor, and partially or a fully loses the function of signal transduction. The EAR of the present disclosure doesn’ t include the truncated EGFR or CAR. An EAR may be a monomer or multimer (e.g. dimer or trimer) formed by two or more polypeptides. The term “an EAR polypeptide” or “apolypeptide of an EAR” refers to a polypeptide in the EAR.
[0048] The term “extracellular domain” or “ectodomain” which can be used interchangeably, as used herein refers to the region of a membrane protein, such as a transmembrane protein, that lies outside the cell membrane. Ectodomains often comprise binding domains that specifically bind to ligands or cell surface receptors, such as via a binding domain that specifically binds to the ligand or cell surface receptor. The term “extracellular antigen-binding domain” refers to an extracellular domain or a part of extracellular domain that is capable of specifically binding to an antigen.
[0049] The term “endodomain” or “intracellular domain” or “cytoplasmic domain” which can be used interchangeably, as used herein refers to the region found in some membrane proteins, such as transmembrane proteins, which extends into the interior space defined by the cell surface membrane. In some cells, the endodomain interacts with intracellular constituents and can play a role in signal transduction and thus, in some cases, can be an intracellular signaling domain. The term “intracellular signaling domain” refers to an intracellular domain which transmits signals.
[0050] The term “transmembrane domain” or “TM” as used herein means a domain found in a membrane protein that substantially or completely spans a lipid bilayer such as those lipid bilayers found in a biological membrane such as a mammalian cell, or in an artificial construct such as a liposome. A transmembrane protein can pass through both layers of the lipid bilayer once or multiple times.
[0051] The term "spacer" or "hinge" as used herein refers to a flexible polypeptide connector region providing structural flexibility and spacing to flanking polypeptide regions and can consist of natural or synthetic polypeptides. In one aspect, the hinge is the part of an antibody heavy chain polypeptide that joins in a wild-type antibody heavy chain the CH1 domain and the CH2 domain.
[0052] The term "flexible polypeptide linker" as used herein refers to a peptide which joins the other peptides to form a functional protein. In the context of an scFv, the flexible polypeptide linker refers to a peptide linker which joins the VH and VL to form an scFv specifically binding to an antigen.
[0053] The term “co-stimulatory signaling domain” , as used herein, refers to a stimulation domain of a CAR that provides a secondary non-specific activation mechanism through the propagation of the primary specific signal. The term “4-1BB” or “CD137” , as used herein, refers to a member of the tumor necrosis factor receptor (TNFR) superfamily with an amino acid sequence provided as UniProt entry Q07011 or a NCBI Ref. No. : NP 001552. In one aspect, the 4-IBB co-stimulatory signaling domain comprises or consists of amino acid residues 214 -255 of 4-1BB full-length polypeptide.
[0054] As used herein, the term "CD2" , "CD8" or "CD28" refers to the protein Cluster of Differentiation 2, 8 or 28 respectively. The term "CD8α" refers to the T-cell surface glycoprotein CD8 alpha chain on the Cluster of Differentiation 8. The term "CD3ζ" or alternatively, "CD3 zeta" or "CD3z" is a protein encoded by the CD247 gene on chromosome 1, together with T cell receptor (TCR) and CD3 (aprotein complex composed of a CD3 gamma, a CD3 delta, and two CD3 epsilon) , forms the TCR complex.
[0055] The term "Fas" as used herein refers to the Fas receptor protein. The Fas receptor (also known as Fas, FasR, APO-1, APT, CD95, and TNFRSF6) is a cell surface receptor protein for Fas ligand (FasL) . Binding of Fas ligand to Fas receptor on a cell leads to apoptosis of the cell.
[0056] The terms "interleukin-7 receptor" , "IL-7 receptor" or “IL-7R” refers to a protein that are present on the cell surface and specifically bind IL-7. The terms “IL-7Rα” refers to the alpha chain of IL-7R.
[0057] The term “expression” refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene. The process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post-translational modification, or any combination thereof.
[0058] The term “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (e.g., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene, cDNA, or RNA, encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system.
[0059] The terms “polypeptide” refers to a compound comprised of amino acid residues covalently linked by peptide bonds. A polypeptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a peptide’s sequence. The term “polypeptide” is also intended to refer to the products of post-expression modifications of the polypeptide, including without limitation glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting / blocking groups, proteolytic cleavage, or modification by non-naturally occurring amino acids. A polypeptide of the disclosure may be of a size of about 3 or more, 5 or more, 10 or more, 20 or more, 25 or more, 50 or more, 75 or more, 100 or more, 200 or more, 500 or more, 1, 000 or more, or 2, 000 or more amino acids. Polypeptides may have a defined three-dimensional structure, although they do not necessarily have such structure. The terms “polypeptide system” refers to a combination of two or more polypeptides. The polypeptides in one system may be fused through a peptide (e.g. 2A) or separated.
[0060] The term “polynucleotide” refers to an isolated nucleic acid molecule or construct, e.g., messenger RNA (mRNA) , virally-derived RNA, or plasmid DNA (pDNA) . A polynucleotide may comprise a conventional phosphodiester bond or a non-conventional bond (e.g., an amide bond, such as found in peptide nucleic acids (PNA) . The term nucleic acid molecule refers to any one or more nucleic acid segments, e.g., DNA or RNA fragments, present in a polynucleotide.
[0061] The term “vector” , as used herein, refers to a nucleic acid molecule capable of propagating another nucleic acid to which it is linked. The term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. Certain vectors are capable of directing the expression of nucleic acids to which they are operatively linked.
[0062] The term “subject” or “individual” is intended to include living organisms in which an immune response can be elicited (e.g., mammals, human) .
[0063] As used herein, “treatment” (and grammatical variations thereof such as “treat” or “treating” ) refers to clinical intervention in an attempt to alter the natural course of a disease in the individual being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
[0064] The term “pharmaceutical composition” refers to a preparation which is in such form as to permit the biological activity of an active ingredient contained therein to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered. A pharmaceutical composition usually comprises one or more pharmaceutically acceptable carrier (s) . A “pharmaceutically acceptable carrier” refers to an ingredient in a pharmaceutical composition, other than an active ingredient, which is nontoxic to a subject. A pharmaceutically acceptable carrier includes, but is not limited to, a buffer, excipient, stabilizer, or preservative.
[0065] The term "pharmaceutical combination or combination product" refers to non-fixed combination products or fixed combination products, including but not limited to drug kits and drug compositions. The term "unfixed combination" means that the active ingredients (for example, (i) the engineered cells in the invention, and (ii) additional therapeutic agents) are administered to patients simultaneously, without specific time limits or at the same or different time intervals, in sequence, in separate entities, where these two or more active agents are administered to provide effective levels of prevention or treatment in patients.
[0066] An “effective amount” of an agent, e.g., a pharmaceutical composition, refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result. II. Polypeptide system
[0067] The present disclosure provides a novel polypeptide system with advantageous properties such as producibility, stability, binding affinity, biological activity, targeting efficiency, reduced toxicity, an extended dosage range that can be given to a patient (e.g. contained in an engineered cell) and thereby an enhanced efficacy. Particularly, the polypeptide systems confer synergistic effects to the engineered cells, such as reduced antigen escape and / or enhanced cell persistence / shielding.
[0068] 2.1 CAR
[0069] In one aspect, provided is the polypeptide system as defined herein before, wherein the polypeptide system comprises at least one CAR. In one aspect, the polypeptide system comprises or consists of a first CAR and an additional polypeptide which is a second CAR or an EAR polypeptide. In one aspect, the polypeptide system comprises or consists of a first CAR and a second CAR. In one aspect, the polypeptide system comprises or consists of a CAR, and one or more EAR polypeptides. In one aspect, the polypeptide system comprises or consists of a first CAR, a second CAR, one or more EAR polypeptides.
[0070] CARs may be chimeric type I trans-membrane proteins which connect an extracellular antigen-recognizing domain (binder) to an intracellular signaling domain (endodomain) . A transmembrane domain anchors the protein in the cell membrane. A spacer domain may be necessary to isolate the binder from the membrane and to allow it a suitable orientation. In one aspect, the CAR comprises, from its N to C terminus in order, an extracellular antigen-binding domain, a spacer, a transmembrane domain and an intracellular signaling domain.
[0071] In one aspect, the extracellular antigen-binding domain may comprise: a single-chain variable fragment (scFv) derived from a monoclonal antibody, a natural ligand of the target antigen, a peptide with sufficient affinity for the target, a single domain binder such as a camelid, an artificial binder single as a Darpin, or a single-chain derived from a T-cell receptor. In one aspect, the antigen binding domain comprises a mono-specific, bispecific or multi-specific antibody molecule.
[0072] In one aspect, the chimeric antigen receptor targets against CD19, CD20, CD22, CD30, BCMA, AFP, ALK, GPC3, HER2, EGFR, 5T4, avβ6 integrin, B7-H3, B7-H6, CA-125, CAIX, CD5, CD13, CD16, CD33, CD44, CD44v6, CD44v7 / 8, CD70, CD79a, CD79b, CD123, CD138, CD160, CD171, CEA, Claudin18.2, CSPG4, DLL3, EGFRvlll, EGP2, EGP40, EPCAM, EphA2, EpCAM, FAP, Folate binding protein, fetal Carbonic anhydrase IX, AchR, FRa, G250, GD2, GD3, MAGE-1, NY-ESO-1, IL-11Rα, IL-13Rα2, Lambda, Lewis-Y, Kappa, Mesothelin, Muc1, Muc16, NCAM, NKG2D Ligands, PRAME, PSCA, PSMA, RORI, SSX, Survivin, TAG72, TEMs, VEGFR2, Vimentin or WT-1. Some antigens are known in the following Table. 2. The antigen-binding domain used in the present invention may be a domain which is capable of binding a tumor-associated antigen (TAA) as indicated therein. Table 2. Type of the TAA
[0073] The CAR may comprise a spacer sequence to connect the antigen-binding domain with the transmembrane domain. A flexible spacer allows the antigen-binding domain to orient in different directions to facilitate binding. In one aspect, the spacer comprises or is at least a portion of a hinge of an immunoglobulin or modified region thereof. In one aspect, the spacer comprises or is a hinge of an immunoglobulin or modified region thereof. In one aspect, the immunoglobulin is IgG, such as IgG1, IgG2, IgG3 or IgG4. In one aspect, the spacer comprises or is at least a portion of a CDS stalk or modified region thereof. In one aspect, the length of the spacer is adjusted to optimize the biophysical synapse distance between the CAR-expressing cell and the target cell. Exemplary spacers include those having about 10 to 200 amino acids, 10 to 100 amino acids, 10 to 50 amino acids, 10 to 40 amino acids, 10 to 30 amino acids, 10 to 30 amino acids, 12 to 40 amino acids, 12 to 30 amino acids, 12 to 20 amino acids. In one aspect, the spacer is at or about 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acids in length. In one aspect, the spacer is at or about 40 amino acids in length.
[0074] The transmembrane domain is the sequence of a classical CAR that spans the membrane. In one aspect, the transmembrane domain may be derived either from a natural or from a recombinant source. In one aspect, the transmembrane domain is a natural peptide derived from any membrane-bound or transmembrane protein. In one aspect, the transmembrane domain may be obtained from a naturally occurring protein or a synthetic, non-naturally occurring protein segment, e.g., a hydrophobic protein segment that is thermodynamically stable in a cell membrane. In one aspect, the transmembrane domain is capable of signaling to the intracellular domain (s) whenever the CAR has bound to a target. A transmembrane domain of particular use in this invention may include at least the transmembrane region (s) of, e.g., the alpha, beta or zeta chain of T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8 (e.g., CD8 alpha, CD8 beta) , CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137, CD154.
[0075] The intracellular signaling domain is generally responsible for activation of at least one of the normal effector functions. In one aspect, the intracellular signaling domains include two distinct classes of cytoplasmic signaling sequences: those that initiate antigen-dependent primary activation through the TCR (primary intracellular signaling domains) and those that act in an antigen-independent manner to provide a secondary or costimulatory signal (secondary cytoplasmic domain, e.g., a costimulatory signaling domain) . In one aspect, the intracellular signaling domain comprises a co-stimulatory signaling domain and a primary intracellular signaling domain. In one aspect, the primary intracellular signaling domain is fused by its N-terminus to the C-terminus of the co-stimulatory signaling domain.
[0076] A primary intracellular signaling domain regulates primary activation of the TCR complex either in a stimulatory way, or in an inhibitory way. Primary intracellular signaling domains that act in a stimulatory manner in CARs may contain signaling motifs which are known as immunoreceptor tyrosine-based activation motifs (ITAMs) . Examples of ITAM containing primary intracellular signaling domains that are of particular use in the invention include those of TCR zeta, FcR gamma, FcR beta, CD3 gamma, CD3 delta , CD3 epsilon, CD5, CD22, CD79a, CD79b, CD278 (also known as “ICOS” ) , FceRI, DAP 10, DAP12, and CD66d. In one aspect, a CAR comprises an intracellular signaling domain, e.g., a primary intracellular signaling domain of CD3ζ. In one aspect, a primary intracellular signaling domain comprises a modified ITAM domain, e.g., a mutated ITAM domain which has altered (e.g., increased or decreased) activity as compared to the native ITAM domain. In one aspect, a primary intracellular signaling domain comprises a modified ITAM-containing primary intracellular signaling domain, e.g., an optimized and / or truncated ITAM-containing primary intracellular signaling domain. In one aspect, the signaling domain of CD3ζ is a mutant CD3ζ or a wild-type human CD3ζ. In one aspect, a primary intracellular signaling domain comprises one, two, three, four or more ITAM motifs. In one aspect, the primary intracellular signaling domain is a functional mutant of the cytoplasmic signaling domain of CD3ζ containing one or more mutations, such as Q65K.
[0077] In one aspect, the intracellular signaling domain of the CAR comprises a costimulatory signaling domain. In one aspect, the costimulatory molecule is a cell surface molecule other than an antigen receptor or its ligands that is required for an efficient response of lymphocytes to an antigen. Examples of such molecules include MHC class I molecule, TNF receptor proteins, Immunoglobulin-like proteins, cytokine receptors, integrins, signaling lymphocytic activation molecules (SEAM proteins) , activating NK cell receptors, BTFA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-l, FFA-l (CD11a / CD18) , 4-1BB (CD137) , B7-H3, CDS, ICAM-l, ICOS (CD278) , GITR, BAFFR, FIGHT, HVEM, KIRDS2, SFAMF7, NKp80 (KFRF1) , NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IF2Rbeta, IF2Rgamma, IF7R alpha, ITGA4, VFA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VFA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAF, FFA-l, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, FFA-l, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE / RANKF, DNAM1 (CD226) , SFAMF4 (CD244, 2B4) , CD84, CD96 (Tactile) , CEACAM1, CRTAM, Fy9 (CD229) , CD160 (BY55) , PSGF1, CD100 (SEMA4D) , CD69, SFAMF6 (NTB-A, Fyl08) , SEAM (SFAMF1, CD150, IPO-3) , BFAME (SFAMF8) , SEFPFG (CD162) , FTBR, FAT, GADS, SFP-76, PAG / Cbp, CD19a, and a ligand that specifically binds with CD83, and the like. The intracellular signaling sequences within the cytoplasmic portion of the CAR of the invention may be linked to each other in a random or specified order. In one aspect, the intracellular signaling domain is designed to comprise two or more, e.g., 2, 3, 4, 5, or more, costimulatory signaling domains.
[0078] 2.1.1 Exemplary CD19 CAR
[0079] In one aspect, the antigen is CD19. CD19 is a co-receptor for B cell antigen receptor (BCR) signal transduction. CD19 regulates B lymphocyte activation and differentiation through modulation of BCR signaling and optimizes immune responses by controlling antigen-independent B cell development, and immunoglobulin-induced B lymphocyte activation. CD19 is expressed on early pro-B cells, late pro-B cells, memory B cells, plasmablasts and some plasma cells. CD19 expression is observed in B-cell leukemia, lymphomas and other cancers. CD19 is expressed on >90%of ALL, B-NHL and CLL. Overexpression of a CD19 in mice can also lead to autoimmune diseases. Human CD19 is about 556 amino acids in length and is encoded by the 7.41 kilobase CD19 gene located on the short arm of chromosome 16.
[0080] In one aspect, the CAR is capable of binding to the same epitope on CD19 as any anti-CD19 antibody in the art (e.g. FMC63, SC25C1) . In one aspect, the antigen-binding domain that specifically binds CD19 is originated from a known antibody that specifically binds CD19, or comprises 1, 2, 3, 4, 5, or 6 CDRs of the known antibody, or comprises the heavy chain variable region and the light chain variable region of the known antibody. In one aspect, the known antibody is disclosed in patents No WO2010095031, WO2014153270, WO2017015783, CN107383196A, CN111848801A, WO2018200496 or WO2022105811. In one aspect, the CAR comprises a VH and a VL of a humanized antibody or a human antibody.
[0081] In one aspect, the extracellular antigen-binding domain is capable of binding to the same epitope on CD19 as a reference antibody that comprises the amino acid sequence of SEQ ID NO: 21. In one aspect, the extracellular antigen-binding domain comprises a CD19-VH and a CD19-VL. In one aspect, the extracellular antigen-binding domain comprises a HCDR1, a HCDR2, a HCDR3, a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 22, SEQ ID NO: 23 or SEQ ID NO: 24. In one aspect, the CD19-VH comprises a HCDR1, a HCDR2 and a HCDR3 contained within the amino acid sequence of SEQ ID NO: 1, and the CD19-VL comprises a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 4. In one aspect, the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2 and LCDR3 are defined according to Kabat, AbM, Chothia, IMGT or Contact numbering. In one aspect, the CD19-VH comprises a HCDR1, a HCDR2 and a HCDR3 comprising or consisting of the amino acid sequences of SEQ ID NO: 5, SEQ ID NO: 6 and SEQ ID NO: 7, respectively; the CD19-VL comprises a LCDR1, a LCDR2 and a LCDR3 comprising or consisting of the amino acid sequences of SEQ ID NO: 8, SEQ ID NO: 9 and SEQ ID NO: 10, respectively.
[0082] In one aspect, the CD19-VH comprises or consists of the amino acid sequence of SEQ ID NO: 1; the CD19-VL comprises or consists of the amino acid sequence of SEQ ID NO: 2. In one aspect, the CD19-VH comprises the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%or 98%sequence identity to SEQ ID NO: 1. In one aspect, the CD19-VL comprises the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%or 98%sequence identity to SEQ ID NO: 2. In one aspect, the CD19-VL comprises the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%or 98%sequence identity to SEQ ID NO: 2, wherein the amino acids of the VL at positions 39 and 80 are R and P, respectively. In one aspect, the CD19-VL comprises the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%or 96%sequence identity to SEQ ID NO: 2, wherein the amino acids of the CD19-VL at positions 39, 80, 100 and 103 are R, P, S and R, respectively. In a particular aspect, the CD19-VH comprises or consists of the amino acid sequence of SEQ ID NO: 1; the CD19-VL comprises or consists of the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 4.
[0083] In one aspect, the extracellular antigen-binding domain comprises or is an antibody. In one aspect, the extracellular antigen-binding domain comprises or is an antibody fragment. In one aspect, the extracellular antigen-binding domain comprises or is a Fab, a scFv or a single-domain antibody. In one aspect, the extracellular antigen-binding domain comprises or is a scFv. In one aspect, the CD19-VH and the CD19-VL are connected via a flexible polypeptide linker. In one aspect, the CD19-VH is fused by its N-terminus via a flexible polypeptide linker to the C-terminus of the CD19-VL (L-H) . In one aspect, the CD19-VL is fused by its N-terminus via a flexible polypeptide linker to the C-terminus of the CD19-VH (H-L) . In one aspect, the flexible polypeptide linker is (G4S) n, (SG4) n or G4 (SG4) n, wherein “n” is 1, 2, 3, 4, 5, 6, 7 or 8, in particular 3. In one aspect, the flexible polypeptide linker comprises or consists of the amino acid sequence of SEQ ID NO: 19 or SEQ ID NO: 20. In one aspect, the flexible polypeptide linker comprises or consists of the amino acid sequence of SEQ ID NO: 19. In one aspect, the scFv comprises or consists of the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%or 98%sequence identity to SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 or SEQ ID NO: 24. In one aspect, the scFv comprises or consists of the amino acid sequence of SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 or SEQ ID NO: 24.Table 3 provides the SEQ ID NOs: of exemplary CD19 scFvs. Table 3. SEQ ID NOs of the exemplary anti-CD19 scFvs
[0084] In one aspect, the spacer comprises or is at least a portion of the IgG3 hinge. In one aspect, the spacer is at or about 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acids in length. In one aspect, the spacer is at or about 15 amino acids in length. In one aspect, the spacer comprises the 15 amino acids of the C terminus of IgG3 hinge. In one aspect, the IgG3 hinge is a modified IgG3 hinge comprising one or more mutations. In one aspect, the spacer comprises or consists of the 15 amino acids of the C terminus of IgG3 hinge and the amino acid at position 2 is S. In one aspect, the spacer comprises or consists of the amino acid sequence of SEQ ID NO: 30.
[0085] In one aspect, the transmembrane domain comprises or consists of the transmembrane domain from CD28 (CD28 transmembrane domain) . In one aspect, the transmembrane domain consists of the transmembrane domain from wild-type CD28. In one aspect, the transmembrane domain is at least approximately 20 amino acids, e.g., at least 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more amino acids. In some specific embodiments, the transmembrane domain comprises or consists of the amino acid sequence having at least 88%, 92%, 96%, sequence identity to SEQ ID NO: 36. In a particular embodiment, the transmembrane domain comprises or consists of the amino acid sequence of SEQ ID NO: 36.
[0086] In one aspect, the intracellular signaling domain comprises a co-stimulatory signaling domain, a primary intracellular signaling domain, or a co-stimulatory signaling domain and a primary intracellular signaling domain. In one aspect, the intracellular signaling domain comprises CD3ζ cytoplasmic signaling domain. In one aspect, the co-stimulatory signaling domain comprises a CD137 co-stimulatory signaling domain or a CD28 co-stimulatory signaling domain. In one aspect, the co-stimulatory signaling domain comprises a CD137 co-stimulatory signaling domain. In one aspect, the intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain and a CD137 co-stimulatory signaling domain or a CD28 co-stimulatory signaling domain. In a particular embodiment, the intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain and a CD137 co-stimulatory signaling domain. In one aspect, the CD3ζ cytoplasmic signaling domain comprises or consists of the amino acid sequence of SEQ ID NO: 38, or an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%identity thereto. In one aspect, the CD137 co-stimulatory signaling domain comprises or consists of the amino acid sequence of SEQ ID NO: 37 or an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%or 97%identity thereto.
[0087] 2.1.2 Exemplary CD20 CAR
[0088] In one aspect, the antigen is CD20. CD20 protein is a hydrophobic transmembrane protein with a molecular weight of approximately 35 kD located on pre-B and mature B lymphocytes. It is present on both normal B cells as well as malignant B cells. In particular, CD20 is expressed on greater than 90%of B cell non-Hodgkin's lymphomas. It is a target for the treatment of autoimmune diseases and cancers.
[0089] In one aspect, the CAR is capable of binding to the same epitope on CD20 as any anti-CD20 antibody in the art (e.g. Ofatumumab, Obinutuzumab, Rituximab, Orelizumab, Veltuzumab, Ibritumomab, Tositumumab, Odronextamab, Ublituximab, Leu16, IF5, 1.5.3, collectively the known antibody) . In one aspect, the antigen-binding domain that specifically binds CD20 is originated from the known antibody that specifically binds CD20, or comprises 1, 2, 3, 4, 5, or 6 CDRs of the known antibody, or comprises the heavy chain variable region and the light chain variable region of the known antibody. In one aspect, the CAR comprises a VH and a VL of a humanized antibody or a human antibody.
[0090] In one aspect, the extracellular antigen-binding domain is capable of binding to the same epitope on CD20 as a reference antibody that comprises the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27. In one aspect, the extracellular antigen-binding domain comprises a CD20-VH and a CD20-VL. In one aspect, the extracellular antigen-binding domain comprises a HCDR1, a HCDR2, a HCDR3, a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27. In one aspect, the CD20-VH comprises a HCDR1, a HCDR2 and a HCDR3 contained within the amino acid sequence of SEQ ID NO: 11, and the CD20-VL comprises a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 12. In one aspect, the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2 and LCDR3 are defined according to Kabat, AbM, Chothia, IMGT or Contact numbering. In one aspect, the CD20-VH comprises a HCDR1, a HCDR2 and a HCDR3 comprising or consisting of the amino acid sequences of SEQ ID NO: 13, SEQ ID NO: 14 and SEQ ID NO: 15, respectively; the CD20-VL comprises a LCDR1, a LCDR2 and a LCDR3 comprising or consisting of the amino acid sequences of SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18, respectively.
[0091] In one aspect, the CD20-VH comprises the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%or 98%sequence identity to SEQ ID NO: 11. In one aspect, the CD20-VL comprises the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%or 98%sequence identity to SEQ ID NO: 12. In one aspect, the CD20-VH comprises or consists of the amino acid sequence of SEQ ID NO: 11; the CD20-VL comprises or consists of the amino acid sequence of SEQ ID NO: 12.
[0092] In one aspect, the extracellular antigen-binding domain comprises or is an antibody. In one aspect, the extracellular antigen-binding domain comprises or is an antibody fragment. In one aspect, the extracellular antigen-binding domain comprises or is a Fab, a scFv or a single-domain antibody. In one aspect, the extracellular antigen-binding domain comprises or is a scFv. In one aspect, the CD20-VH and the CD20-VL are connected via a flexible polypeptide linker. In one aspect, the CD20-VH is fused by its N-terminus via a flexible polypeptide linker to the C-terminus of the CD20-VL (L-H) . In one aspect, the CD20-VL is fused by its N-terminus via a flexible polypeptide linker to the C-terminus of the CD20-VH (H-L) . In one aspect, the flexible polypeptide linker is (G4S) n, (SG4) n or G4 (SG4) n, wherein “n” is 1, 2, 3, 4, 5, 6, 7 or 8, in particular 3. In one aspect, the flexible polypeptide linker comprises or consists of the amino acid sequence of SEQ ID NO: 19 or SEQ ID NO: 20. In one aspect, the flexible polypeptide linker comprises or consists of the amino acid sequence of SEQ ID NO: 20. In one aspect, the scFv comprises or consists of the amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%or 98%sequence identity to SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27. In one aspect, the scFv comprises or consists of the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27.
[0093] In one aspect, the spacer comprises or consists of the hinge domain from CD28. In one aspect, the spacer consists of a CD28 hinge. In one aspect, the spacer consists of the hinge domain from wild-type CD28. In one aspect, the spacer consists of wild-type human CD28 hinge. In one aspect, the spacer consists of an amino acid sequence having at least 90%sequence identity to SEQ ID NO: 34. In one aspect, the spacer consists of the amino acid sequence of SEQ ID NO: 34. In one aspect, the spacer consists of an amino acid sequence that is 12-15 amino acid residues in length. In one aspect, the spacer consists of an amino acid sequence that is 12 amino acid residues in length. In one aspect, the spacer consists of an amino acid sequence that is at least about 90%identical to the amino acid sequence of SEQ ID NO: 33. In one aspect, the spacer consists of the amino acid sequence of SEQ ID NO: 33. In one aspect, the spacer consists of an amino acid sequence that is at least about 90%identical to the amino acid sequence of SEQ ID NO: 32. In one aspect, the spacer consists of the amino acid sequence of SEQ ID NO: 32.
[0094] In one aspect, the transmembrane domain of the CD20 CAR herein is the same as the transmembrane domain of the CD19 CAR as described in section 2.1.1. In one aspect, the transmembrane domain of the CD20 CAR is different from the transmembrane domain of the CD19 CAR. In one aspect, the transmembrane domain comprises or consists of the transmembrane domain from CD28 or CD8α. In one aspect, the transmembrane domain consists of a CD28 transmembrane domain. In one aspect, the transmembrane domain consists of the transmembrane domain from wild-type CD28. In one aspect, the transmembrane domain is at least approximately 20 amino acids, e.g., at least 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more amino acids. In some specific embodiments, the transmembrane domain comprises or consists of the amino acid sequence having at least 88%, 92%, 96%, sequence identity to SEQ ID NO: 36. In a particular embodiment, the transmembrane domain comprises or consists of the amino acid sequence of SEQ ID NO: 36.
[0095] In one aspect, the intracellular signaling domain of the CD20 CAR herein is the same as the intracellular signaling domain of the CD19 CAR as described in section 2.1.1. In one aspect, the intracellular signaling domain comprises a co-stimulatory signaling domain, a primary intracellular signaling domain, or a co-stimulatory signaling domain and a primary intracellular signaling domain. In one aspect, the intracellular signaling domain comprises CD3ζ cytoplasmic signaling domain. In one aspect, the co-stimulatory signaling domain comprises a CD137 co-stimulatory signaling domain or a CD28 co-stimulatory signaling domain. In one aspect, the co-stimulatory signaling domain comprises a CD137 co-stimulatory signaling domain. In one aspect, the intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain and a CD137 co-stimulatory signaling domain or a CD28 co-stimulatory signaling domain. In a particular embodiment, the intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain and a CD137 co-stimulatory signaling domain. In one aspect, the CD3ζ cytoplasmic signaling domain comprises or consists of the amino acid sequence of SEQ ID NO: 38, or an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%identity thereto. In one aspect, the CD137 co-stimulatory signaling domain comprises or consists of the amino acid sequence of SEQ ID NO: 37 or an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%or 97%identity thereto.
[0096] 2.2 EAR
[0097] 2.2.1 Chimeric activation receptor
[0098] In one aspect, provided is the polypeptide system as defined herein before, wherein the polypeptide system comprises at least one polypeptide of chimeric activation receptor. A Chimeric activation receptor of the present disclosure may be designed to transmit a positive signal, by virtue of comprising an intracellular domain associated with the positive signal, and optionally reduce the effects of a negative signal transduction molecule through its extracellular domain associated with the negative signal. In one aspect, the chimeric activation receptor doesn’ t include CD3ζ cytoplasmic signaling domain.
[0099] In one aspect, the polypeptide of an EAR comprises an extracellular domain and an intracellular domain. In one aspect, the extracellular domain is an ectodomain selected from a group consisting of FAS, PD-1, BTLA, CD30, HER2, EGFR, CD34, TGFβR2, TGFβR1, IL-4R, IL-13R1, IL-13R2, IL-8R, IL-10R, LAG3, TIGIT, CTLA4, CD19, CD27, CD28, CD52, CD134, CD137 and NGFR. In one aspect, the EAR is capable of binding Fas ligand. In one aspect, the extracellular domain is a Fas ectodomain. In one aspect, the extracellular domain is a full-length Fas ectodomain. In one aspect, the extracellular domain is a human Fas ectodomain. In one aspect, the extracellular domain is a full-length human Fas ectodomain. In one aspect, the Fas ectodomain includes or doesn’ t include a signal peptide (e.g. SP-3) which usually locates in 1 to 25 amino acids of wild-type Fas with the signal peptide. In one aspect, the Fas ectodomain comprises or consists of an amino acid sequence that is at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity to SEQ ID NO: 50. In one aspect, the Fas ectodomain comprises or consists of the amino acid sequence of SEQ ID NO: 50. In one aspect, the EAR polypeptide comprising the Fas ectodomain loses the function of Fas signal transduction. In one aspect, the EAR polypeptide comprising the Fas ectodomain doesn’ t comprise a Fas endodomain or at least a portion of the Fas endodomain necessary to signaling.
[0100] In one aspect, the transmembrane domain is operably linked to the extracellular domain and the intracellular domain. The transmembrane domain may or may not naturally occurring. In one aspect, the transmembrane domain consists of a transmembrane domain selected from the group consisting of Fas, CD2, CD3s, CD35, CD3C, CD25, CD27, CD28, CD40, CD79A, CD79B, CD80, CD86, OX40, 4-IBB, SLAMF1, CTLA4, CD200R, LAG3, HVEM, BTLA, PD-L2, PD-L1, ICOS, PD-1, CD300, GITR, A2aR, DAP10, FcRα, FcRβ, FcRγ, Fyn, GAL9, KIR, Lck, LAT, LRP, KG2D, NOTCH1, NOTCH2, NOTCH3, NOTCH4, PTCH2, ROR2, Ryk, Slp76, SIRPa, pTa, TCRa, TCRβ, TIM3, TRIM, LPA5 and Zap70. In one aspect, the transmembrane domain is a Fas transmembrane domain. In one aspect, the transmembrane domain is a wild-type Fas transmembrane domain. In some specific embodiments, the transmembrane domain comprises or consists of the amino acid sequence having at least 88%, 92%, 96%, sequence identity to SEQ ID NO: 59. In a particular embodiment, the transmembrane domain comprises or consists of the amino acid sequence of SEQ ID NO: 59. In one aspect, the intracellular domain comprises an intracellular signaling domain selected from the group consisting of CD2, CD27, CD28, CD137, OX40, CD30, CD40, CD3, HVEM, ICOS, Myd88, LFA-1, ICOS, CD7, NKG2C, B7-H3 and Ligands of CD83, and a combination thereof. In one aspect, the intracellular domain comprises a CD2 intracellular signaling domain. In one aspect, the CD2 intracellular signaling domain is a CD2 endodomain. In one aspect, the CD2 endodomain is a human CD2 endodomain. In one aspect, the CD2 endodomain has been modified compared to the naturally occurring CD2 endodomain, as long as it maintains the signaling activity. In one aspect, the CD2 endodomain is a full-length CD2 endodomain. In one aspect, the intracellular domain comprises or consists of an amino acid sequence that is at least 80%, 85%, 90%95%, 96%, 97%, 98%, 99%sequence identity to SEQ ID NO: 55 to SEQ ID NO: 58, respectively. In one aspect, the intracellular domain comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 55 to SEQ ID NO: 58. In one aspect, the intracellular domain comprises or consists of the amino acid sequence of SEQ ID NO: 55. In one aspect, the EAR polypeptide comprises or consists of an amino acid sequence that is at least 80%, 85%, 90%95%, 96%, 97%, 98%, 99%sequence identity to SEQ ID NO: 68. In one aspect, the EAR polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 68.
[0101] In one aspect, the chimeric activation receptor is designed to facilitate downstream signaling without need for binding of the relevant ligand, though it may bind a ligand to neutralize a negative signal meanwhile. A common feature of such chimeric activation receptors is that they are engineered to comprise one or more gain-of-function mutations, e.g., in the transmembrane domain. In one aspect, the transmembrane component is capable of self-oligomerizing. In one aspect, the transmembrane domain consists of any one of the amino acid sequences of SEQ ID NO: 60 to SEQ ID NO: 65. In one aspect, the transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60. In one aspect, the intracellular domain comprises a primary cytokine signaling domain. In one aspect, the intracellular domain comprises an endodomain selected from the group consisting of IL-7Rα, IL-12Rα, IL-15Rα, IL-21Rα and IL-23Rα. In one aspect, the primary cytokine signaling domain comprises or consists of an IL-7R endodomain. In one aspect, the IL-7R endodomain is an IL-7Rα endodomain. In one aspect, the IL-7Rα endodomain is a human IL-7Rαendodomain. In one aspect, the IL-7Rα endodomain has been modified compared to the naturally occurring IL-7Rα endodomain, as long as it maintains the signaling activity. In one aspect, the intracellular domain comprises or consists of an amino acid sequence that is at least 80%, 85%, 90%95%, 96%, 97%, 98%, 99%sequence identity to SEQ ID NO: 54. In one aspect, the intracellular domain comprises or consists of the amino acid sequence of SEQ ID NO: 54. In one aspect, the intracellular domain comprises a primary cytokine signaling domain and one or more co-stimulatory signaling domain. In one aspect, the primary cytokine signaling domain is fused by its C-terminus to the N-terminus of the co-stimulatory signaling domain. In one aspect, the intracellular domain comprises a co-stimulatory signaling domain selected from the group consisting of CD2, CD27, CD28, CD137, OX40, CD30, CD40, CD3, HVEM, ICOS, Myd88, LFA-1, ICOS, CD7, NKG2C, B7-H3 and Ligands of CD83, and a combination thereof. In one aspect, the intracellular domain comprises a CD2 intracellular signaling domain. In one aspect, the CD2 intracellular signaling domain is a CD2 endodomain. In one aspect, the intracellular domain comprises or consists of an IL-7Rαendodomain and a CD2 endodomain. In one aspect, the CD2 endodomain is a human CD2 endodomain. In one aspect, the CD2 endodomain has been modified compared to the naturally occurring CD2 endodomain, as long as it maintains the signaling activity. In one aspect, the CD2 endodomain is a full-length CD2 endodomain. In one aspect, the intracellular domain comprises an amino acid sequence that is at least 80%, 85%, 90%95%, 96%, 97%, 98%, 99%sequence identity to SEQ ID NO: 55 to SEQ ID NO: 58, respectively. In one aspect, the intracellular domain comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 55 to SEQ ID NO: 58. In one aspect, the intracellular domain comprises the amino acid sequence of SEQ ID NO: 55. In one aspect, the EAR polypeptide comprises or consists of an amino acid sequence that is at least 80%, 85%, 90%95%, 96%, 97%, 98%, 99%sequence identity to SEQ ID NO: 66. In one aspect, the EAR polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 66.
[0102] 2.2.2 DNR
[0103] In one aspect, provided is the polypeptide system as defined herein before, wherein the polypeptide system comprises at least one DNR polypeptide. A DNR of the present disclosure may bind a negative signal transduction molecule, e.g., TGFβ, by virtue of an extracellular domain associated with the negative signal and reduce the effect of the negative signal transduction molecule. For example, a modified immune cell comprising a DNR may bind a negative signal transduction molecule in the microenvironment of the modified immune cell and reduce the effect the negative signal transduction molecule may have on the modified immune cell. In one aspect, the DNR polypeptide is a truncated variant of a wild-type protein associated with the negative signal.
[0104] In one aspect, the DNR is capable of binding TGFβ, Fas-L or PD-1L. In one aspect, the DNR is dnTGFβR1, dnTGFβR2, dnFas or dnPD-1. In one aspect, the DNR is dnTGFβR. In one aspect, the DNR polypeptide comprises TGFβR ectodomain. In one aspect, the DNR polypeptide doesn’ t comprise the TGFβR endodomain or at least a portion of the TGFβR endodomain necessary to signaling. In one aspect, the extracellular domain of the DNR polypeptide comprises a TGFβR (e.g. TGFβR1 or TGFβR2) ectodomain. In one aspect, the extracellular domain comprises or is a full-length TGFβR ectodomain. In one aspect, the extracellular domain comprises or is a human TGFβR ectodomain. In one aspect, the TGFβR ectodomain comprises or consists of an amino acid sequence that is at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity to SEQ ID NO: 52. In one aspect, the TGFβR ectodomain comprises or consists of the amino acid sequence of SEQ ID NO: 52. In one aspect, the DNR polypeptide comprising the TGFβR ectodomain loses the function of TGFβR signal transduction. In one aspect, the DNR polypeptide comprising the TGFβR ectodomain doesn’ t comprise a TGFβR endodomain. In one aspect, the DNR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide. In one aspect, the DNR polypeptide is a dnTGFβR2 polypeptide. In one aspect, the DNR polypeptide comprises or consists of an amino acid sequence that is at least 80%, 85%, 90%95%, 96%, 97%, 98%, 99%sequence identity to SEQ ID NO: 69. In one aspect, the DNR polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 69.
[0105] In one aspect, the EAR (e.g. chimeric activation receptor or DNR) polypeptides comprising the Fas ectodomain are capable of segregating together to form a trimeric complex. In one aspect, the trimeric complex is formed on the surface of the engineered cell expressing the EAR. In one aspect, the trimeric complex is formed automatically on the surface of the engineered cell. In one aspect, the Fas ectodomain comprises a cysteine-rich domain 1, a cysteine-rich domain 2 and a cysteine-rich domain 3. Cysteine residues in these cysteine-rich domains contribute to the formation of trimeric complex. In one aspect, the trimeric complex is formed via disulfide bridge (s) between the cysteine-rich domains. In one aspect, the trimeric complex is formed via disulfide bridge (s) between the cysteine-rich domain 1.
[0106] 2.3 Systems
[0107] The polypeptide system of the present disclosure includes any combinations of the polypeptide described in sections 2.1 and / or 2.2. the polypeptides in the system may be separated or linked through a peptide (e.g. self-cleavage peptide) . Exemplary systems are a combination of two or more CARs (e.g. a dual CAR) , two or more EAR polypeptides (e.g. a dual EAR) , or one or more CARs and one or more EAR polypeptides (e.g. a dual CAR and a dual EAR) . In one aspect, the polypeptide system is expressed in one cell (as describe in section 3.1) . In one aspect, the present disclosure also provides a cell comprising the polypeptide system as described in this section. In one aspect, the cell exhibits cytotoxic activity against CD19+ cells, CD20+ cells and / or CD19+ / CD20+ cells.
[0108] 2.3.1 dual CAR
[0109] The dual CAR of the present disclosure may include a first CAR and a second CAR each having an intracellular signaling domain comprising a co-stimulatory signaling domain and / or a primary intracellular signaling domain. Thus, when dual CAR bind antigens (e.g., bispecific) , the T cell signals may be transmitted through two signaling domains from the dual CAR.
[0110] In one aspect, the first CAR comprises, from its N to C terminus in order, a first extracellular antigen-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 31, a first transmembrane domain and a first intracellular signaling domain. In one aspect, the first CAR in the dual CAR herein is described in 2.1.1 In one aspect, the second CAR in the dual CAR herein is described in 2.1.2.
[0111] In one aspect, the first CAR comprises, from its N to C terminus in order, a first extracellular CD20-binding domain, a first spacer of CD28 hinge, a first transmembrane domain and a first intracellular signaling domain. In one aspect, the first CAR in the dual CAR herein is described in 2.1.2, the second CAR in the dual CAR herein is described in 2.1.1.
[0112] In one aspect, the first CAR and the second CAR target different antigens or different epitopes on the same antigen. In one aspect, the first spacer in the first CAR is different from the second spacer in the second CAR. In one aspect, the first intracellular signaling domain in the first CAR is the same as the second intracellular signaling domain in the second CAR. In one aspect, the polypeptide system comprises the polypeptides of the amino acid sequences of SEQ ID NO: 39 and SEQ ID NO: 44. In one aspect, the polypeptide system further comprises EAR polypeptides as described in section 2.2 or 2.3.2.
[0113] 2.3.2 dual EAR
[0114] The polypeptide system categorized in the dual EAR of the present disclosure may include at least two EAR polypeptides. The dual armor may reduce the effects of one or more negative signals and / or transmit one or more positive signal to the armored cells expressing or not expressing a CAR. In one aspect, the EAR polypeptides in the dual Armor herein are described in section 2.2. In one aspect, the polypeptide system further comprises CAR polypeptides as described in section 2.1.
[0115] In one aspect, the polypeptide system, comprising a polypeptide of a first EAR and a polypeptide of a second EAR, wherein the first EAR is capable of binding Fas ligand, the second EAR is capable of binding TGFβ. In one aspect, the first EAR polypeptide comprises a Fas ectodomain, the second EAR polypeptide comprises a TGFβR ectodomain. In one aspect, the first EAR polypeptide comprises, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain, and an intracellular domain. In one aspect, the transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60, and the intracellular domain comprises an IL-7R endodomain and optionally a CD2 intracellular signaling domain. In one aspect, the first EAR polypeptide comprises, from its N to C terminus in order, a Fas ectodomain, a Fas transmembrane domain, and an CD2 intracellular signaling domain. In one aspect, the second EAR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide. In one aspect, the polypeptide system comprises the polypeptides of the amino acid sequence of SEQ ID NO: 66 and SEQ ID NO: 69. In one aspect, the polypeptide system comprises the polypeptides of the amino acid sequences of SEQ ID NO: 68 and SEQ ID NO: 69.
[0116] 2.3.3 Armored CAR
[0117] The polypeptide system of the present disclosure also includes the armored CAR, which comprises at least one CAR as described in section 2.1 or 2.3.1, and at least one EAR polypeptide as described in section 2.2 or 2.3.2. In one aspect, the polypeptide system comprises a first CAR, a second CAR, a first EAR polypeptide and a second EAR polypeptide.
[0118] In one aspect, the first CAR comprises, from its N to C terminus in order, a first extracellular CD19-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 31, a first transmembrane domain and a first intracellular signaling domain; the second CAR comprises, from its N to C terminus in order, a second extracellular CD20-binding domain, a second spacer of CD28 hinge, a second transmembrane domain and a second intracellular signaling domain, wherein the first EAR polypeptide comprises, from its N to C terminus in order, a Fas ectodomain, a Fas transmembrane domain, and an CD2 intracellular signaling domain, the second EAR polypeptide is a dnTGFβR2 polypeptide. In one aspect, the polypeptide system comprises the polypeptides of the amino acid sequences of SEQ ID NO: 39, SEQ ID NO: 44, SEQ ID NO: 68 and SEQ ID NO: 69.
[0119] In one aspect, the first CAR comprises, from its N to C terminus in order, a first extracellular CD19-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, a first transmembrane domain and a first intracellular signaling domain; the second CAR comprises, from its N to C terminus in order, a second extracellular CD20-binding domain, a second spacer of CD28 hinge, a second transmembrane domain and a second intracellular signaling domain, the first EAR polypeptide comprising, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, and an IL-7R endodomain, the second EAR polypeptide is a dnTGFβR2 polypeptide. In one aspect, the polypeptide system comprises the polypeptides of the amino acid sequences of SEQ ID NO: 39, SEQ ID NO: 44, SEQ ID NO: 66 and SEQ ID NO: 69. III. Engineered Cells and preparation thereof
[0120] 3.1 Cells
[0121] In one aspect, the present disclosure provides engineered cells comprising an aforementioned polypeptide system, e.g., engineered immune cells. The source of the engineered immune cells of the present disclosure may be a patient to be treated (i.e., autologous cells) or from a donor who is not the patient to be treated (e.g., allogeneic cells) .
[0122] In one aspect, the cell is an immunoresponsive cell. In one aspect, the cell is a cell of the lymphoid lineage. In one aspect, the engineered immune cells are engineered T cells. In one aspect, the T cells are derived from a mammalian subject. In one aspect, the T cells are derived from a primate subject, such as a human subject. Among the sub-types and subpopulations of T cells and / or of CD4+ and / or of CD8+ T cells are naive T (TN) cells, effector T cells (TEFF) , memory T cells and sub-types thereof, such as stem cell memory T (TSCM) , central memory T (TCM) , effector memory T (TEM) , or terminally differentiated effector memory T cells, tumor-infiltrating lymphocytes (TIL) , immature T cells, mature T cells, helper T cells, cytotoxic T cells, mucosa-associated invariant T (MAIT) cells, naturally occurring and adaptive regulatory T (Treg) cells, helper T cells, such as TH1 cells, TH2 cells, TH3 cells, TH17 cells, TH9 cells, TH22 cells, follicular helper T cells, α / β T cells, and δ / γ T cells. Non-limiting examples of commercially available T-cell lines include lines BCL2 (AAA) Jurkat ( CRL-2902TM) , BCL2 (S70A) Jurkat ( CRL-2900TM) , BCL2 (S87A) Jurkat ( CRL-2901TM) , BCL2 Jurkat ( CRL-2899TM) , Neo Jurkat ( CRL-2898TM) , TALL-104 cytotoxic human T cell line (ATCC #CRL-11386) . Further examples include but are not limited to mature T-cell lines, e.g., such as Deglis, EBT-8, HPB-MLp-W, HUT 78, HUT 102, Karpas 384, Ki 225, My-La, Se-Ax, SKW-3, SMZ-1 and T34; and immature T-cell lines, e.g., ALL-SIL, Be13, CCRF-CEM, CML-T1, DND-41, DU. 528, EU-9, HD-Mar, HPB-ALL, H-SB2, HT-1, JK-T1, Jurkat, Karpas 45, KE-37, KOPT-K1, K-T1, L-KAW, Loucy, MAT, MOLT-1, MOLT 3, MOLT-4, MOLT 13, MOLT-16, MT-1, MT-ALL, P12 / Ichikawa, Peer, PER0117, PER-255, PF-382, PFI-285, RPMI-8402, ST-4, SUP-T1 to T14, TALL-1, TALL-101, TALL-103 / 2, TALL-104, TALL-105, TALL-106, TALL-107, TALL-197, TK-6, TLBR-1, -2, -3, and -4, CCRF-HSB-2 (CCL-120.1) , J. RT3-T3.5 (ATCC TIB-153) , J45.01 (ATCC CRL-1990) , J. CaM1.6 (ATCC CRL-2063) , RS4; 11 (ATCC CRL-1873) , CCRF-CEM (ATCC CRM-CCL-119) ; and cutaneous T-cell lymphoma lines, e.g., HuT78 (ATCC CRM-TIB-161) , MJ[G11] (ATCC CRL-8294) , HuT102 (ATCC TIB-162) . Non-limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection (ATCC) (Manassas, VA) , and the German Collection of Microorganisms and Cell Cultures.
[0123] In certain aspects, the cells are cytotoxic T cells (also known as TC, Cytotoxic T Lymphocyte, CTL, T Killer cell, a lytic T cell, CD8+ T cells or killer T cell) . In certain aspects, the T cell is a CD4+T cell. In certain aspects, the T cell can be a CD4+T cell or a CD8+T cell. In certain aspects, the cell is a tumor-specific T cell.
[0124] In one aspect, the cells are natural killer (NK) cells, Natural Killer T (NKT) cells, cytokine-induced killer (CIK) cells, tumor-infiltrating lymphocytes (TILs) , lymphokine-activated killer (LAK) cells, or the like. NK cells may either be isolated or obtained from a commercially available source. Non-limiting examples of commercial NK cell lines include lines NK-92 ( CRL-2407TM) , NK-92MI ( CRL-2408TM) . Further examples include but are not limited to NK lines HANK1, KHYG-1, NKL, NK-YS, NOI-90, and YT. Non-limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection (ATCC) (Manassas, VA) and the German Collection of Microorganisms and Cell Cultures.
[0125] In one aspect, the cells are B cells, monocytes or granulocytes, e.g., myeloid cells, macrophages, neutrophils, dendritic cells, mast cells, eosinophils, and / or basophils.
[0126] In certain aspects, the cell is a cell of the myeloid lineage. Non-limiting examples of cells of the myeloid lineage include monocytes, macrophages, basophils, neutrophils, eosinophils, mast cell, erythrocytes, megakaryocytes, thrombocytes, and stem cells from which myeloid cells may be differentiated. In certain embodiments, the stem cell is a pluripotent stem cell (e.g., embryonic stem cell or induced pluripotent stem cell) .
[0127] 3.2. Methods for genetic engineering
[0128] In one aspect, the engineered cells are prepared by various methods of the transfer of polynucleotides encoding polypeptides, e.g., CARs or EARs. Physical methods include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Biological methods include the use of DNA and RNA vectors, e.g., a viral vector, e.g., a lentiviral vector. Chemical methods include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. Exemplary methods are shown in Table 4. In some aspects, those well-known methods include transduction via viral e.g., retroviral or lentiviral, transposons, and electroporation. Table 4. Delivery methods for the genome editing systems
[0129] In one aspect, recombinant polynucleotides are transferred into cells using recombinant infectious virus particles, e.g., adenoviral vector, AAV vector, lentiviral vector, retroviral vector, such as gamma-retroviral vectors. In one aspect, the retroviral vector or lentiviral vector has a long terminal repeat sequence (LTR) . In one aspect, the vectors are self-inactivating (SIN) . In one aspect, the vectors are conditionally replicating (mobilizable) vectors. In one aspect, the lentiviral vectors are derived from human, feline or simian lentiviruses. In one aspect, the retroviral vectors are derived from murine retroviruses. In one aspect, the lentiviruses or retroviruses include those derived from any avian or mammalian cell source. In one aspect, the lentiviruses or retroviruses are amphotropic, meaning that they are capable of infecting host cells of several species, including humans. In one aspect, the gene to be expressed replaces the retroviral gag, pol and / or env sequences.
[0130] In one aspect, the vector comprising the polynucleotides encoding the polypeptides e.g., CAR, can contain a promoter and / or enhancer or regulatory elements to regulate expression of the encoded recombinant receptor. In one aspect, the promoter and / or enhancer or regulatory elements can be condition-dependent promoters, enhancers, and / or regulatory elements. In one aspect, the polynucleotides encoding the polypeptides can be operatively linked to a constitutive promoter. In one aspect, the promoter is selected from the group consisting of Cytomegalovirus (CMV) promoter, elongation factors-1 alpha (EF1α) promoter, ubiquitin C promoter (UbiC) , phosphor-glycerokinase promoter (PGK) , simian virus 40 early promoter (SV40) and chicken β-Actin promoter coupled with CMV early enhancer (CAGG) .
[0131] In one aspect, the polynucleotide is operably linked to an inducible promoter. The inducible promoter can be induced by one or more conditions, such as a physical condition, microenvironment of the engineered immune effector cell, or the physiological state of the engineered immune effector cell, an inducer (i.e., an inducing agent) , or a combination thereof. In one aspect, the inducing condition does not induce the expression of endogenous genes in the engineered mammalian cell, and / or in the subject that receives the pharmaceutical composition. In one aspect, the inducing condition is selected from the group consisting of: inducer, irradiation (such as ionizing radiation, light) , temperature (such as heat) , redox state, tumor environment, and the activation state of the engineered mammalian cell.
[0132] In one aspect, the polynucleotide is operatively linked to a Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE) , located downstream of the polynucleotides.
[0133] In one aspect, the vector can contain a single promoter that drives the expression of one or more nucleic acid molecules. In one aspect, such nucleic acid molecules can be multi-cistronic. For example, in one aspect, transcription units can be engineered as a bi-cistronic unit containing an IRES (internal ribosome entry site) , which allows co-expression of gene products (e.g., encoding a first and second CAR) by a message from a single promoter. In one aspect, a single promoter may direct expression of an RNA that contains, in a single open reading frame (ORF) , two or three genes (e.g. encoding a first and second CAR) separated from one another by sequences encoding a self-cleavage peptide or a protease recognition site. In one aspect, the self-cleavage peptide is selected from the group consisting of foot-and-mouth disease virus (F2A) , equine rhinitis A virus (E2A) , Thosea asigna virus (T2A) and porcine teschovirus-1 (P2A) . In one aspect, the T2A comprises or consists of the amino acid sequence of SEQ ID NO: 48, the E2A comprises or consists of the amino acid sequence of SEQ ID NO: 49, the P2A comprises or consists of the amino acid sequence of SEQ ID NO: 70.
[0134] In one aspect, polynucleotides are transferred into T cells via electroporation. In one aspect, polynucleotides are transferred into T cells via transposition. In one aspect, polynucleotides are delivered by means of transposons including a Sleeping Beauty transposon system (SB) and / or a piggyBac (PB) transposon system.
[0135] Polynucleotides encoding polypeptides may be associated with additional coding regions which encode secretory or signal peptides, which direct the secretion of the polypeptide. For example, if secretion of the polypeptide is desired, DNA encoding a signal sequence may be placed upstream of the polypeptide. Those of ordinary skill in the art are aware that polypeptides secreted by vertebrate cells generally have a signal peptide fused to the N-terminus of the polypeptide, which is cleaved from the translated polypeptide to produce a secreted or "mature" form of the polypeptide. In one aspect, the signal peptide comprises a sequence of a human CD2, CD3δ, CD3ε, CD3γ, CD3ζ, CD4, CD8α, CD19, CD28, CD37, CD45, 4-1BB, GM-CSFR, IL-2, CD33, Human IgKVIII, Human IgG2 H, Chymotrypsinogen, trypsinogen-2, HSA, Insulin or tPA signal peptide. Exemplified signal peptides include the amino acid sequence of SEQ ID NO: 45, SEQ ID NO: 46 or SEQ ID NO: 71.
[0136] In one aspect, the polynucleotides encoding the polypeptides contain a nucleic acid sequence encoding one or more markers. In one aspect, the one or more markers is a transduction marker, surrogate marker and / or a selection marker. In one aspect, the polynucleotides encoding the polypeptides contain a nucleic acid sequence encoding one or more additional polypeptides that enhance and / or dampen responses of the cells upon adoptive transfer and encounter with ligand.
[0137] In one aspect, the polynucleotides can also encode one or more surrogate marker (s) . In one aspect, the surrogate markers can include truncated forms of cell surface polypeptides, such as truncated forms that are non-functional and to not transduce or are not capable of transducing a signal or a signal ordinarily transduced by the full-length form of the cell surface polypeptide, and / or do not or are not capable of internalizing. In one aspect, the truncated cell surface polypeptides including truncated forms of growth factors or other receptors such as a truncated human epidermal growth factor receptor 2 (tHER2) , a truncated epidermal growth factor receptor (tEGFR) , a prostate-specific membrane antigen (PSMA) or modified form thereof. tEGFR can be used to identify or select cells that have been engineered with the tEGFR fusion protein and an encoded exogenous protein, and / or to eliminate or separate cells expressing the encoded exogenous protein. In one aspect, the tEGFR comprises or consist of an amino acid sequence of SEQ ID NO: 47.
[0138] In one aspect, the marker is a fluorescent protein, such as green fluorescent protein (GFP) , enhanced green fluorescent protein (EGFP) , such as super-fold GFP (sfGFP) , red fluorescent protein (RFP) , such as tdTomato, mCherry, mStrawberry, AsRed2, DsRed or DsRed2, cyan fluorescent protein (CFP) , blue green fluorescent protein (BFP) , enhanced blue fluorescent protein (EBFP) , and yellow fluorescent protein (YFP) , and variants thereof, including species variants, monomeric variants, and codon-optimized and / or enhanced variants of the fluorescent proteins. In one aspect, the marker is or comprises an enzyme, such as a luciferase, the lacZ gene from E. coli, alkaline phosphatase, secreted embryonic alkaline phosphatase (SEAP) , chloramphenicol acetyl transferase (CAT) . Exemplary light-emitting reporter genes include luciferase (luc) , b-galactosidase, chloramphenicol acetyltransferase (CAT) , b-glucuronidase (GUS) or variants thereof.
[0139] In one aspect, the marker is a selection marker. In one aspect, the selection marker is a polypeptide that confers resistance to exogenous agents or drugs. In one aspect, the selection marker is an antibiotic resistance gene. In one aspect, the selection marker is an antibiotic resistance gene confers antibiotic resistance to a mammalian cell. In one aspect, the selection marker is selected from the group consisting of a Puromycin resistance gene, a Hygromycin resistance gene, a Blasticidin resistance gene, a Neomycin resistance gene, a Geneticin resistance gene or a Zeocin resistance gene or a modified form thereof.
[0140] Alternatively, various assays can be used to confirm the presence of the recombinant DNA sequence in the engineered cell, such as Southern and Northern blotting, RT-PCR and PCR. In one aspect, the polypeptide can be detected by the ability to recognize target cells, or the release of cytokines (e.g., interferon-γ, granulocyte / monocyte colony stimulating factor (GM-CSF) , tumor necrosis factor α (TNF-α) or interleukin 2 (IL-2) ) . In addition, the function of polypeptide can be evaluated by measurement of cellular cytotoxicity.
[0141] 3.3 Preparation of Engineered Cells
[0142] In one aspect, the present disclosure provides a manufacture process of the engineered cells. In one aspect, any known method for preparation may be used. In a particular aspect, the method includes transducing a population of isolated cells with the polynucleotide encoding the polypeptide and selecting a subpopulation of said isolated cells that have been successfully transduced with the polynucleotide thereby producing genetically modified cells, as described above.
[0143] In one aspect, the method includes acquisition, isolation, transduction, expansion steps. In a particular aspect, the method includes the following steps: (i) acquisition of an immune cell population (e.g. blood cells) (ii) isolation of a particular cell population (e.g. T cells and / or NK cells) (iii) transducing a population of isolated cells with the polynucleotide encoding the polypeptide; and (iv) expanding a subpopulation of said isolated cells that have been successfully transduced with said nucleic acid sequence of step (iii) thereby producing genetically modified cells. These different steps are more particularly described below.
[0144] 3.3.1 Cell acquisition
[0145] In one aspect, the subject from which the cell is obtained for introduction of the polypeptide (e.g., CAR) is one having the disease or condition or in need of a cell therapy or to which cell therapy will be administered. In one aspect, the cells can be derived from a healthy donor.
[0146] In one aspect, the cells may be obtained from a sample, such as a biological sample. In one aspect, the samples are selected from whole blood, peripheral blood mononuclear cells (PBMCs) , leukocytes, bone marrow, thymus, tissue biopsy, tumor, leukemia, lymphoma, lymph node, gut associated lymphoid tissue, mucosa associated lymphoid tissue, spleen, other lymphoid tissues, liver, lung, stomach, intestine, colon, kidney, pancreas, breast, bone, prostate, cervix, testes, ovaries, tonsil, or other organ, and / or cells derived therefrom. In one aspect, the cells are primary cells. In one aspect, cells from the circulating blood of a subject are obtained, e.g., by apheresis or leukapheresis. The resulting samples comprise lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and / or platelets, and in some aspects contain cells other than red blood cells and platelets.
[0147] 3.3.2 Cell isolation
[0148] Various methods are readily available for isolating immune cells from a sample, for example using Life Technologies system; STEMcell Technologies EasySepTM, RoboSepTM, RosetteSepTM, SepMateTM; Miltenyi Biotec MACSTM cell separation kits, cell surface marker expression and other commercially available cell separation and isolation kits (e.g., ISOCELL from Pierce, Rockford, IL) . Particular subpopulations of immune cells may be isolated through the use of beads or other binding agents available in such kits specific to unique cell surface markers. For example, MACSTM CD4+ and CD8+MicroBeads may be used to isolate CD4+ and CD8+ T-cells.
[0149] In one aspect, isolation of the cells includes one or more non-affinity-based cell separation steps. In one aspect, cells are washed, centrifuged, and / or incubated in the presence of one or more reagents, for example, to remove unwanted components, enrich for desired components, lyse or remove cells sensitive to particular reagents. In one aspect, cells are separated based on one or more properties, such as density, adherent properties, size, sensitivity and / or resistance to particular components.
[0150] In one aspect, the blood cells collected from the subject are washed, e.g., to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps. In one aspect, the cells are washed with phosphate buffered saline (PBS) . In one aspect, the wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations. Initial activation steps in the absence of calcium may lead to magnified activation. In one aspect, a washing step is accomplished by a semi-automated “flow-through” centrifuge (for example, the Cobe 2991 cell processor, Baxter) according to the manufacturer's instructions. In one aspect, a washing step is accomplished by tangential flow filtration (TFF) according to the manufacturer's instructions. In one aspect, the cells are resuspended in a variety of biocompatible buffers after washing, such as, for example, Ca2+ / Mg2+ free PBS. In certain embodiments, components of a blood cell sample are removed and the cells directly resuspended in culture media. In one aspect, the isolation includes density-based cell separation methods, such as the preparation of white blood cells from peripheral blood by lysing the red blood cells and centrifugation through a Percoll or Ficoll gradient.
[0151] In one aspect, the isolation methods include the separation of different cell types based on the expression or presence in the cell of one or more specific molecules, such as surface markers, e.g., surface proteins, intracellular markers, or nucleic acid. In one aspect, the separation is affinity-or immunoaffinity-based separation. The separation can be based on positive selection, in which the cells having bound the reagents are retained for further use, and / or negative selection, in which the cells having not bound to the antibody or binding partner are retained. The separation needs not result in 100%enrichment or removal of a particular cell population or cells expressing a particular marker.
[0152] In one aspect, one separation step can deplete cells expressing multiple markers simultaneously, such as by incubating cells with a plurality of antibodies or binding partners, each specific for a marker targeted for negative selection. Likewise, multiple cell types can simultaneously be positively selected by incubating cells with a plurality of antibodies or binding partners expressed on the various cell types. In one aspect, multiple rounds of separation steps are carried out, where the positively or negatively selected fraction from one step is subjected to another separation step, such as a subsequent positive or negative selection.
[0153] In some aspects, specific subpopulations of T cells, such as cells positive or expressing high levels of one or more surface markers, e.g., CD3+, CD28+, CD62L+, CCR7+, CD27+, CD127+, CD4+, CD8+, CD45RA+, and / or CD45RO+ T cells, are isolated by positive or negative selection techniques. In one aspect, T cells are isolated by incubation with anti-CD3 / anti-CD28 conjugated particles or beads (e.g., M-450 CD3 / CD28 T Cell Expander, MACSiBeadsTM, etc. ) . In one aspect, the time period of positive selection is about 30 minutes. In a further embodiment, the time period is at least 1, 2, 3, 4, 5, or 6 hours. In one aspect, the time period is 10 to 24 hours. In one aspect, the incubation time period is 24 hours. For isolation of a desired population of cells by positive or negative selection, the concentration of cells and particles can be varied. In certain embodiments, it may be desirable to significantly decrease the volume in which beads and cells are mixed together (i.e., increase the concentration of cells) , to ensure maximum contact of cells and beads. In one aspect, greater than 100 million cells / mL is used.
[0154] In some aspects, T cells are separated from a sample by negative selection of markers expressed on non-T cells, such as B cells, monocytes, or other white blood cells, such as CD14. In some aspects, a CD4 or CD8 selection step is used to separate CD4+ helper and CD8+ cytotoxic T cells. Such CD4+ and CD8+populations can be further sorted into sub-populations by positive or negative selection for markers expressed or expressed to a relatively higher degree on one or more naive, memory, and / or effector T cell subpopulations.
[0155] In some aspects, CD8+ cells are further enriched for or depleted of naive, central memory, effector memory, and / or central memory stem cells, such as by positive or negative selection based on surface antigens associated with the respective subpopulation. In some aspects, enrichment for central memory T (TCM) cells is carried out to increase efficacy, such as to improve long-term survival, expansion, and / or engraftment following administration. In some aspects, combining TCM-enriched CD8+ T cells and CD4+T cells further enhances efficacy.
[0156] In some aspects, memory T cells are present in both CD62L+ and CD62L-subsets of CD8+peripheral blood lymphocytes. PBMC can be enriched for or depleted of CD62L-CD8+ and / or CD62L+CD8 fractions, such as using anti-CD8 and anti-CD62L antibodies.
[0157] In some aspects, the enrichment for central memory T (TCM) cells is based on positive or high surface expression of CD45RO, CD62L, CCR7, CD28, CD3, and / or CD127. In some aspects, it is based on negative selection for cells expressing or highly expressing CD45RA and / or granzyme B. In some aspects, isolation of a CD8+ population enriched for TCM cells is carried out by depletion of cells expressing CD4, CD14, CD45RA, and positive selection or enrichment for cells expressing CD62L. In one aspect, enrichment for central memory T (TCM) cells is carried out starting with a negative fraction of cells selected based on CD4 expression, which is subjected to a negative selection based on expression of CD14 and CD45RA, and a positive selection based on CD62L.
[0158] In one aspect, the enrichment for NK cells is based on positive or high surface expression of CD56 and CD16 and on the negative expression of CD3 and / or optionally on the presence of NKp46 or NKp30 receptors.
[0159] In one aspect, the sample or composition of cells to be separated is incubated with small, magnetizable or magnetically responsive material, such as magnetically responsive particles or microparticles, such as paramagnetic beads (e.g., or beads) . The magnetically responsive material, e.g., particle, generally is directly or indirectly attached to a binding partner, e.g., an antibody, that specifically binds to a molecule, e.g., surface marker, present on the cell, cells, or population of cells that it is desired to separate, e.g., that it is desired to negatively or positively select. In one aspect, the sample is placed in a magnetic field, and those cells having magnetically responsive or magnetizable particles attached thereto will be attracted to the magnet and separated from the unlabeled cells. For positive selection, cells that are attracted to the magnet are retained; for negative selection, cells that are not attracted (unlabeled cells) are retained. In some aspects, a combination of positive and negative selection is performed during the same selection step, where the positive and negative fractions are retained and further processed or subject to further separation steps.
[0160] In one aspect, the magnetically responsive particles are left attached to the cells that are to be subsequently incubated, cultured and / or engineered; in some aspects, the particles are left attached to the cells for administration to a patient. In one aspect, the magnetically responsive particles are removed from the cells. Methods for removing magnetically responsive particles from cells are known and include, e.g., the use of competing non-labeled antibodies, magnetically responsive particles or antibodies conjugated to cleavable linkers, etc. In one aspect, the magnetically responsive particles are biodegradable.
[0161] In one aspect, the affinity-based selection is via magnetic-activated cell sorting (Miltenyi Biotec, Auburn, CA) . Magnetic Activated Cell Sorting systems are capable of high-purity selection of cells having magnetized particles attached thereto. In certain embodiments, operates in a mode wherein the non-target and target species are sequentially eluted after the application of the external magnetic field. That is, the cells attached to magnetized particles are held in place while the unattached species are eluted. Then, after this first elution step is completed, the species that were trapped in the magnetic field and were prevented from being eluted are freed in some manner such that they can be eluted and recovered. In certain embodiments, the non-target cells are labelled and depleted from the heterogeneous population of cells.
[0162] In one aspect, a cell population described herein is collected and enriched (or depleted) via flow cytometry, in which cells stained for multiple cell surface markers are carried in a fluidic stream. In one aspect, a cell population described herein is collected and enriched (or depleted) via preparative scale (FACS) -sorting. In certain embodiments, a cell population described herein is collected and enriched (or depleted) by use of microelectromechanical systems (MEMS) chips in combination with a FACS-based detection system. In both cases, cells can be labeled with multiple markers, allowing for the isolation of well-defined T cell subsets at high purity.
[0163] In one aspect, the preparation methods include steps for freezing, e.g., cryopreserving, the cells, either before or after isolation, incubation, and / or engineering. In one aspect, the freeze and subsequent thaw step removes granulocytes and, to some extent, monocytes in the cell population. In one aspect, the cells are suspended in a freezing solution, e.g., following a washing step to remove plasma and platelets. Any of a variety of known freezing solutions and parameters in some aspects may be used. One example involves using PBS containing 20%DMSO and 8%human serum albumin (HSA) , or other suitable cell freezing media. This is then diluted 1: 1 with media so that the final concentration of DMSO and HSA are 10%and 4%, respectively. The cells are then frozen to -80 ℃ at a rate of 1 ℃ per minute and stored in the vapor phase of a liquid nitrogen storage tank. In one aspect, cryopreserved cells are thawed and washed as described herein and allowed to rest for one hour at room temperature prior to activation.
[0164] 3.3.3 Cell expansion
[0165] In one aspect, the provided methods include cultivation, incubation, culture, and / or genetic engineering steps. In one aspect, the cells are incubated and / or cultured prior to or in connection with genetic engineering. The incubation steps can include culture, cultivation, stimulation, activation, and / or propagation. In one aspect, the cells are incubated in the presence of stimulating conditions or a stimulatory agent. The conditions can include one or more of particular media, temperature, oxygen content, carbon dioxide content, time, agents, e.g., nutrients, amino acids, antibiotics, ions, and / or stimulatory factors, such as cytokines, chemokines, antigens, binding partners, polypeptides, recombinant soluble receptors, and any other agents designed to activate the cells.
[0166] In one aspect, the stimulating conditions or agents include one or more agent, e.g., ligand, which is capable of stimulating or activating an intracellular signaling domain of a TCR complex. In some aspects, the agent turns on or initiates TCR / CD3 intracellular signaling cascade in a T cell. Such agents can include antibodies, such as those specific for a TCR component and / or co-stimulatory receptor, e.g., anti-CD3, anti-CD28, for example, bound to solid support such as a bead (e.g., ) , and / or one or more cytokines. In one aspect, a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 80, 85, 90, 95, 100 125 or 150 million cells / mL is used.
[0167] In one aspect, the mixture may be cultured for several hours (about 3 hours) to about 14 days or any hourly integer value in between. In another embodiment, the mixture may be cultured for 21 days. In one embodiment, the beads and the T cells are cultured together for about eight days. In another embodiment, the beads and cells are cultured together for 2-3 days. Several cycles of stimulation may also be desired such that culture time of T cells can be 60 days or more. Conditions appropriate for T cell culture include an appropriate media that may contain factors necessary for proliferation and viability, including interleukin-2 (IL-2) , insulin, IFN-γ, IL-4, IL-7, GM-CSF, IL-10, IL-12, IL-15, TGFβ, and TNF-α or any other additives. Other additives for the growth of cells include, but are not limited to, surfactant, plasmanate, and reducing agents such as N-acetyl-cysteine and 2-mercaptoethanol. Media can include RPMI 1640, AIM-V, DMEM, MEM, α-MEM, F-12, X-Vivo 15, and X-Vivo 20, optimizer, with added amino acids, sodium pyruvate, and vitamins, either serum-free or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones, and / or an amount of cytokine (s) sufficient for the growth and expansion of T cells. Antibiotics, e.g., penicillin and streptomycin, are included only in experimental cultures, not in cultures of cells that are to be infused into a subject. The target cells are maintained under conditions necessary to support growth, for example, an appropriate temperature (e.g., 37 ℃) and atmosphere (e.g., air plus 5%CO2) .
[0168] In one aspect, NK cell populations can be expanded in vitro using interleukin-2 (IL-2) IL-15, IL-15 / IL-15RA complex, IL-18 and IL-12. In one aspect, the NK cells are ex vivo expanded for at least about 5 days, for example, not less than about 10 days, not less than about 15 days, or not less than about 20 days before administration to the patient. IV. PHARMACEUTICAL COMPOSITION
[0169] Pharmaceutical compositions of the present disclosure may comprise engineered cells in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients. Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide) ; and preservatives. Compositions of the present disclosure are in one aspect formulated for intravenous administration.
[0170] In one aspect, the pharmaceutical composition is substantially free of, e.g., there are no detectable levels of a contaminant, e.g., selected from the group consisting of endotoxin, mycoplasma, replication competent lentivirus (RCL) , p24, VSV-G nucleic acid, HIV gag, residual anti-CD3 / anti-CD28 coated beads, mouse antibodies, pooled human serum, bovine serum albumin, bovine serum, culture media components, vector packaging cell or plasmid components, a bacterium and a fungus. In one aspect, the bacterium is at least one selected from the group consisting of Alcaligenes faecalis, Candida albicans, Escherichia coli, Haemophilus influenza, Neisseria meningitides, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumonia, and Streptococcus pyogenes group A.
[0171] When “an immunologically effective amount” , “an anti-tumor effective amount” , “atumor-inhibiting effective amount” , or “therapeutic amount” is indicated, the precise amount of the compositions of the present disclosure to be administered can be determined by a physician with consideration of individual differences in age, weight, tumor size, extent of infection or metastasis, and condition of the patient (subject) . It can generally be stated that a pharmaceutical composition comprising the T cells described herein may be administered at a dosage of 104 to 109 cells / kg body weight, in some instances 105 to 106 cells / kg body weight, including all integer values within those ranges. T cell compositions may also be administered one time or multiple times at these dosages. The cells can be administered by using infusion techniques that are commonly known in immunotherapy.
[0172] In some embodiments, the present disclosure further provides a pharmaceutical combination or a pharmaceutical combination product, which comprises the polypeptide of the present disclosure or the engineered cells of the present disclosure, and one or more additional therapeutic agents. In one aspect, the therapeutic agent can be any agent that is helpful for treatment, e.g., for treating tumors. In one aspect, the therapeutic agent is selected from chemotherapeutic agents, immunotherapeutic agents, cytotoxic agents, pro-apoptotic or cell cycle regulating agents such as immune checkpoint inhibitor, or small molecule drugs. V. METHOD OF TREATMENT
[0173] Pharmaceutical compositions of the present disclosure may be administered in a manner appropriate to the disease to be treated (or prevented) . In one aspect, the disease is a tumor or an autoimmune disease. In one aspect, the disease is a CD19-associated tumor or a CD19-associated autoimmune disease. In one aspect, the disease is a CD20-associated tumor or a CD20-associated autoimmune disease. In one aspect, the disease is a CD19&CD20-associated tumor or a CD19&CD20-associated autoimmune disease.
[0174] In one aspect, the tumor is TAA positive. In one aspect, the tumor comprises tumor cells that moderately / highly express TAA. In one aspect, the tumor (e.g., cancer) patient has TAA in the tumor tissue at an elevated level as compared to the TAA level in the same tissue of a healthy subject or in a healthy tissue adjacent to the tumor tissue of the patient. In one aspect, the TAA is CD19 and / or CD20. The diseases may comprise solid tumors, such as sarcomas and carcinomas, include fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteosarcoma, and other sarcomas, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, lymphoid malignancy, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer, hepatocellular carcinoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, medullary thyroid carcinoma, papillary thyroid carcinoma, pheochromocytomas sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, Wilms'tumor, cervical cancer, testicular tumor, seminoma, bladder carcinoma, melanoma, and CNS tumors (such as a glioma (such as brainstem glioma and mixed gliomas) , glioblastoma (also known as glioblastoma multiforme) astrocytoma, CNS lymphoma, germinoma, medulloblastoma, Schwannoma craniopharyogioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, neuroblastoma, retinoblastoma and brain metastases) ; the non-solid tumors, such as leukemias, including acute leukemias (such as acute lymphocytic leukemia, acute myelocytic leukemia, acute myelogenous leukemia and myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia) , chronic leukemias (such as chronic myelocytic (granulocytic) leukemia, chronic myelogenous leukemia, and chronic lymphocytic leukemia) , polycythemia vera, lymphoma, Hodgkin's disease, non-Hodgkin's lymphoma (indolent and high grade forms) , multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease, myelodysplastic syndrome, hairy cell leukemia and myelodysplasia. The cancer may be in an early, intermediate or advanced stage or metastatic cancer.
[0175] In one aspect, the autoimmune disease may comprises rheumatoid arthritis and juvenile rheumatoid arthritis, systemic lupus erythematosus, lupus nephritis, Wegener's disease, inflammatory bowel disease, ulcerative colitis, idiopathic thrombocytopenic purpura, thrombotic throbocytopenic purpura, Type 1 diabetes, Pemphigus vulgaris, autoimmune thrombocytopenia, multiple sclerosis, psoriasis, IgA nephropathy, IgM polyneuropathies, ANCA vasculitis, myasthenia gravis, ANCA associated vasculitis, diabetes mellitus, Reynaud's syndrome, Sjogren's syndrome, Neuromyelitis Optica and glomerulonephritis.
[0176] The quantity and frequency of administration will be determined by the condition of the patient, and the type and severity of the patient’s disease, although appropriate dosages may be determined by clinical trials. The administration of the subject compositions may be carried out in any convenient manner, including by aerosol injection, ingestion, transfusion, implantation or transplantation. The compositions described herein may be administered to a patient transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous (i. v. ) injection, or intraperitoneally. In one aspect, the T cell compositions of the present invention are administered to a patient by intradermal or subcutaneous injection. In one aspect, the compositions are directly injected into an organ of interest (e.g., an organ affected by a neoplasm) . Alternatively, the compositions are provided indirectly to the organ of interest, for example, by administration into the circulatory system (e.g., the tumor vasculature) . Expansion and differentiation agents can be provided prior to, during or after administration of the cells or compositions to increase production of T cells or NK cells in vitro or in vivo.
[0177] In one aspect, lymphodepletion is performed on a subject, e.g., prior to administering one or more cells described herein. In one aspect, the lymphodepletion comprises administering one or more of melphalan, cytoxan, cyclophosphamide, and fludarabine.
[0178] In one aspect, the engineered cells are administered as part of a combination treatment, such as simultaneously with or sequentially with, in any order, another therapeutic intervention, such as an antibody or engineered cell or receptor or agent, such as a cytotoxic or therapeutic agent. The cells in some embodiments are co-administered with one or more additional therapeutic agents or in connection with another therapeutic intervention, either simultaneously or sequentially in any order. In one aspect, the cells are co-administered with another therapy sufficiently close in time such that the cell populations enhance the effect of one or more additional therapeutic agents, or vice versa. In one aspect, the cells or antibodies are administered prior to the one or more additional therapeutic agents. In one aspect, the cells or antibodies are administered after to the one or more additional therapeutic agents, such as anti-cancer agents. In the context of the present disclosure, it is contemplated that cell therapy could be used similarly in conjunction with chemotherapeutic, radiotherapeutic, or immunotherapeutic intervention, as well as pro-apoptotic or cell cycle regulating agents such as immune checkpoint inhibitor.
[0179] Alternatively, the present therapy may precede or follow the other agent treatment by intervals ranging from minutes to weeks. In embodiments where the other agent and present disclosure are applied separately to the individual, one would generally ensure that a significant period of time did not expire between the times of each delivery, such that the agent and therapy would still be able to exert an advantageously combined effect on the cell. In such instances, it is contemplated that one may contact the cell with both modalities within about 12-24 h of each other and, more preferably, within about 6-12 h of each other. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2, 3, 4, 5, 6 or 7) to several week (1, 2, 3, 4, 5, 6, 7 or 8) lapse between the respective administrations. It is expected that the treatment cycles would be repeated if necessary. It also is contemplated that various standard therapies, as well as surgical intervention, may be applied in combination with the cell therapy. VI. Sequences Table 5. Sequences of the present disclosure VII. Exemplary Embodiments
[0180] Among the embodiments provided herein are:
[0181] 1. A polypeptide system, comprising a first chimeric antigen receptor (CAR) and one or more additional polypeptides, wherein the first CAR comprises, from its N to C terminus in order, a first extracellular antigen-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 31, a first transmembrane domain and a first intracellular signaling domain; wherein the additional polypeptide is a second CAR or a polypeptide of an engineered armor receptor (EAR) .
[0182] 2. The polypeptide system of embodiment 1, wherein the first extracellular antigen-binding domain is capable of binding CD19, CD20, CD22, CD30, BCMA, AFP, ALK, GPC3, HER2, EGFR, alpha folate receptor, 5T4, avβ6 integrin, B7-H3, B7-H6, CAIX, CD16, CD33, CD44, CD44v6, CD44v7 / 8, CD70, CD79a, CD79b, CD123, CD138, CD171, CEA, Claudin18.2, CSPG4, DLL3, EGFRvlll, EGP2, EGP40, EPCAM, EphA2, EpCAM, FAP, fetal AchR, FRa, GD2, GD3, MAGE-1, NY-ESO-1, IL-11Rα, IL-13Rα2, Lambda, Lewis-Y, Kappa, Mesothelin, Muc1, Muc16, NCAM, NKG2D Ligands, PRAME, PSCA, PSMA, RORI, SSX, Survivin, TAG72, TEMs, VEGFR2 or WT-1.
[0183] 3. The polypeptide system of embodiment 1 or 2, wherein the first extracellular antigen-binding domain is capable of binding CD19.
[0184] 4. The polypeptide system of any one of embodiments 1 to 3, wherein the first extracellular antigen-binding domain is capable of binding to the same epitope on CD19 as a reference antibody that comprises the amino acid sequence of SEQ ID NO: 21.
[0185] 5. The polypeptide system of any one of embodiments 1 to 4, wherein the first extracellular antigen-binding domain comprises a heavy chain variable region (CD19-VH) and a light chain variable region (CD19-VL) .
[0186] 6. The polypeptide system of any one of embodiments 1 to 5, wherein the first extracellular antigen-binding domain is an anti-CD19 scFv.
[0187] 7. The polypeptide system of any one of embodiments 1 to 6, wherein the CD19-VH comprises a HCDR1, a HCDR2 and a HCDR3 contained within the amino acid sequence of SEQ ID NO: 1, and the CD19-VL comprises a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 4.
[0188] 8. The polypeptide system of any one of embodiments 1 to 7, wherein the CD19-VH comprises a HCDR1, a HCDR2 and a HCDR3 comprising the amino acid sequences of SEQ ID NO: 5, SEQ ID NO: 6 and SEQ ID NO: 7, respectively; the CD19-VL comprises a LCDR1, a LCDR2 and a LCDR3 comprising the amino acid sequences of SEQ ID NO: 8, SEQ ID NO: 9 and SEQ ID NO: 10, respectively.
[0189] 9. The polypeptide system of any one of embodiments 1 to 8, wherein the CD19-VH comprises the amino acid sequence of SEQ ID NO: 1; the CD19-VL comprises the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 4.
[0190] 10. The polypeptide system of any one of embodiments 1 to 9, wherein the CD19-VH is fused by its N-terminus via a first flexible polypeptide linker to the C-terminus of the CD19-VL or the CD19-VL is fused by its N-terminus via a first flexible polypeptide linker to the C-terminus of the CD19-VH.
[0191] 11. The polypeptide system of any one of embodiments 1 to 10, wherein the first flexible polypeptide linker comprises the amino acid sequence of SEQ ID NO: 19 or SEQ ID NO: 20.
[0192] 12. The polypeptide system of any one of embodiments 1 to 11, wherein the anti-CD19 scFv comprises the amino acid sequence of SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 or SEQ ID NO: 24.
[0193] 13. The polypeptide system of any one of embodiments 1 to 12, wherein the first transmembrane domain comprises a transmembrane domain of CD28, CD8α, CD4, CD137, CD80, CD86, CD152 or PD1.
[0194] 14. The polypeptide system of any one of embodiments 1 to 13, wherein the first transmembrane domain comprises a CD28 transmembrane domain.
[0195] 15. The polypeptide system of any one of embodiments 1 to 14, wherein the first transmembrane domain comprises the amino acid sequence of SEQ ID NO: 36.
[0196] 16. The polypeptide system of any one of embodiments 1 to 15, wherein the first intracellular signaling domain comprises a first co-stimulatory signaling domain.
[0197] 17. The polypeptide system of any one of embodiments 1 to 16, wherein the first co-stimulatory signaling domain is selected from the group consisting of a signaling domain of CD27, CD28, CD137, OX40, CD30, CD40, CD3, HVEM, ICOS, Myd88, LFA-1, ICOS, CD2, CD7, NKG2C, B7-H3, Ligands of CD83 and a combination thereof.
[0198] 18. The polypeptide system of any one of embodiments 1 to 17, wherein the first co-stimulatory signaling domain is the signaling domain of CD28 or CD137.
[0199] 19. The polypeptide system of any one of embodiments 1 to 18, wherein the first co-stimulatory signaling domain comprises the amino acid sequence of SEQ ID NO: 37.
[0200] 20. The polypeptide system of any one of embodiments 1 to 19, wherein the first intracellular signaling domain comprises a first primary intracellular signaling domain.
[0201] 21. The polypeptide system of any one of embodiments 1 to 20, wherein the first primary intracellular signaling domain is fused by its N-terminus to the C-terminus of the first co-stimulatory signaling domain.
[0202] 22. The polypeptide system of any one of embodiments 1 to 21, wherein the first primary intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain.
[0203] 23. The polypeptide system of any one of embodiments 1 to 22, wherein the first primary intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 38.
[0204] 24. The polypeptide system of any one of embodiments 1 to 23, wherein the second CAR comprising, from its N to C terminus in order, a second extracellular antigen-binding domain, a second spacer, a second transmembrane domain and a second intracellular signaling domain.
[0205] 25. The polypeptide system of any one of embodiments 1 to 24, wherein the second extracellular antigen-binding domain is capable of binding CD20, CD22, CD30, BCMA, AFP, ALK, GPC3, HER2, EGFR, alpha folate receptor, 5T4, avβ6 integrin, B7-H3, B7-H6, CAIX, CD16, CD33, CD44, CD44v6, CD44v7 / 8, CD70, CD79a, CD79b, CD123, CD138, CD171, CEA, Claudin18.2, CSPG4, DLL3, EGFRvlll, EGP2, EGP40, EPCAM, EphA2, EpCAM, FAP, fetal AchR, FRa, GD2, GD3, MAGE-1, NY-ESO-1, IL-11Rα, IL-13Rα2, Lambda, Lewis-Y, Kappa, Mesothelin, Muc1, Muc16, NCAM, NKG2D Ligands, PRAME, PSCA, PSMA, RORI, SSX, Survivin, TAG72, TEMs, VEGFR2 or WT-1.
[0206] 26. The polypeptide system of any one of embodiments 1 to 25, wherein the second extracellular antigen-binding domain is capable of binding CD20.
[0207] 27. The polypeptide system of any one of embodiments 1 to 26, wherein the second extracellular antigen-binding domain is capable of specifically binding to the same epitope on CD20 as a reference antibody that comprises the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27.
[0208] 28. The polypeptide system of any one of embodiments 1 to 27, wherein the second extracellular antigen-binding domain comprises a heavy chain variable region (CD20-VH) and a light chain variable region (CD20-VL) .
[0209] 29. The polypeptide system of any one of embodiments 1 to 28, wherein the second extracellular antigen-binding domain is an anti-CD20 scFv.
[0210] 30. The polypeptide system of any one of embodiments 1 to 29, wherein the CD20-VH comprises a HCDR1, a HCDR2 and a HCDR3 contained within the amino acid sequence of SEQ ID NO: 11, and the CD20-VL comprises a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 12.
[0211] 31. The polypeptide system of any one of embodiments 1 to 30, wherein the CD20-VH comprises a HCDR1, a HCDR2 and a HCDR3 comprising the amino acid sequences of SEQ ID NO: 13, SEQ ID NO: 14 and SEQ ID NO: 15, respectively; the CD20-VL comprises a LCDR1, a LCDR2 and a LCDR3 comprising the amino acid sequences of SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18, respectively.
[0212] 32. The polypeptide system of any one of embodiments 1 to 33, wherein the CD20-VH comprises the amino acid sequence of SEQ ID NO: 11; the CD20-VL comprises the amino acid sequence of SEQ ID NO: 12.
[0213] 33. The polypeptide system of any one of embodiments 1 to 32, wherein the CD20-VH is fused by its N-terminus via a second flexible polypeptide linker to the C-terminus of the CD20-VL, or the CD20-VL is fused by its N-terminus via a second flexible polypeptide linker to the C-terminus of the CD20-VH.
[0214] 34. The polypeptide system of any one of embodiments 1 to 33, wherein the second flexible polypeptide linker comprises the amino acid sequence of SEQ ID NO: 19 or SEQ ID NO: 20.
[0215] 35. The polypeptide system of any one of embodiments 1 to 34, wherein the anti-CD20 scFv comprises the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27.
[0216] 36. The polypeptide system of any one of embodiments 1 to 35, wherein the first spacer and the second spacer are different.
[0217] 37. The polypeptide system of any one of embodiments 1 to 36, wherein the second spacer consists of a CD28 hinge.
[0218] 38. The polypeptide system of any one of embodiments 1 to 37, wherein the second spacer consists of the amino acid sequence of SEQ ID NO: 34.
[0219] 39. The polypeptide system of any one of embodiments 1 to 38, wherein the second transmembrane domain comprises the transmembrane domain of CD8α, CD4, CD28, CD137, CD80, CD86, CD152 or PD1.
[0220] 40. The polypeptide system of any one of embodiments 1 to 39, wherein the second transmembrane domain comprises the CD28 transmembrane domain.
[0221] 41. The polypeptide system of any one of embodiments 1 to 40, wherein the second transmembrane domain comprises the amino acid sequence of SEQ ID NO: 36.
[0222] 42. The polypeptide system of any one of embodiments 1 to 41, wherein the second intracellular signaling domain comprises a second co-stimulatory signaling domain.
[0223] 43. The polypeptide system of any one of embodiments 1 to 42, wherein the second co-stimulatory signaling domain is selected from the group consisting of a signaling domain of CD27, CD28, CD137, OX40, CD30, CD40, CD3, HVEM, ICOS, Myd88, LFA-1, ICOS, CD2, CD7, NKG2C, B7-H3, Ligands of CD83 and a combination thereof.
[0224] 44. The polypeptide system of any one of embodiments 1 to 43, wherein the second co-stimulatory signaling domain is the signaling domain of CD28 or CD137.
[0225] 45. The polypeptide system of any one of embodiments 1 to 44, wherein the second co-stimulatory signaling domain comprises the amino acid sequence of SEQ ID NO: 37.
[0226] 46. The polypeptide system of any one of embodiments 1 to 45, wherein the second intracellular signaling domain comprises a second primary intracellular signaling domain.
[0227] 47. The polypeptide system of any one of embodiments 1 to 46, wherein the second primary intracellular signaling domain is fused by its N-terminus to the C-terminus of the second co-stimulatory signaling domain.
[0228] 48. The polypeptide system of any one of embodiments 1 to 47, wherein the second primary intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain.
[0229] 49. The polypeptide system of any one of embodiments 1 to 48, wherein the second primary intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 38.
[0230] 50. The polypeptide system of any one of embodiments 1 to 49, wherein the EAR is capable of binding a Fas ligand.
[0231] 51. The polypeptide system of any one of embodiments 1 to 50, wherein the EAR polypeptide comprises, from its N to C terminus in order, an extracellular domain, a third transmembrane domain, and an intracellular domain.
[0232] 52. The polypeptide system of any one of embodiments 1 to 51, wherein the extracellular domain is the FAS ectodomain.
[0233] 53. The polypeptide system of any one of embodiments 1 to 52, wherein the extracellular domain comprises the amino acid sequence of SEQ ID NO: 50.
[0234] 54. The polypeptide system of any one of embodiments 1 to 53, wherein the intracellular domain doesn’t comprise a Fas endodomain.
[0235] 55. The polypeptide system of any one of embodiments 1 to 54, wherein the intracellular domain comprises an intracellular signaling domain selected from the group consisting of CD2, CD27, CD28, CD137, OX40, CD30, CD40, CD3, HVEM, ICOS, Myd88, LFA-1, ICOS, CD7, NKG2C, B7-H3 and Ligands of CD83, and a combination thereof.
[0236] 56. The polypeptide system of any one of embodiments 1 to 55, wherein the intracellular domain comprises the CD2 intracellular signaling domain.
[0237] 57. The polypeptide system of any one of embodiments 1 to 56, wherein the intracellular domain comprises any one of the amino acid sequences of SEQ ID NO: 55 to SEQ ID NO: 58.
[0238] 58. The polypeptide system of any one of embodiments 1 to 57, wherein the intracellular domain comprises the amino acid sequences of SEQ ID NO: 55.
[0239] 59. The polypeptide system of any one of embodiments 1 to 58, wherein the third transmembrane domain consists of a transmembrane domain selected from the group consisting of Fas, CD2, CD3s, CD35, CD3C, CD25, CD27, CD28, CD40, CD79A, CD79B, CD80, CD86, OX40, 4-IBB, SLAMF1, CTLA4, CD200R, LAG3, HVEM, BTLA, PD-L2, PD-L1, ICOS, PD-1, CD300, GITR, A2aR, DAP10, FcRα, FcRβ, FcRγ, Fyn, GAL9, KIR, Lck, LAT, LRP, KG2D, NOTCH1, NOTCH2, NOTCH3, NOTCH4, PTCH2, ROR2, Ryk, Slp76, SIRPa, pTa, TCRa, TCRβ, TIM3, TRIM, LPA5 and Zap70.
[0240] 60. The polypeptide system of any one of embodiments 1 to 59, wherein the third transmembrane domain is the Fas transmembrane domain.
[0241] 61. The polypeptide system of any one of embodiments 1 to 60, wherein the third transmembrane domain comprises the amino acid sequence of SEQ ID NO: 59.
[0242] 62. The polypeptide system of any one of embodiments 1 to 61, wherein the intracellular domain comprises an endodomain selected from the group consisting of IL-7Rα, IL-12Rα, IL-15Rα, IL-21Rα and IL-23Rα, or a combination thereof.
[0243] 63. The polypeptide system of any one of embodiments 1 to 62, wherein the intracellular domain comprises the IL-7Rα endodomain.
[0244] 64. The polypeptide system of any one of embodiments 1 to 63, wherein the intracellular domain comprises the amino acid sequence of SEQ ID NO: 54.
[0245] 65. The polypeptide system of any one of embodiments 1 to 64, wherein the intracellular domain comprises the IL-7Rα endodomain and the CD2 intracellular signaling domain.
[0246] 66. The polypeptide system of any one of embodiments 1 to 65, wherein the IL-7Rα endodomain is fused by its C-terminus to the N-terminus of the CD2 intracellular signaling domain.
[0247] 67. The polypeptide system of any one of embodiments 1 to 66, wherein the third transmembrane domain consists of any one of the amino acid sequences of SEQ ID NO: 60 to SEQ ID NO: 65.
[0248] 68. The polypeptide system of any one of embodiments 1 to 67, wherein the third transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60.
[0249] 69. The polypeptide system of any one of embodiments 1 to 68, wherein the EAR polypeptides are capable of segregating together to form a trimer on the cell surface.
[0250] 70. The polypeptide system of any one of embodiments 1 to 69, wherein the EAR polypeptide comprising, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, and an IL-7R endodomain.
[0251] 71. The polypeptide system of any one of embodiments 1 to 70, wherein the EAR polypeptide comprising, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, an IL-7R endodomain and an CD2 intracellular signaling domain.
[0252] 72. The polypeptide system of any one of embodiments 1 to 71, wherein the EAR polypeptide comprising, from its N to C terminus in order, a Fas ectodomain, a Fas transmembrane domain, and a CD2 intracellular signaling domain.
[0253] 73. The polypeptide system of any one of embodiments 1 to 72, wherein the EAR polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 66 to SEQ ID NO: 68.
[0254] 74. The polypeptide system of any one of embodiments 1 to 73, wherein the EAR is capable of binding TGFβ.
[0255] 74. The polypeptide system of any one of embodiments 1 to 73, wherein the EAR polypeptide is a dominant negative receptor (DNR) polypeptide.
[0256] 76. The polypeptide system of any one of embodiments 1 to 75, wherein the DNR polypeptide is a dnTGFβR1 polypeptide or dnTGFβR2 polypeptide.
[0257] 77. The polypeptide system of any one of embodiments 1 to 76, wherein the DNR polypeptide comprises the amino acid sequence of SEQ ID NO: 69.
[0258] 78. The polypeptide system of any one of embodiments 1 to 77, which comprises a first CAR and a second CAR, wherein the first CAR comprises, from its N to C terminus in order, a first extracellular CD19-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, a first transmembrane domain and a first intracellular signaling domain; wherein the second CAR comprises, from its N to C terminus in order, a second extracellular CD20-binding domain, a second spacer of CD28 hinge, a second transmembrane domain and a second intracellular signaling domain.
[0259] 79. The polypeptide system of any one of embodiments 1 to 78, which comprises a first EAR polypeptide and a second EAR polypeptide, wherein the first EAR polypeptide comprises, from its N to C terminus in order, (i) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, and an IL-7R endodomain, or (ii) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, an IL-7R endodomain and an CD2 intracellular signaling domain, or (iii) a Fas ectodomain, a Fas transmembrane domain, and an CD2 intracellular signaling domain, or any combination thereof; wherein the second EAR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide.
[0260] 80. A polypeptide system, comprising a polypeptide of a first EAR and a polypeptide of a second EAR, wherein the first EAR is capable of binding Fas ligand, the second EAR is capable of binding TGFβ.
[0261] 81. The polypeptide system of embodiment 80, wherein the first EAR polypeptide comprises a Fas ectodomain.
[0262] 82. The polypeptide system of embodiment 80 or 81, wherein the Fas ectodomain comprises the amino acid sequence of SEQ ID NO: 50.
[0263] 83. The polypeptide system of any one of embodiments 80 to 82, wherein the first EAR polypeptide comprises, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain, and an intracellular domain.
[0264] 84. The polypeptide system of any one of embodiments 80 to 83, wherein the intracellular domain comprises an intracellular signaling domain selected from the group consisting of CD2, CD27, CD28, CD137, OX40, CD30, CD40, CD3, HVEM, ICOS, Myd88, LFA-1, ICOS, CD7, NKG2C, B7-H3 and Ligands of CD83, and a combination thereof.
[0265] 85. The polypeptide system of any one of embodiments 80 to 84, wherein the intracellular domain comprises the CD2 intracellular signaling domain.
[0266] 86. The polypeptide system of any one of embodiments 80 to 85, wherein the intracellular domain comprises any one of the amino acid sequences of SEQ ID NO: 55 to SEQ ID NO: 58.
[0267] 87. The polypeptide system of any one of embodiments 80 to 86, wherein the intracellular domain comprises the amino acid sequences of SEQ ID NO: 55.
[0268] 88. The polypeptide system of any one of embodiments 80 to 87, wherein the transmembrane domain consists of a transmembrane domain selected from the group consisting of Fas, CD2, CD3s, CD35, CD3C, CD25, CD27, CD28, CD40, CD79A, CD79B, CD80, CD86, OX40, 4-IBB, SLAMF1, CTLA4, CD200R, LAG3, HVEM, BTLA, PD-L2, PD-L1, ICOS, PD-1, CD300, GITR, A2aR, DAP10, FcRα, FcRβ, FcRγ, Fyn, GAL9, KIR, Lck, LAT, LRP, KG2D, NOTCH1, NOTCH2, NOTCH3, NOTCH4, PTCH2, ROR2, Ryk, Slp76, SIRPa, pTa, TCRa, TCRβ, TIM3, TRIM, LPA5 and Zap70.
[0269] 89. The polypeptide system of any one of embodiments 80 to 88, wherein the transmembrane domain is the Fas transmembrane domain.
[0270] 90. The polypeptide system of any one of embodiments 80 to 89, wherein the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 59.
[0271] 91. The polypeptide system of embodiment 80 to 90, wherein the intracellular domain comprises an endodomain selected from the group consisting of IL-7Rα, IL-12Rα, IL-15Rα, IL-21Rα and IL-23Rα.
[0272] 92. The polypeptide system of any one of embodiments 80 to 91, wherein the intracellular domain comprises the IL-7Rα endodomain.
[0273] 93. The polypeptide system of any one of embodiments 80 to 92, wherein the intracellular domain comprises the amino acid sequence of SEQ ID NO: 54.
[0274] 94. The polypeptide system of any one of embodiments 80 to 93, wherein the intracellular domain comprises the IL-7Rα endodomain and the CD2 intracellular signaling domain.
[0275] 95. The polypeptide system of any one of embodiments 80 to 94, wherein the IL-7Rα endodomain is fused by its C-terminus to the N-terminus of the CD2 intracellular signaling domain.
[0276] 96. The polypeptide system of any one of embodiments 80 to 95, wherein the third transmembrane domain consists of any one of the amino acid sequences of SEQ ID NO: 60 to SEQ ID NO: 65.
[0277] 97. The polypeptide system of any one of embodiments 80 to 96, wherein the third transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60.
[0278] 98. The polypeptide system of any one of embodiments 80 to 97, wherein the first EAR polypeptides are capable of segregating together to form a trimer on the cell surface.
[0279] 99. The polypeptide system of any one of embodiments 80 to 98, wherein the first EAR polypeptide comprising, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, and an IL-7R endodomain.
[0280] 100. The polypeptide system of any one of embodiments 80 to 99, wherein the first EAR polypeptide comprising, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, an IL-7R endodomain and an CD2 intracellular signaling domain.
[0281] 101. The polypeptide system of any one of embodiments 80 to 100, wherein the first EAR polypeptide comprising, from its N to C terminus in order, a Fas ectodomain, a Fas transmembrane domain, and an CD2 intracellular signaling domain.
[0282] 102. The polypeptide system of any one of embodiments 80 to 101, wherein the first EAR polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 66 to SEQ ID NO: 68.
[0283] 103. The polypeptide system of any one of embodiments 80 to 102, wherein the second EAR polypeptide comprises a TGFβR ectodomain.
[0284] 104. The polypeptide system of any one of embodiments 80 to 103, wherein the TGFβR ectodomain comprises the amino acid sequence of SEQ ID NO: 52.
[0285] 105. The polypeptide system of any one of embodiments 80 to 104, wherein the second EAR polypeptide is a DNR polypeptide.
[0286] 106. The polypeptide system of any one of embodiments 80 to 105, wherein the DNR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide.
[0287] 107. The polypeptide system of any one of embodiments 80 to 106, wherein the DNR polypeptide comprises the amino acid sequence of SEQ ID NO: 69.
[0288] 108. The polypeptide system of any one of embodiments 80 to 107, which comprises a first EAR polypeptide and a second EAR polypeptide, wherein the first EAR polypeptide comprises, from its N to C terminus in order, (i) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, and an IL-7R endodomain, or (ii) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, an IL-7R endodomain and an CD2 intracellular signaling domain, or (iii) a Fas ectodomain, a Fas transmembrane domain, and an CD2 intracellular signaling domain, or any combination thereof; wherein the second EAR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide.
[0289] 109. The polypeptide system of any one of embodiments 80 to 108, which comprises one or more CARs.
[0290] 110. The polypeptide system of any one of embodiments 80 to 109, wherein the CAR is capable of binding an antigen selected from the group consisting of CD19, CD20, CD22, CD30, BCMA, AFP, ALK, GPC3, HER2, EGFR, alpha folate receptor, 5T4, avβ6 integrin, B7-H3, B7-H6, CAIX, CD16, CD33, CD44, CD44v6, CD44v7 / 8, CD70, CD79a, CD79b, CD123, CD138, CD171, CEA, Claudin18.2, CSPG4, DLL3, EGFRvlll, EGP2, EGP40, EPCAM, EphA2, EpCAM, FAP, fetal AchR, FRa, GD2, GD3, MAGE-1, NY-ESO-1, IL-11Rα, IL-13Rα2, Lambda, Lewis-Y, Kappa, Mesothelin, Muc1, Muc16, NCAM, NKG2D Ligands, PRAME, PSCA, PSMA, RORI, SSX, Survivin, TAG72, TEMs, VEGFR2 and WT-1.
[0291] 111. The polypeptide system of any one of embodiments 80 to 110, which comprises one CAR capable of binding CD19 or CD20, or comprises two CARs capable of binding CD19 and CD20, respectively.
[0292] 112. The polypeptide system of any one of embodiments 80 to 111, which comprises one or more self-cleaving peptides located between the polypeptides contained within the polypeptide system.
[0293] 113. The polypeptide system of any one of embodiments 80 to 112, wherein the self-cleaving peptide is a viral self-cleaving 2A polypeptide.
[0294] 114. The polypeptide system of any one of embodiments 80 to 113, wherein the viral self-cleaving 2A polypeptide is selected from the group consisting of a foot-and-mouth disease virus (FMDV) (F2A) peptide, an equine rhinitis A virus (ERAV) (E2A) peptide, a Thosea asigna virus (TaV) (T2A) peptide, a porcine teschovirus-1 (PTV-1) (P2A) peptide, a Theilovirus 2A peptide, and an encephalomyocarditis virus 2A peptide.
[0295] 115. The polypeptide system of any one of embodiments 80 to 114, which is expressed on the surface of one cell.
[0296] 116. A polynucleotide system encoding the polypeptide system of any one of embodiments 1 to 115.
[0297] 117. A vector system comprising one or more vectors comprising the polynucleotide system of embodiment 116.
[0298] 118. The vector system of embodiments 117, wherein the vector is a retroviral, lentiviral, adenoviral, or adeno-associated viral vector.
[0299] 119. A cell comprising the polypeptide system of any one of embodiments 1 to 115, the polynucleotide system of embodiment 116, or the vector system of embodiment 117 or 118.
[0300] 120. The cell of embodiment 119, wherein the cell is an immune cell.
[0301] 121. The cell of embodiment 119 or 120, wherein the cell is a T-cell, a K cell, a KT cell, an αβ cell, a γδ T-cell, a Mucosa Associated Invariant T-cell (MAIT T-cell) , an innate lymphoid cell, a stem cell, or a progenitor cell.
[0302] 122. A method of treating a disease in a subject, comprising administering a therapeutically effective amount of the cell of any one of embodiments 119 to 121 to the subject.
[0303] 123. The method of embodiment 122, wherein the disease is a cancer or an autoimmune disease.
[0304] 124. The method of embodiment 122 or 123, wherein the cancer is selected from the group consisting of leukemia, lymphoma, lung cancer, melanoma, breast cancer, prostate cancer, colon cancer, renal cell carcinoma, ovarian cancer, neuroblastoma and rhabdomyosarcoma.
[0305] 125. The method of any one of embodiments 122 to 124, wherein the autoimmune disease is selected from the group consisting of systemic lupus erythematosus, lupus nephritis, multiple sclerosis, rheumatoid arthritis, Sjogren’s syndrome, idiopathic thrombocytopenia purpura, Type 1 diabetes, Pemphigus vulgaris, Neuromyelitis optica, ANCA vasculitis, and Myasthenia gravis.
[0306] 126. The method of any one of embodiments 122 to 125, wherein the cancer is leukemia or lymphoma.
[0307] 127. The method of any one of embodiments 122 to 126, wherein the autoimmune disease is systemic lupus erythematosus or lupus nephritis. VIII. Example
[0308] The following examples are included for illustrative purposes only and are not intended to limit the scope of the invention.
[0309] Example 1-1: Generation and assessment of anti-CD19 antibodies
[0310] Antibodies comprising FMC63 scFv, CD19 scFv-1, CD19 scFv-2 or CD19 scFv-3 (sequences shown in Table. 3) fused with human IgG1 Fc fragments were synthetized and examined for affinity to cognate ligand CD19 by surface plasmon resonance (SPR) .
[0311] All SPR experiments were performed on a Biacore T200 (PCytiva) with HBS-EP as running buffer. The antibodies were captured by Protein A chip (LOT#10309880, Cytiva) . Soluble CD19 protein (amino acids 20-291) was used as the analyte at concentrations ranging from 300 nM to 4.69 nM through the flow cells for 120 seconds followed by dissociation analysis for 300 seconds. Association rates (Kon) , dissociation rates (Koff) and the constant Ka (Kon / Koff) were fitted to the results. As can be seen in Figure 1, the antibodies comprising CD19 scFv-1 and CD19 scFv-2 had improved affinity compared to the other binders.
[0312] Example 1-2: Generation and assessment of CD19 CARs
[0313] CD19 CARs in Table 6 were formed through the fusion of a signal peptide (SP-1 for CAR-W, SP-2 for CAR-1 to CAR-13) to either FMC63 scFv, CD19 scFv-1, CD19 scFv-2 or CD19 scFv-3 followed by four different spacers and a transmembrane derived from human CD28 and an endodomain encoding the signaling motifs from 41BB and CD3ζ. Each CAR was co-expressed with a truncated EGFR (tEGFR) , used as a transduction marker. Both CAR and tEGFR were encoded from a single promoter construct separated by a self-cleaving T2A peptide. Table 6. Structures of candidate CD19 CARs (from N-to C-terminus)
[0314] Primary human T cell populations expressing the various CARs were generated. Nucleic acid molecules encoding each fusion protein were individually cloned into a lentiviral vector. T cells, isolated from human PBMC samples obtained from healthy donors, were stimulated with CD3 / CD28 beads ) . One day after the stimulation, the cells were transduced with the lentiviral vector, followed by expansion for 6 days. Cells were stained with EGFR-AF488 and CD19pro-APC and examined by flow cytometry. CD19 binding capacity was used as a surrogate for CAR stability and affinity and examined by analyzing the mean florescent index (MFI) from the CD19 stain after gating on tEGFR positive cells.
[0315] CARs comprising Spacer S-3 (CD19 CAR-3, CD19 CAR-7 and CD19 CAR-11) have an increased capacity to bind CD19 compared to other spacers carrying the same binder (Figure 2) . CD19 CAR-3 displayed the highest binding capacity.
[0316] Example 1-3: Tonic signaling of CD19 CAR constructs
[0317] Certain CARs can exhibit antigen-independent activity or signaling, also known as tonic signaling. Excessive tonic signaling could lead to increased differentiation and T cell exhaustion. To assess tonic signaling of the transduced CAR T cells of Example 1-2, cells were left for 8 days in co-culture in the absence of exogenous stimulation. IFN-γ concentration was then measured by Perkin Elmer AlphaLISA detection kit according to the manufacturer’s instructions.
[0318] In Figure 3, Spacer S-3 (CD19 CAR-3, CD19 CAR-7 and CD19 CAR-11) exhibited low levels of tonic signaling, as indicated by the low level of antigen independent IFN-γ secretion.
[0319] Example 1-4: Killing efficiency and CD69 expression of CD19 CAR constructs
[0320] Primary human T-cells from 4 healthy donors were transduced with lentiviral vectors comprising the polynucleotides encoding the fusion protein CD19 CAR-W, CD19 CAR-3, CD19 CAR-7 or CD19 CAR-11 in Example 1-2 (effector cells) or a lentiviral vector comprising the polynucleotide encoding tEGFR. Transduction efficiency, as assessed by EGFR staining, was normalized to 50%for all samples through the addition of non-transduced cells. Cytotoxicity was then examined after these effector cells were challenged with Raji target cells engineered to express approximately 6, 151 copies or 74, 602 copies of CD19 on their cell surface (Figure 4A) . The effector cells or the vector control cells expressing tEGFR only were co-cultured with the target cells at the E: T of 1: 1. After 20 hours, the cells were isolated and stained with CD3, EGFR and CD20 and CD69.
[0321] The killing efficiency for each CAR T cell sample was calculated as a percentage of remaining target cells from T cells transduced from the tEGFR only control. As shown in Figure 4B, the killing efficiencies of CD19 CAR-3 and CD19 CAR-11 are greater than those observed for CD19 CAR-W. All transduced CAR T cells showed comparable levels of CD69 expression (Figure 4C) .
[0322] Example 1-5: Cytokine release and T cell expansion post target cell stimulation
[0323] The effector cells of Example 1-4 were used to assess the cytokine release. The supernatants in example 1-4 were collected and analyzed for accumulated IFN-γ, TNF-α, and IL-2 cytokines. The results are depicted in Figure 5A-5C. Cells transduced with CD19 CAR-3, CD19 CAR-7 and CD19 CAR-11 showed similar IFN-γ and TNF-α secretion after being challenged with tumor cells. However, CD19 CAR-3 and CD19 CAR-7 produced greater IL-2.
[0324] In an extended assay of Example 1-4, the T cells were allowed to proliferate for 7 days after the initial stimulation with target cells and the number of CAR T cells was assessed. As shown in Figure 5D, T cells transduced with CD19 CAR-3 and CD19 CAR-7 showed significantly higher numbers of T cells compared to the other CAR constructs.
[0325] Example 1-6: Killing efficiency of CD19 CARs at various E: T ratios
[0326] Primary human T-cells from 3 healthy donors were transduced with lentiviral vectors comprising the polynucleotides encoding the fusion protein CD19 CAR-W or CD19 CAR-13 in Example 1-2 (effector cells) or a lentiviral vector comprising the polynucleotide encoding tEGFR. Transduction efficiency, as assessed by EGFR staining, was normalized to 50%for all samples through the addition of non-transduced cells. Cytotoxicity was then examined after these effector cells were challenged with Raji-CD19Lo target cells at various E: T ratios. The effector cells or the vector control cells expressing tEGFR only were co-cultured with Raji-CD19Lo target cells at the E: T ratio of 1: 1, 1: 2, 1: 8. At day 3 of co-culture assay, the cell samples were isolated and stained with CD3, EGFR and CD20.
[0327] The killing efficiency for each CAR-T cell sample was calculated as a percentage of remaining target cells from T cells transduced the tEGFR only control. As shown in Figure 6, the killing efficiencies of both CD19 CAR-W and CD19 CAR-13 decrease with the increase of E: T ratios. However, CD19 CAR-13 shows greater elimination of Raji-CD19Lo target cells than CD19 CAR-W on the E: T ratio of 1: 2 (p=0.0129, CD19 CAR-13 vs. CD19 CAR-W) and 1: 8 (p=0.0367, CD19 CAR-13 vs. CD19 CAR-W) . This data shows the enhanced anti-tumor activity of CD19 CAR-T cells through the S-3 spacer.
[0328] Example 2-1: Generation and assessment of CD20 CARs in Jurkat cells
[0329] CD20 CARs in Table 7 were formed through the fusion of a signal peptide (SP-2) to either RTX-scFv, Obin-scFv, Ofa-scFv followed by three different spacers and a transmembrane derived from human CD28 or CD8 and an endodomain encoding the signaling motifs from 41BB and CD3ζ. Each CAR was co-expressed with a truncated EGFR (tEGFR) , used as a transduction marker. Both CAR and tEGFR were encoded from a single promoter construct separated by a self-cleaving T2A peptide. Table 7. Structures of candidate CARs (from N-to C-terminus)
[0330] Raji cells were purchased from ATCC (Cat No. : CCL-86) . CD20KO Raji cells were generated by knock-out of MS4A1 (gene encoding CD20) through CRISPR-Cas9 mediated gene editing. Different constructs were transduced into CD20KO Raji cells to generate CD20lo Raji cells (Figure 7A) .
[0331] Jurkat 76 cell line (Biovector, Cat#: 921816) was engineered to express a nanoluciferase under the control of a human IL-2 promoter. Nucleic acid molecules encoding each fusion protein were individually cloned into a lentiviral vector and transduced into this IL-2 luciferase reporter Jurkat cell line. The transduced Jurkat cells were then co-cultured with 2 different Raji cells (CD20KO / CD20WT) at the E: T ratio of 5: 1. After 24 hours, the luciferase activity in the supernatant was measured by PE Envision multimode plate reader.
[0332] Jurkat cells transduced with CD20 CAR-4, CD20 CAR-7 and CD20 CAR-8 showed higher luciferase activity when co-cultured with CD20-expressing Raji cells, which indicates higher activation levels (Figure 7B) . CD20 CAR-8 with the CD28 hinge induced strongest activation among CARs containing Ofa-scFv, while CARs with an IgG4 hinge (CD20 CAR-1 and CD20 CAR-4) displayed superior activation signals among CARs containing Obin-scFv or RTX-scFv.
[0333] Example 2-2: Generation and assessment of CD20 CARs in primary human T cells
[0334] Primary human T cell populations expressing the various CARs were generated. T cells, isolated from human PBMC samples obtained from healthy donors, were stimulated with CD3 / CD28 beads Three days after the stimulation, the cells were transduced with lentiviral vector comprising the polynucleotides encoding the fusion protein CD20 CAR-4, CD20 CAR-7 and CD20 CAR-8.Transduction efficiency was determined by EGFR staining 7 days post transduction. Transduced T cells were co-cultured with 3 different Raji cells (CD20WT / CD20lo / CD20KO) at the E: T ratio of 2: 1. After 48 hours, the cells were isolated and stained with CD3, EGFR, CD25, CD69 and Ki67.
[0335] In Figure 8A-8B, CD20 CAR-4 and CD20 CAR-8 showed higher expression of the T cell activation marker CD25 and CD69 compared to CD20 CAR-7 T cells. This is particularly evident when challenged with CD20lo Raji cells. Similarly, CD20 CAR-4 and CD20 CAR-8 showed slight improvements over CAR-7 T cells when challenged with the CD20lo Raji cells and stained for the proliferation marker Ki67 (Figure 8C) .
[0336] Example 2-3: Cytokine release post target cell stimulation
[0337] The effector cells of Example 2-2 were used to assess the cytokine release. The supernatants in Example 2-2 were collected and analyzed for accumulated IFN-γ and IL-2 cytokines. The results are depicted in Figure 9A-9B. Cytokine secretion is positively correlated with the antigen expression. T cells transduced with CD20 CAR-8 showed the highest secretion levels of IFN-γ and IL-2 after co-cultured with either the wild-type or low expressing CD20 tumor cell lines. In contrast, CD20 CAR-4 had lower secretion and CD20 CAR-7 had near background secretion of cytokines when challenged with these low expressing targets.
[0338] Example 2-4: Killing efficiency of CD20 CAR constructs
[0339] Primary human T-cells from 4 healthy donors were transduced with lentiviral vectors comprising the polynucleotides encoding the fusion protein CD20 CAR-4, CD20 CAR-7 and CD20 CAR-8 in Example 2-2. Transduced T cells co-cultured with 3 different Raji cells, which was pre-stained with CellTrace Far Red reagent, at the E: T ratio of 2: 1. CellEvent Caspase3 / 7 Green Detection Reagent was added to the cell mixture to monitor the apoptosis of target cells. The apoptosis cell signal was measured by Incucyte Live-cell Analysis System SX5 for 24 hours with every 4 hours interval.
[0340] The killing score of each CAR-T was calculated as the ratio of Caspase3 / 7 signal from target cell group to the signal from CAR-T alone group. CD20 CAR-8 showed superior kill scores when challenged with CD20lo Raji cells compared to CD20 CAR-4 (Figure 10) . The CD20 CAR-7 killing score when co-cultured with the CD20lo Raji targets was similar to the background CD20KO control levels. CD20 CAR-8 T cells also displayed a slightly lower non-specific killing score on CD20KO Raji cell compared to CD20 CAR-4 and CAR-7 (Figure 10) .
[0341] Example 3-1: Generation of fusion polypeptides
[0342] Plasmid constructs were designed to encode a marker of transduction (tEGFR) on its 3’ of the ORF followed by a sequence encoding a self-cleaving 2A peptide derived from the equine rhinitis A virus. Following this was the sequence encoding the signal peptide (SP-3) and extracellular domain of human Fas followed by a transmembrane sequence (IL-7Rα TM1-1, Fas TM) and then the endodomain of either human IL7Ra or human CD2 endodomain (F-1, F-2) . As a functional negative control, a plasmid encoding only the tEGFR transduction marker was developed (Ctrl) . As a positive control for protection against FasL mediated apoptosis, a plasmid was designed encoding tEGFR (the SP-1 was superseded by SP-2) followed by the 2A sequences from equine rhinitis A virus followed by the signal peptide (SP-3) , extracellular domain, transmembrane and truncated endodomain of human Fas (C-1) . As a positive control for cytokine receptor signaling, a plasmid was designed encoding tEGFR followed by the 2A sequences from equine rhinitis A virus followed by a signal peptide (SP-2) and extracellular domain from human CD34 followed by transmembrane sequence TM1-1 and the endodomain from human IL7Ra (C-2) . The C-3 containing plasmid was designed encoding tEGFR followed by the 2A sequences from equine rhinitis A virus followed by a signal peptide (SP-2) and extracellular domain from human TGFβR followed by transmembrane sequence TM1-1 and the endodomain from human IL7Ra. The C-4 or C-5 containing plasmids were formed similarly. Table 8. Structures of fusion polypeptides (from N-to C-terminus)
[0343] Example 3-2: Apoptosis resistance of engineered T cell
[0344] Over activation / stimulation of T cells by the surrounding tumor can lead to Fas / FasL mediated AICD and can subsequently result in a decreased number of viable T cells. Primary human T-cells from 7 healthy donors were transduced with lentivirus vectors expressing the fusion polypeptides as described in Example 3-1. Transduced T cells (5 × 105 T cells / mL) were added to the wells in the presence of supplemented IL-2 (100 IU / mL) , and then were cultured for 7 days without further stimulation in an incubator.
[0345] At day 1, 3, 7, 8, 10, 15 during incubation, T cells were mixed gently, 60 μL cell suspension was removed for surviving T cell count by High Speed, High Throughput Cell Counter (Nexcelom) . At day 3, 7, 10 after detection of live T cell number, if T cell density over 1 × 106 cells / mL, then will be adjusted to 5 ×105 cells / mL for culture. Live T cell numbers during incubation were made relative to the day 0 analysis to measure proliferation fold difference. Figure 11 shows the growth of transduced T cells (7 healthy donors) after initial seeding (5 × 105 T cells / mL) and left without further stimulation. Here we observe a significant improvement in the expansion of T cells transduced with the F-1 over the control constructs C-1 (p=0.0135, F-1 vs. C-1) and Ctrl (p=0.0063, F-1 vs. Ctrl) . This data shows the enhanced growth capacity of F-1 in unstimulated conditions.
[0346] Example 3-3: Persistence of engineered T cells
[0347] Improved persistence of T cells correlates with clinical efficacy in many settings (10.1186 / s40364-022-00434-9) . In order to expand and maintain durable remission responses, T cells are required to persist in environments with low levels of stimulation and cytokines. To test the ability of the cells to survive these hush conditions we subjected the transduced T cells to starvation assays. Briefly, primary T cells from 4 healthy donors were transduced with either Ctrl, C-2 or F-1. All transduced T cells were spun by centrifugation, stained for EGFR to evaluate the transduction efficiency. And then, the transduced T cells were normalized to be 50%transduced EGFR+ through the addition of non-transduced T cells and then seeded at the same density (1 × 106 T cells / mL) for 7 days in an incubator. At day 3, 7 during incubation, cell suspension was harvest for counting living T cell and EGFR+ T cell enrichment.
[0348] Figure 12B shows that in the absence of cytokine or stimulation, T cells transduced with Ctrl are unable to proliferate and cellular viability decreases dramatically over 7 days to approximately 40%(p=0.0002, C-2 vs. Ctrl; p=0.0003, F-1 vs. Ctrl) . Both C-2 and F-1 have a significant survival advantage over the Ctrl (p<0.0001, C-2 vs. Ctrl; p=0.0002, F-1 vs. Ctrl) , showing linear growth over the 7 day period (p=0.0008, C-2 vs. Ctrl; p=0.0014, F-1 vs. Ctrl) and sustained viability comparable to the same conditions supplemented with external IL-2 (100 IU / mL, Cytiva, #29062790) (Figure 12A and 12B) . In addition, C-2 and F-1 were able to enrich in the transduced T cell population over this period compared to the Ctrl (Figure 12B) or compared to the condition with supplemented IL-2 (100 IU / mL) (Figure 12A) . This demonstrates that T cells transduced with F-1 are able to deliver a cytokine survival signal and promote growth and viability in the absence of exogenous stimulation or cytokines. To further interrogate the constructs’a bility to withstand Fas / FasL mediated apoptosis, the transduced T cells were exposed to trimeric FasL stimulation (50 ng / mL, Adipogene, AG-40B-0130-3010) in the presence of supplemented IL-2 (100 IU / mL) and the cell growth, viability and enrichment was assessed over a 7-day period. Here we demonstrate that T cells transduced with either Ctrl or C-2 are unable to grow and have reduced viability and percentage of the transduced population. In contrast, T cells transduced with F-1 continue to proliferate and grow to similar levels to the condition without FasL (p=0.0035, F-1 vs. Ctrl; p=0.0037, F-1 vs. C-2, (Figure 12C) ) . We also observed a significant improvement in viability (p=0.0007, F-1 vs. Ctrl; p=0.0146, F-1 vs. C-2) and enrichment of EGFR+ T cells (p=0.0003, F-1 vs. Ctrl; p=0.0003, F-1 vs. C-2) over this 7-day period.
[0349] Example 3-4: Persistence of modules post FasL stimulation
[0350] To further interrogate the fusion proteins’ (sharing same extracellular domain of human Fas and different endodomain of either human IL7Ra or CD2) ability to withstand Fas / FasL mediated apoptosis, the transduced T cells (7 healthy donors) were exposed to 50 ng / mL trimeric FasL stimulation in the presence of supplemented IL-2 (100 IU / mL) for 7 days in an incubator. At day 1, 3, 7 during incubation, T cells were mixed gently and removed for surviving T cell count by High Speed, High Throughput Cell Counter (Nexcelom) . Live T cell densities during incubation were made relative to the initial seeding (5 × 105 T cells / mL) of day 0 to measure proliferation fold difference. As shown in Figure 13, the T cells transduced with various fusion proteins (sharing same extracellular domain of human Fas) demonstrate enhanced persistence to FasL induced apoptosis, in which the cells expressing F-1 displayed a slightly higher proliferation level than those with C-1 and F-2.
[0351] Example 3-5: Expansion of modules post non-IL-2 starvation
[0352] To further interrogate the fusion proteins’ (sharing different extracellular domain from either human Fas or TGFβR and same transmembrane domain and endodomain) expansion ability in cytokine starvation, we subjected the transduced T cells to non-IL-2 conditions. Briefly, primary T cells from 4 healthy donors were transduced with either Ctrl, C-3 or F-1. All transduced T cells were spun by centrifugation, stained for EGFR to evaluate the transduction efficiency. And then, the EGFR+ T cells were normalized to be 50%through the addition of non-transduced T cells and then seeded at the same density (1 × 106 T cells / mL) for 7 days in an incubator. At day 3, 7 during incubation, cell suspension was harvested for living T cell counting by Cell Counter and EGFR+ T cell detection by flow cytometry. EGFR+ T cell numbers during incubation were made relative to the day 0 analysis to measure proliferation fold difference.
[0353] Figure 14 shows that T cells transduced with C-3 are unable to proliferate in the absence of cytokine over the 7-day period (C-3 vs. F-1, p=0.0277 at day3, p=0.0060 at day7) . Above results demonstrate that the function of IL-7Rα TM-endo would be prevented by the definite extracellular domain.
[0354] Example 4-1: Killing efficiency of dual CAR
[0355] Plasmid construct of dual CAR was designed to encode SP-2, CD19 CAR-3 followed by a sequence encoding T2A peptide and then SP-2, CD20 CAR-8. Primary human T cell from 6 healthy donors were activated with CD3 / CD28 Dynabeads (Gibco) . One day after the activation, the T cells were transduced with the lentiviral vector, followed by expansion for 7 days. CAR T cells were stained with FMC63-AF647 (Bioswan) and examined by flow cytometry. As shown in Figure 15A, dCAR shows the lower transduction efficiency (dCAR vs. CD19 CAR-3, p<0.0001) and about 50%surface level (dCAR vs. CD19 CAR-3, p=0.0002) of CD19 CAR than CD19 CAR-3.
[0356] Withdraw CD3 / CD28 Dynabeads to rest CAR-T cells for 24h at day 7 after lentivirus transduction. Transduction efficiency of CD19 CAR, as assessed by FMC63 staining, was normalized to 50%for all samples through the addition of non-transduced cells. Cytotoxicity was then examined after these effector cells were challenged by tumor cells with different CD19, CD20 expression levels. The effector cells or the vector control cells expressing tEGFR only were co-cultured with the K562, Raji-CD19Lo, Raji-CD20Lo or Raji-WT tumor cells at the E: T ratio of 1: 1. At day 1 of the co-culture assay, the cell samples were isolated and stained with CD3, CD8 and FMC63.
[0357] The killing efficiency for each CAR-T cell sample was calculated as a percentage of remaining target cells from T cells transduced the tEGFR only control. As shown in Figure 15B, the killing efficiencies of dCAR to K562 tumor cells without surface CD19 or CD20 are significantly lower than CD19 CAR-3 (dCAR vs. CD19 CAR-3, p=0.0130) . The results validate the limitation of dCAR to un-target tumor cells. The dCAR shows significantly higher killing efficiencies of Raji-CD19Lo (dCAR vs. CD19 CAR-3, p=0.0015) and Raji-WT (dCAR vs. CD19 CAR-3, p=0.0010) target cells than CD19 CAR-3 (Figure 15C) . The results demonstrate the more potent anti-tumor activity of dCAR than CD19 CAR. As the surface expression level of dCAR is about 50%of CD19 CAR-3, these data of low non-specific killing and high specific killing clearly illustrate the unexpected synergy of dCAR.
[0358] Example 4-2: Killing efficiency of enhanced dual CAR
[0359] Plasmid construct of dCAR-F1 was designed to encode an ordinal sequence of dCAR, E2A peptide, SP3, F-1, P2A peptide, SP-2 and dnTGFβR2. Plasmid construct of dCAR-F2 was designed to encode an ordinal sequence of dCAR, E2A peptide, SP3, F-2, P2A peptide, SP-2 and dnTGFβR2. Primary human T-cells from 4 healthy donors were transduced with lentiviral vectors of dCAR, dCAR-F1 or dCAR-F2. Transduction efficiency of CD19 CAR, as assessed by FMC63 staining, was normalized to 50%for all samples through the addition of non-transduced cells.
[0360] Cytotoxicity was then examined after these effector cells were challenged with Raji-WT target cells. The effector cells or the vector control cells expressing tEGFR only were co-cultured with Raji-WT cells at the E: T ratio of 1: 2. At day 1 of the co-culture assay, the cells were isolated and stained with CD3, CD8 and FMC63. The killing efficiency for each CAR T cell sample was calculated as a percentage of remaining target cells from T cells transduced the tEGFR only control. As shown in Figure 16, the killing efficiencies of dCAR-F1 and dCAR-F2 are significantly greater than dCAR (dCAR-F1 vs. dCAR, p=0.0127; dCAR-F2 vs.dCAR, p=0.0109) . The results show the increased tumor lysis capability of dCAR-F1 and dCAR-F2 when co-cultured with Raji-WT cells.
[0361] Example 4-3: CAR-T cell expansion post non-IL-2 starvation
[0362] CAR-T cells (normalized to 50%) from Example 4-2 were seeded at the same density (1 × 106 T cells / mL) with supplemented 100 IU / mL IL-2 or non-IL-2 condition for 7 days in an incubator. At day 1, 3, 7 during incubation, cell suspension was harvested for living T cell counting by flow cytometry with Absolute Counting Beads (Invitrogen) and Live / Dead straining. Live T cell numbers during incubation were made relative to the day 0 analysis to measure proliferation fold difference.
[0363] Figure 17 shows that the dCAR are unable to proliferate and cellular viability decreases over 7 days to approximately 40%in the absence of cytokine. However, dCAR-F1 has a significant survival advantage over the dCAR (dCAR-F1 vs. dCAR, p=0.0035 at day3, p=0.0025 at day7) , showing linear growth over the 7-day period (dCAR-F1 vs. dCAR, p=0.0123 at day3, p=0.0262 at day7) . The results demonstrate the strong continuous expansion capabilities of dCAR-F1 after withdrawing IL-2 in T cell culture condition.
[0364] Example 4-4: CAR-T cell persistence post FasL stimulation
[0365] CAR-T cells (normalized to 50%) from Example 4-2 were seeded at the same density (1 × 106 T cells / mL) with 50 ng / mL trimeric FasL stimulation in the presence of supplemented IL-2 (100 IU / mL) for 7 days in an incubator. At day 1, 3, 7 during incubation, cell suspension was harvested for living T cell counting by flow cytometry with Absolute Counting Beads (Invitrogen) and Live / Dead straining. Live T cell numbers during incubation were made relative to the day 0 analysis to measure proliferation fold difference.
[0366] Figure 18A shows that dCAR are unable to proliferate and cellular viability decreases dramatically to approximately 10%at day 1 post FasL stimulation. However, both dCAR-F1 and dCAR-F2 have a significant survival advantage (dCAR-F1 vs. dCAR, p=0.0180 at day1, p=0.0188 at day3, p=0.0346 at day7; dCAR-F2 vs. dCAR, p=0.0026 at day1, p=0.0056 at day3, p=0.0220 at day7) over the dCAR, showing linear growth over the 7 day period (dCAR-F1 vs. dCAR, p=0.0470 at day1, p=0.0286 at day3, p=0.0498 at day7; dCAR-F2 vs. dCAR, p=0.0048 at day1, p=0.0022 at day3, p=0.0119 at day7) . Above results demonstrate the increased persistence of dCAR-F1 and dCAR-F2 with T cell expansion and viability post sFasL treatment.
[0367] CAR-T cells (normalized to 50%) from Example 4-2 were challenged with Raji-FasLOE target cells at the E: T ratios of 1: 1, 1: 2 and 1: 4. At day 1, 3, 7 of the co-culture assay, the cells were isolated and stained with CD3, CD8 and FMC63. The killing efficiency for each CAR-T cell sample was calculated as a percentage of remaining target cells from T cells transduced the tEGFR only control. As shown in Figure 18B, the killing efficiencies of all CAR-T cells decrease with the increase of E: T ratios. However, both dCAR-F1 and dCAR-F2 have a significant enhanced elimination of Raji-FasLOE target cells compared to dCAR. Besides, dCAR-F2 shows more potent resistance to surface FasL induced cell death than dCAR-F1 (E: T=1: 4, dCAR-F2 vs. dCAR-F1, p=0.0026 at day1, p=0.0499 at day3, p=0.0099 at day7) . Above results demonstrate the increased tumor lysis capabilities of dCAR-F1 and dCAR-F2 when co-cultured with Raji-FasLOE cells.
[0368] Example 4-5: CAR-T cell shielding post sTGFβ1 treatment
[0369] CAR-T cells (normalized to 50%) from Example 4-2 were challenged with Raji-WT target cells at the E: T ratio of 1: 2 in the absence / presence of 20 ng / mL TGFβ1 (PeproTech) treatment. At day 3 of the co-culture assay, the cells were isolated and stained with CD3, CD8 and FMC63. The killing efficiency for each CAR T cell sample was calculated as a percentage of remaining target cells from T cells transduced the tEGFR only control. At day 7 of the co-culture assay, cell suspension was harvested for living T cell counting by flow cytometry with Absolute Counting Beads (Invitrogen) and Live / Dead straining. Live T cell numbers during co-culture assay were made relative to the day 0 analysis to measure proliferation fold difference.
[0370] As shown in Figure 19A, the killing efficiencies of dCAR to Raji-WT target cells are suppressed with the TGFβ1 treatment (dCAR TGFβ1+ vs. dCAR TGFβ1-, p=0.0263) at day 3 of co-culture assay. Besides, the T cell expansion (dCAR TGFβ1+ vs. dCAR TGFβ1-, p=0.0219) and CAR-T cell expansion (dCAR TGFβ1+ vs. dCAR TGFβ1-, p=0.0323) are also suppressed with the TGFβ1 treatment at day 7 of co-culture assay (Figure 19B) . However, dCAR-F1 and dCAR-F2 show the constant high killing efficiency and T cell expansion post TGFβ1 treatment (Figure 19A and 19B) . These results show the resistance of dCAR-F1 and dCAR-F2 to the sTGFβ1 treatment.
[0371] Example 4-6: CAR-T cell stimulation by Raji-CD58KO
[0372] CAR-T cells (normalized to 50%) from Example 4-2 were challenged with Raji-CD58KO target cells at the E: T ratio of 1: 2, 1: 4 and 1: 8. At day 1 of the co-culture assay, the cells were isolated and stained with CD3, CD8 and FMC63. The killing efficiency for each CAR T cell sample was calculated as a percentage of remaining target cells from T cells transduced the tEGFR only control.
[0373] As shown in Figure 20, the killing efficiencies of all transduced CAR-T cells are limited with the increase of E: T ratios. However, both dCAR-F1 and dCAR-F2 have a significant enhanced elimination of Raji-CD58KO target cells compared to dCAR. Besides, dCAR-F2 shows more potent killing efficiency of Raji-CD58KO target cells than dCAR-F1 (E: T=1: 4, dCAR-F2 vs. dCAR-F1, p=0.0397) . The results show the increased tumor lysis capabilities dCAR-F1 and dCAR-F2 when co-cultured with Raji-CD58KO cells.
[0374] Example 4-7: Persistence of engineered T cells
[0375] Plasmid construct of dCAR-C4 was designed to encode an ordinal sequence of dCAR, E2A peptide, SP3, C-4, P2A peptide, SP-2 and dnTGFβR2. Plasmid construct of dCAR-C5 (C1) was designed to encode an ordinal sequence of dCAR, E2A peptide, SP-2, C-5, P2A peptide, SP3 and C-1. Plasmid construct of F1, F2 and C4 were designed to replace the dCAR sequence by tEGFR sequence in dCAR-F1, dCAR-F2 and dCAR-C4 plasmid constructs.
[0376] Primary human T-cells from 2 healthy donors were transduced with lentiviral vectors of dCAR, dCAR-F2, dCAR-C4 (dCAR+C-4+dnTGFβR2) , dCAR-C5 (dCAR+C-5+C-1) , F1 (F-1+dnTGFβR2) , F2 (F-2+dnTGFβR2) or C4 (C-4+dnTGFβR2) . Transduction efficiency of CD19 CAR (FMC63+) or tEGFR was normalized to 50%for all samples through the addition of non-transduced cells. Then, T cells were seeded at the same density (4 × 105 T cells / mL) with 50 ng / mL sFasL (Adipogene) stimulation in the presence of supplemented 20 ng / mL TGFβ1 (PeproTech) treatment for 7 days in an incubator. At day 1, 3, 7 during incubation, T cells were mixed gently and removed for surviving T cell count by High Speed, High Throughput Cell Counter (Nexcelom) . At day 3 after the detection of live T cell number, the live T cell density was normalized to 5 × 105 T cells / mL for repetitive 50 ng / mL sFasL and 20 ng / mL sTGFβ1 treatment. Live T cell numbers during incubation were made relative to the day 0 analysis to measure proliferation fold difference.
[0377] As shown in Figure 21 and Figure 22, both dCAR-F2 and F2 engineered T cells displayed the most significant survival advantage and proliferation ability post the repetitive sFasL and sTGFβ1 treatments. These results demonstrate the increased persistence of dCAR-F2 and F2 with enhanced resistance to repetitive sFasL and sTGFβ1 treatments.
[0378] Example 5: In vivo efficacy of dual CAR
[0379] To further investigate the anti-tumor activity of CAR T cells in vivo, luciferase-expressing Raji-WT or Raji-CD19KO tumor cells (5 × 105, i. v. ) were engrafted in NPG (NOD. Cg-Prkdcscid Il2rgtm1 / Vst) mice. The mice were randomized on day 3 post tumor injection and were then treated with the single dose of PBS, UNT (untransduced T cells) , CD19 CAR-W or dCAR (1 × 105 CAR-T cells, i. v. ) . Bioluminescence imaging was performed on days 5, 12, 17, and 20 post T cell injection. The Raji-WT-bearing mice that received CD19 CAR-W or dCAR T cells showed the elimination of tumor cells with no significant toxicity (Figure 23) . However, CD19 CAR-W failed to eradicate the CD19 negative tumor cells. In contrast, dCAR T cells still cleared CD19 negative tumor cells, and no significant toxicity was observed (Figure 24) . These results demonstrate that dCAR can efficiently target malignant B cells and abrogate the effects of CD19-antigen loss in vivo.
[0380] Example 6: In vivo efficacy of enhanced dual CAR
[0381] To determine the in vivo functionality of enhanced dual CAR, NPG (NOD. Cg-Prkdcscid Il2rgtm1 / Vst) mice were injected with luciferase-expressing Raji-WT cells (5 × 105, i. v. ) . The mice were randomized on day 5 post tumor injection and were then treated with the single dose of PBS, dCAR, dCAR-F1 and dCAR-F2 T cells (5 × 104 CAR-T cells, i. v. ) on day 5 after tumor injection. Bioluminescence imaging was performed on days 1, 5, 12, 17, and 23 post T cell injection. As expected, dCAR-F2 administrated the improved activities and the most quickly tumor clearance of a very low dose in Raji-WT animal model, and no significant toxicity was observed (Figure 25) . These data provided the rationale for the development of clinical trials for lymphoma patients.
Claims
1.A polypeptide system, comprising a first chimeric antigen receptor (CAR) and one or more additional polypeptides, wherein the first CAR comprises, from its N to C terminus in order, a first extracellular antigen-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 31, a first transmembrane domain and a first intracellular signaling domain; wherein the additional polypeptide is a second CAR or a polypeptide of an engineered armor receptor (EAR) .2.The polypeptide system of claim 1, wherein the first extracellular antigen-binding domain is capable of binding CD19;preferably, the first extracellular antigen-binding domain is capable of binding to the same epitope on CD19 as a reference antibody that comprises the amino acid sequence of SEQ ID NO: 21;more preferably, the first extracellular antigen-binding domain comprises a heavy chain variable region (CD19-VH) and a light chain variable region (CD19-VL) , wherein the CD19-VH comprises a HCDR1, a HCDR2 and a HCDR3 contained within the amino acid sequence of SEQ ID NO: 1, and the CD19-VL comprises a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 4;more preferably, the CD19-VH comprises a HCDR1, a HCDR2 and a HCDR3 comprising the amino acid sequences of SEQ ID NO: 5, SEQ ID NO: 6 and SEQ ID NO: 7, respectively; the CD19-VL comprises a LCDR1, a LCDR2 and a LCDR3 comprising the amino acid sequences of SEQ ID NO: 8, SEQ ID NO: 9 and SEQ ID NO: 10, respectively;more preferably, the CD19-VH comprises the amino acid sequence of SEQ ID NO: 1; the CD19-VL comprises the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 4;more preferably, the first extracellular antigen-binding domain is an anti-CD19 scFv;more preferably, the anti-CD19 scFv comprises the amino acid sequence of SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 or SEQ ID NO: 24.3.The polypeptide system of claim 1 or 2, wherein the first transmembrane domain comprises a transmembrane domain of CD28, CD8α, CD4, CD137, CD80, CD86, CD152 or PD1;more preferably, the first transmembrane domain comprises a CD28 transmembrane domain;more preferably, the first transmembrane domain comprises the amino acid sequence of SEQ ID NO: 36.4.The polypeptide system of any one of claims 1 to 3, wherein the first intracellular signaling domain comprises a first co-stimulatory signaling domain;preferably, wherein the first co-stimulatory signaling domain is the signaling domain of CD28 or CD137;more preferably, the first co-stimulatory signaling domain comprises the amino acid sequence of SEQ ID NO: 37.5.The polypeptide system of any one of claims 1 to 4, wherein the first intracellular signaling domain comprises a first primary intracellular signaling domain;preferably, the first primary intracellular signaling domain is fused by its N-terminus to the C-terminus of the first co-stimulatory signaling domain;more preferably, the first primary intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain;more preferably, the first primary intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 38.6.The polypeptide system of any one of claims 1 to 5, wherein the second CAR comprising, from its N to C terminus in order, a second extracellular antigen-binding domain, a second spacer, a second transmembrane domain and a second intracellular signaling domain;preferably, the second extracellular antigen-binding domain is capable of binding CD20;more preferably, the second extracellular antigen-binding domain is capable of specifically binding to the same epitope on CD20 as a reference antibody that comprises the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27;more preferably, the second extracellular antigen-binding domain comprises a heavy chain variable region (CD20-VH) and a light chain variable region (CD20-VL) , wherein the CD20-VH comprises a HCDR1, a HCDR2 and a HCDR3 contained within the amino acid sequence of SEQ ID NO: 11, and the CD20-VL comprises a LCDR1, a LCDR2 and a LCDR3 contained within the amino acid sequence of SEQ ID NO: 12;more preferably, the CD20-VH comprises a HCDR1, a HCDR2 and a HCDR3 comprising the amino acid sequences of SEQ ID NO: 13, SEQ ID NO: 14 and SEQ ID NO: 15, respectively; the CD20-VL comprises a LCDR1, a LCDR2 and a LCDR3 comprising the amino acid sequences of SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18, respectively;more preferably, the second extracellular antigen-binding domain is an anti-CD20 scFv;more preferably, the anti-CD20 scFv comprises the amino acid sequence of SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27.7.The polypeptide system of claim 6, wherein the second spacer consists of a CD28 hinge;preferably, the second spacer consists of the amino acid sequence of SEQ ID NO: 34;more preferably, the second transmembrane domain comprises the CD28 transmembrane domain;more preferably, the second transmembrane domain comprises the amino acid sequence of SEQ ID NO: 36.8.The polypeptide system of claim 6 or 7, wherein the second intracellular signaling domain comprises a second co-stimulatory signaling domain;preferably, wherein the second co-stimulatory signaling domain is the signaling domain of CD28 or CD137;more preferably, the second co-stimulatory signaling domain comprises the amino acid sequence of SEQ ID NO: 37.9.The polypeptide system of any one of claims 6 to 8, wherein the second intracellular signaling domain comprises a second primary intracellular signaling domain;preferably, the second primary intracellular signaling domain is fused by its N-terminus to the C-terminus of the second co-stimulatory signaling domain;more preferably, the second primary intracellular signaling domain comprises a CD3ζ cytoplasmic signaling domain;more preferably, the second primary intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 38.10.The polypeptide system of any one of claims 1 to 9, wherein the EAR is capable of binding Fas ligand;preferably, the EAR polypeptide comprises, from its N to C terminus in order, an extracellular domain, a third transmembrane domain, and an intracellular domain;more preferably, the extracellular domain is the Fas ectodomain;more preferably, the extracellular domain comprises the amino acid sequence of SEQ ID NO: 50.11.The polypeptide system of claim 10, wherein the intracellular domain comprises the CD2 intracellular signaling domain;preferably, the intracellular domain comprises the amino acid sequence of SEQ ID NO: 55;more preferably, the third transmembrane domain is the Fas transmembrane domain;more preferably, the third transmembrane domain comprises the amino acid sequence of SEQ ID NO: 59.12.The polypeptide system of claim 10, wherein the intracellular domain comprises the IL-7Rαendodomain;preferably, the intracellular domain comprises the amino acid sequence of SEQ ID NO: 54;more preferably, the third transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60.13.The polypeptide system of claim 10, wherein the intracellular domain comprises the IL-7Rαendodomain and the CD2 intracellular signaling domain, the IL-7Rα endodomain is fused by its C-terminus to the N-terminus of the CD2 intracellular signaling domain;preferably, the CD2 intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 55, the IL-7Rα endodomain comprises the amino acid sequence of SEQ ID NO: 54;more preferably, the third transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60.14.The polypeptide system of any one of claims 1 to 9, wherein the EAR is capable of binding TGFβ;preferably, the EAR polypeptide is a dominant negative receptor (DNR) polypeptide;more preferably, the DNR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide;more preferably, the DNR polypeptide comprises the amino acid sequence of SEQ ID NO: 69.15.The polypeptide system of claims 1, which comprises a first CAR and a second CAR, wherein the first CAR comprises, from its N to C terminus in order, a first extracellular CD19-binding domain, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 31, a first transmembrane domain and a first intracellular signaling domain; wherein the second CAR comprises, from its N to C terminus in order, a second extracellular CD20-binding domain, a second spacer of CD28 hinge, a second transmembrane domain and a second intracellular signaling domain;preferably, the first CAR comprises, from its N to C terminus in order, a first extracellular CD19-binding domain comprising the amino acid sequence of SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 or SEQ ID NO: 24, a first spacer that consists of the amino acid sequence of SEQ ID NO: 30, a CD28 transmembrane domain and a first intracellular signaling domain comprising CD137 co-stimulatory signaling domain and CD3ζ cytoplasmic signaling domain; wherein the second CAR comprises, from its N to C terminus in order, a second extracellular CD20-binding domain comprising the amino acid sequence of SEQ ID NO: 25, a second spacer of CD28 hinge, a CD28 transmembrane domain and a second intracellular signaling domain comprising CD137 co-stimulatory signaling domain and CD3ζ cytoplasmic signaling domain;more preferably, the polypeptide system comprises a first EAR polypeptide and a second EAR polypeptide, wherein the first EAR polypeptide comprises, from its N to C terminus in order, (i) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, and an IL-7R endodomain, or (ii) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, an IL-7R endodomain and an CD2 intracellular signaling domain, or (iii) a Fas ectodomain, a Fas transmembrane domain, and an CD2 intracellular signaling domain, or any combination thereof; wherein the second EAR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide.16.A polypeptide system, comprising a polypeptide of a first EAR and a polypeptide of a second EAR, wherein the first EAR is capable of binding Fas ligand, the second EAR is capable of binding TGFβ;preferably, the first EAR polypeptide comprises a Fas ectodomain, the second EAR polypeptide comprises a TGFβR ectodomain;more preferably, the Fas ectodomain comprises the amino acid sequence of SEQ ID NO: 50, the TGFβR ectodomain comprises the amino acid sequence of SEQ ID NO: 52.17.The polypeptide system of claims 16, wherein the first EAR polypeptide comprises, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain, and a CD2 intracellular signaling domain;preferably, the transmembrane domain is the Fas transmembrane domain;more preferably, the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 59;preferably, the CD2 intracellular signaling domain comprises the amino acid sequences of SEQ ID NO: 55; .18.The polypeptide system of claim 16, wherein the first EAR polypeptide comprises, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain, and an IL-7Rα endodomain;preferably, the transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60;more preferably, the IL-7Rα endodomain comprises the amino acid sequence of SEQ ID NO: 54.19.The polypeptide system of claim 16, wherein the first EAR polypeptide comprises, from its N to C terminus in order, a Fas ectodomain, a transmembrane domain, an IL-7Rα endodomain and a CD2 intracellular signaling domain;preferably, the transmembrane domain consists of the amino acid sequence of SEQ ID NO: 60;more preferably, the CD2 intracellular signaling domain comprises the amino acid sequences of SEQ ID NO: 55, the IL-7Rα endodomain comprises the amino acid sequence of SEQ ID NO: 54.20.The polypeptide system of any one of claims 16 to 19, wherein the second EAR polypeptide is a DNR polypeptide;preferably, the DNR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide;more preferably, the DNR polypeptide comprises the amino acid sequence of SEQ ID NO: 69.21.The polypeptide system of claim 16, which comprises a first EAR polypeptide and a second EAR polypeptide, wherein the first EAR polypeptide comprises, from its N to C terminus in order, (i) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, and an IL-7R endodomain, or (ii) a Fas ectodomain, a transmembrane domain consisting of the amino acid sequence of SEQ ID NO: 60, an IL-7R endodomain and an CD2 intracellular signaling domain, or (iii) a Fas ectodomain, a Fas transmembrane domain, and an CD2 intracellular signaling domain, or any combination thereof; wherein the second EAR polypeptide is a dnTGFβR1 polypeptide or a dnTGFβR2 polypeptide;preferably, the polypeptide system comprises one or more CARs;more preferably, the polypeptide system comprises one CAR capable of binding CD19 or CD20, or comprises two CARs capable of binding CD19 and CD20, respectively.22.The polypeptide system of any one of claims 1 to 21, which comprises one or more self-cleaving peptides located between the polypeptides contained within the polypeptide system;preferably, the self-cleaving peptide is a viral self-cleaving 2A polypeptide;more preferably, the viral self-cleaving 2A polypeptide is selected from the group consisting of a foot-and-mouth disease virus (FMDV) (F2A) peptide, an equine rhinitis A virus (ERAV) (E2A) peptide, a Thosea asigna virus (TaV) (T2A) peptide, a porcine teschovirus-1 (PTV-1) (P2A) peptide, a Theilovirus 2A peptide, and an encephalomyocarditis virus 2A peptide.23.A polynucleotide system encoding the polypeptide system of any one of claims 1 to 22.24.A vector system comprising one or more vectors comprising the polynucleotide system of claim 23;preferably, the vector is a retroviral, lentiviral, adenoviral, or adeno-associated viral vector.25.A cell comprising the polypeptide system of any one of claims 1 to 22, the polynucleotide system of claim 23, or the vector system of claim 24;preferably, the cell is an immune cell;more preferably, the cell is a T-cell, a K cell, a KT cell, an αβ cell, a γδ T-cell, a Mucosa Associated Invariant T-cell (MAIT T-cell) , an innate lymphoid cell, a stem cell, or a progenitor cell.26.A method of treating a disease in a subject, comprising administering a therapeutically effective amount of the cell of claim 25 to the subject;preferably, the disease is a cancer or an autoimmune disease;more preferably, the cancer is selected from the group consisting of leukemia, lymphoma, lung cancer, melanoma, breast cancer, prostate cancer, colon cancer, renal cell carcinoma, ovarian cancer, neuroblastoma and rhabdomyosarcoma, the autoimmune disease is selected from the group consisting of systemic lupus erythematosus, lupus nephritis, multiple sclerosis, rheumatoid arthritis, Sjogren’s syndrome, idiopathic thrombocytopenia purpura, Type 1 diabetes, Pemphigus vulgaris, Neuromyelitis optica, ANCA vasculitis, and Myasthenia gravis;more preferably, the cancer is leukemia or lymphoma, the autoimmune disease is systemic lupus erythematosus or lupus nephritis.
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