Patent Application
20250213615
This application contains a computer readable Sequence Listing which has been submitted in XML file format with this application, the entire content of which is incorporated by reference herein in its entirety. The Sequence Listing XML file submitted with this application is entitled “14735-026-228_SEQ LISTING.xml”, was created on Mar. 28, 2023, and is 347,806 bytes in size.
The invention relates to chimeric antigen receptors (CARs) for natural killer (NK) cells and uses thereof in immunotherapy. In particular, the invention relates to CARs having a cytoplasmic portion that includes a Toll/interleukin-1 (IL-1) receptor (TIR) signaling domain.
NK cells are cytotoxic lymphocytes that constitute a major component of the innate immune system. They were named “natural killers” because of the initial notion that they do not require prior activation in order to kill a target. In humans, a natural killer cell usually expresses the surface markers CD16 (FCyRIII) and CD56. NK cells generally have cytotoxic activity. Endogenous NK cells provide rapid responses to virally infected cells and respond to transformed cells. Small granules in cytoplasm contain perforin, granzymes, and other bioactive molecules. Upon contacting a target cell, the NK cells releases these granules. Perforin forms pores in the cell membrane of the target cell through which the granzymes and associated molecules can enter and act to induce apoptosis of the target cell.
NK cells are considered to be innate lymphoid cells, in contrast to adaptive lymphoid cells (T cells and B cells) and myeloid cells (such as macrophages). Unlike T cells, which specifically detect peptides from pathogens presented by Major Histocompatibility Complex (MHC) molecules on the surface of infected cells, NK cells recognize stressed cells regardless of whether peptides from pathogens are present on MHC molecules. Rather receptors on the cell surface on NK cells that recognize other biomolecules control activation of NK cells.
Artificial NK cells may be made from stem cells, such as induced pluripotent stem cells, by known methods such as those described in Zhu and Kaufman., Methods Mol Biol. 2048:107-119 (2019)). Of particular interest are NK cells having inactivating mutation is the gene encoding cytokine-inducible SH2-containing protein (CISH). These mutations include, but are not limited to substitutions, insertions, and/or deletions. CISH is an important negative regulator of IL-15 signaling. Inactivation of the CISH gene in induced pluripotent stem cells (iPSC) followed by differentiation of iPSC into natural killer (NK) cells results in engineered NK cells having increased persistence and potency relative to NK cells in which CISH has not been inactivated, as described in US 2021/0145883 A1. Inactivation of CISH is also thought to be able to enhance T cell cytotoxicity in cancer therapies.
The innate targeting capacity of NK cells can be redirected to a selected cell population by engineering the NK cells to express a chimeric antigen receptor (CAR). Chimeric antigen receptors have an extracellular portion that includes a ligand-binding domain designed to specifically bind a target antigen; a transmembrane domain; and a cytoplasmic portion that includes one or more signaling domains. Various architectures for the cytoplasmic portion of CARs are known. First generation CARs contained only the signaling domain to the T cell receptor zeta chain, termed a CD3ζ domain. Later generations of CARs incorporated domains from co-stimulatory molecules, notably the signaling domains of Cluster of Differentiation 28 (CD28) and 41BB (also known as CD137).
There remains a need in the art for chimeric antigen receptors for use in engineered natural killer (NK) cells and uses thereof. The present invention addresses that need.
Provided are chimeric antigen receptors for use in engineered natural killer (NK) cells and uses thereof. In one aspect, the disclosure provides chimeric antigen receptors (CARs) having a cytoplasmic portion that includes a Toll/interleukin-1 (IL-1) receptor (TIR) signaling domain.
In an aspect, the disclosure provides CARs having a cytoplasmic portion that includes a Toll-like receptor (TLR) signaling domain. As used herein, the term “TLR signaling domain” refers to the TIR domain of a TLR receptor, or a functional variant thereof. The TLR signaling domain may be a TLR1, TLR2, TLR3, TLR5, TLR6, TLR7, TLR8, TLR9, or TLR10 signaling domain—preferably a TLR2 signaling domain.
Accordingly, the cytoplasmic portion of the CAR may comprise a signaling domain having a polypeptide sequence selected from SEQ ID NOs: 1-10, or a functional variant thereof. The signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 1-10.
In a further aspect, the disclosure provides CARs having a cytoplasmic portion that includes an interleukin-1 receptor (IL-1R) subfamily signaling domain. As used herein, the term “IL-1R subfamily signaling domain” refers to the TIR domain of a member of the IL-1R receptor subfamily, or a functional variant thereof. The IL-1R subfamily signaling domain may an IL-1R signaling domain or an interleukin 18 receptor (IL-18R) signaling domain.
Accordingly, the cytoplasmic portion of the CAR may comprise a signaling domain having a polypeptide sequence selected from SEQ ID NOs: 11 or 12, or a functional variant thereof. The signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 21-22.
In another aspect, the disclosure provides CARs having a cytoplasmic portion that includes a TIR signaling domain and a CD3ζ domain (also referred to herein as “CD3-zeta”)-preferably a CD3ζ domain at the C-terminus of the CAR. The CARs disclosed herein may further comprise one or more other signaling domains. In variations, the cytoplasmic portion of the CAR may comprise a 2B4 signaling domain or an OX40 signaling domain. In further variations, however, the cytoplasmic portion of CAR lacks a 2B4 signaling domain, lacks an OX40 signaling domain, or lacks both 2B4 and OX40 signaling domains.
The CARs disclosed herein further comprise a transmembrane domain. Various suitable transmembrane domains are known in the art. In variations, the transmembrane domain may be the transmembrane domain of CD8 alpha chain (CD8α), CD28, CD16, NKp44, NKp46, TLR, IL-1R subfamily, or functional variant thereof. The transmembrane domain may be an artificial transmembrane domain (termed “aTM”) having the polypeptide sequence NLFVASWIAVMIIFRIGMAVAIFCCFFFP (SEQ ID NO: 41), or a variant with 1, 2, 3, 4, 5 or more substitutions.
In various embodiments, the disclosure provides natural killer (NK) cells engineered to express these CARs, nucleic acids encoding these CARs, vectors for delivery of such nucleic acids to cells, stem cells comprising such nucleic acids, therapeutic compositions, kits, methods of manufacture, and methods of treatment.
In some embodiments, the disclosure provides a natural killer cell, comprising a chimeric antigen receptor (CAR) comprising an extracellular portion, a transmembrane domain, and a cytoplasmic portion, wherein the cytoplasmic portion comprises a Toll/interleukin-1 (IL-1) receptor (TIR) signaling domain extracellular protein comprises a ligand-binding domain. In certain embodiments, the ligand-binding domain specifically binds a CD19 antigen, a CD20 antigen, a Her2 antigen or a BCMA antigen.
In another aspect, provided herein is a chimeric antigen receptor (CAR) comprising an extracellular portion, a transmembrane domain, and a cytoplasmic portion, wherein the cytoplasmic portion comprises a Toll/interleukin-1 (IL-1) receptor (TIR) signaling domain. In some embodiments, the TIR signaling domain is a Toll-like receptor (TLR) signaling domain. In some embodiments, the TLR signaling domain is a TLR2 signaling domain or a functional variant thereof. In some embodiments, the TLR signaling domain has a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 2. In some embodiments, the cytoplasmic portion comprises a CD3ζ signaling domain. In some embodiments, the cytoplasmic portion comprises a 2B4 signaling domain. In some embodiments, the cytoplasmic portion lacks a 2B4 signaling domain. In some embodiments, the cytoplasmic portion consists essentially of, in N- to C-terminal order, a 2B4 signaling domain, an IL-18R signaling domain, and a CD3ζ signaling domain. In some embodiments, the cytoplasmic portion consists essentially of, in N- to C-terminal order, a 2B4 signaling domain, a CD3ζ signaling domain, and a TLR2 signaling domain. In some embodiments, the cytoplasmic portion consists essentially of, in N- to C-terminal order, a 2B4 signaling domain, a TLR2 signaling domain, and a CD3ζ signaling domain.
In some embodiments, the extracellular protein comprises a ligand-binding domain. In some embodiments, the ligand-binding domain comprises an antibody-like domain. In some embodiments, the ligand-binding domain comprises a variable heavy (VH) domain and/or a variable light (VL) domain. In some embodiments, the ligand-binding domain comprises a single-chain variable fragment (scFv). In some embodiments, the ligand-binding domain specifically binds a CD19 antigen, a CD20 antigen, a Her2 antigen, or a BCMA antigen.
In some embodiments, (i) the extracellular domain comprises a polypeptide derived from a CD19 ligand binding domain, a CD20 ligand binding domain, a BCMA binding domain, or a HER2 binding domain; (ii) the transmembrane domain is a transmembrane domain selected from the group consisting of aTM, CD8 alpha chain (CD8α), CD28, CD16, NKp44, NKp46, NKG2, DNAM1, IL-2Rβ, TLR, and IL-1R subfamily; and (iii) the cytoplasmic domain comprises a signaling domain of TLR2, 41BB, or 2B4.
In some embodiments, the cytoplasmic domain further comprises a signaling domain of CD3ζ. In some embodiments, the CAR comprises (i) aTM transmembrane domain, a TLR2 signaling domain, and a CD3zeta signaling domain; or (ii) a CD28 transmembrane domain, a TLR2 signaling domain, and a CD3zeta signaling domain.
In some embodiments, the C-terminus of the extracellular domain is operably linked to the N-terminus or C-terminus of the transmembrane domain without a linker. In some embodiments, the C-terminus of the extracellular domain is operably linked to the N-terminus or C-terminus of the transmembrane domain with a linker or a hinge domain.
In some embodiments, the hinge domain is a CD8a hinge. In some embodiments, the CD8a hinge comprises the amino acid sequence set forth in SEQ ID NO: 158.
In some embodiments, the N-terminus or C-terminus of the transmembrane domain is operably linked to the N-terminus of the cytoplasmic domain, with or without a linker. In some embodiments, the transmembrane domain is operably linked to the cytoplasmic domain with a Gly-Ser linker.
In another aspect, provided herein is a polynucleotide comprising a nucleotide sequence encoding a chimeric antigen receptor of the present disclosure.
In yet another aspect, provided herein is a population of cells comprising an immune cell comprising a chimeric receptor of the present disclosure or a polynucleotide of the present disclosure. In some embodiments, the immune cell is a natural killer (NK) cell. In some embodiments, the NK cell is an induced pluripotent stem cell-derived natural killer (iPSC-NK) cell. In some embodiments, the immune cell comprises homozygous inactivating mutations in a cytokine-inducible SH2-containing protein (CISH) gene. In some embodiments, the immune cell is CISH−/−.
In another aspect, provided herein is a pharmaceutical composition comprising a population of cells of the present disclosure.
In a further aspect, provided herein is a method of killing a target cell comprising contacting a population of target cells with a population of cells of the present disclosure or a pharmaceutical composition of the present disclosure, wherein the ligand-binding domain of the CAR specifically binds on antigen on the target cell, and wherein the cells induce specific killing of the target cells.
In yet another aspect, provided herein is a method of treating cancer in a subject in need thereof, comprising administering a pharmaceutical compositions of the present disclosure to the subject.
Advantages of the invention may include, but are not limited to, increased activity of the disclosed CARs in NK cells or related cell types compared to CARs known in the art.
Other aspects and advantages of the invention, will be apparent from the following description and the accompanying drawings.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
The invention relates to chimeric antigen receptors (CARs) for natural killer (NK) cells and uses thereof in immunotherapy. In some variations, the invention relates to CARs having a cytoplasmic portion that includes a Toll/interleukin-1 (IL-1) receptor (TIR) signaling domain.
In various embodiments, the disclosure provides natural killer (NK) cells engineered to express the disclosed CARs, nucleic acids encoding these CARs, vectors for delivery of such nucleic acids to cells, stem cells comprising such nucleic acids, therapeutic compositions, kits, methods of manufacture, and methods of treatment. As shown in
Illustrative embodiments of CARs are shown in
In endogenous receptors, the TIR signaling domains have shared functional attributes. However, they are diverse at the sequence level.
In one aspect, the disclosure provides natural killer (NK) cells engineered to express the disclosed CARs. The NK cells may be primary NK cells. Primary NK cell mays be isolated from umbilical cord blood or peripheral blood using well-known methods. A polynucleotide encoding the CAR may be introduced into the primary NK cell using a viral vector, a non-viral vector, or electroporation. The NK cells may alternatively be induced pluripotent stem cell (iPSC)-derived NK cells or human embryonic stem cell (hESC)-derived NK cells. Methods for making iPSC-NK cells may be obtained by differentiating iPSCs using known methods. In one variation, iPSC-NK cells are made using embryoid bodies. Exemplary methods are provided in US 2013/0287751 A1 and Zhu et al. Methods Mol. Biol. 2048:107-119 (2019). In another variation, hESC-NK cells are made using single cell differentiation, as described, for example, in Woll et al. Blood 113:6094-6101 (2009). In further variations, iPSC-NK cells are made by differentiating single cells. Exemplary methods are provided in US 2021/0024891 A1 and US 2016/0097035 A1. hESC-/iPSC-derived NK cells may be phenotyped by measuring surface marker expression such as CD16, NKG2D, NKp44, NKp46, TRAIL, FasL, or combinations thereof. Killing activity of hESC-/iPSC-derived NK cells may be assessed. Functional assays to assess differentiation into NK cells include direct cytolytic activity tumor cells (such as killing of K562 cells), Caspase-3/7 flow cytometry assay, immunological assays for cytotoxic granule or cytokine release, or antitumor activity in vivo xenograft models. See, e.g., Woll et al. Blood 113:6094-6101 (2009); Hermanson et al. in Hematopoietic differentiation of human pluripotent stem cells. 69-19 (2015).
In some embodiments, the NK cells are CD45+/CD56+ double-positive. In some embodiments, the immune cell is CD45+. In some embodiments, the immune cell is CD56+. In some embodiments the immune cell is CD45+, CD56+, or CD45+/CD56+. Further illustrative methods for making and using engineered cells are provided in U.S. Pat. Appl. Pub. Nos. US 2018/0298101 A1, US 2021/0230548 A1, and US 2021/0145883 A1; and Int'l. Pat. Appl. Pub. Nos. WO 2018/075664 A1 (corresponding to U.S. patent application Ser. No. 17/481,404) and WO 2020/113029 A2 (corresponding to U.S. patent application Ser. No. 17/309,408), the disclosures of which are incorporated by reference herein in their entireties.
The cell population of the disclosure may be a purified cell population. As used herein, a composition containing a “purified cell population” or “purified cell composition” means that at least 30%, 50%, 60%, typically at least 70%, and more preferably 80%, 90%, 95%, 98%, 99%, or more of the cells in the composition are of a similarly identified cell phenotype.
The cell population may be an isolated cell population. As used herein, the term “isolated” means material that is substantially or essentially free from components that normally accompany it in its native state. In particular embodiments, the term “obtained” or “derived” is used synonymously with isolated.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are within the skill of the art. Such techniques are explained fully in the literature, such as Molecular Cloning: A Laboratory Manual, second edition (Sambrook el al., 1989) Cold Spring Harbor Press; Oligonucleotide Synthesis (M J. Gait, ed., 1984); Methods in Molecular Biology, Humana Press; Cell Biology: A Laboratory Notebook (J. E. Cellis, ed., 1998) Academic Press; Animal Cell Culture (R. I. Freshney. ed., 1987); Introduction to Cell and Tissue Culture (J. P. Mather and P. E. Roberts, 1998) Plenum Press; Cell and Tissue Culture: Laboratory Procedures (A. Doyle. J. B. Griffiths, and D. G. Newell, eds., 1993-1998) J. Wiley and Sons; Methods in Enzymology (Academic Press, Inc.); Handbook of Experimental Immunology (D. M. Weir and CC. Blackwell, eds.); Gene Transfer Vectors for Mammalian Cells (J. M. Miller and M. P. Calos, eds., 1987); Current Protocols in Molecular Biology (F. M. Ausubel el al., eds., 1987); PCR: The Polymerase Chain Reaction, (Mullis et al., eds., 1994); Current Protocols in Immunology (J. E. Coligan el al., eds., 1991); Short Protocols in Molecular Biology (Wiley and Sons, 1999); Immunobiology (C A. Janeway and P. Travers. 1997); Antibodies (P. Finch. 1997); Antibodies: a practical approach (D. Catty., ed., IRL Press, 1988-1989); Monoclonal antibodies: a practical approach (P. Shepherd and C. Dean, eds., Oxford University Press. 2000); Using antibodies: a laboratory manual (E. Harlow and D. Lane (Cold Spring Harbor Laboratory Press, 1999); The Antibodies (M. Zanetti and J. D. Capra, eds., Harwood Academic Publishers, 1995); and Cancer: Principles and Practice of Oncology (V. T. DeVita et al., eds., J. B. Lippincott Company, 1993).
Introduction of a polynucleotide encoding a CAR may be achieved by transduction of either the NK cell or an iPSC or hESC precursor with a viral vector, such as a lentiviral vector. Suitable lentiviral vectors are known in the art and are described in, for example, Zufferey et al., (1997); Dull et al., (1998), U.S. Pat. Nos. 6,013,516A, and 5,994,136A. In variations, a non-viral vector, such as a lipid nanoparticle, a transfection reagent, or electroporation may be used to introduce a polynucleotide into a cell.
In an aspect, the disclosure provides cells comprising the a chimeric antigen receptor as described herein and/or a polynucleotide encoding the chimeric antigen receptor. The cell may be a stem cell or a progenitor cell. In some embodiments, the cell is an induced pluripotent stem cell (iPSC). In some embodiments, the cell is an iPSC-derived NK cell.
In some embodiments, the cell comprises homozygous inactivating mutations in the cytokine-inducible SH2-containing protein (CISH) genes of the cell (e.g., CISH−/−). In some embodiments, the cell comprises expression and/or overexpression of a gene encoding a soluble IL-15 or membrane-bound IL-15.
Provided are chimeric antigen receptors for use in engineered natural killer (NK) cells and uses thereof. In one aspect, the disclosure provides chimeric antigen receptors (CARs) having a cytoplasmic portion that includes a Toll-like/interleukin-1 (IL-1) receptor (TIR) signaling domain.
NK cells are known to express pattern recognitions receptors (PRR), which recognize pathogen-associated molecular patterns (PAMP) on infected cells, including Toll-like Receptors (TLRs). Noh et al. (2020) J. Immunol. Res. 2020:204860.
The Toll/interleukin-1 (IL-1) receptor (TIR) family are defined by have cytoplasmic portions containing structurally homologous signaling domains, termed TIR domains. TIR domains are found in Toll-like Receptors (TLRs) as well as two interleukin receptors, Interleukin-1 Receptor (ILIR) and Interleukin-18 Receptor (IL18), which, though classified as interleukin receptors, participate in signaling pathways similar to those of the TLRs. Accordingly, the TIR family is considered to two subfamilies, defined by the specificity their extracellular domains: (i) the Toll-like receptor (TLR) subfamily and (ii) the IL-1 receptor (IL-1R) subfamily.
In response to extracellular signals, both TLRs can form dimeric receptor complexes, which recruit accessory proteins. Martin et al. (2002) Biochimica et Biophysica Acta 1592:265-280. Humans have ten TLRs, TLR1-TLR10. Signaling by the TLRs depends variously on heterodimerization or homodimerization. TLR4 is known to signal through homodimerization. TLR2 signaling is triggered by heterodimerization with TLR1 or TLR6. It is known that, unlike TLR4, TLR2 does not signal as a homodimer. Zhang, et al. (2002) FEBS Lett. 532:171.
In an aspect, the disclosure provides CARs having a cytoplasmic portion that includes a Toll-like receptor (TLR) signaling domain. As used herein, the term “TLR signaling domain” refers to the TIR domain of a TLR receptor, or a functional variant thereof. The TLR signaling domain may be a TLR1, TLR2, TLR3, TLR5, TLR6, TLR7, TLR8, TLR9, or TLR10 signaling domain-preferably a TLR2 signaling domain.
Accordingly, the cytoplasmic portion of the CAR may comprise a signaling domain having a polypeptide sequence selected from SEQ ID NOs: 1-10, or a functional variant thereof. The signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 1-10.
When receptors containing Toll/interleukin-1 (IL-1) Receptor (TIR) domains are activated, the TIR domain(s) trigger conserved cellular signal transduction pathways control cell function, through recruitment of cytosolic signaling molecules include TIR domain-containing cytosolic adaptor proteins. TIR signaling domains have been characterized, generally, as comprising three conserved regions (e.g., Box 1 motif: (F/Y) DA or FADFISY (SEQ ID NO: 136), Box 2 motif: RDXXPG (SEQ ID NO: 137) or GYKLC-RD-PG (SEQ ID NO: 138), and Box 3 motif: FW or a conserved W neighbored by basic residues) responsible for mediating protein-protein interactions between toll-like receptors (TLRs) and signal-transduction components (Slack, et al., 2000). Each TIR signaling domain comprises five-stranded parallel beta-sheets (A-through-E) and six surrounding alpha-helices (A-through-E) with respective connecting loop structures (Bovijen, et al., 2013). Conserved residues are located in the hydrophobic core and large insertions and deletions may be present in various loop regions of different TIR signaling domains. For example, differences in the Box 2 motif, comprising the “BB loop” region of the signaling domain, are believed to play a role in specificity of TIR-TIR interactions (Xu, et al., 2000; Poltorak, et al., 1998). About twenty receptors that have TIR domains have been identified in humans, including the Toll-Like Receptors (TLRs) and Interleukin-1 Receptors (IL-1Rs). The general structure of the TIR signaling domain comprises conserved residues within a core sequence that ranges from about 125 to about 200 amino acid residues, however, sequence conservation between these domains can be as low as only 20-30%. The exterior residues between TIR domains vary greatly, resulting in differential distribution of electrostatic potential and resulting signaling functionality (Dunne, et al. 2003). Sequence variation between TIR signaling domains may comprise insertions, deletions, and/or mutations in one or more of the alpha-helices, beta-sheets, loops, or box motifs.
In some embodiments, the TIR signaling domain is a Toll-like receptor (TLR) signaling domain. The human Toll-Like Receptors (TLRs 1-10) are single-pass transmembrane proteins that each recognizing unique ligands, which activates intracellular signaling (Armant, M and Fenton, M, 2002) through TIR signaling domains (Xu et al., 2000; Horng et al., 2002; Brown et al., 2006). TLRs 1, 2, 4, 5, 6, and 10 reside in the plasma membrane and recognize extracellular Pathogen Associated Molecular Patterns (PAMPs). TLRs 3, 7, 8, and 9 reside in intracellular endosomes recognize internalized PAMPs (Akira, et al., 2006; Kawai, T. and Akira, S., 2007). TLRs undergo homo- or hetero-dimerization, which initiates their activation (Gay, N. and Gangloff, M., 2007). The signal cascade is followed by TLR signaling via conserved cytosolic TIR domain present in both the cytoplasmic signaling domain and in the TLR adaptor proteins, such as myeloid differentiation factor 88 (MyD88), MyD88-adaptor-like (MAL/TIRAP), the TRIF-related adaptor molecule (TRAM/TICAM2), TIR domain-containing adaptor protein inducing interferon-β (TRIF/TICAM1), and the sterile α- and armadillo-motif containing protein (SARM) (O'Neill, L. and Bowie, A. 2007). The MyD88-dependent pathway signals MyD88 to the phosphorylation of interleukin-1 receptor-associated kinase (IRAK) 4, then to IRAK1 and IRAK2 (Lin et al., 2010). MyD88 and TRIF interact with kinases TRAM and MAL (Yamamoto, et al., 2003; Yamamoto, et al., 2002). The TRAM and TIRAP pathways recruit MyD88 and TRIF to their respective TLRs. All TLRs, except for TLR3, activate the MyD88-dependent pathway (Horng et al., 2002; Kawai and Akira, 2010). The TRIF-dependent pathway signals through downstream kinases, TANK binding kinase 1 (TBK1) and IKKε, to activate IRF3 and subsequently produce type 1 interferons (Yamamoto et al., 2002b; Oshiumi et al., 2003). The SARM pathway functions as a negative regulator of TRIF-dependent Toll-like receptor signaling (Carty, et al. 2006).
The TLR signaling domain may be a TLR2 signaling domain or a functional variant thereof. TLR2 signaling domains are derived from Toll-Like Receptor 2 (TLR2), a type of TLR that interacts with TLR1, TLR6, or TLR10 prior to stimulation with a ligand (Jin, et al, 2007; Toshchakov, V. and Neuwald, A., 2020). Heterodimer formation facilitates interaction with intracellular TIR domains to promote signal initiation. TLR2 acts via MYD88 and TRAF6, leading to activation of transcription factor NF-kappa-B, cytokine secretion and inflammatory response; and may also promote apoptosis in response to lipid moieties of lipoproteins (Brightbill, et al., 1999; Aliprantis, et al., 1999). The TLR2 signaling domain may comprise residues 639-782 (144 aa) of human TLR2 (SEQ ID NO: 26) or a functional variant thereof (ICYDAFVSYSERDAYWVENLMVQELENFNPPFKLCLHKRDFIPGKWIIDNIIDSIEKSHK TVFVLSENFVKSEWCKYELDFSHFRLFDENNDAAILILLEPIEKKAIPQRFCKLRKIMNTK TYLEWPMDEAQREGFWVNLRAAI (SEQ ID NO: 2)). The TIR signaling domain of TLR2 may comprise the polypeptide sequence: ICYDAFVSYSERDAYWVENLMVQELENFNPPFKLCLHKRDFIPGKWIIDNIIDSIEKSHKT VFVLSENFVKSEWCKYELDFSHFRLFDENNDAAILILLEPIEKKAIPQRFCKLRKIMNTKT YLEWPMDEAQREGFWVNLRAAI (SEQ ID NO: 2) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR2 is encoded by the nucleotide sequence set forth in SEQ ID NO: 180. In some embodiments, the TIR signaling domain of TLR2 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 180.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 2. Functional variants and/or some or all of the conserved residues of the TLR2 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR2 signaling pathway. Conserved residues of the TLR2 TIR signaling domain may comprise residues 698-707 (Toshchakov, V. and Neuwald, A., 2020). Further conserved residues of the TLR2 TIR may comprise P681, K709, K714, KK742-743, K751, K754, S636, R677, Y715, and/or R753 (Xu, et al., 2000; Mckelvey, et al., 2016; Ben-Ali, et al., 2011; Kang, et al., 2001; Bochud, et al., 2003; Georgel, et al. 2009).
The TLR signaling domain may be a TLR8 signaling domain or a functional variant thereof. TLR8 signaling domains are derived from Toll-Like Receptor 8 (TLR8), a type of TLR that functions as an endosomal, nucleic acid-sensing, TLR capable of undergoing dimerization in the recruitment of TIR-containing downstream adapter MYD88 via homotypic interaction (Tanji, et al., 2013; Tanji, et al., 2015). Resulting signal propagation through the Myddosome is generated by IRAK4, IRAK1, TRAF6, TRAF3 activating NF-kappa-B and IRF7 inducing proinflammatory cytokines and interferons (Qin, et al. 2006; Doyle, et al. 2007; Zhang, et al., 2018). The TLR8 signaling domain may comprise residues 878-1022 of human TLR8 (SEQ ID NO: 32). The TIR signaling domain of TLR8 may comprise the polypeptide sequence: TFYDAYISYDTKDASVTDWVINELRYHLEESRDKNVLLCLEERDWDPGLAIIDNLMQSI NQSKKTVFVLTKKYAKSWNFKTAFYLALQRLMDENMDVIIFILLEPVLQHSQYLRLRQR ICKSSILQWPDNPKAEGLFWQTLRNVV (SEQ ID NO: 8) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR8 is encoded by the nucleotide sequence set forth in SEQ ID NO: 188. In some embodiments, the TIR signaling domain of TLR8 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 188.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 8. Functional variants and/or some or all of the conserved residues of the TLR8 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR8 signaling pathway. Conserved residues of the TLR8 TIR signaling domain may comprise conserved pattern in the N-terminal half of the BB loop, -E9E9R9D9W9XP9G9-, wherein the glutamate and tryptophan residues remain present; D9 at the C-terminal end of the Beta-sheet A; and/or conserved residues within alpha-helix C and alpha-helix D (Toshchakov, V. and Neuwald, A., 2020)
In some embodiments, the TLR signaling domain is a TLR3 signaling domain or a functional variant thereof. TLR3 signaling domains are derived from Toll-Like Receptor 3 (TLR3), an endosomal, nucleic acid-sensing, TLR that undergoes dimerization, wherein ligand binding results in interaction with TRIF/TICAM1 adapter, resulting in activation of NF-kappa-B, IRF3 nuclear translocation, cytokine secretion and inflammatory responses (Oshiumi, et al. 2003). The TLR3 signaling domain may comprise residues 754-897 of human TLR3 (SEQ ID NO: 27) or a functional variant thereof. The TIR signaling domain of TLR3 may comprise the polypeptide sequence: FEYAAYIIHAYKDKDWVWEHFSSMEKEDQSLKFCLEERDFEAGVFELEAIVNS IKRSRKIIFVITHHLLKDPLCKRFKVHHAVQQAIEQNLDSIILVFLEEIPDYKLNHALCLRR GMFKSHCILNWPVQKERIGAFRHKLQVAL (SEQ ID NO: 3) or a functional variant thereof.
In some embodiments, the TIR signaling domain of TLR3 is encoded by the nucleotide sequence set forth in SEQ ID NO: 183. In some embodiments, the TIR signaling domain of TLR3 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 183.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 3. Functional variants and/or some or all of the conserved residues of the TLR3 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR3 signaling pathway. Conserved residues of the TLR3 TIR signaling domain may comprise N759, Y858, R867, and/or M870 (Sakar, et al., 2007; Hu, et al., 2015; Zhang, et al., 2020).
In some embodiments, the TLR signaling domain is a TLR7 signaling domain or functional variant thereof. TLR7 signaling domains are derived from Toll-Like Receptor 7 (TLR7), an endosomal receptor capable of responding to uridine-containing single strand RNAs or guanosine analogs (Davenne, et al., 2020; Lee, et al., 2003). Association with an agonist results in dimerization allowing for recruitment of TIR-containing adapter MYD88 via homotypic interaction (Zhang, et al. 2016). Myddosome signaling complex interacts with IRAK4, IRAK1, TRAF6, and TRAF3 generating activation of NF-kappa-B and IRF7 to induce cytokines and interferons (Zhang, et al. 2016). The TLR7 signaling domain may comprise residues 889-1033 (145 aa) of human TLR7 (SEQ ID NO: 31). The TIR signaling domain of TLR 7 may comprise the polypeptide sequence: CCYDAFIVYDTKDPAVTEWVLAELVAKLEDPREKHENLCLEE RDWLPGQPVLENLSQSIQLSKKTVFVMTDKYAKTENFKIAFYLSHQRLMDEKVDVIILIF LEKPFQKSKFLQLRKRLCGSSVLEWPTNPQAHPYFWQCLKNAL (SEQ ID NO: 7) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR7 is encoded by the nucleotide sequence set forth in SEQ ID NO: 187. In some embodiments, the TIR signaling domain of TLR7 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 187.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 7. Functional variants and/or some or all of the conserved residues of the TLR7 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR7 signaling pathway. Conserved residues of the TLR7 TIR signaling domain may comprise >90% conserved pattern in the N-terminal half of the BB loop; -E9E9R9D9W9XP9G9-, wherein the glutamate and tryptophan residues remain present D9 at the C-terminal end of the Beta-sheet A; and/or conserved residues within alpha-helix C and alph-helix D (Toshchakov, V. and Neuwald, A., 2020)
The TLR signaling domain may be a TLR4 signaling domain or functional variant thereof. TLR4 signaling domains are derived from Toll-Like Receptor 4 (TLR4), a type of TLR that functions via interacting with K96 and CD14 via homodimerization to initiate response to lipopolysaccharides (LPS) (Tatematsu, et al., 2016). TLR4 interacts with MYD88, TIRAP, and TRAF6, resulting in activation of NF-kappa-B, cytokine secretion, and inflammatory response (Medzhitov, et al, 1997; Arbour, et al, 2000; Tatematsu, et al., 2016). TLR4 may also function via LPS-independent response, wherein activation is triggered by free fatty acids and Ni (2+), which are non-conserved and species-specific (Marc, et al. 2010). The TLR4 signaling domain may comprise residues 672-815 (144 aa) of human TLR4 (SEQ ID NO: 28) or a functional variant thereof. The TIR signaling domain of TLR4 may comprise the polypeptide sequence: NIYDAFVIYSSQDEDWVRNELVKNLEEGVPPFQLCLHYRDFIPGVAIAANIIHEGFHKSR KVIVVVSQHFIQSRWCIFEYEIAQTWQFLSSRAGIIFIVLQKVEKTLLRQQVELYRLLSRN TYLEWEDSVLGRHIFWRRLRKAL (SEQ ID NO: 4) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR4 is encoded by the nucleotide sequence set forth in SEQ ID NO: 184. In some embodiments, the TIR signaling domain of TLR4 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 184.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 4. Functional variants and/or some or all of the conserved residues of the TLR4 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR4 signaling pathway. Variations of the TLR4 TIR signaling domain may comprise R763H and/or Q834H (Smirnova, et al., 2001). Conserved residues of the TLR4 TIR signaling domain may comprise C747 on alpha-helix C; the presence of a WXC747XXE motif; and/or P712 of the BB loop (Shirey, et al. 2020; Poltorak, et al., 1998). Further conserved residues of the TLR4 TIR may comprise residues between the BB loop and alpha-helix E (Toshchakov, et al., 2011).
The TLR signaling domain may be a TLR1 signaling domain or functional variant thereof. TLR1 signaling domains are derived from Toll-Like Receptor 1 (TLR1), a type of TLR that interacts with TLR2 to regulate immune response stimulated by the presence of particular lipopeptides (Lancioni, et al., 2011). The TLR1 signaling domain may comprise residues 635-776 (142 aa) of human TLR1 (SEQ ID NO: 25) or a functional variant thereof (LQFHAFISYSGHDSFWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYKSIF VLSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLEPIPQYSIPSSYHKLKSLMARRTYL EWPKEKSKRGLFWANLRAAI (SEQ ID NO: 1)). The TIR signaling domain of TLR1 may comprise the polypeptide sequence: LQFHAFISYSGHDSFWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFV LSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLEPIPQYSIPSSYHKLKSLMARRTYLE WPKEKSKRGLFWANLRAAI (SEQ ID NO: 1) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR1 is encoded by the nucleotide sequence set forth in SEQ ID NO: 182. In some embodiments, the TIR signaling domain of TLR1 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 182.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 1. Functional variants and/or some or all of the conserved residues of the TLR1 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR1 signaling pathway.
The TLR signaling domain may be a TLR5 signaling domain or functional variant thereof. TLR5 signaling domains are derived from Toll-Like Receptor 5 (TLR5), a type of TLR that has been shown to play a role in immune response via recognition of unique molecular motifs (Bielaszewska, et al., 2018). The TLR5 signaling domain may comprise residues 691-836 (146 aa) of human TLR5 (SEQ ID NO: 29) or a functional variant thereof. The TIR signaling domain of TLR5 may comprise the polypeptide sequence: YKYDAYLCFSSKDFTWVQNALLKHLDTQYSDQNRFNLCFEERDFVPGENRIANIQDAI WNSRKIVCLVSRHFLRDGWCLEAFSYAQGRCLSDLNSALIMVVVGSLSQYQLMKHQSI RGFVQKQQYLRWPEDLQDVGWFLHKLSQQI (SEQ ID NO: 5) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR5 is encoded by the nucleotide sequence set forth in SEQ ID NO: 185. In some embodiments, the TIR signaling domain of TLR5 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 185.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 5. Functional variants and/or some or all of the conserved residues of the TLR5 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR5 signaling pathway.
The TLR signaling domain may be a TLR6 signaling domain or functional variant thereof. TLR6 signaling domains are derived from Toll-Like Receptor 6 (TLR6), a type of TLR that has been shown to play a role in recognition of diacylated and triacylated lipopeptides via interaction with TLR2 (Stewart, et al., 2010; Triantafilou, et al., 2006). The TLR6 signaling domain may comprise residues 640-781 (142 aa) of human TLR6 (SEQ ID NO: 30) or a functional variant thereof. The TIR signaling domain of TLR6 may comprise the polypeptide sequence: LQFHAFISYSEHDSAWVKSELVPYLEKEDIQICLHERNFVPGKSIVENIINCIEKSYKSIFVL SPNFVQSEWCHYELYFAHHNLFHEGSNNLILILLEPIPQNSIPNKYHKLKALMTQRTYLQ WPKEKSKRGLFWANIRAAF (SEQ ID NO: 6) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR6 is encoded by the nucleotide sequence set forth in SEQ ID NO: 186. In some embodiments, the TIR signaling domain of TLR6 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 186.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 6. Functional variants and/or some or all of the conserved residues of the TLR6 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR6 signaling pathway.
The TLR signaling domain may be a TLR9 signaling domain or functional variant thereof. TLR9 signaling domains are derived from Toll-Like Receptor 9 (TLR9), a type of TLR that has been shown to play a role in nucleotide-sensing, stimulated by the presence of unmethylated cytidine-phosphate-guanosine (CpG) dinucleotides (Takeshita, et al., 2001; Doyle, et al., 2007). The TLR9 signaling domain may comprise residues 868-1013 (146 aa) of human TLR9 (SEQ ID NO: 33) or a functional variant thereof. The TIR signaling domain of TLR9 may comprise the polypeptide sequence: LPYDAFVVFDKTQSAVADWVYNELRGQLEECRGRWALRLCLEERDWLPGKTLFENLW ASVYGSRKTLFVLAHTDRVSGLLRASFLLAQQRLLEDRKDVVVLVILSPDGRRSRYVRL RQRLCRQSVLLWPHQPSGQRSFWAQLGMAL (SEQ ID NO: 9) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR9 is encoded by the nucleotide sequence set forth in SEQ ID NO: 189. In some embodiments, the TIR signaling domain of TLR9 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 189.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 9. Functional variants and/or some or all of the conserved residues of the TLR9 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR9 signaling pathway.
The TLR signaling domain may be a TLR10 signaling domain or functional variant thereof. TLR10 signaling domains are derived from Toll-Like Receptor 10 (TLR10), a member of the TLR receptor family involved in detection of unique molecules and regulating immune response. The TLR10 signaling domain may comprise residues 632-775 (144 aa) of human TLR10 (SEQ ID NO: 34) or a functional variant thereof. The TIR signaling domain of TLR 10 may comprise the polypeptide sequence: VRFHAFISYSEHDSLWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIEKSYKSIF VLSPNFVQNEWCHYEFYFAHHNLFHENSDHIILILLEPIPFYCIPTRYHKLKALLEKKAYL EWPKDRRKCGLFWANLRAAI (SEQ ID NO: 10) or a functional variant thereof. In some embodiments, the TIR signaling domain of TLR10 is encoded by the nucleotide sequence set forth in SEQ ID NO: 190. In some embodiments, the TIR signaling domain of TLR10 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 190.
The TLR signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 10. Functional variants and/or some or all of the conserved residues of the TLR10 signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the TLR10 signaling pathway.
In an aspect, the disclosure provides CARs having a cytoplasmic portion that includes an interleukin-1 receptor (IL-1R) subfamily signaling domain. As used herein, the term “IL-1R subfamily signaling domain” refers to the TIR domain of a member of the IL-1R receptor subfamily, or a functional variant thereof. Currently, in humans, ten IL-1R subfamily receptors have been identified (Fields, et al., 2019), nine of which possess a TIR domain. The IL-1R subfamily signaling domain may be an IL-1R signaling domain or an interleukin 18 receptor (IL-18R) signaling domain. In some embodiments, the IL-1R subfamily signaling domain may be an IL-1R4 (IL-33R, ST2) signaling domain, IL-1R6 (IL-36R, IL1-Rrp2) signaling domain, IL-1R3 (IL-1RAcp) signaling domain, IL-1R7 (IL-18Rbeta, AcPl) signaling domain, IL-1R8 (SIGGIR, TIR8) signaling domain, IL-1R9 (IL-1RAPL1, TIGIRR-2) signaling domain, or IL-1R10 (IL-1RAPL2) signaling domain.
Accordingly, the cytoplasmic portion of the CAR may comprise a signaling domain having a polypeptide sequence selected from SEQ ID NOs: 21 or 22, or a functional variant thereof. The signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 21-22.
The cytoplasmic portion of the CAR may comprise a signaling domain having a polypeptide sequence selected from SEQ ID NOs: 143, 144, 145, 146, 147, 148, or 149, or a functional variant thereof. The signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to any one of SEQ ID NOs: 143, 144, 145, 146, 147, 148, or 149.
The IL-1R subfamily signaling domains derive from IL-1R, a superfamily characterized by extracellular immunoglobulin-like (Ig-like) domains and an intracellular Toll/Interleukin 1R (TIR) domain. TIR domains of the IL-1R subfamily share a degree of homology with TIR domains of TLRs and function similarly with regard to signal transduction. IL-1R family members function as heterodimers that recognize cognate cytokines and activate downstream signaling molecules (Boraschi, D. and Tagliabue, A., 2013). Ligand binding results in oligomerization of TIR domains on the receptor, followed by interaction of accessory proteins and adaptor molecules (e.g., MYD88). Heterodimerization with TIR domains results in transduction of downstream cytoplasmic kinases (e.g., IRAKs), and NF-kB activation, which produces an immune response (e.g., cytokine secretion).
The IL-1R subfamily signaling domain may be an IL-1R signaling domain or functional variant thereof. IL-1R signaling domains are derived from Interleukin-1 Receptor (IL-1R), a cytokine receptor that functions by binding interleukin-1 and associates with accessory protein (IL-1RAcP) to form a complex which mediates interaction with TOLLIP, MYD88, and IRAK resulting in MAPK signal transduction and activation of NF-kappa-B (Greenfeder, et al., 1995; Slack, et al., 2000). The IL-1R signaling domain may comprise residues 357-569 (213 aa) of human IL-1R (SEQ ID NO: 35) or functional variant thereof. The IL-1R signaling domain of IL-1R may comprise the polypeptide sequence: KTYDAYILYPKTVGEGSTSDCDIFVFKVLPEVLEKQCGYKLFIYGRDDYVGEDIVEVINE NVKKSRRLIIILVRETSGFSWLGGSSEEQIAMYNALVQDGIKVVLLELEKIQDYEKMPESI KFIKQKHGAIRWSGDFTQGPQSAKTRFWKNVRYHM (SEQ ID NO: 21).
The IL-1R signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 21. Functional variants and/or some or all of the conserved residues of the IL-1R signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the IL-1R signaling pathway. Conserved residues of the IL-1R signaling domain may comprise D369A and/or R428A (Slack, et al. 2000).
The IL-1R subfamily signaling domain may be an Interleukin-18 Receptor (IL-18R) signaling domain. IL-18R signaling domains are derived from Interleukin-18 Receptor (IL-18R), a cytokine receptor that functions by binding a cognate cytokine, associating as a complex with IL-18RAcP accessory protein, and engaging with one or more adaptor proteins, resulting in the signal transduction (Loiarro, et al., 2010). The IL-18R signaling domain may comprise residues 373-520 (148 aa) of human IL-18R (SEQ ID NO: 36) or a functional variant thereof. The IL-18R signaling domain may comprise the polypeptide sequence: KTYDAFVSYLKECRPENGEEHTFAVEILPRVLEKHFGYKLCIFERDVVPGGAVVDEIHSL IEKSRRLIIVLSKSYMSNEVRYELESGLHEALVERKIKIILIEFTPVTDFTFLPQSLKLLKSH RVLKWKADKSLSYNSRFWKNLLYLM (SEQ ID NO: 22) or a functional variant thereof.
The IL-18R signaling domain may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 22. Functional variants and/or some or all of the conserved residues of the IL-18R signaling domain may be retained. Functional variants may include N to C terminal truncations, insertions, and/or mutations. Functional variants may comprise a polypeptide sequence sufficient to promote signal propagation using the IL-18R signaling pathway. Conserved residues of the IL-18R signaling domain may comprise conserved sequences within the BB loop (Ota, et al., 2012).
In another aspect, the disclosure provides CARs having a cytoplasmic portion that includes a TIR signaling domain and a CD3ζ domain—preferably a CD3ζ domain at the C-terminus of the CAR. The CARs disclosed herein may further comprise one or more other signaling domains. In variations, the cytoplasmic portion of the CAR may comprise a 2B4 signaling domain or an OX40 signaling domain. In further variations, however, the cytoplasmic portion of CAR lacks a 2B4 signaling domain, lacks an OX40 signaling domain, or lacks both 2B4 and OX40 signaling domains.
The cytoplasmic portion may comprise the polypeptide sequence: RVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEG LYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR (SEQ ID NO: 64) or a functional variant thereof. The cytoplasmic portion may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 64.
The cytoplasmic portion may comprise the polypeptide sequence: WRRKRKEKQSETSPKEFLTIYEDVKDLKTRRNHEQEQTFPGGGSTIYSMIQSQSSAPTSQ EPAYTLYSLIQPSRKSGSRKRNHSPSFNSTIYEVIGKSQPKAQNPARLSRKELENFDVYS (SEQ ID NO: 65) or a functional variant thereof. The cytoplasmic portion may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 65.
The cytoplasmic portion may comprise the polypeptide sequence: RRDQRLPPDAHKPPGGGSFRTPIQEEQADAHSTLAKI (SEQ ID NO: 66) or a functional variant thereof. The cytoplasmic portion may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 66.
Further cytoplasmic domains that may be used in CARs are provided in U.S. Pat. Pub. US 2017/0233454 and U.S. Pat. No. 10,415,017.
In an aspect, the disclosure provides CARs having an extracellular portion comprising a ligand-binding domain. The ligand-binding domain of the instant disclosure may comprise an antibody-based binding agent that specifically binds an antigen of interest via an antigen or antigenic fragment thereof. As used herein, the term “antigen” refers to a peptide, polypeptide, glycoprotein, glycan, lipid, glycolipid, or other biomolecule that identifies target cells for treatment by immunotherapy with NK cells.
As used herein, the term “antibody” collectively refers to immunoglobulins or immunoglobulin-like molecules including by way of example and without limitation, IgA, IgD, IgE, IgG and IgM, combinations thereof, and similar molecules produced during an immune response. The term “antigen-binding fragment” refers to a portion of an antibody that specifically bind to an antigen. Specific binding is considered to mean any level of specificity that has clinical utility. Specific binding may mean a binding constant at least 103 M−1 greater, at least 104 M−1 greater, or at least 105 M−1 greater than a binding constant for other molecules in a tissue. The antigen-binding fragment may be an artificial fragment such as humanized or chimeric antigen-binding fragment.
The term “antibody-like domain” refers to recombinant antibody fragments (such as sFv fragments, dsFv fragments, bispecific sFv fragments, bispecific dsFv fragments, F (ab)′2 fragments, single chain Fv proteins (“scFv”), disulfide stabilized Fv proteins (“dsFv”), diabodies, and triabodies (as are known in the art), and camelid antibodies, that retain antigen-binding properties (see, for example, U.S. Pat. Nos. 6,015,695; 6,005,079; 5,874,541; 5,840,526; 5,800,988; and 5,759,808). The antibody-like domain may be expressed as a fusion protein to form the singe-chain CAR, or it may be associated with the other polypeptide(s) through other known means, forming a multipartite CAR. An illustrative example of a multipartite CAR as described, e.g., in Int'l Pat. Pub. No. PCT/US2021/05676.
The antibody-like domain may be a single-chain variable fragment (scFv). An scFv protein is a fusion protein in which a light chain variable region (VL) of an antibody and a heavy chain variable region (VH) of an antibody expressed as fusion polypeptide, optionally with an intervening link, such as a Gly-Ser linker, in either VH-VL or VL-VH orientation. The scFv may be an dsFvs, the chains have been mutated to introduce a disulfide bond to stabilize the association of the chains.
When the ligand-binding domain is an antigen-like domain, it may comprise the complementarity determine regions CDR-H1, CDR-H2, CDR-H3, CDR-L1, CDR-L2, and CDR-L3. In some embodiments, the binding domain comprises VH and/or VL chains. In some embodiments, the ligand-binding domain comprises a single polypeptide chain. The ligand binding domain may be an scFv.
Ligand Binding Domain that Specifically Binds CD19
In an aspect, the disclosure provides chimeric antigen receptors that specifically bind CD19. The ligand binding domain may be an anti-CD19 scFv comprising the polypeptide sequence set forth in SEQ ID NO: 73 or a functional variant thereof having a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 73, or other scFv's or VH/VL pairs generated from SEQ ID NO: 73. The ligand binding domain may comprise a VH sequence according to SEQ ID NO: 74 and/or a VL sequence according to SEQ ID NO: 75, or a functional variants thereof having a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 74 and SEQ ID NO: 75, respectively.
The ligand binding domain (e.g., an scFv) may comprise the CDR sequences in Table 1, or functional variants with 1, 2, 3 or more substitutions.
In variations, the ligand binding domain may comprise CDRs extracted from SEQ ID NO: 109 by known methods (e.g., Chothia, Martin, Kabat, AHo and IMGT numbering available at, for example abysis.org; see Swindells et al. J. Mol. Bio. 429 (3): 356-365 (2017)).
In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence set forth in SEQ ID NO: 152. In some embodiments, the extracellular domain of a chimeric receptor consists of an amino acid sequence set forth in SEQ ID NO: 152. In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 152.
In some embodiments, the extracellular domain of a chimeric receptor is encoded by the nucleotide sequence set forth in SEQ ID NO: 153. In some embodiments, the extracellular domain of a chimeric receptor is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 153.
Ligand Binding Domain that Specifically Binds CD20
CD20 is a B-cell lineage-specific antigens expressed on the cell surface of most B-cell lymphomas, particularly in late stages of B-cell lymphogenesis. In an aspect, the disclosure provides chimeric antigen receptors that specifically bind CD20. The ligand binding domain may be an anti-CD20 scFv comprising the polypeptide sequence set forth in SEQ ID NO: 139 or a functional variant thereof having a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 139, or other scFv's or VH/VL pairs generated from SEQ ID NO: 139.
In variations, the ligand binding domain may comprise CDRs extracted from SEQ ID NO: 139 by known methods (e.g., Chothia, Martin, Kabat, AHo and IMGT numbering available at, for example abysis.org; see Swindells et al. J. Mol. Bio. 429 (3): 356-365 (2017)). In some embodiments, the ligand binding domain may be an anti-CD20 scFv comprising SEQ ID NO: 139.
In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence set forth in SEQ ID NO: 156. In some embodiments, the extracellular domain of a chimeric receptor consists of an amino acid sequence set forth in SEQ ID NO: 156. In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 156. The ligand binding domain may comprise a VH sequence according to SEQ ID NO: 154 and/or a VL sequence according to SEQ ID NO: 155, or a functional variants thereof having a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 154 and SEQ ID NO: 155, respectively.
In some embodiments, the extracellular domain of a chimeric receptor is encoded by the nucleotide sequence set forth in SEQ ID NO: 157. In some embodiments, the extracellular domain of a chimeric receptor is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 157.
Ligand Binding Domain that Specifically Binds HER2
In certain embodiments, the ligand-binding domain may bind a cancer antigen. In specific embodiments, the ligand-binding domain may bind an antigen associated with a solid cancer, e.g., an antigen present on a tumor cell. For example, functional activation of human epidermal growth factor receptor 2 (HER2) has been shown to strongly promote carcinogenesis. In an aspect, the disclosure provides chimeric antigen receptors that specifically bind HER2. The ligand binding domain may be an anti-HER2 scFv comprising the polypeptide sequence set forth in SEQ ID NOs: 140-142 or a functional variant thereof having a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NOs: 140-142, or other scFv's or VH/VL pairs generated from SEQ ID NOs: 140-142. The ligand binding domain (e.g., an scFv) may comprise CDR sequences in or functional variants with 1, 2, 3 or more substitutions.
In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence set forth in SEQ ID NOs: 140, 141, or 142. In some embodiments, the extracellular domain of a chimeric receptor consists of an amino acid sequence set forth in SEQ ID NOs: 140, 141, or 142. In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NOs: 140, 141, or 142.
In some embodiments, the extracellular domain of a chimeric receptor is encoded by the nucleotide sequence set forth in SEQ ID NOs: 198,199, or 200. In some embodiments, the extracellular domain of a chimeric receptor is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO:: 198, 199, or 200.
In variations, the ligand binding domain may comprise CDRs extracted from SEQ ID NOs: 140-142 by known methods (e.g., Chothia, Martin, Kabat, AHo and IMGT numbering available at, for example abysis.org; see Swindells et al. J. Mol. Bio. 429 (3): 356-365 (2017)). In some embodiments, the ligand binding domain may be an anti-HER2 scFv comprising SEQ ID NO: 140. In some other embodiments, the ligand binding domain may be an anti-HER2 scFv comprising SEQ ID NO: 141. In some embodiments, the ligand binding domain may be an anti-HER2 scFv comprising SEQ ID NO: 142.
In some embodiments, the CAR comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NOs: 202-207. In some embodiments, the CAR comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 202 (HER2-2-CD8-aTM-TLR2-CD3ζ without sIL15). In some embodiments, the CAR comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 203 (HER2-2-CD8-aTM-TLR2-CD3ζ-sIL15). In some embodiments, the CAR comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 204 (HER2-3-CD8-aTM-TLR2-CD3ζ without sIL15). In some embodiments, the CAR comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 205 (HER2-3-CD8-aTM-TLR2-CD3ζ-sIL15). In some embodiments, the CAR comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 206 (HER2-5-CD8-aTM-TLR2-CD3ζ without sIL 15). In some embodiments, the CAR comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 207 (HER2-5-CD8-aTM-TLR2-CD3ζ-sIL15).
Ligand Binding Domain that Specifically Binds B-Cell Maturation Antigen (BCMA)
In some embodiments, a chimeric receptor described herein comprises an extracellular domain comprising an ligand binding domain or binding fragment thereof of BCMA. BCMA is preferentially expressed in mature B lymphocytes and is important for B cell development.
In some embodiments, a chimeric receptor as described herein comprises an extracellular domain comprising a ligand binding domain or binding fragment thereof of BCMA.
In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence set forth in SEQ ID NO: 210,212, 214, or 216. In some embodiments, the extracellular domain of a chimeric receptor consists of an amino acid sequence set forth in SEQ ID NOs: 210, 212, 214, or 216. In some embodiments, the extracellular domain of a chimeric receptor comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NOs: 210, 212,214, or 216.
In some embodiments, the extracellular domain of a chimeric receptor is encoded by the nucleotide sequence set forth in SEQ ID NOs: 209, 211, 213, or 215. In some embodiments, the extracellular domain of a chimeric receptor is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NOs: 209, 211, 213, or 215.
The chimeric antigen receptor may be expressed from a polynucleotide sequence that encodes an N-terminal signal peptide. Signal peptides may direct their fusion partners to be integrated into the plasma membrane of the cell. For example, the signal peptide comprises the sequence MALPVTALLLPLALLLHAARP (SEQ ID NO: 37), or a functional variant with 1, 2, 3 or more amino acid substitutions.
In an aspect, the disclosure provides CARs having a transmembrane portion that includes a transmembrane domain. The CAR can be designed to comprise a transmembrane domain that is fused to the antigen-binding domain of the CAR. In some embodiments, the transmembrane domain that naturally is associated with one of the domains in the CAR is used. In some instances, the transmembrane domain can be selected or modified by amino acid substitution to avoid binding of such domains to the transmembrane domains of the same or different surface membrane proteins to minimize interactions with other members of the receptor complex. In some embodiments, the transmembrane domain is operably linked to the extracellular domain with or without a linker. In some embodiments, the transmembrane domain is operably linked to the extracellular domain via a hinge domain as described herein. In some embodiments, the transmembrane domain is a naturally occurring transmembrane domain derived from a protein. In some embodiments, the transmembrane domain is a synthetic transmembrane domain. In some embodiments, the transmembrane domain comprises a full transmembrane domain of a polypeptide. In some embodiments, the transmembrane domain comprises a fragment of a transmembrane domain of a polypeptide.
The transmembrane domain may be derived either from a natural or from a synthetic source. Transmembrane regions that may be used include the transmembrane domains of CD28, CD3 epsilon, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, CD154, TCR alpha, TCR beta, or CD3ζ, or a functional variant thereof. In variations, the transmembrane domain may be the transmembrane domain of CD8 alpha chain (CD8α), CD28, CD16, NKp44, NKp46, NKG2, DNAM1, IL-2Rβ, TLR, IL-1R subfamily, or functional variant thereof.
Illustrative transmembrane domains are provided in Table 3.
In some embodiments, the transmembrane domain is a transmembrane domain of CD28. In some embodiments, the transmembrane domain is a fragment of a CD28 transmembrane domain. In some embodiments, a CD28 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 43. In some embodiments, a CD28 transmembrane domain consists of the amino acid sequence set forth in SEQ ID NO: 43. In some embodiments, a CD28 transmembrane domain comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 43.
In some embodiments, a CD28 transmembrane domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 160. In some embodiments, a CD28 transmembrane domain is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 160. In some embodiments, a CD28 transmembrane domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 218. In some embodiments, a CD28 transmembrane domain is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 218.
In some embodiments, the transmembrane domain is a transmembrane domain of TLR2. In some embodiments, the transmembrane domain is a fragment of a TLR2 transmembrane domain. In some embodiments, a TLR2 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 46. In some embodiments, a TLR2 transmembrane domain consists of the amino acid sequence set forth in SEQ ID NO: 46. In some embodiments, a TLR2 transmembrane domain comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 46.
In some embodiments, a TLR2 transmembrane domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 161. In some embodiments, a TLR2 transmembrane domain is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 161.
In some embodiments, the transmembrane domain is an aTM domain. In some embodiments, the transmembrane domain is a fragment of an aTM domain. In some embodiments, an aTM domain comprises the amino acid sequence set forth in SEQ ID NO: 41 or SEQ ID NO: 163. In some embodiments, an aTM domain consists of the amino acid sequence set forth in SEQ ID NO: 41. In some embodiments, an aTM domain consists of the amino acid sequence set forth in SEQ ID NO: 163. In some embodiments, an aTM domain comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 41. In some embodiments, an aTM domain comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 163.
In some embodiments, an aTM domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 164 or 165. In some embodiments, an aTM domain is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 164 or 165.
In some embodiments, the transmembrane domain is a transmembrane domain of DNAM1. In some embodiments, the transmembrane domain is a fragment of a DNAM1 transmembrane domain. In some embodiments, a DNAM1 transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 42. In some embodiments, a DNAM1 transmembrane domain consists of the amino acid sequence set forth in SEQ ID NO: 42. In some embodiments, a DNAM1 transmembrane domain comprises an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 42.
In some embodiments, a DNAM1 transmembrane domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 162. In some embodiments, a DNAM1 transmembrane domain is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 162.
In an aspect, the disclosure provides CARs having a portion that includes a hinge domain. The hinge domain of the CAR of the disclosure may comprise a linker or spacer sequence between the extracellular antigen binding domain and the transmembrane domain. One of ordinary skill in the art will appreciate that a hinge domain (e.g., sequence) is a polypeptide segment that, in at least some instances, facilitates flexibility (see, e.g., Woof et al., Nat. Rev. Immunol., 4 (2): 89-99 (2004)). The hinge sequence can be any suitable sequence derived or obtained from any suitable molecule.
The hinge may be derived from or include at least a portion of an immunoglobulin Fc region, for example, an IgG1 Fc region, an IgG2 Fc region, an IgG3 Fc region, an IgG4 Fc region, an IgE Fc region, an IgM Fc region, or an IgA Fc region. In certain embodiments, the spacer domain includes at least a portion of an IgG1, an IgG2, an IgG3, an IgG4, an IgE, an IgM, or an IgA immunoglobulin Fc region that falls within its CH2 and CH3 domains. In some embodiments, the spacer domain may also include at least a portion of a corresponding immunoglobulin hinge region.
In some embodiments, a portion of the immunoglobulin constant region serves as a hinge region between the antigen binding domain, e.g., scFv, and transmembrane domain. The spacer can be of a length that provides for increased responsiveness of the cell following antigen binding, as compared to in the absence of the spacer. Exemplary hinges include those having at least about 10 to 229 amino acids, about 10 to 200 amino acids, about 10 to 175 amino acids, about 10 to 150 amino acids, about 10 to 125 amino acids, about 10 to 100 amino acids, about 10 to 75 amino acids, about 10 to 50 amino acids, about 10 to 40 amino acids, about 10 to 30 amino acids, about 10 to 20 amino acids, or about 10 to 15 amino acids, and including any integer between the endpoints of any of the listed ranges. In some embodiments, a hinge has about 12 amino acids or less, about 119 amino acids or less, or about 229 amino acids or less. In some embodiments, the hinge is at or about 12 amino acids in length. Exemplary spacers include, but are not limited to, those described in Hudecek et al. (2013) Clin. Cancer Res., 19:3153, international patent application publication number WO2014031687, U.S. Pat. Pub. No. US 2014/0271635.
The CARs of the disclosure may comprise a hinge domain isolated or derived from CD4, CD8α, CD28, IgG1, IgG2, IgG4, or IgD.
In some embodiments, the hinge domain is isolated or derived from the human CD8a molecule. The hinge domain may comprise the polypeptide sequence: TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACD (SEQ ID NO: 38) or a variant with 1, 2, 3, 4, 5 or more substitutions.
In some embodiments, the hinge domain is isolated or derived from the human CD28 molecule. The hinge domain may comprise the polypeptide sequence: CTIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKP (SEQ ID NO: 39) or a variant with 1, 2, 3, 4, 5 or more substitutions. The hinge domain may comprise the polypeptide sequence: LDNEKSNGTIIHVKGKHLCPSPLFPGPSKP (SEQ ID NO: 217) or a variant with 1, 2, 3, 4, 5 or more substitutions.
In some embodiments, the hinge domain is isolated or derived from the human IgG4 molecule. The hinge domain may comprise the polypeptide sequence: ESKYGPPCPPCP (SEQ ID NO: 40) or a variant with 1, 2, 3, 4, 5 or more substitutions.
In some embodiments, the hinge domain is isolated or derived from the human CD8 molecule. The hinge domain may comprise the polypeptide sequence: TTTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACD (SEQ ID NO: 158) or a variant with 1, 2, 3, 4, 5 or more substitutions.
In some embodiments, a chimeric receptor described herein comprises one or more linkers between the components of the receptors. In some embodiments, a chimeric receptor described herein comprises a linker between the extracellular domain and the transmembrane domain. In some embodiments, a chimeric receptor described herein comprises a linker between the transmembrane domain and the cytoplasmic domain. In some embodiments, a chimeric receptor described herein comprises a linker between two or more intracellular signaling domains of the cytoplasmic domain.
Linkers suitable for joining polypeptide sequences are known to those of skill in the art. Exemplary linkers include gly-ser polypeptide linkers, glycine-proline polypeptide linkers, and proline-alanine polypeptide linkers. In certain embodiments, the linker is a gly-ser polypeptide linker, i.e., a peptide that consists of glycine and serine residues.
As used herein, the term “gly-ser linker” refers to a peptide that consists of glycine and serine residues. An exemplary gly-ser polypeptide linker comprises the amino acid sequence Ser (Gly4Ser)n. In some embodiments, n=1. In certain embodiments, n=2. In certain embodiments, n=3, i.e., Ser (Gly4Ser) 3. In some embodiments, n=4, i.e., Ser (Gly4Ser) 4. In certain embodiments, n=5. In certain embodiments, n=6. In some embodiments, n=7. In some embodiments, n=8. In some embodiments, n=9. In certain embodiments, n=10. Another exemplary gly-ser polypeptide linker comprises the amino acid sequence (Gly4Ser)n. In some embodiments, n=1. In certain embodiments, n=2. In certain embodiments, n=3. In some embodiments, n=4. In certain embodiments, n=5. In certain embodiments, n=6. Another exemplary gly-ser polypeptide linker comprises the amino acid sequence (Gly3Ser)n. In some embodiments, n=1. In some embodiments, n=2. In some embodiments, n=3. In some embodiments, n=4. In some embodiments, n=5. In some embodiments, n=6. Exemplary gly-ser polypeptide linkers comprise the amino acid sequence Ser (Gly4Ser)n. In some embodiments, n=1. In some embodiments, n=2. In some embodiments, n=3, i.e., Ser (Gly4Ser) 3. In some embodiments, n=4, i.e., Ser (Gly4Ser) 4. In some embodiments, n=5. In certain embodiments, n=6. In some embodiments, n=7. In some embodiments, n=8. In certain embodiments, n=9. In some embodiments, n=10. Another exemplary gly-ser polypeptide linker comprises the amino acid sequence Ser (Gly4Ser)n. In certain embodiments, n=1. In some embodiments, n=2. In some embodiments, n=3. In certain embodiments, n=4. In some embodiments, n=5. In certain embodiments, n=6. Another exemplary gly-ser polypeptide linker comprises (Gly4Ser)n. In some embodiments, n=1. In some embodiments, n=2. In certain embodiments, n=3. In some embodiments, n=4. In some embodiments, n=5. In certain embodiments, n=6. Another exemplary gly-ser polypeptide linker comprises (Gly3Ser)n. In some embodiments, n=1. In some embodiments, n=2. In certain embodiments, n=3. In certain embodiments, n=4. In some embodiments, n=5. In some embodiments n=6.
In some embodiments, a chimeric receptor described herein comprises a gly-ser linker as set forth in SEQ ID NO: 166. In some embodiments, the gly-ser linker is encoded by the nucleotide sequence of SEQ ID NO: 167. In some embodiments, a chimeric receptor described herein comprises a gly-ser linker as set forth in SEQ ID NO: 168. In some embodiments, the gly-ser linker is encoded by the nucleotide sequence of SEQ ID NO: 169. In some embodiments, a chimeric receptor described herein comprises a gly-ser linker as set forth in SEQ ID NO: 170. In some embodiments, the gly-ser linker is encoded by the nucleotide sequence of SEQ ID NO: 171. In some embodiments, a chimeric receptor described herein comprises a gly-ser linker as set forth in SEQ ID NO: 172. In some embodiments, the gly-ser linker is encoded by the nucleotide sequence of SEQ ID NO: 173.
Additional inkers suitable for joining polypeptide sequences to allow bi-cistronic expression are known to those of skill in the art. Exemplary linkers include Furin GSG-T2A.
In some embodiments, a chimeric receptor described herein comprises a gly-ser linker as set forth in SEQ ID NO: 174. In some embodiments, the gly-ser linker is encoded by the nucleotide sequence of SEQ ID NO: 175.
While the disclosure contemplates the combination of the signaling domains disclosure in any order and combined with any transmembrane and extracellular domains, the disclosure provides, at least, the constructs listed in Table 4.
In each case, the CAR polypeptide may comprises, in consecutive order, a CD8 hinge domain, an artificial transmembrane domain (“aTM”), and one or more signaling domain and/or other cytoplasmic domains as indicate in the first columns of Table 4. It may have a polypeptide sequence according to the second column, or a functional variant having at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identity thereto. In variations, the CAR polypeptide comprises a ligand binding domain specific to CD19. Examples are provided in the third column of each table. In each case, the CAR polypeptide may comprises have a polypeptide sequence according to the third column, or a functional variant having at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identity thereto. The fourth column provides corresponding illustrative polynucleotide sequences for each. In some other variations, the CAR polypeptide comprises a ligand binding domain specific to CD20. In still some other variations, the CAR polypeptide comprises a ligand binding domain specific to HER2
In an aspect, the NK CAR cells of the disclosure are engineered to co-express additional proteins (either membrane bound or secreted). Exemplary compositions and methods are provided in US 2017/0073638 A1.
In some variations, the NK cells of the disclosure are engineered to express Interleukin-15 (IL-15) (either membrane bound or secreted). IL-15 is a cytokine that plays a role in regulating immune response. Without being bound by theory, expression of IL-15 may improve NK cell function. The IL-15 may the comprise polypeptide sequence: MRISKPHLRSISIQCYLCLLLNSHFLTEAGIHVFILGCFSAGLPKTEANWVNVISDLKKIED LIQSMHIDATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLSS NGNVTESGCKECEELEEKNIKEFLQSFVHIVQMFINTS (SEQ ID NO: 58). The IL-15 may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 58. In some embodiments, the IL-15 is encoded by the nucleotide sequence set forth in SEQ ID NO: 208. In some embodiments, the IL-15 is encoded by a nucleotide sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity to SEQ ID NO: 208.
Alternatively, the IL-15 may comprise the polypeptide sequence: MALPVTALLLPLALLLHAARPNWVNVISDLKKIEDLIQSMHIDATLYTESDVHPSCKVTA MKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEELEEKNIKEFLQ SFVHIVQMFINTSTTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACDIYI WAPLAGTCGVLLLSLVITLYC (SEQ ID NO: 57). The IL-15 may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 57.
In some variations, the NK cells of the disclosure are engineered to express Interleukin-18 (IL-18) (either membrane bound or secreted). IL-18 is a pro-inflammatory cytokine that plays a role in immune cell activation and response. Without being bound by theory, expression of IL-18 may enhance NK cell proliferation, maturation, and cytotoxicity. The IL-18 may comprise the polypeptide sequence: MAAEPVEDNCINFVAMKFIDNTLYFIAEDDENLESDYFGKLESKLSVIRNLNDQVLFIDQ GNRPLFEDMTDSDCRDNAPRTIFIISMYKDSQPRGMAVTISVKCEKISTLSCENKIISFKE MNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLACEKERDLFKLILKKEDELG DRSIMFTVQNED (SEQ ID NO: 60). The IL-18 may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 60. Alternatively, the IL-18 may comprise the polypeptide sequence: MWLQSLLLLGTVACSISYFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDCRDNA PRTIFIISMYKDSQPRGMAVTISVKCEKISTLSCENKIISFKEMNPPDNIKDTKSDIIFFQRS VPGHDNKMQFESSSYEGYFLACEKERDLFKLILKKEDELGDRSIMFTVQNEDSGGGSGG GGSGGGGSGGGGSGGGSLQAESCTSRPHITVVEGEPFYLKHCSCSLAHEIETTTKSWYKS SGSQEHVELNPRSSSRIALHDCVLEFWPVELNDTGSYFFQMKNYTQKWKLNVIRRNKHS CFTERQVTSKIVEVKKFFQITCENSYYQTLVNSTSLYKNCKKLLLENNKNPTIKKNAEFE DQGYYSCVHFLHHNGKLFNITKTFNITIVEDRSNIVPVLLGPKLNHVAVELGKNVRLNCS ALLNEEDVIYWMFGEENGSDPNIHEEKEMRIMTPEGKWHASKVLRIENIGESNLNVLYN CTVASTGGTDTKSFILVRKADMADIPGHVFTRGMIIAVLILVAVVCLVTVCVIYRVDLVL FYRHLTRRDETLTDGKTYDAFVSYLKECRPENGEEHTFAVEILPRVLEKHFGYKLCIFER DVVPGGAVVDEIHSLIEKSRRLIIVLSKSYMSNEVRYELESGLHEALVERKIKIILIEFTPVT DFTFLPQSLKLLKSHRVLKWKADKSLSYNSRFWKNLLYLMPAKTVKPGRDEPEVLPVL SES (SEQ ID NO: 59). The IL-18 may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 59.
The co-expressed proteins of the NK cells of the instant disclosure may be fusion proteins. A “fusion protein”, as used herein, refers to an expression product resulting from the fusion of at least two genes. The fusion protein may be a chimeric polypeptide comprising two or more unrelated protein, or protein fragments, conjugated to one another. The co-expressed polypeptides may be linked to the polypeptide encoding the CAR of the disclosure via a self-cleaving peptide, such as a self-cleaving (2A) peptide, or functional variant thereof.
In some variations, the NK cells of the disclosure are engineered to express Interleukin-15/Interleukin-15R (IL15/IL15R) fusion protein. Interleukin-15 Receptor (IL-15R) has been shown to play a role in stimulation of proliferation of immune cells. Without being bound by theory, expression of IL-15/IL15R may improve NK cell function. The IL15/IL15R fusion protein may comprise the polypeptide sequence: MLLLVTSLLLCELPHPAFLLIPNWVNVISDLKKIEDLIQSMHIDATLYTESDVHPSCKVTA MKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEELEEKNIKEFLQ SFVHIVQMFINTSSGGGSGGGGSGGGGSGGGGSGGGSLQITCPPPMSVEHADIWVKSYS LYSRERYICNSGFKRKAGTSSLTECVLNKATNVAHWTTPSLKCIRDPALVHQRPAPPSTV TTAGVTPQPESLSPSGKEPAASSPSSNNTAATTAAIVPGSQLMPSKSPSTGTTEISSHESSH GTPSQTTAKNWELTASASHQPPGVYPQGHSDTTVAISTSTVLLCGLSAVSLLACYLKSR QTPPLASVEMEAMEALPVTWGTSSRDEDLENCSHHLDYKDDDDKDYKDDDDKDYKD DDDK (SEQ ID NO: 62). The IL15/IL15R fusion protein may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 62.
In some variations, the NK cells of the disclosure are engineered to express Interleukin-18/Interleukin-18R (IL18/IL18R) fusion protein. Interleukin-18 Receptor (IL-18R) has been shown to play a role in immune cell activation and promotion of cytotoxic activity. Without being bound by theory, expression of IL18/IL18R may enhance NK cell proliferation, maturation, and cytotoxicity. The IL18/IL18R fusion protein may comprise the polypeptide sequence: MLLLVTSLLLCELPHPAFLLIPYFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDCR DNAPRTIFIISMYKDSQPRGMAVTISVKCEKISTLSCENKIISFKEMNPPDNIKDTKSDIIFF QRSVPGHDNKMQFESSSYEGYFLACEKERDLFKLILKKEDELGDRSIMFTVQNEDSGGG SGGGGSGGGGSGGGGSGGGSLQAESCTSRPHITVVEGEPFYLKHCSCSLAHEIETTTKSW YKSSGSQEHVELNPRSSSRIALHDCVLEFWPVELNDTGSYFFQMKNYTQKWKLNVIRRN KHSCFTERQVTSKIVEVKKFFQITCENSYYQTLVNSTSLYKNCKKLLLENNKNPTIKKNA EFEDQGYYSCVHFLHHNGKLFNITKTFNITIVEDRSNIVPVLLGPKLNHVAVELGKNVRL NCSALLNEEDVIYWMFGEENGSDPNIHEEKEMRIMTPEGKWHASKVLRIENIGESNLNV LYNCTVASTGGTDTKSFILVRKADMADIPGHVFTRGMIIAVLILVAVVCLVTVCVIYRVD LVLFYRHLTRRDETLTDGKTYDAFVSYLKECRPENGEEHTFAVEILPRVLEKHFGYKLCI FERDVVPGGAVVDEIHSLIEKSRRLIIVLSKSYMSNEVRYELESGLHEALVERKIKIILIEFT PVTDFTFLPQSLKLLKSHRVLKWKADKSLSYNSRFWKNLLYLMPAKTVKPGRDEPEVL PVLSESDYKDDDDKDYKDDDDKDYKDDDDK (SEQ ID NO: 63). The IL18/IL18R fusion protein may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 63.
In some variations, the NK cells of the disclosure are engineered to express OX40. OX40 (CD134) is a member of the tumor necrosis factor receptor (TNFR) family that plays a role in signal transduction and priming of immune cells. Without being bound by theory, expression of OX40 may enhance activation of MAPK/ERK, NFkB, and AKT pathways; and/or induce proliferation and cytokine release. The OX40 may comprise the polypeptide sequence: MCVGARRLGRGPCAALLLLGLGLSTVTGLHCVGDTYPSNDRCCHECRPGNGMVSRCSR SQNTVCRPCGPGFYNDVVSSKPCKPCTWCNLRSGSERKQLCTATQDTVCRCRAGTQPL DSYKPGVDCAPCPPGHFSPGDNQACKPWTNCTLAGKHTLQPASNSSDAICEDRDPPATQ PQETQGPPARPITVQPTEAWPRTSQGPSTRPVEVPGGRAVAAILGLGLVLGLLGPLAILL ALYLLRRDQRLPPDAHKPPGGGSFRTPIQEEQADAHSTLAKIDYKDDDDKDYKDDDDK DYKDDDDK (SEQ ID NO: 61). The OX40 may have a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 61.
Any combination of extracellular ligand-binding domain, hinge domain, transmembrane domain, intracellular/cytoplasmic signaling domain, and co-expressed proteins described herein are envisaged within the scope of the CARs of the instant disclosure.
Polynucleotides of the disclosure may be delivered to cells as an isolated nucleic acid or in a vector. In an aspect, the disclosure provides a vector comprising polynucleotides comprising the CARs of the disclosure. In some embodiments, the vector comprises a polynucleotide encoding the co-expressed partners of the disclosure. Additional elements present in the vectors of the disclosure may also comprise a selectable marker and other components, such as enhancers, promoters and termination sequences, necessary for the expression of proteins. The polynucleotides of the disclosure may comprise flanking left and right arms for homology-directed repair. The polynucleotide may comprise a promoter operatively linked to the polynucleotide sequence encoding the CAR.
Polynucleotide of the disclosure may also be used for gene-editing. For example, homology directed repair may be used to insert a polynucleotide into a desired genomic loci. The polynucleotide may include a promoter and other genetic elements, or the repair template may omit these and instead rely on the host genome sequences for transcription.
Physical methods for introducing a polynucleotide into a host 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, for example, Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York). One method for the introduction of a polynucleotide into a host cell is calcium phosphate transfection.
Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and especially retroviral vectors, have become the most widely used method for inserting genes into mammalian, e.g., human cells. Other viral vectors can be derived from lentivirus, poxviruses, herpes simplex virus I, adenoviruses and adeno-associated viruses, and the like. See, for example, U.S. Pat. Nos. 5,350,674 and 5,585,362.
Chemical means for introducing a polynucleotide into a host 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. An exemplary colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (e.g., an artificial membrane vesicle).
Regardless of the method used to introduce exogenous nucleic acids into a host cell, in order to confirm the presence of the recombinant DNA sequence in the host cell, a variety of assays may be performed. Such assays 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 means (ELISAs and Western blots) or other assays.
Polynucleotides comprising the CARs, or parts thereof, are provided. Polynucleotides encoding any combination of extracellular ligand-binding domain, hinge domain, transmembrane domain, intracellular/cytoplasmic signaling domain, and co-expressed proteins described herein are envisaged within the scope of the instant disclosure.
Methods for making a modified cell (e.g., a stem cell, a progenitor cell, or an immune effector cell) are known to those of skill in the art. Methods for making cells expressing polypeptides, such as the chimeric receptors or fusion polypeptides described herein, are known in the art. Exemplary methods are described herein.
In some embodiments, the disclosure provides a modified cell (e.g., a modified stem cell, a modified progenitor cell, or a modified immune effector cells) expressing a chimeric antigen receptor described herein. In some embodiments, the disclosure provides a modified cell (e.g., a modified stem cell, a modified progenitor cell, or a modified immune effector cells) comprising a polynucleotide sequence encoding a chimeric antigen receptor described herein. In some embodiments, the modified cell (e.g., a modified stem cell, a modified progenitor cell, or a modified immune effector cells) is a CISH knock out cell.
In some embodiments, a cell comprises a chimeric antigen receptor described herein comprising a ligand binding domain, a transmembrane domain, and an intracellular signaling domain comprising a TLR2 signaling domain. In some embodiments, a cell comprises a chimeric antigen receptor described herein comprising a ligand binding domain, a transmembrane domain, and an intracellular signaling domain comprising a TLR2 signaling domain and a CD3zeta signaling domain. In some embodiments, a cell comprises a chimeric antigen receptor described herein comprising a ligand binding domain, a transmembrane domain selected from CD8 alpha chain (CD8α), CD28, CD16, NKp44, NKp46, NKG2, DNAM1, IL-2Rβ, TLR, IL-1R subfamily, or functional variant thereof, and an intracellular signaling domain comprising a TLR2 signaling domain and a CD3zeta signaling domain.
In some embodiments, the polynucleotides of the disclosure comprise a sequence encoding a signaling domain of the disclosure. In some embodiments, the polynucleotides encode a TLR signaling domain. In some embodiments, the polynucleotides encode an IL-1R subfamily signaling domain.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR2 signaling domain. The polynucleotide sequence encoding the TLR2 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 12. The polynucleotide sequence encoding the TLR2 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 12.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR8 signaling domain. The polynucleotide sequence encoding the TLR8 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 18. The polynucleotide sequence encoding the TLR8 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 18.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR3 signaling domain. The polynucleotide sequence encoding the TLR3 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 13. The polynucleotide sequence encoding the TLR3 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 13.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR7 signaling domain. The polynucleotide sequence encoding the TLR7 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 17. The polynucleotide sequence encoding the TLR7 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 17.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR4 signaling domain. The polynucleotide sequence encoding the TLR4 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 14. The polynucleotide sequence encoding the TLR4 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 14.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR1 signaling domain. The polynucleotide sequence encoding the TLR1 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 11. The polynucleotide sequence encoding the TLR1 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 11.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR5 signaling domain. The polynucleotide sequence encoding the TLR5 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 15. The polynucleotide sequence encoding the TLR5 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 15.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR6 signaling domain. The polynucleotide sequence encoding the TLR6 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 16. The polynucleotide sequence encoding the TLR6 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 16.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR9 signaling domain. The polynucleotide sequence encoding the TLR9 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 19. The polynucleotide sequence encoding the TLR9 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 19.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding a TLR10 signaling domain. The polynucleotide sequence encoding the TLR10 signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 20. The polynucleotide sequence encoding the TLR10 signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 20.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding an IL-1R signaling domain. The polynucleotide sequence encoding the IL-1R signaling domain may comprise a nucleic acid sequence that encodes for the polypeptide set forth in SEQ ID NO: 21. The polynucleotide sequence encoding the IL-1R signaling domain may have a polynucleotide sequence that encodes a polypeptide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 21.
In some embodiments, the polynucleotide sequence encoding the signaling domain of the disclosure comprises a nucleic acid sequence encoding an IL-18R signaling domain. The polynucleotide sequence encoding the IL-18R signaling domain may comprise the nucleic acid sequence set forth in SEQ ID NO: 24. The polynucleotide sequence encoding the IL-1R signaling domain may have a polynucleotide sequence at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identical to SEQ ID NO: 24.
The cytoplasmic portion of the CAR may further comprise one or more of the domains listed in Table 6, or a functional variant having at least 55%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95%, or 100% identity thereto.
In some embodiments, a chimeric receptor described herein comprises a cytoplasmic domain. In some embodiments, the cytoplasmic domain is operably linked to the TIR signaling domain with a linker. In some embodiments, the cytoplasmic domain is operably linked to the TIR signaling domain without a linker. In some embodiments, the N-terminus of the cytoplasmic domain is operably linked to the C-terminus of the TIR signaling domain. In some embodiments, the C-terminus of the cytoplasmic domain is operably linked to the N-terminus of the TIR signaling domain.
In some embodiments, the cytoplasmic domain is a 2B4 signaling domain. In some embodiments, the 2B4 cytoplasmic domain comprises the amino acid sequence set forth in SEQ ID NO: 65. In some embodiments, the 2B4 cytoplasmic domain consists of amino acid sequence set forth in SEQ ID NO: 65. In some embodiments, the 2B4 cytoplasmic domain comprises an amino acid sequence 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 65. In some embodiments, the 2B4 cytoplasmic domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 179. In some embodiments, the 2B4 cytoplasmic domain is encoded by a nucleotide sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 179.
In some embodiments, the cytoplasmic domain is a CD3ζ cytoplasmic domain. In some embodiments, the CD3ζ cytoplasmic domain comprises the amino acid sequence set forth in SEQ ID NO: 64. In some embodiments, the CD3ζ cytoplasmic domain consists of amino acid sequence set forth in SEQ ID NO: 64. In some embodiments, the CD3ζ cytoplasmic domain comprises an amino acid sequence 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 64. In some embodiments, the CD3ζ cytoplasmic domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 181. In some embodiments, the CD3ζ cytoplasmic domain is encoded by a nucleotide sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 181.
In some embodiments, the cytoplasmic domain is a 41BB cytoplasmic domain. In some embodiments, the 41BB signaling domain comprises the amino acid sequence set forth in SEQ ID NO: 176. In some embodiments, the 41BB cytoplasmic domain consists of amino acid sequence set forth in SEQ ID NO: 176. In some embodiments, the 41BB cytoplasmic domain comprises an amino acid sequence 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 176. In some embodiments, the 41BB cytoplasmic domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 177. In some embodiments, the 41BB cytoplasmic domain is encoded by a nucleotide sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 177.
In some embodiments, the cytoplasmic domain is a CD28 cytoplasmic domain. In some embodiments, the CD28 cytoplasmic domain comprises the amino acid sequence set forth in SEQ ID NO: 68. In some embodiments, the cytoplasmic domain is a CD28 cytoplasmic domain. In some embodiments, the CD28 cytoplasmic domain comprises the amino acid sequence set forth in SEQ ID NO: 220. In some embodiments, the CD28 cytoplasmic domain consists of amino acid sequence set forth in SEQ ID NO: 68. In some embodiments, the CD28 cytoplasmic domain consists of amino acid sequence set forth in SEQ ID NO: 220. In some embodiments, the CD28 cytoplasmic domain comprises an amino acid sequence 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 68. In some embodiments, the CD28 cytoplasmic domain comprises an amino acid sequence 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 220. In some embodiments, the CD28 cytoplasmic domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 178. In some embodiments, the CD28 cytoplasmic domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 219. In some embodiments, the CD28 cytoplasmic domain is encoded by a nucleotide sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 178. In some embodiments, the CD28 cytoplasmic domain is encoded by a nucleotide sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 219.
Activity of NK cells may be increased by co-expressing various factors, including but not limited to those provided in Table 7.
In some embodiments, a chimeric antigen receptor described herein comprises a ligand binding domain, a transmembrane domain, and an intracellular signaling domain comprising a TLR2 signaling domain. In some embodiments, a chimeric antigen receptor described herein comprises a ligand binding domain, a transmembrane domain, and an intracellular signaling domain comprising a TLR2 signaling domain and a CD3zeta signaling domain. In some embodiments, a chimeric antigen receptor described herein comprises (a) a ligand binding domain, (b) a transmembrane domain selected from the group consisting of CD8 alpha chain (CD8α), CD28, CD16, NKp44, NKp46, NKG2D, DNAM1, IL-2Rβ, TLR, IL-1R subfamily, or functional variant thereof, and (c) an intracellular signaling domain comprising a TLR2 signaling domain and a CD3ζ signaling domain. Exemplary, non-limiting examples include, for example, a chimeric antigen receptor described herein comprises a ligand binding domain, an aTM domain, and an intracellular signaling domain comprising a TLR2 signaling domain and a CD3ζ signaling domain. A further exemplary chimeric antigen receptor comprises a ligand binding domain, a CD28 transmembrane domain, and an intracellular signaling domain comprising a TLR2 signaling domain and a CD3ζ signaling domain.
In an aspect, the disclosure provides a kit comprising the CAR NK cells or the pharmaceutical composition of the disclosure and instructions for use.
In an aspect, the disclosure provides a method of treating or preventing a disease or disorder in a subject in need thereof, comprising administering the CAR NK cell of the disclosure or the pharmaceutical composition of the disclosure to the subject.
In an aspect, the disclosure provides a method of killing a target cell comprising contacting a population of target cells with a population of natural killer cells of the disclosure, wherein the chimeric antigen receptors of the natural killer cell comprise a ligand binding domain that specifically binds an antigen on the target cell, and wherein the natural killer cells induce specific killing of the target cells.
In an aspect, the disclosure provides method of killing a target cell comprising contacting a population of target cells with a population of NK cells.
Cell killing may be assessed by assays known in the art, including but not limited to those described in the examples.
The cancer may result from proliferation of tumor cells that display an antigen specifically bound by the CAR or an NK cell expressing the CAR. The CARs provided herein include CARs having a ligand-binding domain that specifically binds CD19, CD20, and/or HER2. CD19 and CD20 can be expressed on tumor cells of various indolent and aggressive subtypes of B cell lymphomas and leukemias, including Non-Hodgkin's lymphoma (NHL), B-cell Chronic lymphocytic leukemia (CLL), and non-T acute lymphoblastic leukemia (ALL). Accordingly, the CARs described herein may be used to kill CD19+ and/or CD20+ tumor cells and/or treat cancer in subjects having Non-Hodgkin's lymphoma (NHL), B-cell Chronic lymphocytic leukemia (CLL), and non-T acute lymphoblastic leukemia (ALL). HER2 expression has been found in several tumor types including, but not limited to, breast, esophageal, lung, cervical, endometrial and ovarian cancer. Accordingly, the CARs described herein may be used to kill HER2+ tumor cells and/or treat cancer in subjects having breast, esophageal, lung, cervical, endometrial and/or ovarian cancer.
In an aspect, the disclosure provides methods of treating cancer in a subject in need thereof, comprising administering a population of NK cells, or pharmaceutical compositions comprising a population of NK cells.
The terms “subject,” “patient”, and “individual” are used interchangeably herein to refer to a vertebrate, such as a mammal, e.g., a human
As used herein, the term “treatment” or “treating” embraces at least an amelioration of the symptoms associated with a disease or condition in the patient, where amelioration is used in a broad sense to refer to at least a reduction in the magnitude of a parameter, e.g., a symptom associated with the condition being treated. As such, “treatment” or “treating” also includes situations where the disease, disorder, or pathological condition, or at least symptoms associated therewith, are completely inhibited (e.g., prevented from happening) or stopped (e.g., terminated) such that the patient no longer suffers from the condition, or at least the symptoms that characterize the condition.
In some embodiments, the method of treating cancer in a subject in need thereof comprises administering a therapeutically effective amount of CAR NK cells and/or pharmaceutical composition of the disclosure to the subject.
As used herein, “therapeutically effective” refers to an amount of cells or pharmaceutical composition that is sufficient to treat or ameliorate, or in some manner reduce the symptoms associated with a disease, such as cancer/
In some embodiments, the CAR NK cells and pharmaceutical compositions comprising the same described herein are used as part of a combination therapy. In some embodiments, the CAR NK cells or pharmaceutical compositions of the instant disclosure are co-administered to the subject with tumor targeting antibodies.
In some embodiments, the CAR NK cells or pharmaceutical compositions of the instant disclosure exhibit increased cytotoxicity relative to cells or pharmaceutical compositions in which the cells have not been engineered in such a way as the instant disclosure. In some embodiments, the cells or pharmaceutical compositions of the instant disclosure exhibit increased effectiveness relative to equivalent cells or pharmaceutical compositions in cells have not been engineered in such a way as the instant disclosure.
The population of NK cells or pharmaceutical composition may be administered in an amount effective to kill target cells and/or in a therapeutically effective amount for treatment of the cancer.
In an aspect, the disclosure provides a pharmaceutical composition comprising the CAR NK cell or cell population of the disclosure and one or more pharmaceutically acceptable excipients or diluents.
As used herein, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopoeia, other generally recognized pharmacopoeia in addition to other formulations that are safe for use in animals, and more particularly in humans and/or non-human mammals.
As used herein, the term “pharmaceutically acceptable excipients or diluents” refers to an excipient, diluent, preservative, solubilizer, emulsifier, adjuvant, and/or vehicle with which a cell of the disclosure is administered. The use of such media and agents for pharmaceutically active substances is well known in the art. See, e.g., Remington, The Science and Practice of Pharmacy, 20th ed., (Lippincott, Williams & Wilkins 2003).
The compositions of the present invention may additionally contain other adjunct components conventionally found in pharmaceutical compositions. Thus, for example, the compositions may contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or may contain additional materials useful in physically formulating various dosage forms of the compositions.
In an aspect, the disclosure provides methods of making NK cells comprising providing a stem or progenitor cell, such as an induced pluripotent stem cell (iPSC) or embryonic stem cell (ESC) and differentiating the stem or progenitor cell into a NK cell. The stem or progenitor cell may be genetically modified to comprise a polynucleotide encoding a CAR prior to or after the differentiation stem. Known vectors may be used to deliver a polynucleotide, which may be stably maintained by the cell and/or integrated into the genome of the cell. The stem or progenitor cells may be CISH−/− iPSCs and used to generate CISH−/− iPSC-NK cells. The stem or progenitor cells may be soluble IL-15 or membrane-bound IL-15 knock-in iPSCs and used to generate IL-15 knock-in iPSC-NK cells. In some embodiments, iPSCs may be edited to not express CISH, express soluble IL-15 or membrane-bound IL-15, and express any one or more of the CAR constructs disclosed herein.
In some embodiments, the disclosure provides a method of treating cancer with the chimeric receptor expressing cells provided herein or pharmaceutical compositions or formulations thereof. In some embodiments, the method comprises administering the chimeric receptor expressing cells provided herein, pharmaceutical compositions or formulations described herein to a subject in need thereof. The terms “administration” and “administering,” as used herein, refer to the delivery of a bioactive composition or formulation by an administration route comprising, but not limited to intravenous, intramuscular, intraperitoneal, subcutaneous, and intramuscular, or combinations thereof. The term includes, but is not limited to, administering by a medical professional and self-administering.
In some embodiments, a cell expressing a chimeric receptor described herein exhibits enhanced anti-tumor efficacy relative to a cell lacking the chimeric receptor. Methods for measuring anti-tumor efficacy in vitro and in vivo are known to those of skill in the art and include, for example, in vitro killing assays and implanting tumors into mouse models.
Cell killing may be assessed by assays known in the art, including but not limited to those described in the examples.
In some embodiments, a cell expressing a chimeric receptor described herein exhibits enhanced cell killing by about 1%, about 5%, about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 100%, or about 1000% compared to a cell that that lacks the chimeric receptor and/or fusion polypeptide.
In some embodiments, a cell expressing a chimeric receptor described herein exhibits enhanced cell killing by between 1% to 5%, between 5% to 10%, between 10% to 20%, between 20% to 30%, between 30% to 40%, between 40% to 50%, between 50% to 60%, between 60% to 70%, between 70% to 80%, between 80% to 90%, between 90% to 100%, or between 100% to 1000% compared to a cell that that lacks the chimeric receptor and/or fusion polypeptide.
In some embodiments, a cell expressing a chimeric receptor described herein exhibits enhanced specific killing by about 1%, about 5%, about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 100%, or about 1000% compared to a cell that that lacks the chimeric receptor and/or fusion polypeptide.
In some embodiments, a cell expressing a chimeric receptor described herein exhibits enhanced specific killing by between 1% to 5%, between 5% to 10%, between 10% to 20%, between 20% to 30%, between 30% to 40%, between 40% to 50%, between 50% to 60%, between 60% to 70%, between 70% to 80%, between 80% to 90%, between 90% to 100%, or between 100% to 1000% compared to a cell that that lacks the chimeric receptor and/or fusion polypeptide.
All publications, patents and patent applications, including any drawings and appendices therein, are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent or patent application, drawing, or appendix was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.
The reference in this specification to any prior publication (or information derived from it), or to any matter which is known, is not, and should not be taken as an acknowledgment or admission or any form of suggestion that that prior publication (or information derived from it) or known matter forms part of the common general knowledge in the field of endeavor to which this specification relates.
All embodiments of any aspect of the invention can be used in combination, unless the context clearly dictates otherwise.
Unless the context clearly requires otherwise, throughout the description and the claims, the words “comprise,” “comprising,” and the like are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense; that is to say, in the sense of “including, but not limited to.”
As used herein, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. “And” as used herein is interchangeably used with “or” unless expressly stated otherwise. Words using the singular or plural number also include the plural and singular number, respectively.
Section headings are for convenience only and combination of elements from different sections is contemplated. Additionally, the words “herein,” “above,” “below,” and words of similar import, when used in this application, refer to this application as a whole and not to any particular portions of the application.
The term “functional variant” refers to a homology (by sequence or structure) of a domain that retains sufficient signaling activity to activate an NK cell.
The term “sequence identity” refers to the percentage identity of a polypeptide or polynucleotide sequence of interest to a reference sequence, calculated as 100 times the number of exact matches in an optimum alignment of the sequence of interest to the reference sequence divided by the total length of the reference sequence (including gaps). An optimum alignment of the sequences may be generated using the European Molecular Biology Open Software Suite (EMBOSS) needle program available at www.ebi.ac.uk, as described in Maderia et al. Nucleic Acids Res. 47 (W1): W636-W641 (2019).
As used herein, the term “inactivating mutation” refers to a mutation in a genomic sequence that disrupts a function of a gene. The inactivating mutation can be in any sequence region (e.g., coding or non-coding) that contributes to gene expression. Examples include, but are not limited to, cis-acting elements (enhancers) or sequences that are subject to transcription (e.g., mRNA transcript sequences). An inactivating mutation includes mutations that render a gene or its encoded protein non-functional or that reduce the function of the gene or its encoded protein.
The disclosure is now described with reference to the following Examples. These Examples are provided for the purpose of illustration only and the disclosure should in no way be construed as being limited to these Examples, but rather should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.
Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the methods of the present disclosure and practice the claimed methods. The following working examples therefore specifically point out embodiments of the present disclosure and are not to be construed as limiting in any way the remainder of the disclosure.
The materials and methods employed in these experiments are now described.
This example describes design and testing of chimerical antigen receptors in induced pluripotent stem cell (iPSC)-derived natural killer (NK cells). We constructed a library of 44 novel CAR constructs containing signaling modules from diverse NK cell specific signaling receptors. Next, we developed a viral-based CAR expression protocol in mature iPSC-derived NK cells that yields high CAR expression (>75% CAR+) while maintaining high viability (>90%). We then screened for CAR activity using two co-culture target cell killing assays (eSight impedance assay and caspase 3/7 killing assay) and two NK cell-resistant CD19+ target cell lines (Raji and SupB15). The tested constructs, all with an anti-CD19 scFv as the ligand-binding domain, are provided as SEQ ID NOs: 100-117. Our screen identified 7 novel CAR signaling modules that performed better than both a second-generation T-cell CAR (CD28-zeta) and three previously described NK cell-CARs (2B4-zeta, OX40-zeta, and OX40L-zeta). These results were consistent across both functional assays and both target cell lines tested adding support to our findings.
Designed CAR sequences were C-terminal linked via a self-cleaving (2A) peptide to a membrane bound IL-15 (mbIL-15) for co-expression in natural killer cells. Lentiviral particles were generated and concentrated ˜100× to facilitate the high viral titers required to transduce iPSC-derived NK cells.
Concentrated viral stocks were loaded onto retronectin-coated 96-well plates by centrifugation, IL-2 activated iPSC-derived NK cells were added and centrifuged in the presence of viral supernatant, and incubated in the presence of IL-2 for 72 hrs. CAR expression was detected by flow cytometry using an HA-tag engineered into the extracellular portion of the CAR polypeptide (
We screened for CAR activity using two co-culture target cell killing assays (eSight impedance assay and Caspase 3/7 killing assay) and two NK cell resistant CD19+ target cell lines (Raji and SupB15). Results of the screen are shown in
Selected data comparing CAR designs with and without a 2B4 domain is shown in
Overall, we have successfully developed a CAR screening platform in a therapeutically relevant allogenic cell source and have identified NK optimized CARs that enable increased potency of NK cells compared to current CAR solutions. Of note, intracellular signaling modules from Toll-like receptors and IL-1R subfamily receptors showed enhanced NK CAR activity compared to CARs containing canonical NK cell activation receptor domains used in previously developed NK optimized CAR designs—i.e., 2B4 (shown in figures), FCER1G, DNAM1, DAP10. These findings validate the use of diverse immune cell signaling domains in NK optimized CARs.
Construction of lentiviral expression vectors and viral packaging: Polypeptide sequences of all candidate CAR components were obtained from Ensemble™ database (Howe et al. Nucleic Acids Res. 2021, vol. 49 (1): 884-891) and assembled into complete CAR designs using SnapGene™ molecular biology software. Nucleic acid sequences were determined using a publicly available codon optimization tool (Integrated DNA Technologies™). All CAR constructs included, as representative ligand binding domain, a CD19 scFv binder (FMC63; SEQ ID NO: 109), mbIL-15 co-expressed partner (SEQ ID NO: 48), and an HA-tag for CAR detection. CAR constructs were synthesized and cloned into a lentiviral expression vector under the EF-1 alpha promoter (pCDH-EF1α-MCS-T2A-Puro; System Biosciences™), and maxi-preps were produced and sequence verified. Lentiviral particles were generated using the constructs described above, packaging plasmids (Rev, gag-pol, and VSVG; Cell Biolabs™), and the Lenti-X™ 293T cell line (Takara™). Viral supernatants were concentrated ˜100× using a PEG-based concentration solution (Takara™) and viral titers were determined using Lenti-X GoStix Plus™ (Takara™).
Generation of iPSC-NK cells: iPSCs are collected and transferred to culture in serum-free media and formed into embryoid bodies by spin aggregation. Upon the appearance of CD34+ cells inside the Embryoid Body (EB) at day 6, EB are transferred into NK cell differentiation medium containing: a 2:1 mixture of Dulbecco modified Eagle medium/Ham F12), 2 mM L-, 1% penicillin/streptomycin, 25 mM b-mercaptoethanol, 20% heat-inactivated human serum AB, 5 ng/ml sodium selenite, 50 mM ethanolamine, 20 mg/mL ascorbic acid, interleukin-3; for first week only, stem cell factor, interleukin-15, Fms-like tyrosine kinase 3 ligand, and interleukin-7. The EB is left in these conditions for 28 days receiving weekly media changes to produce NK cells (CD45+CD56+CD33−CD3− cells, as determined by flow cytometry). Then NK cells are harvested for expansion.
Expansion: After differentiation, an immortalized leukemia cell line, K562 expressing mbIL21 and 4-1BB ligand (CD137), is used to stimulate NK cell expansion. NK cells are seeded with K562-41BBL-mbIL21 feeder cells and incubated at 1:2 ratio in Stromal Cell Growth Medium (SCGM) with 100 U/mL IL-2. Non-adherent cells are removed and analyzed by flow cytometry to determine the purity of CD56+NK cells. These cells are then stimulated with 2:1 aAPCs (irradiated at 10,000 Gy) to NK cells at 350,000 NK cells/mL of media containing RPMI 1640, 2 mM L-glutamine, 1% penicillin/streptomyocin, 1% non-essential amino acids, and 10% standard FBS or 10% human serum AB), supplemented with 50-100 U/mL IL-2.
Transduction of iPSC-NK cells: Non-treated 96-well plates were coated with Retronectin (Takara). Equal amount of concentrated lentivirus was added to plates and centrifuged at 2000×g at 32° C. for 2 hrs. iPSC-derived NK cells (6e4 cells) were added to each well in media containing IL-2 (50 U/ml) and centrifuged at 800×g at 32° C. for 1 hr. Cells were incubated at 37° C. for 48 hrs. Fresh media (with IL-2) was added, and cells were incubated for an additional 24 hrs. CAR expression was determined at 72 hrs post-transduction using flow cytometry to detect the HA-tag engineered into the extracellular domain of each CAR. CAR+ cells were used for functional assay within 24 hrs of CAR detection.
Long-term target cell killing assay using eSight™: RTCA E-plates were coated with CD40 tethering reagent (Agilent™) diluted in PBS overnight at 4° C. Plates were washed with PBS, target cells (either CD19+ target cells (Raji; ATCC™) or HER2+ target cells (BT474 clone5) were added to each well, and impedance readings were allowed to equilibrate for 2-4 hrs. CAR+ iPSC-NK cells were added to each well at the indicated E:T ratio and impedance readings were measured every 15 min for 24 hrs. NK-specific killing was determined by normalizing impedance readings to “target cells alone” control wells and plotted as frequency of target killing.
4 hr Caspase 3/7 cytotoxicity assay: SupB15 (CD19+ target cells) were pre-stained with CellTrace™ Violet at a final concentration of 5 μM in PBS for 15 min at 37° C., followed by washing in complete culture medium. CAR+iPSC-NK cells were added to each well at 2:1 E:T ratio in a final volume of 100 μl. Co-cultures were centrifuged at 100×g for 1 min and incubated at 37° C. for 3.5 hrs. Following incubation, CellEvent® Caspase-3/7 Green Detection Reagent and SYTOX™ AADvanced™ dead cell stain solution was added to co-cultures and incubated for an additional 30 min at 37° C. After staining, assays are read on a NovoCyte Advanteon and analyzed by FlowJo software. NK-specific killing was determined by normalizing impedance readings to “target cells alone” control wells and plotted as frequency of target killing.
iPSC derived NK cells expressing functional CAR constructs (determined by results from in vitro assays) are tested for in vivo efficacy using a CD19 expressing model of B cell malignancies. To initiate disease, 10-12 week-old NOD-SCID-gamma−/− (NSG) mice (Jackson Laboratory) are injected intravenously with luciferase expressing Raji cells (CD19 positive). After 1 day, the mice are administered iPSC-derived NK cells engineered to express (a) no CAR (negative control); (b) a 2nd generation T cell CAR (benchmark control); or (c) an NK CAR (test group). Subject mice are administered IL-2 every other day for the remainder of the experiment. Disease progression is monitored by survival, weight loss, and bioluminescent imaging of tumor burden (measured weekly). To assess the number of infused NK cells present during the course of the experiment, CD45+CD56+CD3− cells from peripheral blood are quantified weekly.
Concentrated lentiviral stocks comprising different CARs having a HER2 scFv binder were loaded onto retronectin-coated 96-well plates by centrifugation. IL-2 activated iPSC-derived NK cells were added and centrifuged in the presence of viral supernatant, and incubated in the presence of IL-2 for 72 hrs. CAR expression was detected by flow cytometry using an HA-tag engineered into the extracellular portion of the CAR polypeptide. CAR expression was uniform across most of the CAR constructs (
CAR activity was screened using a co-culture target cell killing assay (eSight impedance assay) on a NK cell resistant HER2+ target cell line (BT474). Results of the screen are shown in
Similarly, the CD8-aTM-TLR2-CD3ζ construct having a CD19 scFv exhibited robust cell killing of Raji 2.0 cells at multiple effector to target cell rations (data not shown). The CD8-CD28TM-TLR2-CD3ζ construct also exhibited similar activity.
Next, CAR-HER2 activity was screened using stress test killing assays. Briefly, CISH KO iPSC-derived NK cells were transduced using retrovirus with one of three different CAR constructs having the same HER2 scFv binding domain (HER2v3), and different intracellular domains. (
The results using different CAR constructs having the same HER2 scFv binding domain (HER2v3) identified CD8-aTM-TLR2-CD3ζ (SEQ ID NO: 82) as the top NK optimized CAR-HER2 construct tested (
CAR activity for the CD8-aTM-TLR2-CD3ζ CAR constructs having different HER2 scFv binding domains was also assessed in a caspase 3/7 killing assay using a NK cell resistant HER2+ target cell line (BT474) (
Next, the killing activity of CISH KO iPSC-derived NK cells expressing the CD8-aTM-TLR2-CD3ζ CAR and one of three different HER2 scFv binding domains (HER2v2, HER2v3, or HER2v5) were tested in 3D single tumor spheroids. In brief, BT474 cells, which are human HER+ductal carcinoma cells, were seeded and cultured using standard protocols for spheroid formation. After spheroids were formed (approximately 36 hours after seeding), cells were co-cultured with CISH KO iPSC-derived NK cells: 1) not expressing a CAR; 2) expressing a HER2v2-CD8-aTM-TLR2-CD3ζ CAR; 3) expressing a HER2v3-CD8-aTM-TLR2-CD3ζ CAR; or 4) expressing a HER2v5-CD8-aTM-TLR2-CD3ζ CAR.
Using iPSC-derived NK cells transduced with the HER2v3-CD8-aTM-TLR2-CD3ζ construct, a cell serial killing assay (eSight impedance assay) was performed in real time. In brief, repeat killing of a HER2+ target cell line (SKOV3) and exhaustion profiles were observed by repeatedly adding HER2v3-CD8-aTM-TLR2-CD3ζ CISH KO iPSC-derived NK cells to the target cells. As shown in
Killing activity of the HER2v3-CD8-aTM-TLR2-CD3ζ-expressing CISH KO iPSC-derived NK cells was tested in 3D single HER+ tumor spheroids. After spheroids were formed, target cells were co-cultured with different ratios of either 1) CISH KO iPSC-derived NK cells that were not transduced with a CAR construct (untransduced NKs or “UT”) or 2) CISH KO iPSC-derived NK cells that express HER2v3-CD8-aTM-TLR2-CD3ζ. The ratio of effector cells (untransduced CISH KO iPSC-derived NK cells or HER2v3-CD8-aTM-TLR2-CD3ζ CISH KO iPSC-derived NK cells) added to target cells (BT474 cells) was either 5:1, 2.5:1, or 1.25:1. Killing of spheroid cells was monitored at day 0 and day 3 after NK cells were added.
To examine the effect of sIL-15 on CAR-HER2 activity, a CAR expression assay
Taken together, these results demonstrate that CISH KO iPSC-derived NK cells expressing HER2-CD8-aTM-TLR2-CD3ζ CARs demonstrate robust activity against NK cell resistant solid tumor target cells.
This example describes testing of CISH KO iPSC-derived NK cells expressing a HER2 scFv-CAR and soluble IL-15 demonstrated potent killing of solid tumor target cell lines.
First, triple-edited (TE) iPSCs were generated using a gene editing method by introducing into CISH KO iPSCs a HER2-CAR sequence that was C-terminal linked via a self-cleaving (2A) peptide to a soluble IL-15 (sIL-15). The resulting TE iPSCs: 1) did not express the CISH gene (CISH KO); 2) expressed HER2v3-CD8-aTM-TLR2-CD3ζ (HER-CAR) and 3) expressed soluble IL-15 (SEQ ID NO: 58), allowing for IL-15 secretion (
To determine if triple editing of the iPSCs resulted in an altered NK phenotype, NK cell marker expression was measured in the TE iPSC-derived NK cells by flow cytometry. As shown in
TE iPSC-derived NK cell function was assessed in a spheroid killing assay. In brief, HER2+ (BT474 clone 5) target cell spheroids were prepared as described in the examples herein. Either wild type (WT) NK cells, NKs differentiated from iPSCs having only the CISH KO, or NKs differentiated from the TE iPSCs were added to the HER2+ spheroids (10:1 E:T). NK-mediated killing of the HER2+ spheroids, monitored using an eSight impedance assay, showed that the TE iPSC-derived NK cells were effective at killing the NK resistant HER2+ solid tumor target (
Taken together, the data demonstrates that TE iPSC-derived NK cells potently kill solid tumor target cell lines.
While the invention has been described in connection with proposed specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims.
This application claims the benefit of U.S. Provisional Application No. 63/325,441, filed Mar. 30, 2022, and U.S. Provisional Application No. 63/440,169, filed Jan. 20, 2023, the entirety of which are hereby incorporated by reference herein in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2023/065102 | 3/29/2023 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63325441 | Mar 2022 | US | |
| 63440169 | Jan 2023 | US |
