WO2024046468A1 - Protéines de fusion ciblant la voie de dégradation lysosomale - Google Patents

Protéines de fusion ciblant la voie de dégradation lysosomale Download PDF

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WO2024046468A1
WO2024046468A1 PCT/CN2023/116513 CN2023116513W WO2024046468A1 WO 2024046468 A1 WO2024046468 A1 WO 2024046468A1 CN 2023116513 W CN2023116513 W CN 2023116513W WO 2024046468 A1 WO2024046468 A1 WO 2024046468A1
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amino acid
acid sequence
seq
cell
antigen
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PCT/CN2023/116513
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English (en)
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Guodong ZHA
Huihui ZHANG
Ming Zeng
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Nanjing Legend Biotech Co., Ltd.
Legend Biotech Ireland Limited
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Publication of WO2024046468A1 publication Critical patent/WO2024046468A1/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4613—Natural-killer cells [NK or NK-T]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4631—Chimeric Antigen Receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4637—Other peptides or polypeptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • A61K39/464416—Receptors for cytokines
    • A61K39/464417—Receptors for tumor necrosis factors [TNF], e.g. lymphotoxin receptor [LTR], CD30
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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A61K47/6811—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates the drug being a protein or peptide, e.g. transferrin or bleomycin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6843—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70521—CD28, CD152
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2896—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against molecules with a "CD"-designation, not provided for elsewhere
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/62—DNA sequences coding for fusion proteins
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A61K2039/507—Comprising a combination of two or more separate antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterised by the cancer treated
    • A61K2239/48—Blood cells, e.g. leukemia or lymphoma
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/54—Interleukins [IL]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2851—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the lectin superfamily, e.g. CD23, CD72
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2878—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/06—Fusion polypeptide containing a localisation/targetting motif containing a lysosomal/endosomal localisation signal

Definitions

  • the present disclosure relates to fusion proteins for degradation of target proteins through lysosomal degradation pathway, and cells comprising such fusion proteins (e.g., chimeric antigen receptors (CAR) -expressing cells) .
  • fusion proteins e.g., chimeric antigen receptors (CAR) -expressing cells
  • the present disclosure further relates to methods of using such cells for treatments.
  • Targeted protein degradation is a promising approach to remove undesired proteins (e.g., disease-associated proteins) by exploiting cells’ own destruction machinery without editing genes encoding these proteins. Lysosomes can mediate the intracellular degradation of membrane and extracellular proteins. Targeted protein degradation strategies via the lysosomal degradation pathways have emerged in recent years, but have limited efficacy and stability.
  • a fusion protein comprising (i) an antigen-binding domain that binds to a target protein; and (ii) a lysosome-targeting domain that comprises a lysosome-related membrane protein or a fragment thereof.
  • the antigen-binding domain comprises an antibody fragment that binds to the target protein, wherein optionally the target protein is expressed on a cell.
  • the target protein is selected from CD38, CD7, CD3, PD-1, TGF-beta receptor, Killer-cell immunoglobulin-like receptor, CS-1, TCR, CD4, CD5, CD8, CD25, CD30, CD52, CD56, CD70, 4-1BB, NKG2A, NKG2D, CD16, NKp46, CD56, CD138, SLAM family members (such as 2B4, Ly-9, CD84 and CD319) , CD226, Kir family members (such as KIR2DL1, KIR2DS1, KIR2DL2/L3, KIR2DS2, KIR2DS4, KIR3DL1, and KIR3DL2) , the natural cytotoxicity receptors (such as NKp30, NKp44 and NKp46) , PD-1, TIM3, TIGIT, MHCI, MHCII
  • the antibody fragment is selected from the group consisting of Fab, Fab’, F (ab’) 2 , scFv, Fv, dsFv, sdAb, V H H, V NAR , nanobodies, diabodies, triabodies, tetrabodies, and HcAb.
  • the antibody fragment comprises at least one scFv or least one sdAb, wherein optionally the sdAb comprises a V H H.
  • the target protein is CD38.
  • the antibody fragment comprises the scFv comprising: (i) an HCDR1, an HCDR2 and an HCDR3 as set forth in a heavy chain variable domain (V H ) comprising the amino acid sequence of SEQ ID NO: 52; and an LCDR1, an LCDR2 and an LCDR3 as set forth in a light chain variable domain (V L ) comprising the amino acid sequence of SEQ ID NO: 53; and wherein optionally the HCDR1 comprises the amino acid sequence of SEQ ID NO: 34, the HCDR2 comprises the amino acid sequence of SEQ ID NO: 35, the HCDR3 comprises the amino acid sequence of SEQ ID NO: 36, the LCDR1 comprises the amino acid sequence of SEQ ID NO: 37, the LCDR2 comprises the amino acid sequence of SEQ ID NO: 38, and the LCDR3 comprises the amino acid sequence of SEQ ID NO: 39; (ii) a V H comprising the amino acid sequence of SEQ ID NO: 52 and
  • the antibody fragment comprises one or more of sdAb selected from the group consisting of: (i) a V H H comprises a CDR1, a CDR2, and a CDR3 as set forth in a V H H comprising the amino acid sequence of SEQ ID NO: 20, wherein optionally the CDR1 comprises the amino acid sequence of SEQ ID NO: 40, the CDR2 comprises the amino acid sequence of SEQ ID NO: 41, and the CDR3 comprises the amino acid sequence of SEQ ID NO: 42, and wherein optionally the V H H comprises an amino acid sequence having at least about 80%identity to the amino acid sequence of SEQ ID NO: 20 or the amino acid sequence of SEQ ID NO: 20; (ii) a V H H comprises a CDR1, a CDR2, and a CDR3 as set forth in a V H H comprising the amino acid sequence of SEQ ID NO: 54, wherein optionally the CDR1 comprises the amino acid sequence of SEQ ID NO: 43, the CDR2 comprises the amino acid sequence of
  • the target protein is CD7, and further wherein the antibody fragment comprises a V H H comprises a CDR1, a CDR2, and a CDR3 as set forth in a V H H comprising the amino acid sequence of SEQ ID NO: 22, wherein optionally the CDR1 comprises the amino acid sequence of SEQ ID NO: 49, the CDR2 comprises the amino acid sequence of SEQ ID NO: 50, and the CDR3 comprises the amino acid sequence of SEQ ID NO: 51; and wherein optionally the V H H comprises an amino acid sequence having at least about 80%identity to the amino acid sequence of SEQ ID NO: 22 or the amino acid sequence of SEQ ID NO: 22.
  • the lysosome-related membrane protein is selected from the group consisting of transferrin receptor (TfR) , low density lipoprotein receptor (LDLR) , neonatal Fc receptor (FcRn) , very low density lipoprotein receptor (VLDLR) , LDL receptor related protein 8 (LRP8) , LDL receptor related protein 5 (LRP5) , asialoglycoprotein receptor 1 (ASGR1) , asialoglycoprotein receptor 2 (ASGR2) , cation-dependent mannose-6-phosphate receptor (MPRD) , vascular endothelial growth factor receptor 2 (VEGFR2) , integrin alpha-V (ITAV) , integrin beta-3 (ITB3) , arrestin beta 2 (ARRB2) , and glucose transporter type 4 (GLUT4) .
  • TfR transferrin receptor
  • LDLR low density lipoprotein receptor
  • FcRn neonatal Fc receptor
  • VLDLR very low density lipoprotein receptor
  • LRP8 LDL
  • the lysosome-related membrane protein is TfR, LDLR, FcRn, or mutation thereof. In some embodiments, the lysosome-related membrane protein or fragment thereof comprises a transmembrane domain, an intracellular domain, or a combination thereof. In some embodiments, the lysosome-related membrane protein or fragment thereof comprises an amino acid sequence having at least about 80%identity to the amino acid sequence set forth in any of SEQ ID NOs: 1-17 and 78-80, or the amino acid sequence set forth in any of SEQ ID NOs: 1-17 and 78-80.
  • the fusion protein provided herein further comprises a linker between the antigen-binding domain and the lysosome-targeting domain.
  • the antigen-binding domain is N-terminal to the lysosome-related membrane protein or C-terminal to the lysosome-related membrane protein.
  • the lysosome-related membrane protein comprises a transmembrane domain and an intracellular domain, and further wherein the transmembrane domain is N-terminal to the intracellular domain or C-terminal to the intracellular domain.
  • the polypeptide provided herein further comprises a signal peptide, wherein the signal peptide is covalently jointed to the N-terminus of the antigen-binding domain or the N-terminus of the lysosome-related membrane protein.
  • the fusion protein or the polypeptide provided herein comprises an amino acid sequence having at least about 80%identity to the amino acid sequence set forth in any one of SEQ ID NOs: 23-27 and 81-94, or the amino acid sequence set forth in any one of SEQ ID NOs: 23-27 and 81-94.
  • nucleic acid molecule encoding the fusion protein or the polypeptide provided herein.
  • the nucleic acid molecule provided herein further comprises a second nucleic acid sequence encoding an antigen-recognizing receptor that binds to an antigen; optionally wherein the antigen-recognizing receptor is a chimeric antigen receptor (CAR) .
  • the nucleic acid molecule further comprises a third nucleic acid sequence encoding an exogenous cytokine, or a fragment thereof; optionally wherein the exogenous cytokine is IL-15.
  • nucleic acid molecule provided herein.
  • a cell comprising the fusion protein or the polypeptide, the nucleic acid molecule, or the vector provided herein.
  • the cell further comprises an antigen-recognizing receptor that binds to an antigen.
  • the antigen-recognizing receptor is a T cell receptor (TCR) , a chimeric antigen receptor (CAR) , a chimeric TCR (cTCR) , or a T cell antigen coupler (TAC) -like chimeric receptor.
  • TCR T cell receptor
  • CAR chimeric antigen receptor
  • cTCR chimeric TCR
  • TAC T cell antigen coupler
  • the antigen-recognizing receptor is a CAR.
  • the CAR comprises an extracellular antigen binding domain binding to an antigen
  • the antigen is a tumor antigen selected from the group consisting of BCMA, CLL1, CD4, GPC3, GPRC5D, GU2CYC, CD19, MUC16, MUC1, CAIX, CEA, CD8, CD7, CD10, CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD133, CD138, EGP-2, EGP-40, EpCAM, ERBB2, ERBB3, ERBB4, FBP, fetal acetylcholine receptor, folate receptor- ⁇ , GD2, GD3, HER-2, hTERT, IL-13R- ⁇ 2, ⁇ -light chain, KDR, LeY, L1 cell adhesion molecule, MAGE-A1, mesothelin, MAGEA3, p53, MART1, GP100, proteinase-3 (PR3) , ty
  • the antigen
  • the tumor antigen is BCMA or CLL1.
  • the CAR comprises a transmembrane domain, wherein the transmembrane domain is derived from a molecule selected the group consisting of CD8 ⁇ , CD4, CD28, CD137, CD80, CD86, CD152 and PD1.
  • the CAR comprises an intracellular signaling domain comprising a primary intracellular domain.
  • the primary intracellular domain is derived from CD3 ⁇ .
  • the intracellular signaling domain comprises a co-stimulatory signaling domain.
  • the co-stimulatory signaling domain is derived from a co-stimulatory molecule selected from the group consisting of CD27, CD28, CD137, OX40, CD30, CD40, CD3, LFA-1, ICOS, CD2, CD7, LIGHT, NKG2C, B7-H3, ligands of CD83, and combinations thereof.
  • the co-stimulatory signaling domain comprises a cytoplasmic domain of CD28 and/or a cytoplasmic domain of CD137.
  • the CAR comprises an amino acid sequence having at least about 80%identity to the amino acid sequence of SEQ ID NO: 31 or SEQ ID NO: 32, or the amino acid sequence of SEQ ID NO: 31 or SEQ ID NO: 32.
  • the cell provided herein further comprises an exogenous cytokine, or a fragment thereof.
  • the exogenous cytokine is selected from the group consisting of IL-2, IL-3, IL-6, IL-7, IL-11, IL-12, IL-15, IL-17, IL-18, IL-9, and IL-21, and combinations thereof.
  • the cell is an immune effector cell selected from the group consisting of T cells, Natural Killer (NK) cells, cytotoxic T cells (CTL) , regulatory T cells, Natural Killer T (NKT) cells, peripheral blood mononuclear cells (PBMCs) , hematopoietic stem cells, pluripotent stem cells, embryonic stem cells, and combinations thereof.
  • the cell is an NK cell or a T cell.
  • composition comprising the cell provided herein.
  • composition provided herein is a pharmaceutical composition further comprising a pharmaceutically acceptable carrier.
  • a method of treating a disease or a disorder in a subject comprising administering an effective amount of the cell, or the composition provided herein.
  • the subject is receiving or has received an antibody treatment, wherein the antibody treatment targets the antigen bound by the antigen-binding domain of the fusion protein.
  • the antigen is CD38.
  • the antibody treatment is a daratumumab treatment.
  • the disease or disorder is cancer.
  • the cancer is multiple myeloma.
  • a method of producing a cell comprising: introducing into a precursor cell a nucleic acid molecule encoding the fusion protein or the polypeptide provided herein, wherein the fusion protein or the polypeptide upon expression results in down-modulation of a target protein in the cell.
  • the down-modulation comprises reducing cell surface expression of the target protein.
  • the target protein is CD38 or CD7.
  • the method provided herein further comprises introducing into the precursor cell a second nucleic acid sequence encoding an antigen-recognizing receptor that binds to an antigen; optionally wherein the antigen-recognizing receptor is a chimeric antigen receptor (CAR) .
  • CAR chimeric antigen receptor
  • FIG. 1 is a schematic diagram of a non-gene editing approach to modulate target proteins using exemplary fusion proteins of the present disclosure (designated as “PDT” molecules) .
  • the exemplary fusion protein is a chimeric peptide having a binding domain (to recognize the target protein) fused with a transmembrane domain and an intracellular domain derived from a lysosome-related membrane protein.
  • the transmembrane domain may or may not be derived from the same lysosome-related membrane protein as the intracellular domain.
  • FIGs. 2A-2D show the in vitro evaluation of target protein degradation by PDT-1 construct on both NK cells and T cells.
  • FIG. 2A shows that by expressing PDT-1-CD38-1, the expression of CD38 on EGFP+ NK cells decreased.
  • FIG. 2B shows that by expressing PDT-1 (PDT-1-CD38-1 or PDT-1-CD38-2) , the expression of CD38 on BCMA CAR-NK cells decreased.
  • FIG. 2C shows CD38 down-regulated on EGFP+ pan-T cells by expressing PDT-1-CD38-1.
  • FIG. 2D shows that by expressing PDT-1-CD7, the expression of CD7 on EGFP+ NK cells decreased.
  • FIG. 3A-O show the in vitro evaluation of target protein degradation by PDT constructs on BCMA CAR-NK cells. By expressing PDT constructs, the expression of CD38 on BCMA CAR-NK cells decreased.
  • FIG. 3A shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-2 construct.
  • FIG. 3B shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-4 construct.
  • FIG. 3C shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-5 construct.
  • FIG. 3D shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-6 construct.
  • FIG. 3E shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-7 construct.
  • FIG. 3F shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-8 construct.
  • FIG. 3G shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-9 construct.
  • FIG. 3H shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-10 construct.
  • FIG. 3I shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-11 construct.
  • FIG. 3J shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-12 construct.
  • FIG. 3K shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-13 construct.
  • FIG. 3L shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-14 construct.
  • FIG. 3M shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-15 construct.
  • FIG. 3N shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-16 construct.
  • FIG. 3O shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-17 construct.
  • FIG. 4 shows CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-3 construct. CD38 expression was detected on day 4, day 7 and day 10 after transduction. Compared to BCMA CAR-NK cells, the CD38 expression on PDT-3-CD38-3/BCMA CAR-NK cells decreased.
  • FIGs. 5A-5C show in vitro HvG MLR evaluation. Allogeneic PBMCs were cocultured with Un-NK, BCMA CAR-NK or PCT-1-CD38-1/BCMA CAR-NK, with Dara treatment. There were four different co-culture systems in this experiment: Group 1: PBMCs (HLA-A2-) and Un-NK cells; Group 2: PBMCs (HLA-A2-) , Dara (200 g/mL) and Un-NK cells; Group 3: PBMCs (HLA-A2-) , Dara (200 g/mL) and BCMA CAR-NK cells; Group 4: PBMCs (HLA-A2-) , Dara (200 g/mL) and PDT-1-CD38-1/BCMA CAR-NK cells.
  • Group 1 PBMCs (HLA-A2-) and Un-NK cells
  • Group 2 PBMCs (HLA-A2-) , Dara (200 g/mL) and Un-
  • FIGs. 5A &5B show that PCT-1-CD38-1 construct can improve the survival of BCMA CAR-NK cells from Dara induced depletion in a HvG MLR assay.
  • FIG. 5C shows that the CAR positive NK cells were enriched during Dara treatment.
  • FIGs. 6A and 6B show peripheral blood PK of CLL-1 CAR-NK cells and PDT-1-CD38-1/CLL-1 CAR-NK cells (expressing PDT-1-CD38-1 construct) with Dara treatment in vivo.
  • FIG. 6A shows the CAR-NK cells expansion in peripheral blood of mice treated with CLL-1 CAR-NK cells only or treated with PDT-1-CD38-1/CLL-1 CAR-NK cells and Dara.
  • FIG. 6B shows the remaining CD38+ NK cells in mouse peripheral blood.
  • the present disclosure relates to fusion proteins for degradation of target proteins through lysosomal degradation pathway.
  • the fusion proteins comprise (i) an antigen-binding domain that binds to a target protein; and (ii) a lysosome-targeting domain that comprises a lysosome-related membrane protein or a fragment thereof.
  • Such fusion proteins can be used for removing undesired proteins (e.g., proteins lead to cell death or disease-associated) in a non-gene editing way.
  • the present disclosure further relates to cells comprising such fusion proteins and the uses of such cells for treatments.
  • the fusion proteins provided herein provide various benefits and can be used to degrade different targets according to different needs.
  • cells comprising the fusion protein further express an antigen recognizing receptor (e.g., a chimeric antigen receptor (CAR) ) , wherein the fusion protein improves the cytotoxicity, proliferation and/or persistence of the CAR-expressing cells.
  • an antigen recognizing receptor e.g., a chimeric antigen receptor (CAR)
  • the fusion proteins provided herein can be expressed in cells and used in combination with antibodies to avoid cell removal.
  • the fusion proteins provided herein can be used to enhance cellular functions, such as targeting immnosuppresive molecules.
  • a CAR targets to a protein that is also expressed by immune cells themselves (such as CD7, CD38, CD70, CD4, CD56, etc.
  • co-expressing the fusion protein (which reduces the target protein from cell membrane) and the CAR may avoid fratricide of the CAR-expressing cells.
  • CD38-or CD7-targeting fusion proteins efficiently reduced the surface expression of CD38 or CD7 respectively in NK cells or T cells, including CAR-NK cells.
  • CAR-NK cells expressing the CD38-targeting fusion protein were able to overcome the killing effects of anti-CD38 antibody (e.g., daratumumab) , and maintain good expansion and survival.
  • anti-CD38 antibody e.g., daratumumab
  • antibody immunoglobulin, ” or “Ig” is used interchangeably herein, and is used in the broadest sense and specifically covers, for example, monoclonal antibodies (including agonist, antagonist, neutralizing antibodies, full length or intact monoclonal antibodies) , antibody compositions with polyepitopic or monoepitopic specificity, polyclonal or monovalent antibodies, multivalent antibodies, multispecific antibodies (e.g., bispecific antibodies so long as they exhibit the desired biological activity) , formed from at least two intact antibodies, single chain antibodies, and fragments thereof (e.g., domain antibodies) , as described below.
  • an antibody can be human, humanized, chimeric and/or affinity matured, as well as an antibody from other species, for example, mouse, rabbit, llama, etc.
  • the term “antibody” is intended to include a polypeptide product of B cells within the immunoglobulin class of polypeptides that is able to bind to a specific molecular antigen and is composed of two identical pairs of polypeptide chains, wherein each pair has one heavy chain (about 50-70 kDa) and one light chain (about 25 kDa) , each amino-terminal portion of each chain includes a variable region of about 100 to about 130 or more amino acids, and each carboxy-terminal portion of each chain includes a constant region.
  • Antibodies also include, but are not limited to, synthetic antibodies, recombinantly produced antibodies, antibodies including from Camelidae species (e.g., llama or alpaca) or their humanized variants, intrabodies, anti-idiotypic (anti-Id) antibodies, and functional fragments (e.g., antigen binding fragments) of any of the above, which refers to a portion of an antibody heavy or light chain polypeptide that retains some or all of the binding activity of the antibody from which the fragment was derived.
  • Camelidae species e.g., llama or alpaca
  • anti-Id anti-idiotypic antibodies
  • functional fragments e.g., antigen binding fragments
  • Non-limiting examples of functional fragments include single-chain Fvs (scFv) (e.g., including monospecific, bispecific, etc. ) , Fab fragments, F (ab’) fragments, F (ab) 2 fragments, F (ab’) 2 fragments, disulfide-linked Fvs (dsFv) , Fd fragments, Fv fragments, diabody, triabody, tetrabody, and minibody.
  • scFv single-chain Fvs
  • Fab fragments fragments
  • F (ab’) fragments fragments
  • F (ab) 2 fragments F (ab’) 2 fragments
  • dsFv disulfide-linked Fvs
  • antibodies provided herein include immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, for example, antigen-binding domains or molecules that contain an antigen-binding site that binds to an antigen (e.g., one or more CDRs of an antibody) .
  • an antigen e.g., one or more CDRs of an antibody
  • Such antibody fragments can be found in, for example, Harlow and Lane, Antibodies: A Laboratory Manual (1989) ; Mol. Biology and Biotechnology: A Comprehensive Desk Reference (Myers ed., 1995) ; Huston et al., 1993, Cell Biophysics 22: 189-224; Plückthun and Skerra, 1989, Meth. Enzymol. 178: 497-515; and Day, Advanced Immunochemistry (2d ed. 1990) .
  • the antibodies provided herein can be of any class (e.g., IgG, IgE, IgM, IgD, and IgA) or any subclass (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2) of immunoglobulin molecule.
  • Antibodies may be agonistic antibodies or antagonistic antibodies .
  • Antibodies may be neither agonistic nor antagonistic.
  • an “antigen” is a structure to which an antibody can selectively bind.
  • a target antigen may be a polypeptide, carbohydrate, nucleic acid, lipid, hapten, or other naturally occurring or synthetic compound.
  • the target antigen is a polypeptide.
  • an antigen is associated with a cell, for example, is present on or in a cell.
  • an “intact” antibody is one comprising an antigen-binding site as well as a CL and at least heavy chain constant regions, CH1, CH2 and CH3.
  • the constant regions may include human constant regions or amino acid sequence variants thereof.
  • an intact antibody has one or more effector functions.
  • Single-chain Fv also abbreviated as “sFv” or “scFv” are antibody fragments that comprise the V H and V L antibody domains connected into a single polypeptide chain.
  • the sFv polypeptide further comprises a polypeptide linker between the V H and V L domains which enables the sFv to form the desired structure for antigen binding.
  • HcAb heavy chain-only antibody
  • a functional antibody which comprises heavy chains, but lacks the light chains usually found in 4-chain antibodies.
  • Camelid animals (such as camels, llamas, or alpacas) are known to produce HcAbs.
  • binding refers to an interaction between molecules including, for example, to form a complex. Interactions can be, for example, non-covalent interactions including hydrogen bonds, ionic bonds, hydrophobic interactions, and/or van der Waals interactions. A complex can also include the binding of two or more molecules held together by covalent or non-covalent bonds, interactions, or forces. The strength of the total non-covalent interactions between a single antigen-binding site on an antibody and a single epitope of a target molecule, such as an antigen, is the affinity of the antibody or functional fragment for that epitope.
  • the ratio of dissociation rate (k off ) to association rate (k on ) of a binding molecule (e.g., an antibody) to a monovalent antigen (k off /k on ) is the dissociation constant K D , which is inversely related to affinity.
  • K D the dissociation constant
  • the value of K D varies for different complexes of antibody and antigen and depends on both k on and k off .
  • the dissociation constant K D for an antibody provided herein can be determined using any method provided herein or any other method well known to those skilled in the art.
  • the affinity at one binding site does not always reflect the true strength of the interaction between an antibody and an antigen.
  • binding molecules described herein terms such as “bind to, ” “that specifically bind to, ” and analogous terms are also used interchangeably herein and refer to binding molecules of antigen binding domains that specifically bind to an antigen, such as a polypeptide.
  • a binding molecule or antigen binding domain that binds to or specifically binds to an antigen can be identified, for example, by immunoassays, or other techniques known to those of skill in the art.
  • a binding molecule or antigen binding domain binds to or specifically binds to an antigen when it binds to an antigen with higher affinity than to any cross-reactive antigen as determined using experimental techniques, such as radioimmunoassay (RIA) and enzyme linked immunosorbent assay (ELISA) .
  • RIA radioimmunoassay
  • ELISA enzyme linked immunosorbent assay
  • a specific or selective reaction will be at least twice background signal or noise and may be more than 10 times background. See, e.g., Fundamental Immunology 332-36 (Paul ed., 2d ed. 1989) for a discussion regarding binding specificity.
  • the extent of binding of a binding molecule or antigen binding domain to a “non-target” protein is less than about 10%of the binding of the binding molecule or antigen binding domain to its particular target antigen, for example, as determined by fluorescence activated cell sorting (FACS) analysis or RIA.
  • a binding molecule or antigen binding domain that binds to an antigen includes one that is capable of binding the antigen with sufficient affinity such that the binding molecule is useful, for example, as a therapeutic and/or diagnostic agent in targeting the antigen.
  • a binding molecule or antigen binding domain that binds to an antigen has a dissociation constant (K D ) of less than or equal to 1 ⁇ M, 800 nM, 600 nM, 550 nM, 500 nM, 300 nM, 250 nM, 100 nM, 50 nM, 10 nM, 5 nM, 4 nM, 3 nM, 2 nM, 1 nM, 0.9 nM, 0.8 nM, 0.7 nM, 0.6 nM, 0.5 nM, 0.4 nM, 0.3 nM, 0.2 nM, or 0.1 nM.
  • K D dissociation constant
  • a binding molecule or antigen binding domain binds to an epitope of an antigen that is conserved among the antigen from different species.
  • the binding molecules or antigen binding domains can comprise “chimeric” sequences in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain (s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see U.S. Pat. No. 4,816,567; and Morrison et al., 1984, Proc. Natl. Acad. Sci. USA 81: 6851-55) .
  • Chimeric sequences may include humanized sequences.
  • the binding molecules or antigen binding domains can comprise portions of “humanized” forms of nonhuman (e.g., camelid, murine, non-human primate) antibodies that include sequences from human immunoglobulins (e.g., recipient antibody) in which the native CDR residues are replaced by residues from the corresponding CDR of a nonhuman species (e.g., donor antibody) such as camelid, mouse, rat, rabbit, or nonhuman primate having the desired specificity, affinity, and capacity.
  • a nonhuman species e.g., donor antibody
  • one or more FR region residues of the human immunoglobulin sequences are replaced by corresponding nonhuman residues.
  • humanized antibodies can comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance.
  • a humanized antibody heavy or light chain can comprise substantially all of at least one or more variable regions, in which all or substantially all of the CDRs correspond to those of a nonhuman immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence.
  • the humanized antibody will comprise at least a portion of an immunoglobulin constant region (Fc) , typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • the binding molecules or antigen binding domains can comprise portions of a “fully human antibody” or “human antibody, ” wherein the terms are used interchangeably herein and refer to an antibody that comprises a human variable region and, for example, a human constant region.
  • the binding molecules may comprise an antibody sequence.
  • the terms refer to an antibody that comprises a variable region and constant region of human origin.
  • Fully human antibodies in certain embodiments, can also encompass antibodies which bind polypeptides and are encoded by nucleic acid sequences which are naturally occurring somatic variants of human germline immunoglobulin nucleic acid sequence.
  • the term “fully human antibody” includes antibodies having variable and constant regions corresponding to human germline immunoglobulin sequences as described by Kabat et al.
  • a “human antibody” is one that possesses an amino acid sequence which corresponds to that of an antibody produced by a human and/or has been made using any of the techniques for making human antibodies. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues.
  • Human antibodies can be produced using various techniques known in the art, including phage-display libraries (Hoogenboom and Winter, J. Mol. Biol. 227: 381 (1991) ; Marks et al., J. Mol. Biol.
  • Human antibodies can be prepared by administering the antigen to a transgenic animal that has been modified to produce such antibodies in response to antigenic challenge, but whose endogenous loci have been disabled, e.g., mice (see, e.g., Jakobovits, Curr. Opin. Biotechnol. 6 (5) : 561-66 (1995) ; Brüggemann and Taussing, Curr. Opin. Biotechnol. 8 (4) : 455-58 (1997) ; and U.S. Pat. Nos. 6,075,181 and 6,150,584 regarding XENOMOUSE TM technology) . See also, for example, Li et al., Proc. Natl. Acad. Sci. USA 103: 3557-62 (2006) regarding human antibodies generated via a human B-cell hybridoma technology.
  • the binding molecules or antigen binding domains can comprise portions of a “recombinant human antibody, ” wherein the phrase includes human antibodies that are prepared, expressed, created or isolated by recombinant means, such as antibodies expressed using a recombinant expression vector transfected into a host cell, antibodies isolated from a recombinant, combinatorial human antibody library, antibodies isolated from an animal (e.g., a mouse or cow) that is transgenic and/or transchromosomal for human immunoglobulin genes (see, e.g., Taylor, L.D. et al., Nucl. Acids Res.
  • human antibodies prepared, expressed, created or isolated by any other means that involves splicing of human immunoglobulin gene sequences to other DNA sequences.
  • Such recombinant human antibodies can have variable and constant regions derived from human germline immunoglobulin sequences (See Kabat, E.A. et al. (1991) Sequences of Proteins of Immunological Interest , Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242) .
  • such recombinant human antibodies are subjected to in vitro mutagenesis (or, when an animal transgenic for human Ig sequences is used, in vivo somatic mutagenesis) and thus the amino acid sequences of the V H and V L regions of the recombinant antibodies are sequences that, while derived from and related to human germline V H and V L sequences, may not naturally exist within the human antibody germline repertoire in vivo.
  • the binding molecules or antigen binding domains can comprise a portion of a “monoclonal antibody, ” wherein the term as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, e.g., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts or well-known post-translational modifications such as amino acid iomerizatio or deamidation, methionine oxidation or asparagine or glutamine deamidation, each monoclonal antibody will typically recognize a single epitope on the antigen.
  • a “monoclonal antibody, ” as used herein is an antibody produced by a single hybridoma or other cell.
  • the term “monoclonal” is not limited to any particular method for making the antibody.
  • the monoclonal antibodies useful in the present disclosure may be prepared by the hybridoma methodology first described by Kohler et al., Nature 256: 495 (1975) , or may be made using recombinant DNA methods in bacterial or eukaryotic animal or plant cells (see, e.g., U.S. Pat. No. 4,816,567) .
  • the “monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature 352: 624-28 (1991) and Marks et al., J. Mol. Biol. 222: 581-97 (1991) , for example.
  • a typical 4-chain antibody unit is a heterotetrameric glycoprotein composed of two identical light (L) chains and two identical heavy (H) chains.
  • the 4-chain unit is generally about 150,000 daltons.
  • Each L chain is linked to an H chain by one covalent disulfide bond, while the two H chains are linked to each other by one or more disulfide bonds depending on the H chain isotype.
  • Each H and L chain also has regularly spaced intrachain disulfide bridges.
  • Each H chain has at the N-terminus, a variable domain (VH) followed by three constant domains (CH) for each of the ⁇ and ⁇ chains and four CH domains for ⁇ and ⁇ isotypes.
  • Each L chain has at the N-terminus, a variable domain (VL) followed by a constant domain (CL) at its other end.
  • VL variable domain
  • CL constant domain
  • the V L is aligned with the VH
  • the CL is aligned with the first constant domain of the heavy chain (CH1) .
  • Particular amino acid residues are believed to form an interface between the light chain and heavy chain variable domains.
  • the pairing of a V H and V L together forms a single antigen-binding site.
  • Fab refers to an antibody region that binds to antigens.
  • a conventional IgG usually comprises two Fab regions, each residing on one of the two arms of the Y-shaped IgG structure.
  • Each Fab region is typically composed of one variable region and one constant region of each of the heavy and the light chain. More specifically, the variable region and the constant region of the heavy chain in a Fab region are V H and CH1 regions, and the variable region and the constant region of the light chain in a Fab region are V L and CL regions.
  • the VH, CH1, VL, and CL in a Fab region can be arranged in various ways to confer an antigen binding capability according to the present disclosure.
  • V H and CH1 regions can be on one polypeptide, and V L and CL regions can be on a separate polypeptide, similarly to a Fab region of a conventional IgG.
  • VH, CH1, V L and CL regions can all be on the same polypeptide and oriented in different orders as described in more detail the sections below.
  • variable region refers to a portion of the light or heavy chains of an antibody that is generally located at the amino-terminal of the light or heavy chain and has a length of about 120 to 130 amino acids in the heavy chain and about 100 to 110 amino acids in the light chain, and are used in the binding and specificity of each particular antibody for its particular antigen.
  • the variable region of the heavy chain may be referred to as “VH. ”
  • the variable region of the light chain may be referred to as “VL. ”
  • variable refers to the fact that certain segments of the variable regions differ extensively in sequence among antibodies. The V region mediates antigen binding and defines specificity of a particular antibody for its particular antigen.
  • variable regions consist of less variable (e.g., relatively invariant) stretches called framework regions (FRs) of about 15-30 amino acids separated by shorter regions of greater variability (e.g., extreme variability) called “hypervariable regions” that are each about 9-12 amino acids long.
  • FRs framework regions
  • hypervariable regions that are each about 9-12 amino acids long.
  • the variable regions of heavy and light chains each comprise four FRs, largely adopting a ⁇ sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases form part of, the ⁇ sheet structure.
  • the hypervariable regions in each chain are held together in close proximity by the FRs and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site of antibodies (see, e.g., Kabat et al., Sequences of Proteins of Immunological Interest (5th ed. 1991) ) .
  • the constant regions are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody dependent cellular cytotoxicity (ADCC) and complement dependent cytotoxicity (CDC) .
  • the variable regions differ extensively in sequence between different antibodies.
  • the variable region is a human variable region.
  • variable region residue numbering refers to the numbering system used for heavy chain variable regions or light chain variable regions of the compilation of antibodies in Kabat et al., supra. Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, an FR or CDR of the variable domain.
  • a heavy chain variable domain may include a single amino acid insert (residue 52a according to Kabat) after residue 52 and three inserted residues (e.g., residues 82a, 82b, and 82c, etc. according to Kabat) after residue 82.
  • the Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a “standard” Kabat numbered sequence.
  • the Kabat numbering system is generally used when referring to a residue in the variable domain (approximately residues 1-107 of the light chain and residues 1-113 of the heavy chain) (e.g., Kabat et al., supra) .
  • the “EU numbering system” or “EU index” is generally used when referring to a residue in an immunoglobulin heavy chain constant region (e.g., the EU index reported in Kabat et al., supra) .
  • the “EU index as in Kabat” refers to the residue numbering of the human IgG 1 EU antibody. Other numbering systems have been described, for example, by AbM, Chothia, Contact, IMGT, and AHon.
  • the term “heavy chain” when used in reference to an antibody refers to a polypeptide chain of about 50-70 kDa, wherein the amino-terminal portion includes a variable region of about 120 to 130 or more amino acids, and a carboxy-terminal portion includes a constant region.
  • the constant region can be one of five distinct types, (e.g., isotypes) referred to as alpha ( ⁇ ) , delta ( ⁇ ) , epsilon ( ⁇ ) , gamma ( ⁇ ) , and mu ( ⁇ ) , based on the amino acid sequence of the heavy chain constant region.
  • the distinct heavy chains differ in size: ⁇ , ⁇ , and ⁇ contain approximately 450 amino acids, while ⁇ and ⁇ contain approximately 550 amino acids.
  • IgA immunoglobulin A
  • IgD immunoglobulin D
  • IgE immunoglobulin G
  • IgM immunoglobulin M
  • light chain when used in reference to an antibody refers to a polypeptide chain of about 25 kDa, wherein the amino-terminal portion includes a variable region of about 100 to about 110 or more amino acids, and a carboxy-terminal portion includes a constant region.
  • the approximate length of a light chain is 211 to 217 amino acids.
  • CDR refers to one of three hypervariable regions (H1, H2 or H3) within the non-framework region of the immunoglobulin (Ig or antibody) V H ⁇ -sheet framework, or one of three hypervariable regions (L1, L2 or L3) within the non-framework region of the antibody V L ⁇ -sheet framework.
  • CDR1, CDR2 and CDR3 in V H domain are also referred to as HCDR1, HCDR2 and HCDR3, respectively.
  • CDR1, CDR2 and CDR3 in V L domain are also referred to as LCDR1, LCDR2 and LCDR3, respectively. Accordingly, CDRs are variable region sequences interspersed within the framework region sequences.
  • CDR regions are well known to those skilled in the art and have been defined by well-known numbering systems.
  • the Kabat Complementarity Determining Regions are based on sequence variability and are the most commonly used (see, e.g., Kabat et al., supra; Nick Deschacht et al., J Immunol 2010; 184: 5696-5704) .
  • Chothia refers instead to the location of the structural loops (see, e.g., Chothia and Lesk, J. Mol. Biol. 196: 901-17 (1987) ) .
  • the end of the Chothia CDR-H1 loop when numbered using the Kabat numbering convention varies between H32 and H34 depending on the length of the loop (this is because the Kabat numbering scheme places the insertions at H35A and H35B; if neither 35A nor 35B is present, the loop ends at 32; if only 35A is present, the loop ends at 33; if both 35A and 35B are present, the loop ends at 34) .
  • the AbM hypervariable regions represent a compromise between the Kabat CDRs and Chothia structural loops, and are used by Oxford Molecular’s AbM antibody modeling software (see, e.g., Antibody Engineering Vol. 2 (Kontermann and Dübel eds., 2d ed.
  • IMGT ImMunoGeneTics
  • IG immunoglobulins
  • TCR T-cell receptors
  • MHC major histocompatibility complex
  • CDR complementary determining region
  • individual CDRs e.g., CDR-H1, CDR-H2
  • the scheme for identification of a particular CDR or CDRs is specified, such as the CDR as defined by the IMGT, Kabat, Chothia, or Contact method. In other cases, the particular amino acid sequence of a CDR is given.
  • CDR regions may also be defined by a combination of various numbering systems, e.g., a combination of Kabat and Chothia numbering systems, or a combination of Kabat and IMGT numbering systems. Therefore, the term such as “a CDR1 as set forth in a specific VH” includes any CDR1 as defined by the exemplary CDR numbering systems described above, but is not limited thereby.
  • a variable region e.g., a V H or VL
  • the CDRs of V H H are defined according to Kabat numbering referring to Deschacht et al., 2010. J Immunol 184: 5696-704.
  • Hypervariable regions may comprise “extended hypervariable regions” as follows: 24-36 or 24-34 (L1) , 46-56 or 50-56 (L2) , and 89-97 or 89-96 (L3) in the VL, and 26-35 or 26-35A (H1) , 50-65 or 49-65 (H2) , and 93-102, 94-102, or 95-102 (H3) in the VH.
  • constant region refers to a carboxy terminal portion of the light and heavy chain which is not directly involved in binding of the antibody to antigen but exhibits various effector function, such as interaction with the Fc receptor.
  • the term refers to the portion of an immunoglobulin molecule having a more conserved amino acid sequence relative to the other portion of the immunoglobulin, the variable region, which contains the antigen binding site.
  • the constant region may contain the CH1, CH2, and CH3 regions of the heavy chain and the CL region of the light chain.
  • FR refers to those variable region residues flanking the CDRs. FR residues are present, for example, in chimeric, humanized, human, domain antibodies, diabodies, linear antibodies, and bispecific antibodies. FR residues are those variable domain residues other than the hypervariable region residues or CDR residues.
  • Fc region herein is used to define a C-terminal region of an immunoglobulin heavy chain, including, for example, native sequence Fc regions, recombinant Fc regions, and variant Fc regions. Although the boundaries of the Fc region of an immunoglobulin heavy chain might vary, the human IgG heavy chain Fc region is often defined to stretch from an amino acid residue at position Cys226, or from Pro230, to the carboxyl-terminus thereof.
  • the C-terminal lysine (residue 447 according to the EU numbering system) of the Fc region may be removed, for example, during production or purification of the antibody, or by recombinantly engineering the nucleic acid encoding a heavy chain of the antibody.
  • a composition of intact antibodies may comprise antibody populations with all K447 residues removed, antibody populations with no K447 residues removed, and antibody populations having a mixture of antibodies with and without the K447 residue.
  • a “functional Fc region” possesses an “effector function” of a native sequence Fc region.
  • exemplary “effector functions” include C1q binding; CDC; Fc receptor binding; ADCC; phagocytosis; downregulation of cell surface receptors (e.g., B cell receptor) , etc.
  • effector functions generally require the Fc region to be combined with a binding region or binding domain (e.g., an antibody variable region or domain) and can be assessed using various assays known to those skilled in the art.
  • a “variant Fc region” comprises an amino acid sequence which differs from that of a native sequence Fc region by virtue of at least one amino acid modification (e.g., substituting, addition, or deletion) .
  • the variant Fc region has at least one amino acid substitution compared to a native sequence Fc region or to the Fc region of a parent polypeptide, for example, from about one to about ten amino acid substitutions, or from about one to about five amino acid substitutions in a native sequence Fc region or in the Fc region of a parent polypeptide.
  • the variant Fc region herein can possess at least about 80%homology with a native sequence Fc region and/or with an Fc region of a parent polypeptide, or at least about 90%homology therewith, for example, at least about 95%homology therewith.
  • an “epitope” is a term in the art and refers to a localized region of an antigen to which a binding molecule (e.g., an antibody) can specifically bind.
  • An epitope can be a linear epitope or a conformational, non-linear, or discontinuous epitope.
  • an epitope can be contiguous amino acids of the polypeptide (a “linear” epitope) or an epitope can comprise amino acids from two or more non-contiguous regions of the polypeptide (a “conformational, ” “non-linear” or “discontinuous” epitope) .
  • a linear epitope may or may not be dependent on secondary, tertiary, or quaternary structure.
  • a binding molecule binds to a group of amino acids regardless of whether they are folded in a natural threedimensional protein structure.
  • a binding molecule requires amino acid residues making up the epitope to exhibit a particular conformation (e.g., bend, twist, turn or fold) in order to recognize and bind the epitope.
  • down-modulation when used in the context of a target protein (e.g., endogenous CD38 or CD7) in cells refers to down-regulate or reduce expression (e.g., cell surface expression) of the target protein, for example, via degradation through, e.g., lysosomal degradation pathway.
  • a target protein e.g., endogenous CD38 or CD7
  • reduce expression e.g., cell surface expression
  • 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 MEGALIGN TM (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.
  • an amino acid sequence thereof disclosed herein comprises amino acid sequences with certain percent identity relative to any sequences provided herein.
  • the determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • a non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, Proc. Natl. Acad. Sci. U.S.A. 87: 2264 2268 (1990) , modified as in Karlin and Altschul, Proc. Natl. Acad. Sci. U.S.A. 90: 5873 5877 (1993) .
  • Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., J.
  • Gapped BLAST can be utilized as described in Altschul et al., Nucleic Acids Res. 25: 3389 3402 (1997) .
  • PSI BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id. ) .
  • the default parameters of the respective programs e.g., of XBLAST and NBLAST
  • NCBI National Center for Biotechnology Information
  • Another non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, CABIOS 4: 11-17 (1998) .
  • Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package.
  • a PAM120 weight residue table When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.
  • the percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
  • the term “specificity” refers to selective recognition of an antigen binding protein (such as a CAR or an antibody) for a particular epitope of an antigen. Natural antibodies, for example, are monospecific.
  • the term “multispecific” as used herein denotes that an antigen binding protein (such as a CAR or an antibody) has two or more antigen-binding sites of which at least two bind different antigens.
  • Bispecific as used herein denotes that an antigen binding protein (such as a CAR or an antibody) has two different antigen-binding specificities.
  • the term “monospecific” CAR as used herein denotes an antigen binding protein (such as a CAR or an antibody) that has one or more binding sites each of which bind the same antigen.
  • valent denotes the presence of a specified number of binding sites in an antigen binding protein (such as a CAR or an antibody) .
  • a natural antibody for example or a full length antibody has two binding sites and is bivalent.
  • trivalent tetravalent
  • pentavalent hexavalent
  • CAR Chimeric antigen receptor
  • CAR genetically engineered receptors, which can be used to graft one or more antigen specificity onto immune effector cells, such as T cells. Some CARs are also known as “artificial T-cell receptors, ” “chimeric T cell receptors, ” or “chimeric immune receptors. ”
  • the CAR comprises an extracellular antigen binding domain specific for one or more antigens (such as tumor antigens) , a transmembrane domain, and an intracellular signaling domain of a T cell and/or other receptors.
  • CAR-T cell refers to a T cell that expresses a CAR.
  • CAR-NK cell refers to a NK cell that expresses a CAR.
  • polypeptide and “peptide” and “protein” are used interchangeably herein and refer to polymers of amino acids of any length.
  • the polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids.
  • the terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification.
  • polypeptides containing one or more analogs of an amino acid including but not limited to, unnatural amino acids, as well as other modifications known in the art. It is understood that, because the polypeptides of this disclosure may be based upon antibodies or other members of the immunoglobulin superfamily, in certain embodiments, a “polypeptide” can occur as a single chain or as two or more associated chains.
  • Polynucleotide or “nucleic acid, ” as used interchangeably herein, refers to polymers of nucleotides of any length and includes DNA and RNA.
  • the nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase or by a synthetic reaction.
  • a polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs.
  • Oligonucleotide refers to short, generally single-stranded, synthetic polynucleotides that are generally, but not necessarily, fewer than about 200 nucleotides in length.
  • oligonucleotide and “polynucleotide” are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.
  • a cell that produces a binding molecule of the present disclosure may include a parent hybridoma cell, as well as bacterial and eukaryotic host cells into which nucleic acids encoding the antibodies have been introduced.
  • the left-hand end of any single-stranded polynucleotide sequence disclosed herein is the 5’ end; the left-hand direction of double-stranded polynucleotide sequences is referred to as the 5’ direction.
  • the direction of 5’ to 3’ addition of nascent RNA transcripts is referred to as the transcription direction; sequence regions on the DNA strand having the same sequence as the RNA transcript that are 5’ to the 5’ end of the RNA transcript are referred to as “upstream sequences” ; sequence regions on the DNA strand having the same sequence as the RNA transcript that are 3’ to the 3’ end of the RNA transcript are referred to as “downstream sequences. ”
  • an “isolated nucleic acid” is a nucleic acid, for example, a RNA, DNA, or a mixed nucleic acids, which is substantially separated from other genome DNA sequences as well as proteins or complexes such as ribosomes and polymerases, which naturally accompany a native sequence.
  • An “isolated” nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid molecule.
  • an “isolated” nucleic acid molecule, such as a cDNA molecule can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • nucleic acid molecules encoding an antibody as described herein are isolated or purified.
  • the term embraces nucleic acid sequences that have been removed from their naturally occurring environment, and includes recombinant or cloned DNA isolates and chemically synthesized analogues or analogues biologically synthesized by heterologous systems.
  • a substantially pure molecule may include isolated forms of the molecule.
  • an “isolated” nucleic acid molecule encoding a CAR or an antibody described herein is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the environment in which it was produced.
  • nucleotide sequence encoding an amino acid sequence includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence.
  • the phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some versions contain an intron (s) .
  • control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism.
  • the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
  • Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
  • operatively linked, ” and similar phrases when used in reference to nucleic acids or amino acids, refer to the operational linkage of nucleic acid sequences or amino acid sequence, respectively, placed in functional relationships with each other.
  • an operatively linked promoter, enhancer elements, open reading frame, 5' and 3' UTR, and terminator sequences result in the accurate production of a nucleic acid molecule (e.g., RNA) .
  • operatively linked nucleic acid elements result in the transcription of an open reading frame and ultimately the production of a polypeptide (i.e., expression of the open reading frame) .
  • an operatively linked peptide is one in which the functional domains are placed with appropriate distance from each other to impart the intended function of each domain.
  • vector refers to a substance that is used to carry or include a nucleic acid sequence, including for example, a nucleic acid sequence encoding a binding molecule (e.g., an antibody) as described herein, in order to introduce a nucleic acid sequence into a host cell.
  • Vectors applicable for use include, for example, expression vectors, plasmids, phage vectors, viral vectors, episomes, and artificial chromosomes, which can include selection sequences or markers operable for stable integration into a host cell’s chromosome. Additionally, the vectors can include one or more selectable marker genes and appropriate expression control sequences.
  • Selection control sequences can include constitutive and inducible promoters, transcription enhancers, transcription terminators, and the like, which are well known in the art.
  • both nucleic acid molecules can be inserted, for example, into a single expression vector or in separate expression vectors.
  • the encoding nucleic acids can be operationally linked to one common expression control sequence or linked to different expression control sequences, such as one inducible promoter and one constitutive promoter.
  • nucleic acid molecules into a host cell can be confirmed using methods well known in the art. Such methods include, for example, nucleic acid analysis such as Northern blots or polymerase chain reaction (PCR) amplification of mRNA, immunoblotting for expression of gene products, or other suitable analytical methods to test the expression of an introduced nucleic acid sequence or its corresponding gene product. It is understood by those skilled in the art that the nucleic acid molecules are expressed in a sufficient amount to produce a desired product and it is further understood that expression levels can be optimized to obtain sufficient expression using methods well known in the art.
  • nucleic acid analysis such as Northern blots or polymerase chain reaction (PCR) amplification of mRNA
  • immunoblotting for expression of gene products or other suitable analytical methods to test the expression of an introduced nucleic acid sequence or its corresponding gene product.
  • host refers to an animal, such as a mammal (e.g., a human) .
  • host cell refers to a particular subject cell that may be transfected with a nucleic acid molecule and the progeny or potential progeny of such a cell. Progeny of such a cell may not be identical to the parent cell transfected with the nucleic acid molecule due to mutations or environmental influences that may occur in succeeding generations or integration of the nucleic acid molecule into the host cell genome.
  • autologous is meant to refer to any material derived from the same individual to whom it is later to be re-introduced into the individual.
  • Allogeneic refers to a graft derived from a different individual of the same species.
  • transfected or “transformed” or “transduced” as used herein refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell.
  • a “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid.
  • the cell includes the primary subject cell and its progeny.
  • pharmaceutically acceptable means being approved by a regulatory agency of the Federal or a state government, or listed in United States Pharmacopeia, European Pharmacopeia, or other generally recognized Pharmacopeia for use in animals, and more particularly in humans.
  • Excipient means a pharmaceutically-acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, solvent, or encapsulating material.
  • Excipients include, for example, encapsulating materials or additives such as absorption accelerators, antioxidants, binders, buffers, carriers, coating agents, coloring agents, diluents, disintegrating agents, emulsifiers, extenders, fillers, flavoring agents, humectants, lubricants, perfumes, preservatives, propellants, releasing agents, sterilizing agents, sweeteners, solubilizers, wetting agents and mixtures thereof.
  • the term “excipient” can also refer to a diluent, adjuvant (e.g., Freunds’ adjuvant (complete or incomplete) or vehicle.
  • excipients are pharmaceutically acceptable excipients.
  • pharmaceutically acceptable excipients include buffers, such as phosphate, citrate, and other organic acids; antioxidants, including ascorbic acid; low molecular weight (e.g., fewer than about 10 amino acid residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers, such as polyvinylpyrrolidone; amino acids, such as glycine, glutamine, asparagine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates, including glucose, mannose, or dextrins; chelating agents, such as EDTA; sugar alcohols, such as mannitol or sorbitol; salt-forming counterions, such as sodium; and/or nonionic surfactants, such as TWEEN TM , polyethylene glycol (PEG) , and PLURONICS TM .
  • buffers such as phosphate,
  • each component is “pharmaceutically acceptable” in the sense of being compatible with the other ingredients of a pharmaceutical formulation, and suitable for use in contact with the tissue or organ of humans and animals without excessive toxicity, irritation, allergic response, immunogenicity, or other problems or complications, commensurate with a reasonable benefit/risk ratio.
  • pharmaceutically acceptable excipients are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed.
  • a pharmaceutically acceptable excipient is an aqueous pH buffered solution.
  • excipients are sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil, and the like.
  • Water is an exemplary excipient when a composition (e.g., a pharmaceutical composition) is administered intravenously.
  • Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid excipients, particularly for injectable solutions.
  • An excipient can also include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol, and the like.
  • the composition if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.
  • Compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations, and the like.
  • Oral compositions, including formulations can include standard excipients such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc.
  • compositions including pharmaceutical compounds, may contain a binding molecule (e.g., an antibody) , for example, in isolated or purified form, together with a suitable amount of excipients.
  • a binding molecule e.g., an antibody
  • an effective amount or “therapeutically effective amount” as used herein refers to the amount of an antibody or a therapeutic molecule comprising an agent and the antibody or pharmaceutical composition provided herein which is sufficient to result in the desired outcome.
  • a subject is a mammal, such as a non-primate or a primate (e.g., human) .
  • the subject is a human.
  • the subject is a mammal, e.g., a human, diagnosed with a disease or disorder.
  • the subject is a mammal, e.g., a human, at risk of developing a disease or disorder.
  • administer refers to the act of injecting or otherwise physically delivering a substance as it exists outside the body into a patient, such as by mucosal, intradermal, intravenous, intramuscular delivery, and/or any other method of physical delivery described herein or known in the art.
  • treat, ” “treatment” and “treating” refer to the reduction or amelioration of the progression, severity, and/or duration of a disease or condition resulting from the administration of one or more therapies. Treating may be determined by assessing whether there has been a decrease, alleviation and/or mitigation of one or more symptoms associated with the underlying disorder such that an improvement is observed with the patient, despite that the patient may still be afflicted with the underlying disorder.
  • Treating includes both managing and ameliorating the disease.
  • the terms “manage, ” “managing, ” and “management” refer to the beneficial effects that a subject derives from a therapy which does not necessarily result in a cure of the disease.
  • prevent, ” and “prevention” refer to reducing the likelihood of the onset (or recurrence) of a disease, disorder, condition, or associated symptom (s) (e.g., diabetes or a cancer) .
  • “delaying” the development of cancer means to defer, hinder, slow, retard, stabilize, and/or postpone development of the disease. This delay can be of varying lengths of time, depending on the history of the disease and/or individual being treated. As is evident to one skilled in the art, a sufficient or significant delay can, in effect, encompass prevention, in that the individual does not develop the disease.
  • a method that "delays" development of cancer is a method that reduces probability of disease development in a given time frame and/or reduces the extent of the disease in a given time frame, when compared to not using the method. Such comparisons are typically based on clinical studies, using a statistically significant number of individuals.
  • Cancer development can be detectable using standard methods, including, but not limited to, computerized axial tomography (CAT Scan) , Magnetic Resonance Imaging (MRI) , abdominal ultrasound, clotting tests, arteriography, or biopsy. Development may also refer to cancer progression that may be initially undetectable and includes occurrence, recurrence, and onset.
  • the terms “about” and “approximately” mean within 20%, within 15%, within 10%, within 9%, within 8%, within 7%, within 6%, within 5%, within 4%, within 3%, within 2%, within 1%, or less of a given value or range.
  • the present disclosure provides fusion proteins for degradation of target proteins through lysosomal degradation pathway.
  • the present disclosure also provides the polypeptide of the fusion proteins.
  • the fusion proteins comprise (i) an antigen-binding domain that binds to a target protein; and (ii) a lysosome-targeting domain that comprises a lysosome-related membrane protein or a fragment thereof.
  • the presently disclosed fusion proteins comprise an antigen-binding domain that binds to a target protein.
  • the antigen-binding domain comprises an antibody or a fragment thereof.
  • the target protein is expressed on a cell. In certain embodiments, the target protein is expressed on the surface of a cell. In certain embodiments, the target protein is expressed on an immune cell. In certain embodiments, the target protein is expressed on a NK cell or a T cell. In certain embodiments, the target protein is a diseased cell surface antigen, e.g., a tumor antigen. In certain embodiments, the target protein is a tumor-associated antigen (an antigen which is also present in other organs and tissues or heterogeneous and allogeneic normal cells, or an antigen which is expressed on the way of development and differentiation) . In some embodiments, the target protein is an immnosuppresive molecule.
  • the target protein is associated with graft-versus-host disease (GvHD) and/or host-versus-graft disease (HvGD) in a cell therapy.
  • target proteins bound by the antigen-binding domain of the presently disclosed fusion protein include CD38, CD7, PD-1, TGF-beta receptor, Killer-cell immunoglobulin-like receptor, CS-1, TCR, CD3, CD4, CD5, CD8, CD25, CD30, CD52, CD56, CD70, 4-1BB, NKG2A, NKG2D, CD16, CD138, SLAM family members (such as 2B4, Ly-9, CD84 and CD319) , CD226, Kir family members (such as KIR2DL1, KIR2DS1, KIR2DL2/L3, KIR2DS2, KIR2DS4, KIR3DL1, and KIR3DL2) , the natural cytotoxicity receptors (such as NKp30, NKp44 and NKp46) , TIM3, TIGIT,
  • the target protein is CD38.
  • CD38 also known as cyclic ADP ribose hydrolase, is a glycoprotein expressed on the surface of plasma cells and other lymphoid and myeloid cell populations, including T cells, B cells, and NK cells. CD38 is also expressed at a high level on myeloma cells, and thus is a good target of immunotherapeutic strategies for treating multiple myeloma.
  • the target protein is CD7.
  • CD7 also known as GP40, TP41, Tp40, and LEU-9, is expressed on thymocytes, mature T cells, and NK cells. It plays an essential role in T-cell interactions and also in T-cell/B-cell interaction during early lymphoid development.
  • the antigen-binding domain comprises an antibody or an antibody fragment thereof that binds to the target protein.
  • antibody also includes various antibody fragments thereof.
  • Antibodies provided herein include, but are not limited to, immunoglobulin molecules and immunologically active portions of immunoglobulin molecules.
  • the immunoglobulin molecules provided herein can be of any class (e.g., IgG, IgE, IgM, IgD, and IgA) or any subclass (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2) of immunoglobulin molecule.
  • the antibody is an IgG antibody.
  • the IgG antibody is an IgG1 antibody.
  • the IgG antibody is an IgG2, IgG3, or IgG4 antibody.
  • the antigen-binding domain comprises an antibody fragments that binds to the target protein.
  • Non-limiting exemplary antibody fragments that can be used with the present disclosure include Fab, Fab’, F (ab’) 2 , scFv, Fv, dsFv, sdAb, V H H, V NAR , nanobodies, diabodies, triabodies, tetrabodies, Fab2, Fab3, and combinations thereof.
  • Single domain antibody also known as sdAb, is a single antigen-binding polypeptide having three complementary determining regions (CDRs) .
  • the sdAb alone is capable of binding to the antigen without pairing with a corresponding CDR-containing polypeptide.
  • Examples of sdAb include, but are not limited to, antibodies naturally devoid of light chains such as those from Camelidae species (e.g., V H H) and Elasmobranchii (e.g., V NAR ) , single domain antibodies derived from conventional 4-chain antibodies, human single-domain antibodies produced by transgenic mice or rats expressing human heavy chain segments, and engineered antibodies and single domain scaffolds other than those derived from antibodies.
  • a single domain antibody can be derived from antibodies raised in Camelidae species, for example in camel, llama, dromedary, alpaca and guanaco. Other species besides Camelidae (e.g., sharks) may produce heavy chain antibodies naturally devoid of light chain. Any sdAbs known in the art or developed by the present disclosure, including the single domain antibodies described in the present disclosure, may be used to construct the fusion protein described herein.
  • Nanobody is the variable domain of heavy-chain-only antibody (HcAb) .
  • HcAb heavy-chain-only antibody
  • Examples of nanobodies include V H H and V NAR.
  • V H H variable domain derived from a HcAb naturally devoid of light chain
  • a V H H molecule can be derived from antibodies raised in Camelidae species, for example, camel, llama, vicuna, dromedary, alpaca and guanaco.
  • Camelidae species for example, camel, llama, vicuna, dromedary, alpaca and guanaco.
  • Other species besides Camelidae may produce heavy chain molecules naturally devoid of light chain, and such V H Hs are within the scope of the present disclosure.
  • humanized versions of V H Hs as well as other modifications and variants are also contemplated and within the scope of the present disclosure.
  • Camelid sdAb i.e., V H H
  • V H H is one of the smallest known antigen-binding antibody fragments (see, e.g., Hamers-Casterman et al., Nature 363: 446-8 (1993) ; Greenberg et al., Nature 374: 168-73 (1995) ; Hassanzadeh-Ghassabeh et al., Nanomedicine (Lond) , 8: 1013-26 (2013) ) .
  • a basic V H H has the following structure from the N-terminus to the C-terminus: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4, in which FR1 to FR4 refer to framework regions 1 to 4, respectively, and in which CDR1 to CDR3 refer to the complementarity determining regions 1 to 3.
  • sdAbs e.g., V H Hs
  • V NAR is the variable domain of IgNAR, which is an unconventional antibody identified in sharks and other cartilaginous fish. IgNAR exists in a homodimer that is naturally devoid of light chain. Each chain in IgNAR consists of five constant domains followed by one variable domain. V NAR contains only two complementarity-determining regions (CDRs) , as known as CDR1 and CDR3. See Cheong et al.., Int J Biol Macromol. 2020; 147: 369–375 for a review of V NAR , the content of which is incorporated by reference in its entirety.
  • CDRs complementarity-determining regions
  • Fab refers to an antibody fragment containing a single antigen-binding domain comprising a Fab and an additional portion of the heavy chain through the hinge region) .
  • F (ab’) 2 refers to an antibody fragment containing two Fab’ molecules joined by interchain disulfide bonds in the hinge regions of the heavy chains.
  • the Fab’ molecules may be directed toward the same or different epitopes.
  • Single chain variable fragment also known as scFv, is an antibody fragment that comprises the V H and V L antibody domains connected into a single polypeptide chain.
  • the scFv further comprises a polypeptide linker between the V H and V L domains which enables the scFv to form the desired structure for antigen binding.
  • Bispecific scFv or a dsFv is an antibody fragment having two antigen-binding domains, each of which can be directed to a different epitope.
  • Disulfide-linked Fv also known as dsFv, is an antibody fragment where the variable, antigen-binding determinative regions of a single light and heavy chain of an antibody are linked together by a disulfide bond.
  • Diabody is a dimerized scFv which is formed when the V H domain of a first scFv assembles with the V L domain of a second scFv and the V L domain of the first scFv assembles with the V H domain of the second scFv.
  • the two antigen-binding regions of the diabody can be directed towards the same or different epitopes.
  • Triabody is a trimerized scFv, formed in a manner similar to a diabody, but in which three antigen-binding domains are created in a single complex.
  • the three antigen binding domains can be directed towards the same or different epitopes.
  • Tetrabody is tetramerized scFv, formed in a manner similar to a diabody, but in which four antigen-binding domains are created in a single complex.
  • the four antigen binding domains may be directed towards the same or different epitopes.
  • an antibody is a single chain Fv fragment (scFv) (see, e.g., WO 93/16185; U.S. Pat. Nos.
  • Fv and scFv have intact combining sites that are devoid of constant regions; thus, they may be suitable for reduced nonspecific binding during in vivo use.
  • scFv fusion proteins may be constructed to yield fusion of an effector protein at either the amino or the carboxy terminus of an scFv (See, e.g., Borrebaeck ed., supra) .
  • the antibody fragment may also be a “linear antibody, ” for example, as described in the references cited above. Such linear antibodies may be monospecific or multi-specific, such as bispecific.
  • the presently disclosed antigen-binding domain comprises an antibody fragment.
  • Table 2 below provides the amino acid sequences of exemplary antibody fragments. The CDRs are defined according to Kabat numbering.
  • the antibody fragment comprises an scFv.
  • the scFv binds to CD38.
  • An exemplary anti-CD38 scFv is designated as “CD38-1 binding domain” , as disclosed in Examples of the present disclosure.
  • the anti-CD38 scFv comprises the HCDR1, HCDR2, and HCDR3 of SEQ ID NO: 52; and/or the LCDR1, LCDR2, and LCDR3 of SEQ ID NO: 53. In certain embodiments, the anti-CD38 scFv comprises the HCDR1, HCDR2, and HCDR3 of SEQ ID NO: 52; and the LCDR1, LCDR2, and LCDR3 of SEQ ID NO: 53.
  • the anti-CD38 scFv comprises an HCDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 34, an HCDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 35, and an HCDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 36, and a LCDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 37, a LCDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 38, and a LCDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 39.
  • the anti-CD38 scFv comprises a VH domain comprising an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 52; and/or a VL domain comprising an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at
  • the anti-CD38 scFv comprises a VH domain comprising the amino acid sequence of SEQ ID NO: 52 and a VL domain comprising the amino acid sequence of SEQ ID NO: 53.
  • the anti-CD38 scFv comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 19.
  • the anti-CD38 scFv comprises the amino acid sequence of SEQ ID NO: 19.
  • the antibody fragment comprises at least one sdAb.
  • the sdAb comprise an V H H.
  • the antibody fragment comprises one sdAb.
  • the sdAb comprise an anti-CD38 V H H.
  • An exemplary anti-CD38 V H H is designated as “CD38-2 binding domain” , as disclosed in Examples of the present disclosure.
  • the anti-CD38 V H H is an anti-CD38 V H H disclosed in International Patent Publication No. WO2017081211, the content of which is incorporated by reference in its entirety.
  • the anti-CD38 V H H is an anti-CD38 V H H disclosed in International Patent Publication No. WO201702503, the content of which is incorporated by reference in its entirety.
  • the anti-CD38 V H H comprises the CDR1, CDR2, and CDR3 of SEQ ID NO: 20, SEQ ID NO: 54 or SEQ ID NO: 55.
  • the anti-CD38 V H H comprises a CDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 40, a CDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 41, and a CDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 42.
  • the anti-CD38 V H H comprises a CDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 43, a CDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 44, and a CDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 45.
  • the anti-CD38 V H H comprises a CDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 46, a CDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 47, and a CDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 48.
  • the anti-CD38 V H H comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 20, SEQ ID NO: 54 or SEQ ID NO: 55.
  • the anti-CD38 V H H comprises the amino acid sequence of SEQ ID NO: 20, SEQ ID NO: 54 or SEQ ID NO: 55.
  • the antibody fragment comprises two sdAbs.
  • each of the two sdAbs comprises an V H H that binds to CD38.
  • the antibody fragment comprises a first anti-CD38 V H H (V H H1) , and a second anti-CD38 V H H (V H H2) .
  • An exemplary anti-CD38 antibody fragment comprising two sdAbs is designated as “CD38-3 binding domain” , as disclosed in the Examples of the present disclosure.
  • the anti-CD38 antibody fragment is an anti-CD38 antibody fragment disclosed in International Patent Publication No. WO201702503, the content of which is incorporated by reference in its entirety.
  • the anti-CD38 V H H1 comprises the CDR1, CDR2, and CDR3 of SEQ ID NO: 54.
  • the anti-CD38 V H H1 comprises a CDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 43, a CDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 44, and a CDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 45.
  • the anti-CD38 V H H1 comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 54.
  • the anti-CD38 V H H1 comprises the amino acid sequence of SEQ ID NO: 54.
  • the anti-CD38 V H H2 comprises the CDR1, CDR2, and CDR3 of SEQ ID NO: 55.
  • the anti-CD38 V H H2 comprises a CDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 46, a CDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 47, and a CDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 48.
  • the anti-CD38 V H H2 comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 55.
  • the anti-CD38 V H H2 comprises the amino acid sequence of SEQ ID NO: 55.
  • the antibody fragment comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 21.
  • the antibody fragment comprises the amino acid sequence of SEQ ID NO: 21.
  • the antibody fragment binds to CD7.
  • the antibody fragment comprises an sdAb that binds to CD7.
  • the sdAb is an V H H.
  • An exemplary anti-CD7 V H H is designated as “CD7 V H H” , as disclosed in Examples of the present disclosure.
  • the anti-CD7 V H H is an anti-CD7 V H H disclosed in International Patent Publication No. WO2020135870, the content of which is incorporated by reference in its entirety.
  • the anti-CD7 V H H comprises the CDR1, CDR2, and CDR3 of SEQ ID NO: 22.
  • the anti-CD7 V H H comprises a CDR1 comprising or consisting of the amino acid sequence of SEQ ID NO: 49, a CDR2 comprising or consisting of the amino acid sequence of SEQ ID NO: 50, and a CDR3 comprising or consisting of the amino acid sequence of SEQ ID NO: 51.
  • the anti-CD7 V H H comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 22.
  • the anti-CD7 V H H comprises the amino acid sequence of SEQ ID NO: 22.
  • the antibody provide herein contains substitutions (e.g., conservative substitutions) , insertions, or deletions relative to the reference sequence, but the antibody comprising that sequence retains the ability to bind to the target protein.
  • substitutions e.g., conservative substitutions
  • a total of 1 to 10 amino acids have been substituted, inserted and/or deleted in a reference amino acid sequence.
  • substitutions, insertions, or deletions occur in regions outside the CDRs (i.e., in the FRs) .
  • the antibody provided herein includes post-translational modifications of a reference sequence.
  • CDR sequences can be determined according to well-known numbering systems.
  • the CDRs are according to IMGT numbering.
  • the CDRs are according to Kabat numbering.
  • the CDRs are according to AbM numbering.
  • the CDRs are according to Chothia numbering.
  • the CDRs are according to Contact numbering.
  • the antibody fragment is humanized.
  • the antibody fragment comprises an acceptor human framework, e.g., a human immunoglobulin framework or a human consensus framework.
  • humanized antibodies can be generated using the method exemplified in the section below.
  • Framework regions described herein are determined based upon the boundaries of the CDR numbering system. In other words, if the CDRs are determined by, e.g., Kabat, IMGT, or Chothia, then the framework regions are the amino acid residues surrounding the CDRs in the variable region in the format, from the N-terminus to C-terminus: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4.
  • FR1 is defined as the amino acid residues N-terminal to the CDR1 amino acid residues as defined by, e.g., the Kabat numbering system, the IMGT numbering system, or the Chothia numbering system
  • FR2 is defined as the amino acid residues between CDR1 and CDR2 amino acid residues as defined by, e.g., the Kabat numbering system, the IMGT numbering system, or the Chothia numbering system
  • FR3 is defined as the amino acid residues between CDR2 and CDR3 amino acid residues as defined by, e.g., the Kabat numbering system, the IMGT numbering system, or the Chothia numbering system
  • FR4 is defined as the amino acid residues C-terminal to the CDR3 amino acid residues as defined by, e.g., the Kabat numbering system, the IMGT numbering system, or the Chothia numbering system.
  • the antibodies described herein include humanized antibodies.
  • Humanized antibodies such as the humanized antibodies disclosed herein can be produced using a variety of techniques known in the art, including but not limited to, CDR-grafting (European Patent No. EP 239, 400; International publication No. WO 91/09967; and U.S. Patent Nos. 5,225,539, 5,530,101, and 5,585,089) , veneering or resurfacing (European Patent Nos.
  • antibodies provided herein can be humanized antibodies.
  • Various methods for humanizing non-human antibodies are known in the art.
  • a humanized antibody can have one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain.
  • Humanization may be performed, for example, following the method of Jones et al., Nature 321: 522-25 (1986) ; Riechmann et al., Nature 332: 323-27 (1988) ; and Verhoeyen et al., Science 239: 1534-36 (1988) ) , by substituting hypervariable region sequences for the corresponding sequences of a human antibody.
  • humanization of the antibody provided herein is performed as described in the sections below.
  • the humanized antibodies are constructed by CDR grafting, in which the amino acid sequences of the CDRs of the parent non-human antibody are grafted onto a human antibody framework.
  • CDR grafting in which the amino acid sequences of the CDRs of the parent non-human antibody are grafted onto a human antibody framework.
  • Padlan et al. determined that only about one third of the residues in the CDRs actually contact the antigen, and termed these the “specificity determining residues, ” or SDRs (Padlan et al., FASEB J. 9: 133-39 (1995) ) .
  • SDR grafting only the SDR residues are grafted onto the human antibody framework (see, e.g., Kashmiri et al., Methods 36: 25-34 (2005) ) .
  • variable domains can be important to reduce antigenicity.
  • sequence of the variable domain of a non-human antibody is screened against the entire library of known human variable-domain sequences.
  • the human sequence that is closest to that of the non-human antibody may be selected as the human framework for the humanized antibody (Sims et al., J. Immunol. 151: 2296-308 (1993) ; and Chothia et al., J. Mol. Biol. 196: 901-17 (1987) ) .
  • Another method uses a particular framework derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains.
  • the same framework may be used for several different humanized antibodies (Carter et al., Proc. Natl. Acad. Sci. USA 89: 4285-89 (1992) ; and Presta et al., J. Immunol. 151: 2623-32 (1993) ) .
  • the framework is derived from the consensus sequences of the most abundant human subclasses, V L 6 subgroup I (V L 6I) and VH subgroup III (V H III) .
  • human germline genes are used as the source of the framework regions.
  • FR homology is irrelevant.
  • the method consists of comparison of the non-human sequence with the functional human germline gene repertoire. Those genes encoding the same or closely related canonical structures to the murine sequences are then selected. Next, within the genes sharing the canonical structures with the non-human antibody, those with highest homology within the CDRs are chosen as FR donors. Finally, the non-human CDRs are grafted onto these FRs (see, e.g., Tan et al., J. Immunol. 169: 1119-25 (2002) ) .
  • humanized antibodies are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences.
  • Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art.
  • Computer programs are available which illustrate and display probable three-dimensional conformational structures of selected candidate immunoglobulin sequences. These include, for example, WAM (Whitelegg and Rees, Protein Eng. 13: 819-24 (2002) ) , Modeller (Sali and Blundell, J. Mol. Biol.
  • FR residues can be selected and combined from the recipient and import sequences so that the desired antibody characteristic, such as increased affinity for the target antigen (s) , is achieved.
  • the hypervariable region residues are directly and most substantially involved in influencing antigen binding.
  • HSC Human String Content
  • Antibody variants may be isolated from phage, ribosome, and yeast display libraries as well as by bacterial colony screening (see, e.g., Hoogenboom, Nat. Biotechnol. 23: 1105-16 (2005) ; Dufner et al., Trends Biotechnol. 24: 523-29 (2006) ; Feldhaus et al., Nat. Biotechnol. 21: 163-70 (2003) ; and Schlapschy et al., Protein Eng. Des. Sel. 17: 847-60 (2004) ) .
  • residues to be substituted may include some or all of the “Vernier” residues identified as potentially contributing to CDR structure (see, e.g., Foote and Winter, J. Mol. Biol. 224: 487-99 (1992) ) , or from the more limited set of target residues identified by Baca et al. J. Biol. Chem. 272: 10678-84 (1997) .
  • FR shuffling whole FRs are combined with the non-human CDRs instead of creating combinatorial libraries of selected residue variants (see, e.g., Dall’Acqua et al., Methods 36: 43-60 (2005) ) .
  • a one-step FR shuffling process may be used. Such a process has been shown to be efficient, as the resulting antibodies exhibited improved biochemical and physicochemical properties including enhanced expression, increased affinity, and thermal stability (see, e.g., Damschroder et al., Mol. Immunol. 44: 3049-60 (2007) ) .
  • the “humaneering” method is based on experimental identification of essential minimum specificity determinants (MSDs) and is based on sequential replacement of non-human fragments into libraries of human FRs and assessment of binding. This methodology typically results in epitope retention and identification of antibodies from multiple subclasses with distinct human V-segment CDRs.
  • the “human engineering” method involves altering a non-human antibody or antibody fragment by making specific changes to the amino acid sequence of the antibody so as to produce a modified antibody with reduced immunogenicity in a human that nonetheless retains the desirable binding properties of the original non-human antibodies.
  • the technique involves classifying amino acid residues of a non-human antibody as “low risk, ” “moderate risk, ” or “high risk” residues. The classification is performed using a global risk/reward calculation that evaluates the predicted benefits of making particular substitution (e.g., for immunogenicity in humans) against the risk that the substitution will affect the resulting antibody’s folding.
  • the particular human amino acid residue to be substituted at a given position (e.g., low or moderate risk) of a non-human antibody sequence can be selected by aligning an amino acid sequence from the non-human antibody’s variable regions with the corresponding region of a specific or consensus human antibody sequence.
  • the amino acid residues at low or moderate risk positions in the non-human sequence can be substituted for the corresponding residues in the human antibody sequence according to the alignment.
  • a composite human antibody can be generated using, for example, Composite Human Antibody TM technology (Antitope Ltd., Cambridge, United Kingdom) .
  • variable region sequences are designed from fragments of multiple human antibody variable region sequences in a manner that avoids T cell epitopes, thereby minimizing the immunogenicity of the resulting antibody.
  • a deimmunized antibody is an antibody in which T-cell epitopes have been removed. Methods for making deimmunized antibodies have been described. See, e.g., Jones et al., Methods Mol Biol. 525: 405-23 (2009) , xiv, and De Groot et al., Cell. Immunol. 244: 148-153 (2006) ) .
  • Deimmunized antibodies comprise T-cell epitope-depleted variable regions and human constant regions. Briefly, variable regions of an antibody are cloned and T-cell epitopes are subsequently identified by testing overlapping peptides derived from the variable regions of the antibody in a T cell proliferation assay.
  • T cell epitopes are identified via in silico methods to identify peptide binding to human MHC class II. Mutations are introduced in the variable regions to abrogate binding to human MHC class II. Mutated variable regions are then utilized to generate the deimmunized antibody.
  • amino acid sequence modification (s) of the antibodies comprised in the antigen-binding domains of the fusion proteins are contemplated.
  • variants of the antibodies described herein can be prepared.
  • antibody variants can be prepared by introducing appropriate nucleotide changes into the encoding DNA, and/or by synthesis of the desired antibody or polypeptide. Those skilled in the art who appreciate that amino acid changes may alter post-translational processes of the antibody.
  • the antibodies provided herein are chemically modified, for example, by the covalent attachment of any type of molecule to the antibody.
  • the antibody derivatives may include antibodies that have been chemically modified, for example, by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, or conjugation to one or more immunoglobulin domains (e.g., Fc or a portion of an Fc) . Any of numerous chemical modifications may be carried out by known techniques, including, but not limited to, specific chemical cleavage, acetylation, formulation, metabolic synthesis of tunicamycin, etc. Additionally, the antibody may contain one or more non-classical amino acids.
  • an antibody provided herein is altered to increase or decrease the extent to which the antibody is glycosylated.
  • Addition or deletion of glycosylation sites to an antibody may be conveniently accomplished by altering the amino acid sequence such that one or more glycosylation sites is created or removed.
  • the carbohydrate attached thereto may be altered.
  • Native antibodies produced by mammalian cells typically comprise a branched, biantennary oligosaccharide that is generally attached by an N-linkage to Asn297 of the CH2 domain of the Fc region. See, e.g., Wright et al. TIBTECH 15: 26-32 (1997) .
  • the oligosaccharide may include various carbohydrates, e.g., mannose, N-acetyl glucosamine (GlcNAc) , galactose, and sialic acid, as well as a fucose attached to a GlcNAc in the “stem” of the biantennary oligosaccharide structure.
  • modifications of the oligosaccharide in the binding molecules provided herein may be made in order to create variants with certain improved properties.
  • antibody variants provided herein may have a carbohydrate structure that lacks fucose attached (directly or indirectly) to said Fc region.
  • the amount of fucose in such antibody may be from 1%to 80%, from 1%to 65%, from 5%to 65%or from 20%to 40%.
  • the amount of fucose is determined by calculating the average amount of fucose within the sugar chain at Asn297, relative to the sum of all glycostructures attached to Asn 297 (e.g., complex, hybrid and high mannose structures) as measured by MALDI-TOF mass spectrometry, as described in WO 2008/077546, for example.
  • Asn297 refers to the asparagine residue located at about position 297 in the Fc region (EU numbering of Fc region residues) ; however, Asn297 may also be located about ⁇ 3 amino acids upstream or downstream of position 297, i.e., between positions 294 and 300, due to minor sequence variations in antibodies. Such fucosylation variants may have improved ADCC function. See, e.g., US Patent Publication Nos. US 2003/0157108 and US 2004/0093621.
  • Examples of publications related to “defucosylated” or “fucose-deficient” antibody variants include: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614; US 2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US 2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO 2005/035586; WO 2005/035778; WO2005/053742; WO2002/031140; Okazaki et al. J. Mol. Biol. 336: 1239-1249 (2004) ; Yamane-Ohnuki et al. Biotech.
  • Examples of cell lines capable of producing defucosylated antibodies include Lec13 CHO cells deficient in protein fucosylation (Ripka et al. Arch. Biochem. Biophys. 249: 533-545 (1986) ; US Patent Application No. US 2003/0157108; and WO 2004/056312, and knockout cell lines, such as alpha-1, 6-fucosyltransferase gene, FUT8, knockout CHO cells (see, e.g., Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614 (2004) ; Kanda, Y. et al., Biotechnol. Bioeng., 94 (4) : 680-688 (2006) ; and WO2003/085107) .
  • the binding molecules comprising an antibody provided herein are further provided with bisected oligosaccharides, e.g., in which a biantennary oligosaccharide attached to the Fc region is bisected by GlcNAc.
  • Such variants may have reduced fucosylation and/or improved ADCC function. Examples of such variants are described, e.g., in WO 2003/011878 (Jean-Mairet et al. ) ; US Patent No. 6,602,684 (Umana et al. ) ; and US 2005/0123546 (Umana et al. ) .
  • Variants with at least one galactose residue in the oligosaccharide attached to the Fc region are also provided. Such variants may have improved CDC function. Such variants are described, e.g., in WO 1997/30087; WO 1998/58964; and WO 1999/22764.
  • the Fc region variant may comprise a human Fc region sequence (e.g., a human IgG1, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g., a substitution) at one or more amino acid positions.
  • a human Fc region sequence e.g., a human IgG1, IgG2, IgG3 or IgG4 Fc region
  • an amino acid modification e.g., a substitution
  • the present application contemplates variants that possesses some but not all effector functions, which make it a desirable candidate for applications in which the half-life of the binding molecule in vivo is important yet certain effector functions (such as complement and ADCC) are unnecessary or deleterious.
  • In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/depletion of CDC and/or ADCC activities.
  • Fc receptor (FcR) binding assays can be conducted to ensure that the binding molecule lacks Fc ⁇ R binding (hence likely lacking ADCC activity) , but retains FcRn binding ability.
  • FcR Fc receptor
  • Patent No. 5,500,362 see, e.g. Hellstrom, I. et al. Proc. Nat’l Acad. Sci. USA 83: 7059-7063 (1986) ) and Hellstrom, I et al., Proc. Nat’l Acad. Sci. USA 82: 1499-1502 (1985) ; 5, 821, 337 (see Bruggemann, M. et al., J. Exp. Med. 166: 1351-1361 (1987) ) .
  • non-radioactive assays methods may be employed (see, for example, ACTI TM non-radioactive cytotoxicity assay for flow cytometry (CellTechnology, Inc.
  • PBMC peripheral blood mononuclear cells
  • NK Natural Killer
  • ADCC activity of the molecule of interest may be assessed in vivo, e.g., in an animal model such as that disclosed in Clynes et al. Proc. Nat’l Acad. Sci. USA 95: 652-656 (1998) .
  • C1q binding assays may also be carried out to confirm that the antibody is unable to bind C1q and hence lacks CDC activity.
  • a CDC assay may be performed (see, for example, Gazzano-Santoro et al., J. Immunol. Methods 202: 163 (1996) ; Cragg, M.S. et al., Blood 101: 1045-1052 (2003) ; and Cragg, M.S. and M.J. Glennie, Blood 103: 2738-2743 (2004) ) .
  • FcRn binding and in vivo clearance/half-life determinations can also be performed using methods known in the art (see, e.g., Petkova, S.B. et al., Int’l. Immunol. 18 (12) : 1759-1769 (2006) ) .
  • Binding molecules with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Patent No. 6,737,056) .
  • Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called “DANA” Fc mutant with substitution of residues 265 and 297 to alanine (US Patent No. 7,332,581) .
  • a variant comprises an Fc region with one or more amino acid substitutions which improve ADCC, e.g., substitutions at positions 298, 333, and/or 334 of the Fc region (EU numbering of residues) .
  • alterations are made in the Fc region that result in altered (i.e., either improved or diminished) C1q binding and/or Complement Dependent Cytotoxicity (CDC) , e.g., as described in US Patent No. 6,194,551, WO 99/51642, and Idusogie et al. J. Immunol. 164: 4178-4184 (2000) .
  • CDC Complement Dependent Cytotoxicity
  • Binding molecules with increased half-lives and improved binding to the neonatal Fc receptor (FcRn) which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 117: 587 (1976) and Kim et al., J. Immunol. 24: 249 (1994) ) , are described in US2005/0014934A1 (Hinton et al. ) . Those molecules comprise an Fc region with one or more substitutions therein which improve binding of the Fc region to FcRn.
  • Such Fc variants include those with substitutions at one or more of Fc region residues: 238, 256, 265, 272, 286, 303, 305, 307, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424 or 434, e.g., substitution of Fc region residue 434 (US Patent No. 7,371,826) . See also Duncan &Winter, Nature 322: 738-40 (1988) ; U.S. Patent No. 5,648,260; U.S. Patent No. 5,624,821; and WO 94/29351 concerning other examples of Fc region variants.
  • cysteine engineered antibodies in which one or more residues of an antibody are substituted with cysteine residues.
  • the substituted residues occur at accessible sites of the antibody.
  • reactive thiol groups are thereby positioned at accessible sites of the antibody and may be used to conjugate the antibody to other moieties, such as drug moieties or linker-drug moieties, to create an immunoconjugate, as described further herein.
  • Variations may be a substitution, deletion, or insertion of one or more codons encoding the antibody or polypeptide that results in a change in the amino acid sequence as compared with the original antibody or polypeptide.
  • Sites of interest for substitutional mutagenesis include the CDRs and FRs.
  • Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, e.g., conservative amino acid replacements.
  • Standard techniques known to those of skill in the art can be used to introduce mutations in the nucleotide sequence encoding a molecule provided herein, including, for example, site-directed mutagenesis and PCR-mediated mutagenesis which results in amino acid substitutions. Insertions or deletions may optionally be in the range of about 1 to 5 amino acids.
  • the substitution, deletion, or insertion includes fewer than 25 amino acid substitutions, fewer than 20 amino acid substitutions, fewer than 15 amino acid substitutions, fewer than 10 amino acid substitutions, fewer than 5 amino acid substitutions, fewer than 4 amino acid substitutions, fewer than 3 amino acid substitutions, or fewer than 2 amino acid substitutions relative to the original molecule.
  • the substitution is a conservative amino acid substitution made at one or more predicted non-essential amino acid residues. The variation allowed may be determined by systematically making insertions, deletions, or substitutions of amino acids in the sequence and testing the resulting variants for activity exhibited by the parental antibodies.
  • Amino acid sequence insertions include amino-and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing multiple residues, as well as intrasequence insertions of single or multiple amino acid residues.
  • terminal insertions include an antibody with an N-terminal methionyl residue.
  • Antibodies generated by conservative amino acid substitutions are included in the present disclosure.
  • a conservative amino acid substitution an amino acid residue is replaced with an amino acid residue having a side chain with a similar charge.
  • families of amino acid residues having side chains with similar charges have been defined in the art.
  • amino acids with basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid, glutamic acid
  • uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine
  • nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan
  • beta-branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
  • mutations can be introduced randomly along all or part of the coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for biological activity to identify mutants that retain activity.
  • the encoded protein can be expressed and the activity of the protein can be determined.
  • Conservative (e.g., within an amino acid group with similar properties and/or side chains) substitutions may be made, so as to maintain or not significantly change the properties. Exemplary substitutions are shown in Table 3 below.
  • Amino acids may be grouped according to similarities in the properties of their side chains (see, e.g., Lehninger, Biochemistry 73-75 (2d ed. 1975) ) : (1) non-polar: Ala (A) , Val (V) , Leu (L) , Ile (I) , Pro (P) , Phe (F) , Trp (W) , Met (M) ; (2) uncharged polar: Gly (G) , Ser (S) , Thr (T) , Cys (C) , Tyr (Y) , Asn (N) , Gln (Q) ; (3) acidic: Asp (D) , Glu (E) ; and (4) basic: Lys (K) , Arg (R) , His(H) .
  • Naturally occurring residues may be divided into groups based on common side-chain properties: (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; and (6) aromatic: Trp, Tyr, Phe.
  • any cysteine residue not involved in maintaining the proper conformation of the antibody also may be substituted, for example, with another amino acid, such as alanine or serine, to improve the oxidative stability of the molecule and to prevent aberrant crosslinking.
  • Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
  • substitutional variant involves substituting one or more hypervariable region residues of a parent antibody (e.g., a humanized or human antibody) .
  • a parent antibody e.g., a humanized or human antibody
  • the resulting variant (s) selected for further study will have modifications (e.g., improvements) in certain biological properties (e.g., increased affinity, reduced immunogenicity) relative to the parent antibody and/or will have substantially retained certain biological properties of the parent antibody.
  • An exemplary substitutional variant is an affinity matured antibody, which may be conveniently generated, e.g., using phage display-based affinity maturation techniques such as those described herein. Briefly, one or more CDR residues are mutated and the variant antibodies displayed on phage and screened for a particular biological activity (e.g. binding affinity) .
  • Alterations may be made in CDRs, e.g., to improve antibody affinity. Such alterations may be made in CDR “hotspots, ” i.e., residues encoded by codons that undergo mutation at high frequency during the somatic maturation process (see, e.g., Chowdhury, Methods Mol. Biol. 207: 179-196 (2008) ) , and/or SDRs (a-CDRs) , with the resulting variant antibody or fragment thereof being tested for binding affinity.
  • CDR “hotspots i.e., residues encoded by codons that undergo mutation at high frequency during the somatic maturation process (see, e.g., Chowdhury, Methods Mol. Biol. 207: 179-196 (2008) )
  • SDRs a-CDRs
  • affinity maturation diversity is introduced into the variable genes chosen for maturation by any of a variety of methods (e.g., error-prone PCR, chain shuffling, or oligonucleotide-directed mutagenesis) .
  • a secondary library is then created. The library is then screened to identify any antibody variants with the desired affinity.
  • Another method to introduce diversity involves CDR-directed approaches, in which several CDR residues (e.g., 4-6 residues at a time) are randomized. CDR residues involved in antigen binding may be specifically identified, e.g., using alanine scanning mutagenesis or modeling. More detailed description regarding affinity maturation is provided in the section below.
  • substitutions, insertions, or deletions may occur within one or more CDRs so long as such alterations do not substantially reduce the ability of the antibody to bind antigen.
  • conservative alterations e.g., conservative substitutions as provided herein
  • binding affinity may be made in CDRs.
  • each CDR either is unaltered, or contains no more than one, two or three amino acid substitutions.
  • a useful method for identification of residues or regions of an antibody that may be targeted for mutagenesis is called “alanine scanning mutagenesis” as described by Cunningham and Wells, Science, 244: 1081-1085 (1989) .
  • a residue or group of target residues e.g., charged residues such as Arg, Asp, His, Lys, and Glu
  • a neutral or negatively charged amino acid e.g., alanine or polyalanine
  • Further substitutions may be introduced at the amino acid locations demonstrating functional sensitivity to the initial substitutions.
  • a crystal structure of an antigen-antibody complex to identify contact points between the antibody and antigen. Such contact residues and neighboring residues may be targeted or eliminated as candidates for substitution.
  • Variants may be screened to determine whether they contain the desired properties.
  • Amino acid sequence insertions include amino-and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues.
  • terminal insertions include an antibody with an N-terminal methionyl residue.
  • Other insertional variants of the antibody molecule include the fusion to the N-or C-terminus of the antibody to an enzyme (e.g., for ADEPT) or a polypeptide which increases the serum half-life of the antibody.
  • the variations can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis.
  • Site-directed mutagenesis see, e.g., Carter, Biochem J. 237: 1-7 (1986) ; and Zoller et al., Nucl. Acids Res. 10: 6487-500 (1982)
  • cassette mutagenesis see, e.g., Wells et al., Gene 34: 315-23 (1985)
  • other known techniques can be performed on the cloned DNA to produce the antibody variant DNA.
  • antibody variants having an improved property such as affinity, stability, or expression level as compared to a parent antibody may be prepared by in vitro affinity maturation.
  • in vitro affinity maturation is based on the principles of mutation and selection.
  • Libraries of antibodies are displayed on the surface of an organism (e.g., phage, bacteria, yeast, or mammalian cell) or in association (e.g., covalently or non-covalently) with their encoding mRNA or DNA.
  • Affinity selection of the displayed antibodies allows isolation of organisms or complexes carrying the genetic information encoding the antibodies.
  • Two or three rounds of mutation and selection using display methods such as phage display usually results in antibody fragments with affinities in the low nanomolar range.
  • Affinity matured antibodies can have nanomolar or even picomolar affinities for the target antigen.
  • Phage display is a widespread method for display and selection of antibodies.
  • the antibodies are displayed on the surface of Fd or M13 bacteriophages as fusions to the bacteriophage coat protein.
  • Selection involves exposure to antigen to allow phage-displayed antibodies to bind their targets, a process referred to as “panning. ”
  • Phage bound to antigen are recovered and used to infect bacteria to produce phage for further rounds of selection. For review, see, for example, Hoogenboom, Methods. Mol. Biol. 178: 1-37 (2002) ; and Bradbury and Marks, J. Immunol. Methods 290: 29-49 (2004) .
  • the antibody may be fused to the adhesion subunit of the yeast agglutinin protein Aga2p, which attaches to the yeast cell wall through disulfide bonds to Aga1p.
  • Display of a protein via Aga2p projects the protein away from the cell surface, minimizing potential interactions with other molecules on the yeast cell wall. Magnetic separation and flow cytometry are used to screen the library to select for antibodies with improved affinity or stability.
  • Binding to a soluble antigen of interest is determined by labeling of yeast with biotinylated antigen and a secondary reagent such as streptavidin conjugated to a fluorophore. Variations in surface expression of the antibody can be measured through immunofluorescence labeling of either the hemagglutinin or c-Myc epitope tag flanking the single chain antibody (e.g., scFv) . Expression has been shown to correlate with the stability of the displayed protein, and thus antibodies can be selected for improved stability as well as affinity (see, e.g., Shusta et al., J. Mol. Biol. 292: 949-56 (1999) ) .
  • yeast display An additional advantage of yeast display is that displayed proteins are folded in the endoplasmic reticulum of the eukaryotic yeast cells, taking advantage of endoplasmic reticulum chaperones and quality-control machinery. Once maturation is complete, antibody affinity can be conveniently “titrated” while displayed on the surface of the yeast, eliminating the need for expression and purification of each clone.
  • a theoretical limitation of yeast surface display is the potentially smaller functional library size than that of other display methods; however, a recent approach uses the yeast cells’ mating system to create combinatorial diversity estimated to be 1014 in size (see, e.g., U.S. Pat. Publication 2003/0186374; and Blaise et al., Gene 342: 211–18 (2004) ) .
  • antibody-ribosome-mRNA (ARM) complexes are generated for selection in a cell-free system.
  • the DNA library coding for a particular library of antibodies is genetically fused to a spacer sequence lacking a stop codon. This spacer sequence, when translated, is still attached to the peptidyl tRNA and occupies the ribosomal tunnel, and thus allows the protein of interest to protrude out of the ribosome and fold.
  • the resulting complex of mRNA, ribosome, and protein can bind to surface-bound ligand, allowing simultaneous isolation of the antibody and its encoding mRNA through affinity capture with the ligand.
  • ribosome-bound mRNA is then reverse transcribed back into cDNA, which can then undergo mutagenesis and be used in the next round of selection (see, e.g., Fukuda et al., Nucleic Acids Res. 34: e127 (2006) ) .
  • mRNA display a covalent bond between antibody and mRNA is established using puromycin as an adaptor molecule (Wilson et al., Proc. Natl. Acad. Sci. USA 98: 3750-55 (2001) ) .
  • the diversity of the library is not limited by the transformation efficiency of bacterial cells, but only by the number of ribosomes and different mRNA molecules present in the test tube.
  • random mutations can be introduced easily after each selection round, for example, by non-proofreading polymerases, as no library must be transformed after any diversification step.
  • mammalian display systems may be used.
  • Diversity may also be introduced into the CDRs of the antibody libraries in a targeted manner or via random introduction.
  • the former approach includes sequentially targeting all the CDRs of an antibody via a high or low level of mutagenesis or targeting isolated hot spots of somatic hypermutations (see, e.g., Ho et al., J. Biol. Chem. 280: 607-17 (2005) ) or residues suspected of affecting affinity on experimental basis or structural reasons.
  • Diversity may also be introduced by replacement of regions that are naturally diverse via DNA shuffling or similar techniques (see, e.g., Lu et al., J. Biol. Chem. 278: 43496-507 (2003) ; U.S. Pat. Nos. 5,565,332 and 6,989,250) .
  • Screening of the libraries can be accomplished by various techniques known in the art.
  • antibodies can be immobilized onto solid supports, columns, pins, or cellulose/poly (vinylidene fluoride) membranes/other filters, expressed on host cells affixed to adsorption plates or used in cell sorting, or conjugated to biotin for capture with streptavidin-coated beads or used in any other method for panning display libraries.
  • Covalent modifications of antibodies are included within the scope of the present disclosure. Covalent modifications include reacting targeted amino acid residues of an antibody with an organic derivatizing agent that is capable of reacting with selected side chains or the N-or C-terminal residues of the antibody. Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, respectively, hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the ⁇ -amino groups of lysine, arginine, and histidine side chains (see, e.g., Creighton, Proteins: Structure and Molecular Properties 79-86 (1983) ) , acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group.
  • covalent modification of the antibody included within the scope of this present disclosure include altering the native glycosylation pattern of the antibody or polypeptide as described above (see, e.g., Beck et al., Curr. Pharm. Biotechnol. 9: 482-501 (2008) ; and Walsh, Drug Discov. Today 15: 773-80 (2010) ) , and linking the antibody to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG) , polypropylene glycol, or polyoxyalkylenes, in the manner set forth, for example, in U.S. Pat. Nos.
  • PEG polyethylene glycol
  • polypropylene glycol polypropylene glycol
  • polyoxyalkylenes polyoxyalkylenes
  • the antibody may also be genetically fused or conjugated to one or more immunoglobulin constant regions or portions thereof (e.g., Fc) to extend half-life and/or to impart known Fc-mediated effector functions.
  • Fc immunoglobulin constant regions or portions thereof
  • Antibodies may be obtained using methods known in the art such as by immunizing a Camelid species (such as camel or llama) and obtaining hybridomas therefrom, or by cloning a library of antibodies using molecular biology techniques known in the art and subsequent selection by ELISA with individual clones of unselected libraries or by using phage display.
  • Antibodies provided herein may be produced by culturing cells transformed or transfected with a vector containing an antibody-encoding nucleic acids.
  • Polynucleotide sequences encoding polypeptide components of the antibody of the present disclosure can be obtained using standard recombinant techniques. Desired polynucleotide sequences may be isolated and sequenced from antibody producing cells such as hybridomas cells or B cells. Alternatively, polynucleotides can be synthesized using nucleotide synthesizer or PCR techniques. Once obtained, sequences encoding the polypeptides are inserted into a recombinant vector capable of replicating and expressing heterologous polynucleotides in host cells.
  • Host cells suitable for expressing antibodies of the present disclosure include prokaryotes such as Archaebacteria and Eubacteria, including Gram-negative or Gram-positive organisms, eukaryotic microbes such as filamentous fungi or yeast, invertebrate cells such as insect or plant cells, and vertebrate cells such as mammalian host cell lines.
  • Host cells are transformed with the above-described expression vectors and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • Antibodies produced by the host cells are purified using standard protein purification methods as known in the art.
  • antibodies may be prepared by direct peptide synthesis using solid-phase techniques (see, e.g., Stewart et al., Solid-Phase Peptide Synthesis (1969) ; and Merrifield, J. Am. Chem. Soc. 85:2149-54 (1963) ) .
  • In vitro protein synthesis may be performed using manual techniques or by automation.
  • Various portions of the antibody may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the desired antibody.
  • antibodies may be purified from cells or bodily fluids, such as milk, of a transgenic animal engineered to express the antibody, as disclosed, for example, in U.S. Pat. Nos. 5,545,807 and 5,827,690.
  • Polyclonal antibodies are generally raised in animals by multiple subcutaneous (sc) or intraperitoneal (ip) injections of the relevant antigen and an adjuvant. It may be useful to conjugate the relevant antigen to a protein that is immunogenic in the species to be immunized, e.g., keyhole limpet hemocyanin (KLH) , serum albumin, bovine thyroglobulin, or soybean trypsin inhibitor, using a bifunctional or derivatizing agent, e.g., maleimidobenzoyl sulfosuccinimide ester (conjugation through cysteine residues) , N-hydroxysuccinimide (through lysine residues) , glutaraldehyde, succinic anhydride, SOCl2, or R1N ⁇ C ⁇ NR, where R and R1 are independently lower alkyl groups.
  • KLH keyhole limpet hemocyanin
  • serum albumin serum albumin
  • adjuvants examples include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate) .
  • the immunization protocol may be selected by one skilled in the art without undue experimentation.
  • the animals are immunized against the antigen, immunogenic conjugates, or derivatives by combining, e.g., 100 ⁇ g or 5 ⁇ g of the protein or conjugate (for rabbits or mice, respectively) with 3 volumes of Freund's complete adjuvant and injecting the solution intradermally at multiple sites.
  • the animals are boosted with 1/5 to 1/10 the original amount of peptide or conjugate in Freund's complete adjuvant by subcutaneous injection at multiple sites.
  • the animals are bled and the serum is assayed for antibody titer. Animals are boosted until the titer plateaus.
  • Conjugates also can be made in recombinant cell culture as protein fusions. Also, aggregating agents such as alum are suitable to enhance the immune response.
  • Monoclonal antibodies are obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations and/or post-translational modifications (e.g., isomerizations, amidations) that may be present in minor amounts.
  • the modifier “monoclonal” indicates the character of the antibody as not being a mixture of discrete antibodies.
  • the monoclonal antibodies may be made using the hybridoma method first described by Kohler et al., Nature, 256: 495 (1975) , or may be made by recombinant DNA methods (U.S. Pat. No. 4,816,567) .
  • lymphocytes that produce or are capable of producing antibodies that will specifically bind the protein used for immunization.
  • lymphocytes may be immunized in vitro. Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986) .
  • the immunizing agent will typically include the antigenic protein or a fusion variant thereof. Goding, Monoclonal Antibodies: Principles and Practice, Academic Press (1986) , pp. 59-103. Immortalized cell lines are usually transformed mammalian cells. The hybridoma cells thus prepared are seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells. Preferred immortalized myeloma cells are those that fuse efficiently, support stable high-level production of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium.
  • Culture medium in which hybridoma cells are growing is assayed for production of monoclonal antibodies directed against the antigen.
  • the culture medium in which the hybridoma cells are cultured can be assayed for the presence of monoclonal antibodies directed against the desired antigen.
  • binding affinity may be determined by the Scatchard analysis of Munson et al., Anal. Biochem., 107: 220 (1980) .
  • the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, supra) .
  • Suitable culture media for this purpose include, for example, D-MEM or RPMI-1640 medium.
  • the hybridoma cells may be grown in vivo as tumors in a mammal.
  • the monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
  • Monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567, and as described above.
  • DNA encoding the monoclonal antibodies is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies) .
  • the hybridoma cells serve as a preferred source of such DNA.
  • the DNA may be placed into expression vectors, which are then transfected into host cells such as E.
  • antibodies can be isolated from antibody phage libraries generated using the techniques described in McCafferty et al., Nature, 348: 552-554 (1990) . Clackson et al., Nature, 352: 624-628 (1991) and Marks et al., J. Mol. Biol., 222: 581-597 (1991) . Subsequent publications describe the production of high affinity (nM range) human antibodies by chain shuffling (Marks et al., Bio/Technology, 10: 779-783 (1992) ) , as well as combinatorial infection and in vivo recombination as a strategy for constructing very large phage libraries (Waterhouse et al., Nucl. Acids Res., 21: 2265-2266 (1993) ) . Thus, these techniques are viable alternatives to traditional monoclonal antibody hybridoma techniques for isolation of monoclonal antibodies.
  • the DNA also may be modified, for example, by substituting the coding sequence (U.S. Pat. No. 4,816,567; Morrison, et al., Proc. Natl Acad. Sci. USA, 81: 6851 (1984) ) , or by covalently joining to the coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide.
  • Such non-immunoglobulin polypeptides can be substituted to create a chimeric bivalent antibody comprising one antigen-combining site having specificity for an antigen and another antigen-combining site having specificity for a different antigen.
  • Chimeric or hybrid antibodies also may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents.
  • immunotoxins may be constructed using a disulfide-exchange reaction or by forming a thioether bond.
  • suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate.
  • Polynucleic acid sequences encoding the antibodies of the present disclosure can be obtained using standard recombinant techniques. Desired polynucleic acid sequences may be isolated and sequenced from antibody producing cells such as hybridoma cells. Alternatively, polynucleotides can be synthesized using nucleotide synthesizer or PCR techniques. Once obtained, sequences encoding the polypeptides are inserted into a recombinant vector capable of replicating and expressing heterologous polynucleotides in prokaryotic hosts. Many vectors that are available and known in the art can be used for the purpose of the present disclosure.
  • Selection of an appropriate vector will depend mainly on the size of the nucleic acids to be inserted into the vector and the particular host cell to be transformed with the vector.
  • Each vector contains various components, depending on its function (amplification or expression of heterologous polynucleotide, or both) and its compatibility with the particular host cell in which it resides.
  • the vector components generally include, but are not limited to, an origin of replication, a selection marker gene, a promoter, a ribosome binding site (RBS) , a signal sequence, the heterologous nucleic acid insert and a transcription termination sequence.
  • plasmid vectors containing replicon and control sequences which are derived from species compatible with the host cell are used in connection with these hosts.
  • the vector ordinarily carries a replication site, as well as marking sequences which are capable of providing phenotypic selection in transformed cells.
  • E. coli is typically transformed using pBR322, a plasmid derived from an E. coli species. Examples of pBR322 derivatives used for expression of particular antibodies are described in detail in Carter et al., U.S. Pat. No. 5,648,237.
  • phage vectors containing replicon and control sequences that are compatible with the host microorganism can be used as transforming vectors in connection with these hosts.
  • bacteriophage such as GEM TM -11 may be utilized in making a recombinant vector which can be used to transform susceptible host cells such as E. coli LE392.
  • the expression vector of the present application may comprise two or more promoter-cistron pairs, encoding each of the polypeptide components.
  • a promoter is an untranslated regulatory sequence located upstream (5′) to a cistron that modulates its expression.
  • Prokaryotic promoters typically fall into two classes, inducible and constitutive. Inducible promoter is a promoter that initiates increased levels of transcription of the cistron under its control in response to changes in the culture condition, e.g. the presence or absence of a nutrient or a change in temperature.
  • promoters recognized by a variety of potential host cells are well known.
  • the selected promoter can be operably linked to cistron DNA encoding the present antibody by removing the promoter from the source DNA via restriction enzyme digestion and inserting the isolated promoter sequence into the vector of the present application.
  • Both the native promoter sequence and many heterologous promoters may be used to direct amplification and/or expression of the target genes.
  • heterologous promoters are utilized, as they generally permit greater transcription and higher yields of expressed target gene as compared to the native target polypeptide promoter.
  • Promoters suitable for use with prokaryotic hosts include the PhoA promoter, the -galactamase and lactose promoter systems, a tryptophan (trp) promoter system and hybrid promoters such as the tac or the trc promoter.
  • trp tryptophan
  • other promoters that are functional in bacteria such as other known bacterial or phage promoters
  • Their nucleic acid sequences have been published, thereby enabling a skilled worker operably to ligate them to cistrons encoding the target peptide (Siebenlist et al. Cell 20: 269 (1980) ) using linkers or adaptors to supply any required restriction sites.
  • each cistron within the recombinant vector comprises a secretion signal sequence component that directs translocation of the expressed polypeptides across a membrane.
  • the signal sequence may be a component of the vector, or it may be a part of the target polypeptide DNA that is inserted into the vector.
  • the signal sequence selected for the purpose of this disclosure should be one that is recognized and processed (i.e. cleaved by a signal peptidase) by the host cell.
  • the signal sequence can be substituted by a prokaryotic signal sequence selected, for example, from the group consisting of the alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II (STII) leaders, LamB, PhoE, PelB, OmpA and MBP.
  • a prokaryotic signal sequence selected, for example, from the group consisting of the alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II (STII) leaders, LamB, PhoE, PelB, OmpA and MBP.
  • STII heat-stable enterotoxin II
  • the production of the antibodies according to the present disclosure can occur in the cytoplasm of the host cell, and therefore does not require the presence of secretion signal sequences within each cistron.
  • Certain host strains e.g., the E. coli trxB-strains
  • Prokaryotic host cells suitable for expressing the antibodies of the present disclosure include Archaebacteria and Eubacteria, such as Gram-negative or Gram-positive organisms.
  • useful bacteria include Escherichia (e.g., E. coli) , Bacilli (e.g., B. subtilis) , Enterobacteria, Pseudomonas species (e.g., P. aeruginosa) , Salmonella typhimurium, Serratia marcescans, Klebsiella, Proteus, Shigella, Rhizobia, Vitreoscilla, or Paracoccus.
  • gram-negative cells are used.
  • E. coli cells are used as hosts. Examples of E.
  • coli strains include strain W3110 (Bachmann, Cellular and Molecular Biology, vol. 2 (Washington, D.C.: American Society for Microbiology, 1987) , pp. 1190-1219; ATCC Deposit No. 27, 325) and derivatives thereof, including strain 33D3 having genotype W3110 AfhuA (AtonA) ptr3 lac Iq lacL8 AompT A (nmpc-fepE) degP41 kanR (U.S. Pat. No. 5,639,635) .
  • Other strains and derivatives thereof such as E. coli 294 (ATCC 31, 446) , E. coli B, E. coli 1776 (ATCC 31, 537) and E.
  • coli RV308 (ATCC 31, 608) are also suitable. These examples are illustrative rather than limiting. Methods for constructing derivatives of any of the above-mentioned bacteria having defined genotypes are known in the art and described in, for example, Bass et al., Proteins, 8: 309-314 (1990) . It is generally necessary to select the appropriate bacteria taking into consideration replicability of the replicon in the cells of a bacterium. For example, E. coli, Serratia, or Salmonella species can be suitably used as the host when well-known plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon.
  • plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon.
  • the host cell should secrete minimal amounts of proteolytic enzymes, and additional protease inhibitors may desirably be incorporated in the cell culture.
  • Host cells are transformed with the above-described expression vectors and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • Transformation means introducing DNA into the prokaryotic host so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integrant.
  • transformation is done using standard techniques appropriate to such cells.
  • the calcium treatment employing calcium chloride is generally used for bacterial cells that contain substantial cell-wall barriers.
  • Another method for transformation employs polyethylene glycol/DMSO.
  • Yet another technique used is electroporation.
  • Prokaryotic cells used to produce the antibodies of the present application are grown in media known in the art and suitable for culture of the selected host cells.
  • suitable media include luria broth (LB) plus necessary nutrient supplements.
  • the media also contains a selection agent, chosen based on the construction of the expression vector, to selectively permit growth of prokaryotic cells containing the expression vector. For example, ampicillin is added to media for growth of cells expressing ampicillin resistant gene.
  • any necessary supplements besides carbon, nitrogen, and inorganic phosphate sources may also be included at appropriate concentrations introduced alone or as a mixture with another supplement or medium such as a complex nitrogen source.
  • the culture medium may contain one or more reducing agents selected from the group consisting of glutathione, cysteine, cystamine, thioglycollate, dithioerythritol and dithiothreitol.
  • the prokaryotic host cells are cultured at suitable temperatures and pHs.
  • an inducible promoter is used in the expression vector of the present application, protein expression is induced under conditions suitable for the activation of the promoter.
  • PhoA promoters are used for controlling transcription of the polypeptides.
  • the transformed host cells are cultured in a phosphate-limiting medium for induction.
  • the phosphate-limiting medium is the C.R.A.P medium (see, e.g., Simmons et al., J. Immunol. Methods 263: 133-147 (2002) ) .
  • a variety of other inducers may be used, according to the vector construct employed, as is known in the art.
  • the expressed antibodies of the present disclosure are secreted into and recovered from the periplasm of the host cells. Protein recovery typically involves disrupting the microorganism, generally by such means as osmotic shock, sonication or lysis. Once cells are disrupted, cell debris or whole cells may be removed by centrifugation or filtration. The proteins may be further purified, for example, by affinity resin chromatography. Alternatively, proteins can be transported into the culture media and isolated therein. Cells may be removed from the culture and the culture supernatant being filtered and concentrated for further purification of the proteins produced. The expressed polypeptides can be further isolated and identified using commonly known methods such as polyacrylamide gel electrophoresis (PAGE) and Western blot assay.
  • PAGE polyacrylamide gel electrophoresis
  • protein production is conducted in large quantity by a fermentation process.
  • Various large-scale fed-batch fermentation procedures are available for production of recombinant proteins.
  • various fermentation conditions can be modified.
  • the chaperone proteins have been demonstrated to facilitate the proper folding and solubility of heterologous proteins produced in bacterial host cells. Chen et al. J Bio Chem 274: 19601-19605 (1999) ; U.S. Pat. No. 6,083,715; U.S. Pat. No. 6,027,888; Bothmann and Pluckthun, J. Biol. Chem. 275: 17100-17105 (2000) ; Ramm and Pluckthun, J. Biol. Chem. 275: 17106-17113 (2000) ; Arie et al., Mol. Microbiol. 39:199-210 (2001) .
  • certain host strains deficient for proteolytic enzymes can be used for the present disclosure, as described in, for example, U.S. Pat. No. 5,264,365; U.S. Pat. No. 5,508,192; Hara et al., Microbial Drug Resistance, 2: 63-72 (1996) .
  • E. coli strains deficient for proteolytic enzymes and transformed with plasmids overexpressing one or more chaperone proteins may be used as host cells in the expression system encoding the antibodies of the present application.
  • the antibodies produced herein can be further purified to obtain preparations that are substantially homogeneous for further assays and uses.
  • Standard protein purification methods known in the art can be employed. The following procedures are exemplary of suitable purification procedures: fractionation on immunoaffinity or ion-exchange columns, ethanol precipitation, reverse phase HPLC, chromatography on silica or on a cation-exchange resin such as DEAE, chromatofocusing, SDS-PAGE, ammonium sulfate precipitation, and gel filtration using, for example, Sephadex G-75.
  • Protein A immobilized on a solid phase for example can be used in certain embodiments for immunoaffinity purification of binding molecules of the present disclosure.
  • the solid phase to which Protein A is immobilized is preferably a column comprising a glass or silica surface, more preferably a controlled pore glass column or a silicic acid column.
  • the column has been coated with a reagent, such as glycerol, in an attempt to prevent nonspecific adherence of contaminants.
  • the solid phase is then washed to remove contaminants non-specifically bound to the solid phase. Finally the antibody of interest is recovered from the solid phase by elution.
  • the vector components generally include, but are not limited to, one or more of the following, a signal sequence, an origin of replication, one or more marker genes, and enhancer element, a promoter, and a transcription termination sequence.
  • a vector for use in a eukaryotic host may also an insert that encodes a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide.
  • the heterologous signal sequence selected preferably is one that is recognized and processed (i.e., cleaved by a signal peptidase) by the host cell.
  • mammalian signal sequences as well as viral secretory leaders, for example, the herpes simplex gD signal are available.
  • the DNA for such precursor region can be ligated in reading frame to DNA encoding the antibodies of the present application.
  • the origin of replication component is not needed for mammalian expression vectors (the SV40 origin may typically be used only because it contains the early promoter) .
  • Selection genes may encode proteins that confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline; complement auxotrophic deficiencies; or supply critical nutrients not available from complex media.
  • One example of a selection scheme utilizes a drug to arrest growth of a host cell. Those cells that are successfully transformed with a heterologous gene produce a protein conferring drug resistance and thus survive the selection regimen. Examples of such dominant selection use the drugs neomycin, mycophenolic acid and hygromycin.
  • Suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up nucleic acid encoding the antibodies of the present application.
  • cells transformed with the DHFR selection gene are first identified by culturing all of the transformants in a culture medium that contains methotrexate (Mtx) , a competitive antagonist of DHFR.
  • Mtx methotrexate
  • An exemplary appropriate host cell when wild-type DHFR is employed is the Chinese hamster ovary (CHO) cell line deficient in DHFR activity.
  • host cells transformed or co-transformed with the polypeptide encoding-DNA sequences, wild-type DHFR protein, and another selectable marker such as aminoglycoside 3′-phosphotransferase (APH) can be selected by cell growth in medium containing a selection agent for the selectable marker such as an aminoglycosidic antibiotic.
  • APH aminoglycoside 3′-phosphotransferase
  • Expression and cloning vectors usually contain a promoter that is recognized by the host organism and is operably linked to the nucleic acid encoding the desired polypeptide sequences.
  • Eukaryotic genes have an AT-rich region located approximately 25 to 30 based upstream from the site where transcription is initiated. Another sequence found 70 to 80 bases upstream from the start of the transcription of many genes may be included. The 3′ end of most eukaryotic may be the signal for addition of the poly A tail to the 3′ end of the coding sequence. All of these sequences may be inserted into eukaryotic expression vectors.
  • Polypeptide transcription from vectors in mammalian host cells can be controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2) , bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40) , from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2) , bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40
  • Enhancer sequences are now known from mammalian genes (globin, elastase, albumin, ⁇ -fetoprotein, and insulin) . Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270) , the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. See also Yaniv, Nature 297: 17-18 (1982) on enhancing elements for activation of eukaryotic promoters.
  • the enhancer may be spliced into the vector at a position 5′ or 3′ to the polypeptide encoding sequence, but is preferably located at a site 5′ from the promoter.
  • Expression vectors used in eukaryotic host cells also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the polypeptide-encoding mRNA.
  • One useful transcription termination component is the bovine growth hormone polyadenylation region.
  • Suitable host cells for cloning or expressing the DNA in the vectors herein include higher eukaryote cells described herein, including vertebrate host cells. Propagation of vertebrate cells in culture (tissue culture) has become a routine procedure. Examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651) ; human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., J. Gen Virol. 36: 59 (1977) ); baby hamster kidney cells (BHK, ATCC CCL 10) ; Chinese hamster ovary cells/-DHFR (CHO, Urlaub et al., Proc. Natl.
  • mice sertoli cells TM4, Mather, Biol. Reprod. 23: 243-251 (1980) ) ; monkey kidney cells (CV1 ATCC CCL 70) ; African green monkey kidney cells (VERO-76, ATCC CRL-1587) ; human cervical carcinoma cells (HELA, ATCC CCL 2) ; canine kidney cells (MDCK, ATCC CCL 34) ; buffalo rat liver cells (BRL 3A, ATCC CRL 1442) ; human lung cells (W138, ATCC CCL 75) ; human liver cells (Hep G2, HB 8065) ; mouse mammary tumor (MMT 060562, ATCC CCL51) ; TR1 cells (Mather et al., Annals N. Y. Acad. Sci. 383: 44-68 (1982) ) ; MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2) .
  • MRC 5 cells FS4 cells
  • a human hepatoma line Hep
  • Host cells can be transformed with the above-described expression or cloning vectors for antibodies production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the host cells used to produce the antibodies of the present application may be cultured in a variety of media.
  • Commercially available media such as Ham's F10 (Sigma) , Minimal Essential Medium ( (MEM) , (Sigma) , RPMI-1640 (Sigma) , and Dulbecco's Modified Eagle's Medium ( (DMEM) , Sigma) are suitable for culturing the host cells.
  • MEM Minimal Essential Medium
  • RPMI-1640 Sigma
  • DMEM Dulbecco's Modified Eagle's Medium
  • any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor) , salts (such as sodium chloride, calcium, magnesium, and phosphate) , buffers (such as HEPES) , nucleotides (such as adenosine and thymidine) , antibiotics (such as GENTAMYCIN TM drug) , trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range) , and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art.
  • the culture conditions such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
  • the antibodies can be produced intracellularly, in the periplasmic space, or directly secreted into the medium. If the antibody is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, are removed, for example, by centrifugation or ultrafiltration. Where the antibody is secreted into the medium, supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an Amicon or Millipore Pellicon ultrafiltration unit. A protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
  • a protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
  • the protein composition prepared from the cells can be purified using, for example, hydroxylapatite chromatography, gel electrophoresis, dialysis, and affinity chromatography, with affinity chromatography being the preferred purification technique.
  • the matrix to which the affinity ligand is attached is most often agarose, but other matrices are available.
  • Mechanically stable matrices such as controlled pore glass or poly (styrene-divinyl) benzene allow for faster flow rates and shorter processing times than can be achieved with agarose.
  • the presently disclosed fusion proteins comprise a lysosome-targeting domain.
  • the lysosome-targeting domain comprises a lysosome-related membrane protein or a fragment thereof.
  • the lysosome-related membrane protein or the fragment thereof can transport the target protein and the fusion protein complex to the lysosome for degradation.
  • the lysosome-related membrane protein is selected from transferrin receptor (TfR) , low density lipoprotein receptor (LDLR) , neonatal Fc receptor (FcRn) , very low density lipoprotein receptor (VLDLR) , LDL receptor related protein 8 (LRP8, ApoER2) , LDL receptor related protein 5 (LRP5) , asialoglycoprotein receptor 1 (ASGR1) , asialoglycoprotein receptor 2 (ASGR2) , cation-dependent mannose-6-phosphate receptor (MPRD) , vascular endothelial growth factor receptor 2 (VEGFR2) , integrin alpha-V (ITAV) , integrin beta-3 (ITB3) , arrestin beta 2 (also known as Beta arrestin 2, ARRB2) , and glucose transporter type 4 (GLUT4) .
  • TfR transferrin receptor
  • LDLR low density lipoprotein receptor
  • FcRn neonatal Fc receptor
  • VLDLR very low density lipoprotein receptor
  • the lysosome-related membrane protein is TfR, LDLR, or FcRn.
  • Table 4 shows exemplary lysosome-related membrane proteins and fragments thereof that can be used with the presently disclosed fusion proteins. Sequences for certain exemplary lysosome-related membrane proteins and fragments thereof are also provided.
  • the lysosome-related membrane protein or fragment thereof comprises a transmembrane domain, an intracellular domain, or a combination thereof. In certain embodiments, the lysosome-related membrane protein or fragment thereof comprises a transmembrane domain and an intracellular domain. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In some embodiments, for Type I transmembrane proteins, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID. In other embodiments, for Type II transmembrane proteins, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM.
  • the lysosome-targeting domain comprises TfR or a fragment thereof.
  • the TfR is wild-type.
  • the intracellular domain of TfR comprises a mutation.
  • the mutant TfR is m1TfR, which can be constructed by replacing NADN at position 47-50 with YTRF, wherein numbering of the amino acid residue positions is according to SEQ ID NO: 1.
  • the mutant TfR is m2TfR, which can be constructed by replacing GDNS at position 31-34 with YTRF, wherein numbering of the amino acid residue positions is according to SEQ ID NO: 1 (see J Biol Chem.
  • the lysosome-targeting domain comprises a transmembrane domain of TfR.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 80.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 80. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of TfR. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of TfR. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 2, SEQ ID NO: 8 or SEQ ID NO: 9.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 8 or SEQ ID NO: 9.
  • the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises TfR.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 1.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 1.
  • the lysosome-targeting domain comprises LDLR or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of LDLR. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of LDLR. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of LDLR. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 3.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 3.
  • the lysosome-targeting domain comprises LDLR.
  • the lysosome-targeting domain comprises FcRn or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of FcRn. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of FcRn. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of FcRn. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 4.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 4.
  • the lysosome-targeting domain comprises FcRn.
  • the lysosome-targeting domain comprises VLDLR or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of VLDLR. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of VLDLR. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of VLDLR. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 5.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 5.
  • the lysosome-targeting domain comprises VLDLR.
  • the lysosome-targeting domain comprises LRP8 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of LRP8. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of LRP8. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of LRP8. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 6.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 6.
  • the lysosome-targeting domain comprises LRP8.
  • the lysosome-targeting domain comprises LRP5 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of LRP5. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of LRP5. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of LRP5. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 7.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 7.
  • the lysosome-targeting domain comprises LRP5.
  • the lysosome-targeting domain comprises ASGR1 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of ASGR1. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of ASGR1. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of ASGR1. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 10.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 10.
  • the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises ASGR1.
  • the lysosome-targeting domain comprises ASGR2 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of ASGR2. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of ASGR2. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of ASGR2. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 11.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 11.
  • the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises ASGR2.
  • the lysosome-targeting domain comprises MPRD or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of MPRD. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of MPRD. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of MPRD. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 12.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 12.
  • the lysosome-targeting domain comprises MPRD.
  • the lysosome-targeting domain comprises VEGFR2 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of VEGFR2. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of VEGFR2. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of VEGFR2. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 13.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 13.
  • the lysosome-targeting domain comprises VEGFR2.
  • the lysosome-targeting domain comprises GLUT4 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of GLUT4. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of GLUT4. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of GLUT4. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises GLUT4. In certain embodiments, the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 14. In certain embodiments, the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 14.
  • the lysosome-targeting domain comprises ARRB2 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of ARRB2. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of ARRB2. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of ARRB2. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises ARRB2.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 15.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 15.
  • the lysosome-targeting domain comprises ITAV or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of ITAV. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of ITAV. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of ITAV. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 16.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 16.
  • the lysosome-targeting domain comprises ITAV.
  • the lysosome-targeting domain comprises ITB3 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of ITB3. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of ITB3. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of ITB3. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises ITB3. In certain embodiments, the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% sequence identity to SEQ ID NO: 17. In certain embodiments, the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 17.
  • the lysosome-targeting domain comprises (i) ITAV or a fragment thereof; and (ii) ITB3 or a fragment thereof.
  • the lysosome-targeting domain comprises an ITAV fragment and ITB3.
  • the ITAV fragment comprises an intracellular domain and a transmembrane domain.
  • the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the ITAV fragment and ITB3 are positioned from N-terminus to C-terminus as ITAV fragment-ITB3.
  • a self-cleaving peptide is positioned between the ITAV fragment and ITB3.
  • the self-cleaving peptide is or is derived from P2A, for example SEQ ID NO: 75 or 76. In other embodiments, the self-cleaving peptide is or is derived from T2A, for example, SEQ ID NO: 77.
  • the lysosome-targeting domain comprises (i) an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 16;and (ii) an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%se
  • the lysosome-targeting domain comprises (i) the amino acid sequence of SEQ ID NO: 16, and (ii) the amino acid sequence of SEQ ID NO: 17.
  • the lysosome-targeting domain comprises ApoER2 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of ApoER2. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of ApoER2. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of ApoER2. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 78.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 78.
  • the lysosome-targeting domain comprises ApoER2.
  • the lysosome-targeting domain comprises Beta arrestin 2 or a fragment thereof. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain of Beta arrestin 2. In certain embodiments, the lysosome-targeting domain comprises an intracellular domain of Beta arrestin 2. In certain embodiments, the lysosome-targeting domain comprises a transmembrane domain and an intracellular domain of Beta arrestin 2. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as ID-TM. In certain embodiments, the transmembrane domain and the intracellular domain are positioned from N-terminus to C-terminus as TM-ID.
  • the lysosome-targeting domain comprises Beta arrestin 2.
  • the lysosome-targeting domain comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 79.
  • the lysosome-targeting domain comprises the amino acid sequence of SEQ ID NO: 79.
  • the lysosome-related membrane protein or fragment provided herein contains substitutions (e.g., conservative substitutions) , insertions, or deletions relative to the reference sequence, but the lysosome-related membrane protein or fragment comprising that sequence retains the ability to induce protein degradation through lysosomal degradation pathway.
  • a total of 1 to 10 amino acids have been substituted, inserted and/or deleted in a reference amino acid sequence.
  • the lysosome-related membrane protein or fragment provided herein includes post-translational modifications of a reference sequence.
  • the position of the antigen binding-domain and the lysosome targeting domain are positioned from N-terminus to C-terminus as antigen binding-domain-lysosome targeting domain, or lysosome targeting domain -antigen binding-domain.
  • the lysosome targeting domain comprises an intracellular domain and a transmembrane domain of a lysosome-related membrane protein.
  • the antigen binding-domain and the domains of the lysosome-related membrane protein are positioned from N-terminus to C-terminus as the intracellular domain of the lysosome-related membrane protein-the transmembrane domain of the lysosome-related membrane protein-the antigen-binding domain.
  • the antigen binding-domain and the domains of the lysosome-related membrane protein are positioned from N-terminus to C-terminus as the antigen-binding domain -the transmembrane domain of the lysosome-related membrane protein -the intracellular domain of the lysosome-related membrane protein.
  • the fusion protein further comprises a linker between the antigen-binding domain and the lysosome-targeting domain.
  • linkers include a GS linker, an ⁇ -helical linker, a glycine-alanine polymer linker, an alanine-serine polymer linker, and an IgG4-Fc linker.
  • the linker comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 72, SEQ ID NO: 73 or SEQ ID NO: 74.
  • the linker comprises the amino acid sequence of SEQ ID NO: 72, SEQ ID NO: 73 or SEQ ID NO: 74.
  • the fusion protein further comprises a signal peptide.
  • the signal peptide is located at the N-terminus of the fusion protein.
  • the signal peptide provided herein is a signal peptide of the lysosome-related membrane protein (for example for Type I transmembrane proteins) .
  • a signal peptide provided herein is derived from CD8 ⁇ or IL-2 (for example for Type II transmembrane proteins or other proteins) .
  • the signal peptide comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 28, SEQ ID NO: 29, or SEQ ID NO: 30.
  • the linker comprises the amino acid sequence of SEQ ID NO: 28, SEQ ID NO: 29, or SEQ ID NO: 30.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, an intracellular domain of TfR, a transmembrane domain of TfR, a linker, the CD38-1 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 23.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 23.
  • the fusion protein is designated as “PDT-1-CD38-1” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, an intracellular domain of TfR, a transmembrane domain of TfR, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 24.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 24.
  • the fusion protein is designated as “PDT-1-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, an intracellular domain of TfR, a transmembrane domain of TfR, a linker, the CD7 V H H.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 25.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 25.
  • the fusion protein is designated as “PDT-1-CD7” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-3 binding domain, a linker, a transmembrane domain of LDLR, an intracellular domain of LDLR.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 26.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 26.
  • the fusion protein is designated as “PDT-2-CD38-3” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-3 binding domain, a linker, a transmembrane domain of FcRn, an intracellular domain of FcRn.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 27.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 27.
  • the fusion protein is designated as “PDT-3-CD38-3” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-2 binding domain, a linker, a transmembrane domain of VLDLR, an intracellular domain of VLDLR.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 81.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 81.
  • the fusion protein is designated as “PDT-4-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-2 binding domain, a linker, a transmembrane domain of LRP5, an intracellular domain of LRP5.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 82.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 82.
  • the fusion protein is designated as “PDT-5-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, an intracellular domain of m1TfR, a transmembrane domain of m1TfR, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 83.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 83.
  • the fusion protein is designated as “PDT-6-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, an intracellular domain of m2TfR, a transmembrane domain of m2TfR, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 84.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 84.
  • the fusion protein is designated as “PDT-7-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, an intracellular domain of ASGR1, a transmembrane domain of ASGR1, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 85.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 85.
  • the fusion protein is designated as “PDT-8-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, an intracellular domain of ASGR2, a transmembrane domain of ASGR2, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 86.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 86.
  • the fusion protein is designated as “PDT-9-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-2 binding domain, a linker, a transmembrane domain of MPRD, an intracellular domain of MPRD.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 87.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 87.
  • the fusion protein is designated as “PDT-10-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-2 binding domain, a linker, a transmembrane domain of VEGFR2, an intracellular domain of VEGFR2.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 88.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 88.
  • the fusion protein is designated as “PDT-11-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-2 binding domain, a linker, a transmembrane domain of ITAV, an intracellular domain of ITAV, a self cleaving peptide, an ITB3.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 89.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 89.
  • the fusion protein is designated as “PDT-12-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, a TfR, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 90.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 90.
  • the fusion protein is designated as “PDT-13-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-2 binding domain, a linker, a GLUT4.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 91.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 91.
  • the fusion protein is designated as “PDT-14-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, the CD38-2 binding domain, a linker, a transmembrane domain of ApoER2, an intracellular domain of ApoER2.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 92.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 92.
  • the fusion protein is designated as “PDT-15-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, a Beta arrestin 2, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 93.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 93.
  • the fusion protein is designated as “PDT-16-CD38-2” in the presently disclosed Examples.
  • the fusion protein comprises, from N-terminus to C-terminus, a signal peptide, a transmembrane domain of TfR, a linker, the CD38-2 binding domain.
  • the fusion protein comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 94.
  • the fusion protein comprises or consists of the amino acid sequence of SEQ ID NO: 94.
  • the fusion protein is designated as “PDT-17-CD38-2” in the presently disclosed Examples.
  • the present disclosure provides cells comprising the presently disclosed fusion protein (e.g., fusion proteins disclosed in Section 5.2 of the present disclosure) .
  • the cells further comprise an antigen-recognizing receptor.
  • the antigen recognizing receptor is a T cell receptor (TCR) or a chimeric antigen receptor (CAR) .
  • the cells of the disclosure have enhanced therapeutic efficacy.
  • Non-limiting exemplary enhanced therapeutic efficacies include one or more of reduced graft-versus-host disease (GvHD) or host-versus-graft disease (HvGD) in the host, reduced or eliminated rejection by the host, prolonged survival in the host, reduced suppression by tumors in the host, reduced self-killing in the host, reduced inflammatory cascades in the host, or sustained CAR-mediated signal transduction in the host.
  • GvHD reduced graft-versus-host disease
  • HvGD host-versus-graft disease
  • TCR T-Cell Receptor
  • the antigen recognizing receptor is a TCR.
  • a TCR is a disulfide-linked heterodimeric protein consisting of two variable chains expressed as part of a complex with the invariant CD3 chain molecules.
  • a TCR is found on the surface of T cells, and is responsible for recognizing antigens as peptides bound to major histocompatibility complex (MHC) molecules.
  • MHC major histocompatibility complex
  • a TCR comprises an alpha chain and a beta chain (encoded by TRA and TRB, respectively) .
  • a TCR comprises a gamma chain and a delta chain (encoded by TRG and TRD, respectively) .
  • Each chain of a TCR is composed of two extracellular domains: Variable (V) region and a Constant (C) region.
  • the Constant region is proximal to the cell membrane, followed by a transmembrane region and a short cytoplasmic tail.
  • the Variable region binds to the peptide/MHC complex.
  • the variable domain of both chains each has three complementarity determining regions (CDRs) .
  • a TCR can form a receptor complex with three dimeric signaling modules CD3 ⁇ / ⁇ , CD3 ⁇ / ⁇ and CD247 ⁇ / ⁇ or ⁇ / ⁇ .
  • a TCR complex engages with its antigen and MHC (peptide/MHC)
  • MHC peptide/MHC
  • the presently disclosed subject matter provides a recombinant TCR.
  • the TCR is a non-naturally occurring TCR.
  • the TCR differs from any naturally occurring TCR by at least one amino acid residue.
  • the TCR differs from any naturally occurring TCR by at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 or more amino acid residues.
  • the TCR is modified from a naturally occurring TCR by at least one amino acid residue.
  • the TCR is modified from a naturally occurring TCR by at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 or more amino acid residues.
  • the antigen recognizing receptor is a CAR.
  • CARs are engineered receptors, which graft or confer a specificity of interest onto an immune effector cell.
  • CARs can be used to graft the specificity of a monoclonal antibody onto a T cell; with transfer of their coding sequence facilitated by retroviral vectors.
  • the CAR comprises (a) an extracellular antigen binding domain binding to an antigen; (b) a transmembrane domain; and (c) an intracellular signaling domain.
  • the CAR comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to the amino acid sequence of SEQ ID NO: 31.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 31.
  • the CAR comprises an amino acid sequence having at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to the amino acid sequence of SEQ ID NO: 32.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 32.
  • the extracellular antigen-binding domain specifically binds to an antigen.
  • the extracellular antigen-binding domain comprises at least one sdAb.
  • the extracellular antigen-binding domain comprises at least two sdAb.
  • the sdAb is V H H.
  • the extracellular antigen-binding domain is an extracellular antigen-binding domain disclosed in international Publication No. WO2021121228.
  • the extracellular antigen-binding domain is an extracellular antigen-binding domain disclosed in international Publication No. WO2020052542.
  • the extracellular antigen-binding domain is an scFv. In certain embodiments, the scFv is a human scFv. In certain embodiments, the scFv is a humanized scFv. In certain embodiments, the extracellular antigen-binding domain is a Fab, which is optionally crosslinked. In certain embodiments, the extracellular binding domain is a F (ab) 2 . In certain embodiments, any of the foregoing molecules may be comprised in a fusion protein with a heterologous sequence to form the extracellular antigen-binding domain. In certain embodiments, the scFv is identified by screening scFv phage library with an antigen-Fc fusion protein.
  • the antigen is a tumor antigen. In certain embodiments, the antigen is a pathogen antigen.
  • tumor antigen include BCMA, CLL1, CD4, GPC3, GPRC5D, GU2CYC, CD19, MUC16, MUC1, CAIX, CEA, CD8, CD7, CD10, CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD133, CD138, EGP-2, EGP-40, EpCAM, ERBB2, ERBB3, ERBB4, FBP, fetal acetylcholine receptor, folate receptor- ⁇ , GD2, GD3, HER-2, hTERT, IL-13R- ⁇ 2, ⁇ -light chain, KDR, LeY, L1 cell adhesion molecule, MAGE-A1, mesothelin, MAGEA3, p53, MART1, GP100, proteinase-3 (PR3) , ty
  • CD19 CARs or BCMA CARs Many CARs targeting different tumor antigens have been widely disclosed in the field, such as CD19 CARs or BCMA CARs.
  • the extracellular antigen-binding domain of CD19 CARs can be or include the CD19 binding fragment (e.g., FMC63, SJ25C1, or those disclosed in different patents such as WO 2022/012683, etc) .
  • BCMA CARs also have been well described, related patents include but not limited to WO 2016/014789, WO 2016/014565, WO 2013/154760, and WO 2018/028647, etc.
  • the antigen is BCMA. In certain embodiments, the antigen is CLL1. In some embodiments, the CAR comprises (a) an extracellular antigen binding domain comprising at least two anti-BCMA sdAbs; (b) a transmembrane domain; and (c) an intracellular signaling domain, wherein the first anti-BCMA sdAb comprises a CDR1, a CDR2, and a CDR3 as set forth in an sdAb comprising the amino acid sequence of SEQ ID NO: 62 and the second anti-BCMA sdAb comprises a CDR1, a CDR2, and a CDR3 as set forth in an sdAb comprising the amino acid sequence of SEQ ID NO: 63.
  • the first anti-BCMA sdAb comprises a CDR1 comprising the amino acid sequence of SEQ ID NO: 56; a CDR2 comprising the amino acid sequence of SEQ ID NO: 57; and a CDR3 comprising the amino acid sequence of SEQ ID NO: 58; and the second anti-BCMA sdAb comprises a CDR1 comprising the amino acid sequence of SEQ ID NO: 59; a CDR2 comprising the amino acid sequence of SEQ ID NO: 60; and a CDR3 comprising the amino acid sequence of SEQ ID NO: 61.
  • the two VHH domains can be in any order in the extracellular domain, i.e., either the first or the second VHH domain can be at the N-terminus in the extracellular domain.
  • the CAR comprises (a) an extracellular antigen binding domain comprising at least two anti-BCMA sdAbs; (b) a transmembrane domain; and (c) an intracellular signaling domain, wherein the first anti-BCMA sdAb comprises an amino acid sequence of SEQ ID NO: 62, and the second anti-BCMA sdAb comprises an amino acid sequence of SEQ ID NO: 63.
  • the CAR comprises (a) an extracellular antigen binding domain comprising an anti-CLL1 sdAb; (b) a transmembrane domain; and (c) an intracellular signaling domain, wherein the anti-CLL1 sdAb comprises a CDR1, a CDR2 and a CDR3 as set forth in an sdAb comprising the amino acid sequence of SEQ ID NO: 67.
  • the sdAb comprises a CDR1 comprising the amino acid sequence of SEQ ID NO: 64; a CDR2 comprising the amino acid sequence of SEQ ID NO: 65; and a CDR3 comprising the amino acid sequence of SEQ ID NO: 66.
  • the CAR comprises (a) an extracellular antigen binding domain comprising an anti-CLL1 sdAb; (b) a transmembrane domain; and (c) an intracellular signaling domain, wherein the anti-CLL1 sdAb comprises an amino acid sequence of SEQ ID NO: 67.
  • the CAR provided herein may further comprise one or more of the following: a linker (e.g., a peptide linker) , a transmembrane domain, a hinge region, a signal peptide, an intracellular signaling domain, a co-stimulatory signaling domain, each of which is described in more detail below.
  • a linker e.g., a peptide linker
  • the various antibodies may be fused to each other via peptide linkers.
  • the antibodies are directly fused to each other without any peptide linkers.
  • the peptide linkers connecting different antibodies may be the same or different.
  • Different domains of the CARs may also be fused to each other via peptide linkers.
  • Each peptide linker in a CAR may have the same or different length and/or sequence depending on the structural and/or functional features of the antibodies and/or the various domains. Each peptide linker may be selected and optimized independently. The length, the degree of flexibility and/or other properties of the peptide linker (s) used in the CARs may have some influence on properties, including but not limited to the affinity, specificity or avidity for one or more particular antigens or epitopes. For example, longer peptide linkers may be selected to ensure that two adjacent domains do not sterically interfere with one another. In certain embodiments, a short peptide linker may be disposed between the transmembrane domain and the intracellular signaling domain of a CAR.
  • a peptide linker comprises flexible residues (such as glycine and serine) so that the adjacent domains are free to move relative to each other.
  • a glycine-serine doublet can be a suitable peptide linker.
  • the peptide linker can be of any suitable length. In certain embodiments, the peptide linker is at least about any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 50, 75, 100 or more amino acids long. In certain embodiments, the peptide linker is no more than about any of 100, 75, 50, 40, 35, 30, 25, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5 or fewer amino acids long.
  • the length of the peptide linker is any of about 1 amino acid to about 10 amino acids, about 1 amino acids to about 20 amino acids, about 1 amino acid to about 30 amino acids, about 5 amino acids to about 15 amino acids, about 10 amino acids to about 25 amino acids, about 5 amino acids to about 30 amino acids, about 10 amino acids to about 30 amino acids long, about 30 amino acids to about 50 amino acids, about 50 amino acids to about 100 amino acids, or about 1 amino acid to about 100 amino acids.
  • the peptide linker may have a naturally occurring sequence, or a non-naturally occurring sequence.
  • a sequence derived from the hinge region of heavy chain only antibodies may be used as the linker. See, for example, WO1996/34103.
  • the peptide linker is a flexible linker.
  • Exemplary flexible linkers include but not limited to glycine polymers (G) n , glycine-serine polymers, glycine-alanine polymers, alanine-serine polymers, and other flexible linkers known in the art.
  • the CARs of the present disclosure comprise a transmembrane domain that can be directly or indirectly fused to the extracellular antigen binding domain.
  • the transmembrane domain may be derived either from a natural or from a synthetic source.
  • a “transmembrane domain” refers to any protein structure that is thermodynamically stable in a cell membrane, preferably an eukaryotic cell membrane.
  • Transmembrane domains compatible for use in the CARs described herein may be obtained from a naturally occurring protein. Alternatively, it can be a synthetic, non-naturally occurring protein segment, e.g., a hydrophobic protein segment that is thermodynamically stable in a cell membrane.
  • Transmembrane domains are classified based on the three dimensional structure of the transmembrane domain.
  • transmembrane domains may form an alpha helix, a complex of more than one alpha helix, a beta-barrel, or any other stable structure capable of spanning the phospholipid bilayer of a cell.
  • transmembrane domains may also or alternatively be classified based on the transmembrane domain topology, including the number of passes that the transmembrane domain makes across the membrane and the orientation of the protein. For example, single-pass membrane proteins cross the cell membrane once, and multi-pass membrane proteins cross the cell membrane at least twice (e.g., 2, 3, 4, 5, 6, 7 or more times) .
  • Membrane proteins may be defined as Type I, Type II or Type III depending upon the topology of their termini and membrane-passing segment (s) relative to the inside and outside of the cell.
  • Type I membrane proteins have a single membrane-spanning region and are oriented such that the N-terminus of the protein is present on the extracellular side of the lipid bilayer of the cell and the C-terminus of the protein is present on the cytoplasmic side.
  • Type II membrane proteins also have a single membrane-spanning region but are oriented such that the C-terminus of the protein is present on the extracellular side of the lipid bilayer of the cell and the N-terminus of the protein is present on the cytoplasmic side.
  • Type III membrane proteins have multiple membrane-spanning segments and may be further sub-classified based on the number of transmembrane segments and the location of N-and C-termini.
  • the transmembrane domain of the CAR described herein is derived from a Type I single-pass membrane protein.
  • transmembrane domains from multi-pass membrane proteins may also be compatible for use in the CARs described herein.
  • Multi-pass membrane proteins may comprise a complex (at least 2, 3, 4, 5, 6, 7 or more) alpha helices or a beta sheet structure.
  • the N-terminus and the C-terminus of a multi-pass membrane protein are present on opposing sides of the lipid bilayer, e.g., the N-terminus of the protein is present on the cytoplasmic side of the lipid bilayer and the C-terminus of the protein is present on the extracellular side.
  • the transmembrane domain of the CAR comprises a transmembrane domain chosen from the transmembrane domain of an alpha, beta or zeta chain of a T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137, CD154, KIRDS2, OX40, CD2, CD27, LFA-1 (CDl la, CD18) , ICOS (CD278) , 4-1BB (CD137) , GITR, CD40, BAFFR, HVEM (LIGHTR) , SLAMF7, NKp80 (KLRFl) , CD160, GPC3, IL-2R beta, IL-2R gamma, IL-7Ra, ITGA1, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CDl
  • the transmembrane domain is derived from a molecule selected from the group consisting of CD8 ⁇ , CD4, CD28, CD137, CD80, CD86, CD152 and PD1. In some embodiments, the transmembrane domain is derived from CD8 ⁇ . In some embodiments, the transmembrane domain is a transmembrane domain of CD8 ⁇ comprising the amino acid sequence of SEQ ID NO: 69.
  • Transmembrane domains for use in the CARs described herein can also comprise at least a portion of a synthetic, non-naturally occurring protein segment.
  • the transmembrane domain is a synthetic, non-naturally occurring alpha helix or beta sheet.
  • the protein segment 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. Examples of synthetic transmembrane domains are known in the art, for example in U.S. Patent No. 7,052,906 and PCT Publication No. WO 2000/032776, the relevant disclosures of which are incorporated by reference herein.
  • the transmembrane domain provided herein may comprise a transmembrane region and a cytoplasmic region located at the C-terminal side of the transmembrane domain.
  • the cytoplasmic region of the transmembrane domain may comprise three or more amino acids and, in certain embodiments, helps to orient the transmembrane domain in the lipid bilayer.
  • one or more cysteine residues are present in the transmembrane region of the transmembrane domain.
  • one or more cysteine residues are present in the cytoplasmic region of the transmembrane domain.
  • the cytoplasmic region of the transmembrane domain comprises positively charged amino acids.
  • the cytoplasmic region of the transmembrane domain comprises the amino acids arginine, serine, and lysine.
  • the transmembrane region of the transmembrane domain comprises hydrophobic amino acid residues.
  • the transmembrane domain of the CAR provided herein comprises an artificial hydrophobic sequence.
  • a triplet of phenylalanine, tryptophan and valine may be present at the C terminus of the transmembrane domain.
  • the transmembrane region comprises mostly hydrophobic amino acid residues, such as alanine, leucine, isoleucine, methionine, phenylalanine, tryptophan, or valine.
  • the transmembrane region is hydrophobic.
  • the transmembrane region comprises a poly-leucine-alanine sequence.
  • the hydropathy, or hydrophobic or hydrophilic characteristics of a protein or protein segment can be assessed by any method known in the art, for example the Kyte and Doolittle hydropathy analysis.
  • the CARs of the present disclosure comprise an intracellular signaling domain (ISD) .
  • the intracellular signaling domain is responsible for activation of at least one of the normal effector functions of the immune effector cell expressing the CARs.
  • effector function refers to a specialized function of a cell. Effector function of a T cell, for example, may be cytolytic activity or helper activity including the secretion of cytokines.
  • cytoplasmic signaling domain refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function. While usually the entire cytoplasmic signaling domain can be employed, in many cases it is not necessary to use the entire chain.
  • cytoplasmic signaling domain is thus meant to include any truncated portion of the cytoplasmic signaling domain sufficient to transduce the effector function signal.
  • the intracellular signaling domain comprises a primary intracellular signaling domain of an immune effector cell.
  • the CAR comprises an intracellular signaling domain consisting essentially of a primary intracellular signaling domain of an immune effector cell.
  • Primary intracellular signaling domain refers to cytoplasmic signaling sequence that acts in a stimulatory manner to induce immune effector functions.
  • the primary intracellular signaling domain contains a signaling motif known as immunoreceptor tyrosine-based activation motif, or ITAM.
  • ITAM immunoreceptor tyrosine-based activation motif
  • ITAM immunoreceptor tyrosine-based activation motif
  • the motif may comprise two repeats of the amino acid sequence YxxL/I separated by 6-8 amino acids, wherein each x is independently any amino acid, producing the conserved motif YxxL/Ix (6-8) YxxL/I.
  • ITAMs within signaling molecules are important for signal transduction within the cell, which is mediated at least in part by phosphorylation of tyrosine residues in the ITAM following activation of the signaling molecule. ITAMs may also function as docking sites for other proteins involved in signaling pathways.
  • Exemplary ITAM-containing primary cytoplasmic signaling sequences include those derived from CD3 ⁇ , FcR gamma (FCER1G) , FcR beta (Fc Epsilon Rib) , CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b, and CD66d.
  • the primary intracellular signaling domain is derived from CD3 ⁇ .
  • the intracellular signaling domain consists of the cytoplasmic signaling domain of CD3 ⁇ .
  • the primary intracellular signaling domain is a cytoplasmic signaling domain of wild-type CD3 ⁇ .
  • the primary intracellular signaling domain of wild-type CD3 ⁇ comprises the amino acid sequence of SEQ ID NO: 71.
  • the primary intracellular signaling domain is a functional mutant of the cytoplasmic signaling domain of CD3 ⁇ containing one or more mutations, such as Q65K.
  • the CAR comprises at least one co-stimulatory signaling domain.
  • co-stimulatory signaling domain refers to at least a portion of a protein that mediates signal transduction within a cell to induce an immune response such as an effector function.
  • the co-stimulatory signaling domain of the chimeric receptor described herein can be a cytoplasmic signaling domain from a co-stimulatory protein, which transduces a signal and modulates responses mediated by immune cells, such as T cells, NK cells, macrophages, neutrophils, or eosinophils.
  • “Co-stimulatory signaling domain” can be the cytoplasmic portion of a co-stimulatory molecule.
  • co-stimulatory molecule refers to a cognate binding partner on an immune cell (such as T cell) that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the immune cell, such as, but not limited to, proliferation and survival.
  • the intracellular signaling domain comprises a single co-stimulatory signaling domain. In certain embodiments, the intracellular signaling domain comprises two or more (such as about any of 2, 3, 4, or more) co-stimulatory signaling domains. In certain embodiments, the intracellular signaling domain comprises two or more of the same co-stimulatory signaling domains. In certain embodiments, the intracellular signaling domain comprises two or more co-stimulatory signaling domains from different co-stimulatory proteins, such as any two or more co-stimulatory proteins described herein. In certain embodiments, the intracellular signaling domain comprises a primary intracellular signaling domain (such as cytoplasmic signaling domain of CD3 ⁇ ) and one or more co-stimulatory signaling domains.
  • a primary intracellular signaling domain such as cytoplasmic signaling domain of CD3 ⁇
  • the one or more co-stimulatory signaling domains and the primary intracellular signaling domain are fused to each other via optional peptide linkers.
  • the primary intracellular signaling domain, and the one or more co-stimulatory signaling domains may be arranged in any suitable order.
  • the one or more co-stimulatory signaling domains are located between the transmembrane domain and the primary intracellular signaling domain (such as cytoplasmic signaling domain of CD3 ⁇ ) .
  • Multiple co-stimulatory signaling domains may provide additive or synergistic stimulatory effects.
  • Activation of a co-stimulatory signaling domain in a host cell may induce the cell to increase or decrease the production and secretion of cytokines, phagocytic properties, proliferation, differentiation, survival, and/or cytotoxicity.
  • the co-stimulatory signaling domain of any co-stimulatory molecule may be compatible for use in the CARs described herein.
  • the type (s) of co-stimulatory signaling domain is selected based on factors such as the type of the immune effector cells in which the effector molecules would be expressed (e.g., T cells, NK cells, macrophages, neutrophils, or eosinophils) and the desired immune effector function (e.g., ADCC effect) .
  • co-stimulatory signaling domains for use in the CARs can be the cytoplasmic signaling domain of co-stimulatory proteins, including, without limitation, members of the B7/CD28 family (e.g., B7-1/CD80, B7-2/CD86, B7-H1/PD-L1, B7-H2, B7-H3, B7-H4, B7-H6, B7-H7, BTLA/CD272, CD28, CTLA-4, Gi24/VISTA/B7-H5, ICOS/CD278, PD-1, PD-L2/B7-DC, and PDCD6) ; members of the TNF superfamily (e.g., 4-1BB/TNFSF9/CD137, 4-1BB Ligand/TNFSF9, BAFF/BLyS/TNFSF13B, BAFF R/TNFRSF13C, CD27/TNFRSF7, CD27 Ligand/TNFSF7, CD30/TNFRSF8, CD30 Ligand/TNFSF8, CD40/TN
  • the one or more co-stimulatory signaling domains are selected from the group consisting of CD27, CD28, CD137, OX40, CD30, CD40, CD3, lymphocyte function-associated antigen-1 (LFA-1) , CD2, CD7, LIGHT, NKG2C, B7-H3 and ligands that specially bind to CD83 (such as CD83 and MD2) .
  • the intracellular signaling domain in the CAR of the present disclosure comprises a co-stimulatory signaling domain derived from CD137 (i.e., 4-1BB) .
  • the intracellular signaling domain comprises a cytoplasmic signaling domain of CD3 ⁇ and a co-stimulatory signaling domain of CD137.
  • the intracellular signaling domain comprises a co-stimulatory signaling domain of CD137 comprising the amino acid sequence of SEQ ID NO: 70.
  • the co-stimulatory signaling domains comprises up to 10 amino acid residue variations (e.g., 1, 2, 3, 4, 5, or 8) as compared to a wild-type counterpart.
  • Such co-stimulatory signaling domains comprising one or more amino acid variations may be referred to as variants. Mutation of amino acid residues of the co-stimulatory signaling domain may result in an increase in signaling transduction and enhanced stimulation of immune responses relative to co-stimulatory signaling domains that do not comprise the mutation. Mutation of amino acid residues of the co-stimulatory signaling domain may result in a decrease in signaling transduction and reduced stimulation of immune responses relative to co-stimulatory signaling domains that do not comprise the mutation.
  • the CARs of the present disclosure may comprise a hinge domain that is located between the extracellular antigen binding domain and the transmembrane domain.
  • a hinge domain is an amino acid segment that is generally found between two domains of a protein and may allow for flexibility of the protein and movement of one or both of the domains relative to one another. Any amino acid sequence that provides such flexibility and movement of the extracellular antigen binding domain relative to the transmembrane domain of the effector molecule can be used.
  • the hinge domain may contain about 10-100 amino acids, e.g., about any one of 15-75 amino acids, 20-50 amino acids, or 30-60 amino acids. In certain embodiments, the hinge domain may be at least about any one of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, or 75 amino acids in length.
  • the hinge domain is a hinge domain of a naturally occurring protein. Hinge domains of any protein known in the art to comprise a hinge domain are compatible for use in the chimeric receptors described herein. In certain embodiments, the hinge domain is at least a portion of a hinge domain of a naturally occurring protein and confers flexibility to the chimeric receptor. In certain embodiments, the hinge domain is derived from CD8 ⁇ . In certain embodiments, the hinge domain is a portion of the hinge domain of CD8 ⁇ , e.g., a fragment containing at least 15 (e.g., 20, 25, 30, 35, or 40) consecutive amino acids of the hinge domain of CD8 ⁇ . In some embodiments, the hinge domain of CD8 ⁇ comprises the amino acid sequence of SEQ ID NO: 68.
  • Hinge domains of antibodies are also compatible for use in the pH-dependent chimeric receptor systems described herein.
  • the hinge domain is the hinge domain that joins the constant domains CH1 and CH2 of an antibody.
  • the hinge domain is of an antibody and comprises the hinge domain of the antibody and one or more constant regions of the antibody.
  • the hinge domain comprises the hinge domain of an antibody and the CH3 constant region of the antibody.
  • the hinge domain comprises the hinge domain of an antibody and the CH2 and CH3 constant regions of the antibody.
  • the antibody is an IgG, IgA, IgM, IgE, or IgD antibody. In certain embodiments, the antibody is an IgG antibody. In certain embodiments, the antibody is an IgG1, IgG2, IgG3, or IgG4 antibody. In certain embodiments, the hinge region comprises the hinge region and the CH2 and CH3 constant regions of an IgG1 antibody. In certain embodiments, the hinge region comprises the hinge region and the CH3 constant region of an IgG1 antibody.
  • Non-naturally occurring peptides may also be used as hinge domains for the chimeric receptors described herein.
  • the hinge domain between the C-terminus of the extracellular ligand-binding domain of an Fc receptor and the N-terminus of the transmembrane domain is a peptide linker, such as a (GxS) n linker, wherein x and n, independently can be an integer between 3 and 12, including 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more.
  • the CARs of the present disclosure may comprise a signal peptide (also known as a signal sequence) at the N-terminus of the polypeptide.
  • signal peptides are peptide sequences that target a polypeptide to the desired site in a cell.
  • the signal peptide targets the effector molecule to the secretory pathway of the cell and will allow for integration and anchoring of the effector molecule into the lipid bilayer.
  • Signal peptides including signal sequences of naturally occurring proteins or synthetic, non-naturally occurring signal sequences, which are compatible for use in the CARs described herein will be evident to one of skill in the art.
  • the signal peptide is derived from a molecule selected from the group consisting of CD8 ⁇ , GM-CSF receptor ⁇ , and IgG1 heavy chain. In certain embodiments, the signal peptide is derived from CD8 ⁇ . In some embodiments, the signal peptide of CD8 ⁇ comprises the amino acid sequence of SEQ ID NO: 28.Costimulatory Ligands
  • a presently disclosed immune effector cell can further include at least one recombinant or exogenous co-stimulatory ligand.
  • a presently disclosed immune effector cell can be further transduced with at least one co-stimulatory ligand, such that the immune effector cell co-expresses or is induced to co-express the at least one co-stimulatory ligand.
  • co-stimulatory ligands include, but are not limited to, members of the tumor necrosis factor (TNF) superfamily, and immunoglobulin (Ig) superfamily ligands.
  • TNF tumor necrosis factor
  • Ig immunoglobulin
  • TNF superfamily members include, without limitation, nerve growth factor (NGF) , CD40L (CD40L) /CD154, CD137L/4-1BBL, TNF- ⁇ , CD134L/OX40L/CD252, CD27L/CD70, Fas ligand (FasL) , CD30L/CD153, tumor necrosis factor beta (TNFP) /lymphotoxin-alpha (LT ⁇ ) , lymphotoxin-beta (ITG ⁇ ) , CD257/B cell-activating factor (BAFF) /Blys/THANK/Tall-1, glucocorticoid-induced TNF Receptor ligand (GITRL) , and TNF-related apoptosis-inducing ligand (TRAIL) , LIGHT (TNF) , TNF-related apoptosis-inducing ligand (TRAIL) , LIGHT (TN FGF) , TNF-related apoptosis-
  • immunoglobulin (Ig) superfamily is a large group of cell surface and soluble proteins that are involved in the recognition, binding, or adhesion processes of cells. These proteins share structural features with immunoglobulin, they possess an immunoglobulin domain (fold) .
  • Immunoglobulin superfamily ligands include, but are not limited to, CD80 and CD86, both ligands for CD28, PD-L1/ (B7-H1) that ligands for PD-1.
  • the at least one co-stimulatory ligand is selected from the group consisting of 4-1BBL, CD80, CD86, CD70, OX40L, CD48, TNFRSF14, PD-L1, and combinations thereof.
  • the immune effector cell comprises one recombinant co-stimulatory ligand that is 4-1BBL. In certain embodiments, the immune effector cell comprises two recombinant co-stimulatory ligands that are 4-1BBL and CD80.
  • a presently disclosed immune effector cell can further comprise at least one exogenous cytokine.
  • a presently disclosed immune effector cell can be further transduced with at least one cytokine, such that the immune effector cell secretes the at least one cytokine as well as expresses the CAR.
  • the at least one cytokine is selected from the group consisting of IL-2, IL-3, IL-6, IL-7, IL-11, IL-12, IL-15, IL-17, IL-18, IL-9 and IL-21.
  • the cytokine is IL-15.
  • the exogenous cytokine comprises an amino acid sequence having at least 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100%sequence identity to SEQ ID NO: 33.
  • the exogenous cytokine comprises the amino acid sequence of SEQ ID NO: 33.
  • the present disclosure provides vectors for cloning and expressing any one of the fusion proteins and CARs described herein.
  • the vector is suitable for replication and integration in eukaryotic cells, such as mammalian cells.
  • the vector is a viral vector.
  • viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, lentiviral vector, retroviral vectors, vaccinia vector, herpes simplex viral vector, and derivatives thereof.
  • Viral vector technology is well known in the art and is described, for example, in Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York) , and in other virology and molecular biology manuals.
  • retroviruses provide a convenient platform for gene delivery systems.
  • the heterologous nucleic acid can be inserted into a vector and packaged in retroviral particles using techniques known in the art.
  • the recombinant virus can then be isolated and delivered to the engineered mammalian cell in vitro or ex vivo.
  • retroviral systems are known in the art.
  • adenovirus vectors are used.
  • a number of adenovirus vectors are known in the art.
  • lentivirus vectors are used.
  • self-inactivating lentiviral vectors are used.
  • self-inactivating lentiviral vectors carrying the immunomodulator (such as immune checkpoint inhibitor) coding sequence and/or self-inactivating lentiviral vectors carrying chimeric antigen receptors can be packaged with protocols known in the art.
  • the resulting lentiviral vectors can be used to transduce a mammalian cell (such as primary human T cells) using methods known in the art.
  • Vectors derived from retroviruses such as lentivirus are suitable tools to achieve long-term gene transfer, because they allow long-term, stable integration of a transgene and its propagation in progeny cells.
  • Lentiviral vectors also have low immunogenicity, and can transduce non-proliferating cells.
  • the vector comprises any one of the nucleic acids encoding a fusion protein and/or a CAR described herein.
  • the nucleic acid can be cloned into the vector using any known molecular cloning methods in the art, including, for example, using restriction endonuclease sites and one or more selectable markers.
  • the nucleic acid is operably linked to a promoter. Varieties of promoters have been explored for gene expression in mammalian cells, and any of the promoters known in the art may be used in the present disclosure. Promoters may be roughly categorized as constitutive promoters or regulated promoters, such as inducible promoters.
  • the nucleic acid encoding the fusion protein and/or a CAR is operably linked to a constitutive promoter.
  • Constitutive promoters allow heterologous genes (also referred to as transgenes) to be expressed constitutively in the host cells.
  • Exemplary constitutive promoters contemplated herein include, but are not limited to, Cytomegalovirus (CMV) promoters, human elongation factors-1 alpha (hEF1 ⁇ ) , ubiquitin C promoter (UbiC) , phosphoglycerokinase promoter (PGK) , simian virus 40 early promoter (SV40) , and chicken ⁇ -Actin promoter coupled with CMV early enhancer (CAGG) .
  • CMV Cytomegalovirus
  • hEF1 ⁇ human elongation factors-1 alpha
  • UbiC ubiquitin C promoter
  • PGK phosphoglycerokinase promoter
  • SV40 simian virus
  • the efficiencies of such constitutive promoters on driving transgene expression have been widely compared in a huge number of studies. For example, Michael C. Milone et al compared the efficiencies of CMV, hEF1 ⁇ , UbiC and PGK to drive chimeric antigen receptor expression in primary human T cells, and concluded that hEF1 ⁇ promoter not only induced the highest level of transgene expression, but was also optimally maintained in the CD4 and CD8 human T cells (Molecular Therapy, 17 (8) : 1453-1464 (2009) ) .
  • the nucleic acid encoding the CAR is operably linked to a hEF1 ⁇ promoter.
  • the nucleic acid encoding the fusion protein and/or a CAR is operably linked to an inducible promoter.
  • Inducible promoters belong to the category of regulated promoters.
  • 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.
  • 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.
  • 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.
  • the vector also contains a selectable marker gene or a reporter gene to select cells expressing the fusion protein and/or a CAR from the population of host cells transfected through lentiviral vectors.
  • selectable markers and reporter genes may be flanked by appropriate regulatory sequences to enable expression in the host cells.
  • the vector may contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the nucleic acid sequences.
  • the vector comprises more than one nucleic acid encoding the fusion protein and/or a CAR, or a TCR.
  • the vector comprises a nucleic acid comprising a first nucleic acid sequence encoding a fusion protein and a second nucleic acid sequence encoding a CAR, wherein the first nucleic acid is operably linked to the second nucleic acid via a third nucleic acid sequence encoding a self-cleaving peptide.
  • the self-cleaving peptide is selected from the group consisting of T2A, P2A and F2A.
  • the self-cleaving peptide comprises the amino acid sequence of SEQ ID NO: 75, SEQ ID NO: 76 or SEQ ID NO: 77.
  • Immuno effector cells are immune cells that can perform immune effector functions.
  • the immune effector cells express at least Fc ⁇ RIII and perform ADCC effector function.
  • immune effector cells which mediate ADCC include peripheral blood mononuclear cells (PBMC) , natural killer (NK) cells, monocytes, cytotoxic T cells, neutrophils, and eosinophils.
  • the immune effector cells are T cells.
  • the T cells are CD4+/CD8-, CD4-/CD8+, CD4+/CD8+, CD4-/CD8-, or combinations thereof.
  • the T cells produce IL-2, TFN, and/or TNF upon expressing the CAR and binding to the target cells.
  • the CD8+ T cells lyse antigen-specific target cells upon expressing the CAR and binding to the target cells.
  • the immune effector cells are NK cells.
  • the immune effector cells can be established cell lines, for example, NK-92 cells.
  • the immune effector cells are differentiated from a stem cell, such as a hematopoietic stem cell, a pluripotent stem cell, an iPS, or an embryonic stem cell.
  • a stem cell such as a hematopoietic stem cell, a pluripotent stem cell, an iPS, or an embryonic stem cell.
  • the engineered immune effector cells are prepared by introducing the CARs into the immune effector cells, such as T cells.
  • the CAR is introduced to the immune effector cells by transfecting any one of the isolated nucleic acids or any one of the vectors described above.
  • the CAR is introduced to the immune effector cells by inserting proteins into the cell membrane while passing cells through a microfluidic system, such as CELL (see, e.g., U.S. Patent Application Publication No. 20140287509) .
  • vectors or isolated nucleic acids into a mammalian cell are known in the art.
  • the vectors described can be transferred into an immune effector cell by physical, chemical, or biological methods.
  • Physical methods for introducing the vector into an immune effector cell include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and/or exogenous nucleic acids are well-known in the art. See, e.g., Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York. In certain embodiments, the vector is introduced into the cell by electroporation.
  • Biological methods for introducing the vector into an immune effector cell include the use of DNA and RNA vectors.
  • Viral vectors have become the most widely used method for inserting genes into mammalian, e.g., human cells.
  • Chemical means for introducing the vector into an immune effector cell 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.
  • colloidal dispersion systems such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes.
  • An exemplary colloidal system for use as a delivery vehicle in vitro is a liposome (e.g., an artificial membrane vesicle) .
  • RNA molecules encoding any of the CARs described herein may be prepared by a conventional method (e.g., in vitro transcription) and then introduced into the immune effector cells via known methods such as mRNA electroporation. See, e.g., Rabinovich et al., Human Gene Therapy 17: 1027-1035 (2006) .
  • the transduced or transfected immune effector cell is propagated ex vivo after introduction of the vector or isolated nucleic acid.
  • the transduced or transfected immune effector cell is cultured to propagate for at least about any of 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, or 14 days.
  • the transduced or transfected immune effector cell is further evaluated or screened to select the engineered mammalian cell.
  • Reporter genes may be used for identifying potentially transfected cells and for evaluating the functionality of regulatory sequences.
  • a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells.
  • Suitable reporter genes may include genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et al. FEBS Letters 479: 79-82 (2000) ) .
  • Suitable expression systems are well known and may be prepared using known techniques or obtained commercially.
  • nucleic acid encoding the fusion protein and/or CARs in the engineered immune effector cell include, for example, molecular biological assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR; biochemical assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological methods (such as ELISAs and Western blots) .
  • molecular biological assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR
  • biochemical assays such as detecting the presence or absence of a particular peptide, e.g., by immunological methods (such as ELISAs and Western blots) .
  • a source of T cells is obtained from a subject.
  • T cells can be obtained from a number of sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
  • any number of T cell lines available in the art may be used.
  • T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled artisan, such as Ficoll TM separation.
  • cells from the circulating blood of an individual are obtained by apheresis.
  • the apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets.
  • the cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps.
  • the cells are washed with phosphate buffered saline (PBS) .
  • 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.
  • a washing step may be accomplished by methods known to those in the art, such as by using a semi-automated “flow-through” centrifuge (for example, the Cobe 2991 cell processor, the Baxter CytoMate, or the Haemonetics Cell Saver 5) according to the manufacturer's instructions.
  • a semi-automated “flow-through” centrifuge for example, the Cobe 2991 cell processor, the Baxter CytoMate, or the Haemonetics Cell Saver 5
  • the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca 2+ -free, Mg 2+ -free PBS, PlasmaLyte A, or other saline solution with or without buffer.
  • the undesirable components of the apheresis sample may be removed and the cells directly resuspended in culture media.
  • T cells are isolated from peripheral blood lymphocytes by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLL TM gradient or by counterflow centrifugal elutriation.
  • a specific subpopulation of T cells such as CD3+, CD28+, CD4+, CD8+, CD45RA+, and CD45RO+T cells, can be further isolated by positive or negative selection techniques.
  • T cells are isolated by incubation with anti-CD3/anti-CD28 (i.e., 3 ⁇ 28) -conjugated beads, such as M-450 CD3/CD28 T, for a time period sufficient for positive selection of the desired T cells.
  • the time period is about 30 minutes. In a further embodiment, the time period ranges from 30 minutes to 36 hours or longer and all integer values there between. In a further embodiment, the time period is at least 1, 2, 3, 4, 5, or 6 hours. In certain embodiments, the time period is 10 to 24 hours. In certain embodiments, the incubation time period is 24 hours. For isolation of T cells from patients with leukemia, use of longer incubation times, such as 24 hours, can increase cell yield. Longer incubation times may be used to isolate T cells in any situation where there are few T cells as compared to other cell types, such in isolating tumor infiltrating lymphocytes (TIL) from tumor tissue or from immune-compromised individuals.
  • TIL tumor infiltrating lymphocytes
  • T cells can be preferentially selected for or against at culture initiation or at other time points during the process.
  • subpopulations of T cells can be preferentially selected for or against at culture initiation or at other desired time points.
  • multiple rounds of selection can also be used. In certain embodiments, it may be desirable to perform the selection procedure and use the “unselected” cells in the activation and expansion process. “Unselected” cells can also be subjected to further rounds of selection.
  • Enrichment of a T cell population by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells.
  • One method is cell sorting and/or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected.
  • a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CD11b, CD16, HLA-DR, and CD8.
  • T regulatory cells are depleted by anti-C25 conjugated beads or other similar method of selection.
  • the concentration of cells and surface can be varied.
  • it may be desirable to significantly decrease the volume in which beads and cells are mixed together i.e., increase the concentration of cells
  • a concentration of 2 billion cells/ml is used.
  • a concentration of 1 billion cells/ml is used.
  • greater than 100 million cells/ml is used.
  • a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/ml is used.
  • a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/ml is used. In further embodiments, concentrations of 125 or 150 million cells/ml can be used.
  • concentrations may result in increased cell yield, cell activation, and cell expansion. Further, use of high cell concentrations may allow more efficient capture of cells that may weakly express target antigens of interest, such as CD28-negative T cells, or from samples where there are many tumor cells present (i.e., leukemic blood, tumor tissue, etc. ) . Such populations of cells may have therapeutic value and would be desirable to obtain. In certain embodiments, using high concentration of cells allows more efficient selection of CD8+ T cells that normally have weaker CD28 expression.
  • the concentration of cells used is 5 ⁇ 10 6 /mL. In certain embodiments, the concentration used can be from about 1 ⁇ 10 5 /mL to 1 ⁇ 10 6 /mL, and any integer value in between.
  • the cells may be incubated on a rotator for varying lengths of time at varying speeds at either 2-10°C, or at room temperature.
  • T cells for stimulation can also be frozen after a washing step.
  • the freeze and subsequent thaw step may provide a more uniform product by removing granulocytes and to some extent monocytes in the cell population.
  • the cells may be suspended in a freezing solution.
  • one method involves using PBS containing 20%DMSO and 8%human serum albumin, or culture media containing 10%dextran 40 and 5%dextrose, 20%human serum albumin and 7.5%DMSO, or 31.25%plasmalyte-A, 31.25%dextrose 5%, 0.45%NaCl, 10%dextran 40 and 5%dextrose, 20%human serum albumin, and 7.5%DMSO or other suitable cell freezing media containing for example, Hespan and PlasmaLyte A.
  • the cells then are frozen to -80°C at a rate of 1° per minute and stored in the vapor phase of a liquid nitrogen storage tank.
  • Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at -20°C or in liquid nitrogen.
  • cryopreserved cells are thawed and washed as described herein and allowed to rest for one hour at room temperature prior to activation.
  • a blood sample or an apheresis product is taken from a generally healthy subject.
  • a blood sample or an apheresis is taken from a generally healthy subject who is at risk of developing a disease, but who has not yet developed a disease, and the cells of interest are isolated and frozen for later use.
  • the T cells may be expanded, frozen, and used at a later time.
  • samples are collected from a patient shortly after diagnosis of a particular disease as described herein but prior to any treatments.
  • the cells are isolated from a blood sample or an apheresis from a subject prior to any number of relevant treatment modalities, including but not limited to treatment with agents such as natalizumab, efalizumab, antiviral agents, chemotherapy, radiation, immunosuppressive agents, such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies, or other immunoablative agents such as CAMPATH, anti-CD3 antibodies, cytoxan, fludarabine, cyclosporin, FK506, rapamycin, mycophenolic acid, steroids, FR901228, and irradiation.
  • agents such as natalizumab, efalizumab, antiviral agents, chemotherapy, radiation, immunosuppressive agents, such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies, or other immunoablative agents such as CAMPATH, anti-CD3
  • the cells are isolated for a patient and frozen for later use in conjunction with (e.g., before, simultaneously or following) bone marrow or stem cell transplantation, T cell ablative therapy using either chemotherapy agents such as, fludarabine, external-beam radiation therapy (XRT) , cyclophosphamide, or antibodies such as OKT3 or CAMPATH.
  • chemotherapy agents such as, fludarabine, external-beam radiation therapy (XRT) , cyclophosphamide, or antibodies such as OKT3 or CAMPATH.
  • T cells are obtained from a patient directly following treatment.
  • the quality of T cells obtained may be optimal or improved for their ability to expand ex vivo.
  • these cells may be in a preferred state for enhanced engraftment and in vivo expansion.
  • mobilization for example, mobilization with GM-CSF
  • conditioning regimens can be used to create a condition in a subject wherein repopulation, recirculation, regeneration, and/or expansion of particular cell types is favored, especially during a defined window of time following therapy.
  • Illustrative cell types include T cells, B cells, dendritic cells, and other cells of the immune system.
  • the T cells prior to or after genetic modification of the T cells with the CARs described herein, can be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and U.S. Patent Application Publication No. 20060121005.
  • T cells can be expanded by contact with a surface having attached thereto an agent that stimulates a CD3/TCR complex associated signal and a ligand that stimulates a co-stimulatory molecule on the surface of the T cells.
  • T cell populations may be stimulated as described herein, such as by contact with an anti-CD3 antibody, or antigen binding fragment thereof, or an anti-CD2 antibody immobilized on a surface, or by contact with a protein kinase C activator (e.g., bryostatin) in conjunction with a calcium ionophore.
  • a ligand that binds the accessory molecule is used for co-stimulation of an accessory molecule on the surface of the T cells.
  • a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells.
  • an anti-CD3 antibody and an anti-CD28 antibody can be used as can other methods commonly known in the art (Graves J, et al., J. Immunol. 146: 2102 (1991) ; Li B, et al., Immunology 116: 487 (2005) ; Rivollier A, et al., Blood 104: 4029 (2004) ) .
  • an anti-CD28 antibody examples include 9.3, B-T3, XR-CD28 (Diaclone, Besancon, France) can be used as can other methods commonly known in the art (Berg et al., Transplant Proc. 30 (8) : 3975-3977 (1998) ; Haanen et al., J. Exp. Med. 190 (9) : 13191328 (1999) ; Garland et al., J. Immunol Meth. 227 (1-2) : 53-63 (1999) ) .
  • the primary stimulatory signal and the co-stimulatory signal for the T cell may be provided by different protocols.
  • the agents providing each signal may be in solution or coupled to a surface. When coupled to a surface, the agents may be coupled to the same surface (i.e., in “cis” formation) or to separate surfaces (i.e., in “trans” formation) . Alternatively, one agent may be coupled to a surface and the other agent in solution.
  • the agent providing the co-stimulatory signal is bound to a cell surface and the agent providing the primary activation signal is in solution or coupled to a surface. In certain embodiments, both agents can be in solution.
  • the agents may be in soluble form, and then cross-linked to a surface, such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents.
  • a surface such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents.
  • aAPCs artificial antigen presenting cells
  • the T cells are combined with agent-coated beads, the beads and the cells are subsequently separated, and then the cells are cultured.
  • the agent-coated beads and cells prior to culture, are not separated but are cultured together.
  • the beads and cells are first concentrated by application of a force, such as a magnetic force, resulting in increased ligation of cell surface markers, thereby inducing cell stimulation.
  • cell surface proteins may be ligated by allowing paramagnetic beads to which anti-CD3 and anti-CD28 are attached (3 ⁇ 28 beads) to contact the T cells.
  • the cells for example, 10 4 to 4 ⁇ 10 8 T cells
  • beads for example, anti-CD3/CD28 MACSiBead particles at a recommended titer of 1: 100
  • a buffer preferably PBS (without divalent cations such as, calcium and magnesium)
  • the target cell may be very rare in the sample and comprise only 0.01%of the sample or the entire sample (i.e., 100%) may comprise the target cell of interest.
  • any cell number is within the context of the present disclosure.
  • it may be desirable to significantly decrease the volume in which particles and cells are mixed together i.e., increase the concentration of cells
  • a concentration of about 2 billion cells/mL is used. In certain embodiments, greater than 100 million cells/mL is used. In a further embodiment, a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/mL is used. In certain embodiments, a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/mL is used. In further embodiments, concentrations of 125 or 150 million cells/mL can be used.
  • Using high concentrations may result in increased cell yield, cell activation, and cell expansion. Further, use of high cell concentrations may allow more efficient capture of cells that may weakly express target antigens of interest, such as CD28-negative T cells. Such populations of cells may have therapeutic value and would be desirable to obtain in certain embodiments. For example, using high concentration of cells allows more efficient selection of CD8+ T cells that normally have weaker CD28 expression.
  • the mixture may be cultured for several hours (about 3 hours) to about 14 days or any hourly integer value in between. In certain embodiments, the mixture may be cultured for 21 days. In certain embodiments, the beads and the T cells are cultured together for about eight days. In certain embodiments, the beads and T 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 (e.g., Minimal Essential Media or RPMI Media 1640 or, X-vivo 15, (Lonza) ) that may contain factors necessary for proliferation and viability, including serum (e.g., fetal bovine or human serum) , interleukin-2 (IL-2) , insulin, IFN- ⁇ , IL-4, IL-7, GM-CSF, IL-10, IL-12, IL-15, TGF ⁇ , and TNF- ⁇ or any other additives for the growth of cells known to the skilled artisan.
  • 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, ⁇ -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 °C) and atmosphere (e.g., air plus 5%CO 2 ) .
  • T cells that have been exposed to varied stimulation times may exhibit different characteristics.
  • typical blood or apheresed peripheral blood mononuclear cell products have a helper T cell population (TH, CD4+) that is greater than the cytotoxic or suppressor T cell population (TC, CD8) .
  • TH, CD4+ helper T cell population
  • TC, CD8 cytotoxic or suppressor T cell population
  • Ex vivo expansion of T cells by stimulating CD3 and CD28 receptors produces a population of T cells that prior to about days 8-9 consists predominately of TH cells, while after about days 8-9, the population of T cells comprises an increasingly greater population of TC cells.
  • infusing a subject with a T cell population comprising predominately of TH cells may be advantageous.
  • an antigen-specific subset of TC cells may be beneficial to expand this subset to a greater degree.
  • CD4 and CD8 markers vary significantly, but in large part, reproducibly during the course of the cell expansion process. Thus, such reproducibility enables the ability to tailor an activated T cell product for specific purposes.
  • the disclosure provides polynucleotides that encode the presently disclosed fusion protein (e.g., fusion proteins disclosed in Section 5.2 of the present disclosure) .
  • the polynucleotides of the disclosure can be in the form of RNA or in the form of DNA.
  • DNA includes cDNA, genomic DNA, and synthetic DNA; and can be double-stranded or single-stranded, and if single stranded can be the coding strand or non-coding (anti-sense) strand.
  • the polynucleotide is in the form of cDNA.
  • the polynucleotide is a synthetic polynucleotide.
  • the disclosure provides polynucleotides that encode the CAR provided herein.
  • the polynucleotides of the disclosure can be in the form of RNA or in the form of DNA.
  • DNA includes cDNA, genomic DNA, and synthetic DNA; and can be double-stranded or single-stranded, and if single stranded can be the coding strand or non-coding (anti-sense) strand.
  • the polynucleotide is in the form of cDNA.
  • the polynucleotide is a synthetic polynucleotide.
  • the present disclosure further relates to variants of the polynucleotides described herein, wherein the variant encodes, for example, fragments, analogs, and/or derivatives of the fusion protein or CAR of the disclosure.
  • the present disclosure provides a polynucleotide comprising a polynucleotide having a nucleotide sequence at least about 75%identical, at least about 80%identical, at least about 85%identical, at least about 90%identical, at least about 95%identical, and in certain embodiments, at least about 96%, 97%, 98%or 99%identical to a polynucleotide encoding the fusion protein or CAR of the disclosure.
  • a polynucleotide having a nucleotide sequence at least, for example, 95% “identical” to a reference nucleotide sequence” is intended to mean that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence can include up to five-point mutations per each 100 nucleotides of the reference nucleotide sequence.
  • a polynucleotide having a nucleotide sequence at least 95%identical to a reference nucleotide sequence up to 5%of the nucleotides in the reference sequence can be deleted or substituted with another nucleotide, or a number of nucleotides up to 5%of the total nucleotides in the reference sequence can be inserted into the reference sequence.
  • These mutations of the reference sequence can occur at the 5’ or 3’ terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.
  • the polynucleotide variants can contain alterations in the coding regions, non-coding regions, or both.
  • a polynucleotide variant contains alterations which produce silent substitutions, additions, or deletions, but does not alter the properties or activities of the encoded polypeptide.
  • a polynucleotide variant comprises silent substitutions that results in no change to the amino acid sequence of the polypeptide (due to the degeneracy of the genetic code) .
  • Polynucleotide variants can be produced for a variety of reasons, for example, to optimize codon expression for a particular host (i.e., change codons in the human mRNA to those preferred by a bacterial host such as E. coli) .
  • a polynucleotide variant comprises at least one silent mutation in a non-coding or a coding region of the sequence.
  • a polynucleotide variant is produced to modulate or alter expression (or expression levels) of the encoded polypeptide. In certain embodiments, a polynucleotide variant is produced to increase expression of the encoded polypeptide. In certain embodiments, a polynucleotide variant is produced to decrease expression of the encoded polypeptide. In certain embodiments, a polynucleotide variant has increased expression of the encoded polypeptide as compared to a parental polynucleotide sequence. In certain embodiments, a polynucleotide variant has decreased expression of the encoded polypeptide as compared to a parental polynucleotide sequence.
  • nucleic acid molecules described herein comprising the nucleic acid molecules described herein.
  • the nucleic acid molecules can be incorporated into a recombinant expression vector.
  • the present disclosure provides recombinant expression vectors comprising any of the nucleic acids of the disclosure.
  • the term “recombinant expression vector” means a genetically-modified oligonucleotide or polynucleotide construct that permits the expression of an mRNA, protein, polypeptide, or peptide by a host cell, when the construct comprises a nucleotide sequence encoding the mRNA, protein, polypeptide, or peptide, and the vector is contacted with the cell under conditions sufficient to have the mRNA, protein, polypeptide, or peptide expressed within the cell.
  • the vectors described herein are not naturally-occurring as a whole; however, parts of the vectors can be naturally-occurring.
  • the described recombinant expression vectors can comprise any type of nucleotides, including, but not limited to DNA and RNA, which can be single-stranded or double-stranded, synthesized or obtained in part from natural sources, and which can contain natural, non-natural or altered nucleotides.
  • the recombinant expression vectors can comprise naturally-occurring or non-naturally-occurring internucleotide linkages, or both types of linkages. The non-naturally occurring or altered nucleotides or internucleotide linkages do not hinder the transcription or replication of the vector.
  • the recombinant expression vector of the disclosure can be any suitable recombinant expression vector, and can be used to transform or transfect any suitable host.
  • Suitable vectors include those designed for propagation and expansion or for expression or both, such as plasmids and viruses.
  • the vector can be selected from the group consisting of the pUC series (Fermentas Life Sciences, Glen Burnie, Md. ) , the pBluescript series (Stratagene, LaJolla, Calif. ) , the pET series (Novagen, Madison, Wis. ) , the pGEX series (Pharmacia Biotech, Uppsala, Sweden) , and the pEX series (Clontech, Palo Alto, Calif.
  • Bacteriophage vectors such as ⁇ GT10, ⁇ GT11, ⁇ EMBL4, and ⁇ NM1149, ⁇ ZapII (Stratagene) can be used.
  • plant expression vectors include pBI01, pBI01.2, pBI121, pBI101.3, and pBIN19 (Clontech) .
  • animal expression vectors include pEUK-Cl, pMAM, and pMAMneo (Clontech) .
  • the recombinant expression vector may be a viral vector, e.g., a retroviral vector, e.g., a gamma retroviral vector.
  • the recombinant expression vectors are prepared using standard recombinant DNA techniques described in, for example, Sambrook et al., supra, and Ausubel et al., supra.
  • Constructs of expression vectors which are circular or linear, can be prepared to contain a replication system functional in a prokaryotic or eukaryotic host cell.
  • Replication systems can be derived, e.g., from ColE1, SV40, 2 ⁇ plasmid, ⁇ , bovine papilloma virus, and the like.
  • the recombinant expression vector may comprise regulatory sequences, such as transcription and translation initiation and termination codons, which are specific to the type of host (e.g., bacterium, plant, fungus, or animal) into which the vector is to be introduced, as appropriate, and taking into consideration whether the vector is DNA-or RNA-based.
  • regulatory sequences such as transcription and translation initiation and termination codons, which are specific to the type of host (e.g., bacterium, plant, fungus, or animal) into which the vector is to be introduced, as appropriate, and taking into consideration whether the vector is DNA-or RNA-based.
  • the recombinant expression vector can include one or more marker genes, which allow for selection of transformed or transfected hosts.
  • Marker genes include biocide resistance, e.g., resistance to antibiotics, heavy metals, etc., complementation in an auxotrophic host to provide prototrophy, and the like.
  • Suitable marker genes for the described expression vectors include, for instance, neomycin/G418 resistance genes, histidinol x resistance genes, histidinol resistance genes, tetracycline resistance genes, and ampicillin resistance genes.
  • the recombinant expression vector can comprise a native or normative promoter operably linked to the nucleotide sequence of the disclosure.
  • the selection of promoters e.g., strong, weak, tissue-specific, inducible and developmental-specific, is within the ordinary skill of the artisan.
  • the combining of a nucleotide sequence with a promoter is also within the skill of the artisan.
  • the promoter can be a non-viral promoter or a viral promoter, e.g., a cytomegalovirus (CMV) promoter, an RSV promoter, an SV40 promoter, or a promoter found in the long-terminal repeat of the murine stem cell virus.
  • CMV cytomegalovirus
  • the recombinant expression vectors can be designed for either transient expression, for stable expression, or for both. Also, the recombinant expression vectors can be made for constitutive expression or for inducible expression.
  • the recombinant expression vectors can be made to include a suicide gene.
  • suicide gene refers to a gene that causes the cell expressing the suicide gene to die.
  • the suicide gene can be a gene that confers sensitivity to an agent, e.g., a drug, upon the cell in which the gene is expressed, and causes the cell to die when the cell is contacted with or exposed to the agent.
  • Suicide genes are known in the art and include, for example, the Herpes Simplex Virus (HSV) thymidine kinase (TK) gene, cytosine deaminase, purine nucleoside phosphorylase, and nitroreductase.
  • a polynucleotide is isolated. In certain embodiments, a polynucleotide is substantially pure.
  • the host cell may be any cell that contains a heterologous nucleic acid.
  • the heterologous nucleic acid can be a vector (e.g., an expression vector) .
  • a host cell can be a cell from any organism that is selected, modified, transformed, grown, used or manipulated in any way, for the production of a substance by the cell, for example the expression by the cell of a gene, a DNA or RNA sequence, a protein or an enzyme.
  • An appropriate host may be determined.
  • the host cell may be selected based on the vector backbone and the desired result.
  • a plasmid or cosmid can be introduced into a prokaryote host cell for replication of several types of vectors.
  • Bacterial cells such as, but not limited to DH5 ⁇ , JM109, and KCB, Competent Cells, and SOLOPACK Gold Cells, can be used as host cells for vector replication and/or expression.
  • bacterial cells such as E. coli LE392 could be used as host cells for phage viruses.
  • Eukaryotic cells that can be used as host cells include, but are not limited to yeast (e.g., YPH499, YPH500 and YPH501) , insects and mammals.
  • mammalian eukaryotic host cells for replication and/or expression of a vector include, but are not limited to, HeLa, NIH3T3, Jurkat, 293, COS, Saos, PC12, SP2/0 (American Type Culture Collection (ATCC) , Manassas, VA, CRL-1581) , NS0 (European Collection of Cell Cultures (ECACC) , Salisbury, Wiltshire, UK, ECACC No. 85110503) , FO (ATCC CRL-1646) and Ag653 (ATCC CRL-1580) murine cell lines.
  • An exemplary human myeloma cell line is U266 (ATCC CRL-TIB-196) .
  • Other useful cell lines include those derived from Chinese Hamster Ovary (CHO) cells such as CHO-K1SV (Lonza Biologics, Walkersville, MD) , CHO-K1 (ATCC CRL-61) or DG44.
  • the present disclosure further provides pharmaceutical compositions comprising a cell of the present disclosure (e.g., cells disclosed in Section 5.3 of the present disclosure) .
  • a pharmaceutical composition comprises a therapeutically effective amount of the presently disclosed cell (e.g., cells disclosed in Section 5.3 of the present disclosure) and a pharmaceutically acceptable excipient.
  • a pharmaceutical composition comprising a therapeutically effective amount of a nucleic acid provided herein, e.g., in a vector, and a pharmaceutically acceptable excipient, e.g., suitable for gene therapy.
  • excipient can also refer to a diluent, adjuvant (e.g., Freunds’ adjuvant (complete or incomplete) , carrier or vehicle.
  • adjuvant e.g., Freunds’ adjuvant (complete or incomplete)
  • Pharmaceutical excipients can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid excipients.
  • Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
  • the composition if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. Examples of suitable pharmaceutical excipients are described in Remington’s Pharmaceutical Sciences (1990) Mack Publishing Co., Easton, PA. Such compositions will contain a prophylactically or therapeutically effective amount of the active ingredient provided herein, such as in purified form, together with a suitable amount of excipient so as to provide the form for proper administration to the patient.
  • the formulation should suit the mode of administration.
  • the choice of excipient is determined in part by the particular cell, binding molecule, and/or antibody, and/or by the method of administration. Accordingly, there are a variety of suitable formulations.
  • acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers, antioxidants including ascorbic acid, methionine, Vitamin E, sodium metabisulfite; preservatives, isotonicifiers, stabilizers, metal complexes (e.g., Zn-protein complexes) ; chelating agents such as EDTA and/or non-ionic surfactants.
  • Buffers may be used to control the pH in a range which optimizes the therapeutic effectiveness, especially if stability is pH dependent.
  • Suitable buffering agents for use with the present disclosure include both organic and inorganic acids and salts thereof.
  • buffers may comprise histidine and trimethylamine salts such as Tris.
  • Preservatives may be added to retard microbial growth.
  • Suitable preservatives for use with the present disclosure include octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium halides (e.g., chloride, bromide, iodide) , benzethonium chloride; thimerosal, phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol, 3-pentanol, and m-cresol.
  • octadecyldimethylbenzyl ammonium chloride hexamethonium chloride
  • benzalkonium halides e.g., chloride, bromide, iodide
  • benzethonium chloride thimerosal, phenol, butyl or
  • Tonicity agents can be present to adjust or maintain the tonicity of liquid in a composition.
  • stabilizers When used with large, charged biomolecules such as proteins and antibodies, they are often termed “stabilizers” because they can interact with the charged groups of the amino acid side chains, thereby lessening the potential for inter and intra-molecular interactions.
  • exemplary tonicity agents include polyhydric sugar alcohols, trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol and mannitol.
  • excipients include: (1) bulking agents, (2) solubility enhancers, (3) stabilizers and (4) agents preventing denaturation or adherence to the container wall.
  • excipients include: polyhydric sugar alcohols (enumerated above) ; amino acids such as alanine, glycine, glutamine, asparagine, histidine, arginine, lysine, ornithine, leucine, 2-phenylalanine, glutamic acid, threonine, etc.; organic sugars or sugar alcohols such as sucrose, lactose, lactitol, trehalose, stachyose, mannose, sorbose, xylose, ribose, ribitol, myoinisitose, myoinisitol, galactose, galactitol, glycerol, cyclitols (e.g., inositol) , polyethylene glycol; sulfur
  • Non-ionic surfactants or detergents may be present to help solubilize the therapeutic agent as well as to protect the therapeutic protein against agitation-induced aggregation, which also permits the formulation to be exposed to shear surface stress without causing denaturation of the active therapeutic protein or antibody.
  • Suitable non-ionic surfactants include, e.g., polysorbates (20, 40, 60, 65, 80, etc. ) , polyoxamers (184, 188, etc. ) , polyols, polyoxyethylene sorbitan monoethers ( etc.
  • lauromacrogol 400 lauromacrogol 400, polyoxyl 40 stearate, polyoxyethylene hydrogenated castor oil 10, 50 and 60, glycerol monostearate, sucrose fatty acid ester, methyl celluose and carboxymethyl cellulose.
  • Anionic detergents that can be used include sodium lauryl sulfate, dioctyle sodium sulfosuccinate and dioctyl sodium sulfonate.
  • Cationic detergents include benzalkonium chloride or benzethonium chloride.
  • compositions are preferably sterile.
  • the pharmaceutical composition may be rendered sterile by filtration through sterile filtration membranes.
  • the pharmaceutical compositions herein generally can be placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
  • the route of administration is in accordance with known and accepted methods, such as by single or multiple bolus or infusion over a long period of time in a suitable manner, e.g., injection or infusion by subcutaneous, intravenous, intraperitoneal, intramuscular, intraarterial, intralesional or intraarticular routes, topical administration, inhalation or by sustained release or extended-release means.
  • a pharmaceutical composition can be provided as a controlled release or sustained release system.
  • a pump may be used to achieve controlled or sustained release (see, e.g., Sefton, Crit. Ref. Biomed. Eng. 14: 201-40 (1987) ; Buchwald et al., Surgery 88: 507-16 (1980) ; and Saudek et al., N. Engl. J. Med. 321: 569-74 (1989) ) .
  • polymeric materials can be used to achieve controlled or sustained release of a prophylactic or therapeutic agent (e.g., a fusion protein as described herein) or a composition provided herein (see, e.g., Medical Applications of Controlled Release (Langer and Wise eds., 1974) ; Controlled Drug Bioavailability, Drug Product Design and Performance (Smolen and Ball eds., 1984) ; Ranger and Peppas, J. Macromol. Sci. Rev. Macromol. Chem. 23: 61-126 (1983) ; Levy et al., Science 228: 190-92 (1985) ; During et al., Ann. Neurol.
  • a prophylactic or therapeutic agent e.g., a fusion protein as described herein
  • a composition provided herein see, e.g., Medical Applications of Controlled Release (Langer and Wise eds., 1974) ; Controlled Drug Bioavailability, Drug Product Design and Performance (
  • polymers used in sustained release formulations include, but are not limited to, poly (2-hydroxy ethyl methacrylate) , poly (methyl methacrylate) , poly (acrylic acid) , poly (ethylene-co-vinyl acetate) , poly (methacrylic acid) , polyglycolides (PLG) , polyanhydrides, poly (N-vinyl pyrrolidone) , poly (vinyl alcohol) , polyacrylamide, poly (ethylene glycol) , polylactides (PLA) , poly (lactide-co-glycolides) (PLGA) , and polyorthoesters.
  • the polymer used in a sustained release formulation is inert, free of leachable impurities, stable on storage, sterile, and biodegradable.
  • a controlled or sustained release system can be placed in proximity of a particular target tissue, for example, the nasal passages or lungs, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, Medical Applications of Controlled Release Vol. 2, 115-38 (1984) ) . Controlled release systems are discussed, for example, by Langer, Science 249: 1527-33 (1990) . Any technique known to one of skill in the art can be used to produce sustained release formulations comprising one or more agents as described herein (see, e.g., U.S.
  • compositions described herein may also contain more than one active compound or agent as necessary for the particular indication being treated.
  • the composition may comprise a cytotoxic agent, chemotherapeutic agent, cytokine, immunosuppressive agent, or growth inhibitory agent.
  • cytotoxic agent chemotherapeutic agent
  • cytokine cytokine
  • immunosuppressive agent or growth inhibitory agent.
  • growth inhibitory agent Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
  • the active ingredients may also be entrapped in microcapsules prepared, for example, by coascervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly- (methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • compositions and delivery systems are known and can be used with the therapeutic agents provided herein, including, but not limited to, encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the antibody or therapeutic molecule provided herein, construction of a nucleic acid as part of a retroviral or other vector, etc.
  • the pharmaceutical composition provided herein contains the cells in amounts effective to treat or prevent the disease or disorder, such as a therapeutically effective or prophylactically effective amount.
  • Therapeutic or prophylactic efficacy in certain embodiments is monitored by periodic assessment of treated subjects. For repeated administrations over several days or longer, depending on the condition, the treatment is repeated until a desired suppression of disease symptoms occurs. However, other dosage regimens may be useful and can be determined.
  • compositions e.g., compositions disclosed in Section 5.4 of the present disclosure
  • Such methods and uses include therapeutic methods and uses, for example, involving administration of the cells or compositions containing the same, to a subject having a disease, condition, or disorder.
  • the cells and/or composition is administered in an effective amount to effect treatment of the disease or disorder.
  • Uses include uses of the cells and compositions in such methods and treatments, and in the preparation of a medicament in order to carry out such therapeutic methods.
  • the methods are carried out by administering the cells or compositions comprising the same, to the subject having or suspected of having the disease or condition. In certain embodiments, the methods thereby treat the disease or disorder in the subject.
  • the cells are administered as part of a combination treatment, such as simultaneously with or sequentially with, in any order, another therapeutic intervention, such as another antibody or engineered cell or receptor or agent, such as a cytotoxic or therapeutic agent.
  • another therapeutic intervention such as another antibody or engineered cell or receptor or agent, such as a cytotoxic or therapeutic agent.
  • the cells 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 some contexts, 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 certain embodiments, the cells are administered prior to the one or more additional therapeutic agents. In certain embodiments, the cells are administered after to the one or more additional therapeutic agents.
  • the additional therapeutic treatment is an antibody treatment.
  • the antibody treatment targets the antigen bound by the antigen-binding domain of the fusion protein.
  • the fusion protein degrades the antigen expressed on the cells comprising the fusion protein, thus protects the cells from being attacked and/or killed by the antibody treatment.
  • the fusion protein improves the proliferation and persistent of the cells.
  • the antibody is an anti-CD38 antibody.
  • the antibody treatment is a daratumumab treatment.
  • the antibody is an anti-CS-1 antibody (such as elotuzumab) .
  • the antibody is an anti-CD25 antibody (such as daclizumab.
  • the antibody is an anti-CD52 antibody (such as alemtuzumab) .
  • the treatment provided herein cause complete or partial amelioration or reduction of a disease or disorder, or a symptom, adverse effect or outcome, or phenotype associated therewith.
  • 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.
  • the terms include, but do not imply complete curing of a disease or complete elimination of any symptom or effect (s) on all symptoms or outcomes.
  • the treatment provided herein delay development of a disease or disorder, e.g., defer, hinder, slow, retard, stabilize, suppress and/or postpone development of the disease (such as cancer) .
  • This delay can be of varying lengths of time, depending on the history of the disease and/or individual being treated.
  • a sufficient or significant delay can, in effect, encompass prevention, in that the individual does not develop the disease or disorder.
  • a late stage cancer such as development of metastasis, may be delayed.
  • the method or the use provided herein prevents a disease or disorder.
  • the disease or disorder is cancer.
  • Illustrative cancer for which the presently disclosed subject matter can be used include, but are not limited to leukemias (e.g., acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, chronic leukemia, chronic myelocytic leukemia, chronic lymphocytic leukemia) , polycythemia vera, lymphoma (Hodgkin's disease, non-Hodgkin's disease) , Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors such as sarcomas and carcinomas (e.g., fibrosarcoma, myosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma,
  • the cancer is one or more of blood cancer, multiple myeloma, B cell leukemia, multiple myeloma, lymphoblastic leukemia (ALL) , chronic lymphocytic leukemia, non-Hodgkin's lymphoma, and ovarian cancer.
  • the blood cancer is one or more of B cell leukemia, acute lymphoblastic leukemia (ALL) , chronic lymphocytic leukemia, and non-Hodgkin's lymphoma.
  • the cancer is multiple myeloma (MM) , acute leukemias (including but not limited to acute myeloid leukemia (AML) , B-cell acute lymphoid leukemia (BALL) , T-cell acute lymphoid leukemia (TALL) , and acute lymphoid leukemia (ALL) ) , chronic leukemias (including but not limited to chronic myelogenous leukemia (CML) and chronic lymphocytic leukemia (CLL) ) , myelodysplastic syndrome, myeloproliferative neoplasms, chronic myeloid leukemia (CML) , and Blastic plasmacytoid dendritic cell neoplasm.
  • acute leukemias including but not limited to acute myeloid leukemia (AML) , B-cell acute lymphoid leukemia (BALL) , T-cell acute lymphoid leukemia (TALL) , and acute lymphoid leukemia (
  • the methods include adoptive cell therapy, whereby genetically engineered cells expressing the provided fusion proteins and/or CARs are administered to a subject.
  • Such administration can promote activation of the cells (e.g., T cell activation) in a targeted manner, such that the cells of the disease or disorder are targeted for destruction.
  • the methods include administration of the cells or a composition containing the cells to a subject, tissue, or cell, such as one having at risk for, or suspected of having the disease or disorder.
  • the cells, populations, and compositions are administered to a subject having the particular disease or disorder to be treated, e.g., via adoptive cell therapy, such as adoptive T cell therapy.
  • the cells or compositions are administered to the subject, such as a subject having or at risk for the disease or disorder.
  • the methods thereby treat, e.g., ameliorate one or more symptom of the disease or disorder, such as by lessening tumor burden in a cancer.
  • the cell therapy (e.g., adoptive T cell therapy or NK cell therapy) is carried out by autologous transfer, in which the cells are isolated and/or otherwise prepared from the subject who is to receive the cell therapy, or from a sample derived from such a subject.
  • the cells are derived from a subject in need of a treatment and the cells, following isolation and processing are administered to the same subject.
  • the cell therapy (e.g., adoptive T cell therapy or NK cell therapy) is carried out by allogeneic transfer, in which the cells are isolated and/or otherwise prepared from a subject other than a subject who is to receive or who ultimately receives the cell therapy, e.g., a first subject.
  • the cells then are administered to a different subject, e.g., a second subject, of the same species.
  • a different subject e.g., a second subject
  • the first and second subjects are genetically identical.
  • the first and second subjects are genetically similar.
  • the second subject expresses the same HLA class or supertype as the first subject.
  • the cell therapy e.g., adoptive T cell therapy or NK cell therapy
  • the subject, to whom the cells, cell populations, or compositions are administered is a primate, such as a human.
  • the subject can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects.
  • the subject is a validated animal model for disease, adoptive cell therapy, and/or for assessing toxic outcomes.
  • the cells or compositions can be administered by any suitable means, for example, by injection, e.g., intravenous or subcutaneous injections, intraocular injection, periocular injection, subretinal injection, intravitreal injection, trans-septal injection, subscleral injection, intrachoroidal injection, intracameral injection, subconjectval injection, subconjuntival injection, sub-Tenon's injection, retrobulbar injection, peribulbar injection, or posterior juxtascleral delivery.
  • they are administered by parenteral, intrapulmonary, and intranasal, and, if desired for local treatment, intralesional administration.
  • Parenteral infusions include intramuscular, intravenous, intraarterial, intraperitoneal, or subcutaneous administration.
  • the amount of a prophylactic or therapeutic agent provided herein that will be effective in the prevention and/or treatment of a disease or condition can be determined by standard clinical techniques. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems.
  • the appropriate dosage of the binding molecule or cell may depend on the type of disease or disorder to be treated, the type of binding molecule, the severity and course of the disease or disorder, whether the therapeutic agent is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response to the agent, and the discretion of the attending physician.
  • the compositions, molecules and cells are in certain embodiments suitably administered to the patient at one time or over a series of treatments.
  • a subject may be administered the range of about one million to about 100 billion cells and/or that amount of cells per kilogram of body weight.
  • the pharmaceutical composition comprises any one of the engineered immune cells described herein, the pharmaceutical composition is administered at a dosage of at least about any of 10 4 , 10 5 , 10 6 , 10 7 , 10 8 , or 10 9 cells/kg of body weight of the individual. Dosages may vary depending on attributes particular to the disease or disorder and/or patient and/or other treatments.
  • the pharmaceutical composition is administered for a single time. In certain embodiments, the pharmaceutical composition is administered for multiple times (such as any of 2, 3, 4, 5, 6, or more times) . In certain embodiments, the pharmaceutical composition is administered once or multiple times during a dosing cycle.
  • a dosing cycle can be, e.g., 1, 2, 3, 4, 5 or more week (s) , or 1, 2, 3, 4, 5, or more month (s) .
  • the optimal dosage and treatment regime for a particular patient can be determined by one skilled in the art of medicine by monitoring the patient for signs of disease and adjusting the treatment accordingly.
  • the biological activity of the engineered cell populations is measured by any of a number of known methods.
  • Parameters to assess include specific binding of an engineered or natural T cell or other immune cell to antigen, in vivo, e.g., by imaging, or ex vivo, e.g., by ELISA or flow cytometry.
  • the ability of the engineered cells to destroy target cells can be measured using any suitable method known in the art, such as cytotoxicity assays described in, for example, Kochenderfer et al., J. Immunotherapy, 32 (7) : 689-702 (2009) , and Herman et al. J.
  • the biological activity of the cells also can be measured by assaying expression and/or secretion of certain cytokines, such as CD107a, IFN ⁇ , IL-2, and TNF.
  • the biological activity is measured by assessing clinical outcome, such as reduction in tumor burden or load.
  • a method for producing any of the cells described above involves introducing into a precursor cell a nucleic acid molecule encoding any of the fusion protein or the polypeptide described herein, wherein the fusion protein or the polypeptide upon expression results in down-modulation of a target protein in the cell.
  • the down-modulation comprises reducing cell surface expression of a target protein.
  • the method futher comprises introducing into the precursor cell a second nucleic acid sequence encoding an antigen-recognizing receptor that binds to an antigen, optionally wherein the antigen-recognizing receptor is a chimeric antigen receptor (CAR) .
  • CAR chimeric antigen receptor
  • kits, unit dosages, and articles of manufacture comprising any of the fusion proteins and cells described herein.
  • a kit is provided which contains any one of the pharmaceutical compositions described herein and preferably provides instructions for its use.
  • kits of the present application are in suitable packaging.
  • suitable packaging includes, but is not limited to, vials, bottles, jars, flexible packaging (e.g., sealed Mylar or plastic bags) , and the like. Kits may optionally provide additional components such as buffers and interpretative information.
  • the present application thus also provides articles of manufacture, which include vials (such as sealed vials) , bottles, jars, flexible packaging, and the like.
  • the article of manufacture can comprise a container and a label or package insert on or associated with the container.
  • Suitable containers include, for example, bottles, vials, syringes, etc.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition which is effective for treating a disease or disorder (such as cancer) described herein, and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle) .
  • the label or package insert indicates that the composition is used for treating the particular condition in an individual.
  • the label or package insert will further comprise instructions for administering the composition to the individual.
  • the label may indicate directions for reconstitution and/or use.
  • the container holding the pharmaceutical composition may be a multi- use vial, which allows for repeat administrations (e.g., from 2-6 administrations) of the reconstituted formulation.
  • Package insert refers to instructions customarily included in commercial packages of therapeutic products that contain information about the indications, usage, dosage, administration, contraindications and/or warnings concerning the use of such therapeutic products.
  • the article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI) , phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
  • BWFI bacteriostatic water for injection
  • kits or article of manufacture may include multiple unit doses of the pharmaceutical composition and instructions for use, packaged in quantities sufficient for storage and use in pharmacies, for example, hospital pharmacies and compounding pharmacies.
  • the disclosure is generally disclosed herein using affirmative language to describe the numerous embodiments.
  • the disclosure also specifically includes embodiments in which particular subject matter is excluded, in full or in part, such as substances or materials, method steps and conditions, protocols, procedures, assays or analysis.
  • the disclosure is generally not expressed herein in terms of what the disclosure does not include, aspects that are not expressly included in the disclosure are nevertheless disclosed herein.
  • the instant example shows exemplary fusion proteins designed according to the protein degradation technology of the present disclosure.
  • the presently disclosed fusion proteins are designated as PDT molecules in the Examples, see FIG. 1.
  • the target protein in the engineered cells that express the fusion protein is brought to the intracellular lysosome for protein degradation.
  • the target protein is down-regulated in a non-gene editing way.
  • Table 6 shows the constructs of exemplary fusion proteins of the present disclosure.
  • the instant example shows the construction of engineered NK or T cells expressing PDT constructs.
  • a nucleotide sequence encoding a polypeptide comprising from the N-terminus to the C-terminus was chemically synthesized and cloned into a pre-modified retroviral vector (MSCV vector) , downstream and operably linked to a constitutive hEF1 ⁇ promoter for in vitro transcription.
  • the vector comprises a nucleotide sequence encoding a polypeptide of CAR or EGFP (SEQ ID NO: 18) for co-expression with the PDT constructs.
  • the PDT constructs and CAR are linked by a self-cleaving peptide (e.g., P2A, the amino acid sequence is set forth in in SEQ ID NO: 75) .
  • the PDT constructs and EGFP are linked by a self-cleaving peptide (e.g., P2A) .
  • Transient retroviral supernatants were produced as exemplified in Blood (2006) 108 (12) : 3890–3897. To verify the protein degradation function of the PDT molecules, various antibodies were used. Constructs of exemplary PDT molecules are shown in Table 5.
  • CD38-1 binding domain is an anti-CD38 scFv derived from daratumumab and the amino acid sequence of CD38-1 binding domain is shown in SEQ ID NO: 19.
  • CD38-2 binding domain is an anti-CD38 V H H disclosed in International Patent Publication No. WO2017081211, and its amino acid sequence is set forth in SEQ ID NO: 20.
  • CD38-3 binding domain is a multivalent antibody fragment having two anti-CD38 V H Hs, which are disclosed in International Patent Publication No. WO2017025038, and its amino acid sequence is set forth in SEQ ID NO: 21.
  • CD7 binding domain is an ani-CD7 V H H, which is disclosed in International Patent Publication No. WO2020135870, and its amino acid sequence is set forth in SEQ ID NO: 22.
  • the transmembrane domain (TM) and intracellular domain (ID) of TfR has the amino acid sequence of SEQ ID NO: 2;
  • the transmembrane domain (TM) and intracellular domain (ID) of LDLR has the amino acid sequence of SEQ ID NO: 3;
  • the transmembrane domain (TM) and intracellular domain (ID) of FcRn has the amino acid sequence of SEQ ID NO: 4.
  • BCMA CAR is disclosed in International Patent Publication No. WO2021121228 and the amino acid sequence is set forth in SEQ ID NO: 31;
  • CLL-1 CAR is disclosed in International Patent Publication No. WO2020052542 and the amino acid sequence is set forth in SEQ ID NO: 32.
  • PBMCs Human peripheral blood mononuclear cells
  • PBMCs Human peripheral blood mononuclear cells
  • PBMCs were purchased from HemaCare Corporation.
  • PBMCs were thawed and cultured with a K562 genetically modified membrane bound IL-15 and a 4-1BB ligand (i.e., K562-mb15-41BBL) .
  • the cells were expanded using stem cell growth medium (SCGM; Cell Genix, Freiburg) supplemented with 50 IU of IL-2/mL of culture medium.
  • SCGM stem cell growth medium
  • After 7 days of culture cells were collected and purified using anti-CD3 dynabeads (Miltenyi, Cat#11365D) .
  • the resulting NK cells were cultured and expanded in SCGM medium supplemented with 50 IU of IL-2/mL of culture medium.
  • NK cells were collected and suspended at a concentration of 0.25 ⁇ l0 6 cells in 2 mL of RPMI-1640 medium. Retrovirus supernatant was added to the NK cells, and the cells were incubated at 37 °C overnight. Following incubation, the cells were pelleted by centrifugation and medium was replace with fresh SCGM with 200 IU of IL-2/mL culture medium. Transduced NK cells were cultured, and used for experiments following their expansion for 12 to 20 days.
  • PBMCs were thawed in 2 mL 37°C pre-warmed R10 with 100IU/mL IL-2, and the cell pellet was re-suspended softly. Cells were quantified and the PBMC sample was ready for experimentation. Human T cells were purified from PBMCs using Miltenyi Pan T cell isolation kit (Cat#130-096-535) .
  • the prepared T cells were subsequently pre-activated for 48 hours with human T cell Activation/Expansion kit (Milteny#130-091-441) by using one loaded anti-Biotin MACSiBead Particle per two cells (bead-to-cell ratio 1: 2) .
  • the pre-activated T cells were transduced with Retrovirus stock by centrifugation at 1000 g, 32 °C for 1h. The transduced cells were then transferred to the cell culture incubator for transgene expression under suitable conditions. The next day, the transduced cells were centrifuged and replaced with fresh media, the cells concentration was measured every 2 days, and fresh media were added to continue the expansion. 8.3.
  • Example 3 Quantification of receptor expression
  • Cells expressing PDT constructs were evaluated for expression of the system by flow cytometry. An aliquot of cells is collected from the culture, washed, pelleted, and re-suspended in 100 ⁇ L PBS, supplemented with 0.5%FBS and diluted binding antibody (1/100) . Re-suspended cells were in about 100 ⁇ L of staining buffer (including human BCMA protein solution (ACRO Biosystems, Cat#BCA-HF254) and anti-human CD38-multi-epitope antibody (Cytognos, Cat#CYT-38F2-A, incubated at 4°C for 30 minutes. Viability dye eFluor780 or SYTOX Blue viability stain was also added according to manufacturer’s instructions. Post incubation, cells were washed twice in PBS and re-suspended in 100 to 200 ul PBS for analysis. The mean fluorescence of the system was quantified by flow cytometry.
  • staining buffer including human BCMA protein solution (AC
  • FIG. 2A shows CD38 down-regulated on NK cells by expressing PDT-1-CD38-1 construct.
  • the virus By transduction the virus with the design of chimeric TfR (transmembrane &intercellular domain) fused with CD38 antibody on NK cells, the surface expression of CD38 (analyzed with multi-clone CD38 antibody) on transduced NK cells (EGFP+ cells) decreased.
  • FIG. 2B shows CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-1-CD38-1 or PDT-1-CD38-2 construct. Both PDT-1-CD38-1 or PDT-1-CD38-2 could efficiently down-regulate the expression of CD38 on CAR positive NK cells.
  • FIG. 1A shows CD38 down-regulated on NK cells by expressing PDT-1-CD38-1 construct.
  • FIG. 2C shows the surface expression of CD38 on PDT-1-CD38-1/EGFP expressing Pan-T cells.
  • the PDT-1-CD38-1 construct can decrease the expression of CD38 on EGFP+ pan-T cells.
  • FIG. 2D shows the surface CD7 expression was down-regulated on NK cells by expressing PDT-1-CD7 construct. The above results suggest that different target proteins can be down-regulated by PDT-1 construct on both NK and T cells with or without CAR.
  • FIG. 3A shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-2 construct.
  • PDT-2-CD38-3 CD38-3 binding domain fused with LDLR transmembrane and intracellular domain
  • FIG. 3B shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-4 construct.
  • PDT-4 construct By expressing functional peptide PDT-4-CD38-2 (CD38-2 binding domain fused with VLDLR transmembrane and intracellular domain) , the expression of CD38 on CAR-NK cells decreased.
  • FIG. 3C shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-5 construct.
  • PDT-5-CD38-2 CD38-2 binding domain fused with LRP5 transmembrane and intracellular domain
  • FIG. 3D shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-6 construct.
  • PDT-6-CD38-2 CD38-2 binding domain fused with mutant TfR (m1TfR) transmembrane and intracellular domain
  • FIG. 3E shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-7 construct.
  • PDT-7-CD38-2 CD38-2 binding domain fused with mutant TfR (m2TfR) transmembrane and intracellular domain
  • FIG. 3F shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-8 construct.
  • PDT-8-CD38-2 CD38-2 binding domain fused with ASGR1 transmembrane and intracellular domain
  • FIG. 3G shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-9 construct.
  • PDT-9-CD38-2 CD38-2 binding domain fused with ASGR2 transmembrane and intracellular domain
  • FIG. 3H shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-10 construct.
  • PDT-10-CD38-2 CD38-2 binding domain fused with MPRD transmembrane and intracellular domain
  • FIG. 3I shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-11 construct.
  • PDT-11-CD38-2 CD38-2 binding domain fused with VEGFR2 transmembrane and intracellular domain
  • FIG. 3J shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-12 construct.
  • PDT-12-CD38-2 CD38-2 binding domain fused with IntegrinaV transmembrane, intracellular domain and ITB3
  • the expression of CD38 on CAR-NK cells decreased.
  • FIG. 3K shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-13 construct.
  • PDT-13-CD38-2 CD38-2 binding domain fused with TfR
  • FIG. 3L shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-14 construct.
  • PDT-14-CD38-2 CD38-2 binding domain fused with GLUT4
  • the expression of CD38 on CAR-NK cells decreased.
  • FIG. 3M shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-15 construct.
  • PDT-15-CD38-2 CD38-2 binding domain fused with ApoER2 transmembrane and intracellular domain
  • FIG. 3N shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-16 construct.
  • PDT-16-CD38-2 CD38-2 binding domain fused with Beta arrestin 2
  • the expression of CD38 on CAR-NK cells decreased.
  • FIG. 3O shows the in vitro evaluation of CD38 down-regulated on BCMA CAR-NK cells by expressing PDT-17 construct.
  • PDT-17-CD38-2 CD38-2 binding domain fused with TfR transmembrane domain
  • FIG. 4 shows CD38 expression on BCMA CAR-NK cells and PDT-3-CD38-3/BCMA CAR NK cells.
  • the CD38 expression were detected on day 4, day 7 and day 10 after transduction.
  • functional peptide PDT-3 CD38-3 binding domain fused with FcRn transmembrane and intracellular domain
  • CD38 expression on CAR positive cells of PDT-3-CD38-3/BCMA CAR transduced NK cells CD38 + CAR + %) decreased, compared to that on BCMA CAR NK cells.
  • the expression of CD38 were consistently down-regulated on PDT-3-CD38-3/BCMA CAR-NK cells.
  • Un-NK cells Un-transduced NK cells
  • BCMA CAR-NK cells BCMA CAR-NK cells
  • PDT-1-CD38-1/BCMA CAR-NK cells with PCT-1-CD38-1 construct were prepared using PBMCs from HLA-A2 + donor via the method described in Example 2, and as graft cells co-cultured with PBMCs (HLA-A2 - ) and CD38 antibody (200 g/mL) to conduct MLR experiments to evaluate the effect of cell preparations remaining in the presence of both CD38 antibody and host cells.
  • the CD38 antibody used in this experiment was Daratumumab or “Dara” hereinafter, purchased from Janssen Biotech (Darzalex) . There were four different co-culture systems in this experiment:
  • Group 1 PBMCs (HLA-A2 - ) and Un-NK cells;
  • PBMCs HLA-A2 -
  • Dara 200 g/mL
  • Un-NK cells Un-NK cells
  • Group 3 PBMCs (HLA-A2 - ) , Dara (200 g/mL) and BCMA CAR-NK cells;
  • Group 4 PBMCs (HLA-A2 - ) , Dara (200 g/mL) and PDT-1-CD38-1/BCMA CAR-NK cells.
  • HLA-A2 + graft cells
  • HLA-A2 + Un-NK cells, BCMA CAR-NK cells or PDT-1-CD38-1/BCMA CAR-NK cells
  • the ratio was calculated according to the CAR positive cells data. Every 48 hours, the proportion of HLA-A2 + cells were detected by flow cytometry.
  • the experimental results show that in the presence of allogeneic PBMC immune rejection and the treatment of Dara, the proportion of graft cells (HLA-A2 + cells, also labeled as target cells in FIGs. 5A and 5B) of Group 2 was decreased from 19.4% (on Day 0) to 0.055% (on Day 6) and that of Group 3 was decreased from 17.4% (on Day 0) to 0.078% (on Day 6) , which means the proportion of Un-NK cells and BCMA CAR-NK cells (without PDT constructs) significantly decreased ( ⁇ 1%) on day 6 (FIG. 5A and 5B) .
  • the experiment results indicate that NK cells will be cleared by Dara treatment.
  • CAR-NK cells with PDT-1-CD38-1 expression could down-regulate CD38 on NK cells in a NCG mouse model (U937-luc model) with a leukemia cell line tumor xenograft, and the CD38 down-regulated CAR-NK cells survived well with good expansion.
  • Wild type IL-15 (SEQ ID NO: 33) with a signal peptide was co-expressed with CLL-1 CAR via s self-cleaving peptide (e.g., P2A, as shown in SEQ ID NO: 75) for supporting NK cells in vivo expansion in this animal study.
  • CLL-1 CAR-NK cells (armored with IL-15)
  • PDT-1-CD38-1/CLL-1 CAR-NK cells armored with IL-15
  • HLA-A2 + donor were prepared as described in Examples 2.
  • NCG mice were injected intravenously with U937-Luc cells (1 ⁇ 10 6 cells/mouse, CLL-1 positive human monoblastic leukemia cell line, #ATCC CRL-1593.2 TM , transduced with Luciferase) .
  • tumor engrafted mice were infused with 4 M CAR positive CLL-1 CAR-NK cells or PDT-1-CD38-1/CLL-1 CAR-NK cells.
  • Dara (10 mg/kg) was injected (i. p. ) to mice in PDT-1-CD38-1/CLL-1 CAR-NK cells group from day 0 (once dose every 2 to 3 days, 3 times each week) .
  • a HBSS (-/-) vehicle control i.e., “Vehicle, i.v. ”
  • CLL-1 CAR-NK cells and PDT-1-CD38-1/CLL-1 CAR-NK cells showed similar PK in mice peripheral blood, indicating the CD38 down-regulated CAR-NK cells survived well with good expansion under Dara treatment.
  • CD38+/HLA-A2+ By analyzed the percentage of CD38+/HLA-A2+ in mice peripheral blood, there were almost no CD38 + HLA-A2 + cells ( ⁇ 0.5%) in the group of mice treated with PDT-1-CD38-1/CLL-1 CAR-NK cells (as shown in FIG. 6B) .

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Abstract

La présente divulgation concerne des protéines de fusion pour la dégradation de protéines cibles par l'intermédiaire d'une voie de dégradation lysosomale, et des cellules comprenant de telles protéines de fusion (par exemple, des cellules exprimant un récepteur antigénique chimérique (CAR)). La présente divulgation concerne en outre des procédés d'utilisation de telles cellules pour des traitements.
PCT/CN2023/116513 2022-09-02 2023-09-01 Protéines de fusion ciblant la voie de dégradation lysosomale WO2024046468A1 (fr)

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CN2022116821 2022-09-02
CNPCT/CN2022/116821 2022-09-02

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WO2017181119A2 (fr) * 2016-04-15 2017-10-19 Novartis Ag Compositions et méthodes pour l'expression sélective d'une protéine
WO2018136455A1 (fr) * 2017-01-17 2018-07-26 The Texas A&M University System Conjugués de ciblage endolysosomal pour une meilleure distribution de molécules de charge au compartiment endolysosomal de cellules cibles
WO2018170475A1 (fr) * 2017-03-17 2018-09-20 Fred Hutchinson Cancer Research Center Protéines de fusion immunomodulatrices et leurs utilisations

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