WO2021030182A1 - Bifunctional single variable domain t cell receptors and uses thereof - Google Patents

Bifunctional single variable domain t cell receptors and uses thereof Download PDF

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Publication number
WO2021030182A1
WO2021030182A1 PCT/US2020/045373 US2020045373W WO2021030182A1 WO 2021030182 A1 WO2021030182 A1 WO 2021030182A1 US 2020045373 W US2020045373 W US 2020045373W WO 2021030182 A1 WO2021030182 A1 WO 2021030182A1
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tcr
domain
cell
cells
polypeptide
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PCT/US2020/045373
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French (fr)
Inventor
Carl Alexander Kamb
Julyun OH
Dora Toledo WARSHAVIAK
Mikayel MKRTICHYAN
Melanie MUNGUIA
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A2 Biotherapeutics, Inc.
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Publication of WO2021030182A1 publication Critical patent/WO2021030182A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex

Definitions

  • TCRs T cell receptors
  • CARs chimeric antigen receptors
  • pMHCs peptide-MHC complexes
  • pMHCs are the natural ligands for TCRs and, as such, lend themselves to targeting by TCRs and their derivatives.
  • Class I MHC molecules consist of a molecular dimer of an a chain associated with b2 microglobulin. This dimer binds in a degenerate manner to individual short peptides while folding in the endoplasmic reticulum to create the pMHC complex.
  • the pMHC is then transported to the membrane surface where it can be recognized by cognate T cells. If a certain binding threshold is crossed, pMHCs can trigger activation and effector function of T cells through TCRs.
  • TCRs are composed of a complex of eight subunits, comprising six individual polypeptides in the stoichiometry a:b:g:d:2e:2z.
  • the a and b subunits form the central pMHC binding element, which has significant structural similarity to its relative, the antibody antigen-binding fragment (Fab).
  • Both the a and b subunits typically contribute to binding a small region on the class I MHC ligand distal to the membrane that includes residues from the MHC molecule as well as the short peptide in the complex itself.
  • pMHCs afford the option to target peptides derived from proteins that reside in the cytoplasm and are otherwise inaccessible to large molecules, such as monoclonal antibodies.
  • TCR-based binding agents including engineered TCRs.
  • the invention relates generally to polypeptides that comprise at least two antigen-binding domains, at least one of which is a single-variable domain TCR domain (svd-TCR).
  • the disclosure provides a polypeptide, comprising, in N-terminal to C-terminal order, a first antigen binding domain, a linker, and a second antigen-binding domain, wherein either or both of the first and second antigen-binding domains comprise a single-variable domain TCR (svd-TCR).
  • the polypeptide comprises a transmembrane domain C-terminal to the second antigen binding domain.
  • the first and second antigen-binding domains each independently comprise a svd-TCR.
  • the first and second antigen binding domains each independently comprise a svd-TCR, wherein the svd-TCR comprises a variable domain selected from a TCR Va domain, a TCR nb domain, a TCR Vy domain, and a TCR V5 domain, or an antigen-binding fragment thereof.
  • either or both of the first and the second svd-TCRs comprises a TCR constant domain selected from a TCR Ca domain, TCR Cb domain, a TCR Cy domain, and a TCR C5 domain and/or the second antigen-binding domain comprises a TCR constant domain selected from a TCR Ca domain, TCR Cb domain, a TCR Cy domain.
  • the first svd-TCR comprises a first TCR nb domain or an antigen-binding fragment thereof and the second svd-TCR comprises a second TCR nb domain or an antigen-binding fragment thereof.
  • the first and second nb domains each independently comprises a human nb domain.
  • the Ub domains each independently share at least 80% sequence identity to a human Ub domain.
  • the first nb domain share at least 80% sequence identity to TRBV5-8 nb (SEQ ID NO: 30).
  • the second nb domain shares at least 80% sequence identity to TRBV5- 8 nb (SEQ ID NO: 30).
  • the second svd-TCR comprises a TCR Ob domain.
  • the first svd-TCR specifically binds a first peptide:MHC complex comprising a first peptide.
  • the second svd- TCR specifically binds a second peptide:MHC complex comprising a second peptide.
  • the first peptide comprises a tumor antigen.
  • the second peptide comprises a tumor antigen.
  • the first or the second peptide:MHC complex comprises a class I MHC.
  • the first or the second peptide:MHC complex comprises a class II MHC.
  • the linker comprises the amino acid sequence of SEQ ID NO: 31.
  • the transmembrane domain is a TCRa transmembrane domain or a TO Ib transmembrane domain. In some embodiments, the transmembrane domain is a E ⁇ 3z transmembrane domain or a CD28 transmembrane domain.
  • the polypeptides comprise, C- terminal to the transmembrane domain, one or more intracellular signaling domains.
  • the transmembrane domain comprises a CD28 transmembrane domain and wherein the one or more intracellular signaling domains comprise, in any C terminal to N terminal order, a CD28 intracellular domain, or functional fragment thereof, and a E ⁇ 3z intracellular domain, or functional fragment thereof.
  • the transmembrane domain comprises a CD28 transmembrane domain and wherein the one or more intracellular signaling domains comprise, in any C terminal to N terminal order, a CD28 intracellular domain, a 4- IBB intracellular domain, and a E03z intracellular domain, or functional fragments thereof.
  • the first svd-TCR and the second svd-TCR each independently comprise a CDR3 comprising an amino acid sequence selected from SEQ ID NOs: 1-7.
  • the first svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 2 and the second svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 7.
  • the first svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 7 and the second svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID.
  • the disclosure provides polynucleotides comprising a nucleic acid sequence encoding a polypeptide of the disclosure.
  • the nucleic acid sequence is in operative association with a promoter for expression of said nucleic acid.
  • the disclosure provides vectors comprising polynucleotides of the disclosure.
  • the disclosure provides cells comprising the polypeptides of the disclosure.
  • the cell is a T cell.
  • the T cell is a T regulatory (T reg ) cell.
  • the T cell is a non-regulatory T cell.
  • the cell is an NK cell.
  • the disclosure provides pharmaceutical compositions comprising a plurality of the cells of the disclosure and a pharmaceutically acceptable carrier, diluent or excipient.
  • the pharmaceutical compositions comprise a therapeutically effective amount of the cells.
  • the disclosure provides methods of activating a cytotoxic signal in a target cell, comprising contacting, delivering, administering, providing, and/or supplying the cell of the disclosure to the target cell.
  • the cytotoxic signal comprises NFAT signaling.
  • the cytotoxic signal comprises release of IFNy.
  • the disclosure provides methods inducing tolerance in a target cell, comprising contacting, delivering, administering, providing, and/or supplying the cell of the disclosure to the target cell. [0022]
  • the disclosure provides methods of treating and/or preventing cancer in a subject in need thereof, comprising administering to the subject a plurality of the cell of the disclosure or the pharmaceutical composition of the disclosure.
  • kits comprising a plurality of the cell of any one of claims 28-33.
  • the kits further comprise instructions for use.
  • the disclosure provides a vectors, cells, and methods of use including methods of treating diseases or disorders, e.g., cancer.
  • FIG. 1 A shows a schematic of the Ub-TCR and Ub-CAR constructs used in the disclosure.
  • FIG. IB is a series of plots that shows flow cytometry of HEK293 cells transfected with NY- ESO-1 pMHC -targeted constructs. The x-axis reflects the proportion of pMHC probes bound to the cell, and the y-axis reflects the proportion of TCR 3 chain on the cell surface.
  • FIG. 1C is a series of plots that shows flow cytometry of HEK293 cells transfected with MAGE- A3 pMHC-targeted constructs.
  • the x-axis reflects the proportion of pMHC probes bound to cell, and the y-axis reflects the proportion of TCR 3 chain on the cell surface.
  • FIG. ID is a series of plots that shows flow cytometry of Jurkat cells transfected with NY- ESO-1 pMHC-targeted constructs.
  • the x-axis reflects the proportion of pMHC probes bound to the cell.
  • FIG. IE is a series of plots that shows flow cytometry of Jurkat cells transfected with MAGE- A3 pMHC-targeted constructs. The x-axis reflects the proportion of pMHC probes bound to the cell.
  • FIG. 2 is a series of pictures that shows homology models that use the atomic coordinates of the MAGE peptide/HLA-A2 pMHC in complex with a nb5 TCR (5BRZ). The amino acid sequences for a specific TCR representing 3 different nb family segments were threaded onto the crystal structure backbone and refined to eliminate steric clashes (see Methods). Hydrophobic patches on the space-filling surface model are labeled green; charged and neutral surfaces white.
  • FIG. 3 is a pair of plots that shows the NFAT-luciferase signal of Jurkat cells transfected with nb constructs after 6 hours of co-culture with NY-ESO-1 (left panel) or MAGE-A3 (right panel) peptide-loaded T2 cells.
  • FIG. 4A shows a schematic of the nb-TCR constructs used in the current disclosure.
  • FIG. 4B is a series of plots that show pMHC probe binding (top panel) and TCR complex formation (CD3s surface expression, bottom panel) in transfected SUP-T1 cells.
  • FIG. 4C is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6hrs of co-culture with NY-ESO-1 (left) or MAGE-A3 (right) peptide-loaded T2 cells.
  • FIG. 5A is a series of plots that show a flow cytometry of transfected Jurkat cells stained for binding to NY-ESO-1 pMHC probe (y-axis) and MAGE-A3 pMHC probe (x-axis). M refers to MAGE- A3 and N refers to NY-ESO-1.
  • FIG. 5B is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 (left) and MAGE- A3 (right) peptide-loaded T2 cells.
  • FIG. 5C shows a schematic of the constructs presented in this disclosure.
  • M refers to MAGE- A3 and N refers to NY-ESO-1.
  • FIG. 5D is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 (left) and MAGE- A3 (right) peptide-loaded T2 cells.
  • FIG. 6A is a series of plots that show primary T cells transduced with indicated constructs stained with NY-ESO-1 or MAGE- A3, as indicated.
  • FIG. 6B is a pair of plots that show A375 cells expressing nuclear locating GFP loaded with IOmM of NY-ESO-1 (left) or MAGE-A3 (right) peptides were co-cultured with T cells transduced with NY-ESO-1 (left) or MAGE- A3 (right) binding constructs at 1:1 ratios and imaged in IncuCyte for 42 hours. Ratio of total green fluorescent area at each time point divided by time zero value is plotted.
  • FIG. 6C is a plot that shows IFNy measured by the BD cytometric bead array with supernatants from the 24 hour time-point of the co-cultures in FIG. 6B.
  • FIG. 7 is a series of plots that show flow cytometry plots of HEK293T cells transfected with nb-only domains recovered from the HuTARGTM system.
  • the x-axis reflects the amount of target pMHC probes bound to the cell.
  • the y-axis reflects the amount of the TCRP chain on the cell surface.
  • FIG. 8 A shows a schematic of the nb-only CARs in the present disclosure.
  • FIG. 8B is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6hrs of co-culture with NY-ESO-1 (left panel) and MAGE-A3 (right panel) peptide-loaded T2 cells.
  • FIG. 9 is a series of plots that show flow cytometry of Jurkat cells transfected with NY-ESO- 1 or MAGE- A3 pMHC-targeted constructs. The x-axis reflects the proportion of pMHC probes bound to the cell.
  • FIG. 10A is a series of plots that show flow cytometry of CD3 and NY-ESOl pMHC probe binding in SUP-T1 cells.
  • FIG. 10B is a plot that shows the NFAT-luciferase signal of transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 peptide-loaded T2 cells.
  • FIG. 11 A shows a schematic of scFv-CAR and TCR constructs used in FIG. 1 IB.
  • FIG. 1 IB is a plot that shows the NFAT-luciferase signal transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 peptide-loaded T2 cells.
  • TCRs can function as a single binding domain; e.g., as a nb devoid of its normal partner, the a variable domain (Va).
  • Va variable domain
  • shark species have a variety of novel TCRs that are distinct in form from mammalian orthologs (Criscitiello et al, 2006; Greenberg et al., 1995). If such a simplified TCR variable domain that retains binding and functional activity against pMHCs could be defined, it would potentially open a path to engineering smaller, more complex binding capabilities with svd-TCRs.
  • the HuTARG platform is a powerful tool for engineering proteins in a mammalian system due to its ability to screen billions of antigen-binding molecules directly for function.
  • the HuTARG platform was used to generate variable regions of the svd-TCR by using TCR-specific V, D, and J elements.
  • In vitro V(D)J recombination was used to generate sequence diversity in the TCR nb domain while keeping the Va domain constant in a controlled fashion in mammalian cells, and over 100 million TCR-expressing cells were sorted and enriched for their ability to bind peptide in the absence of a second TCR variable domain. See patent applications WO 2009/129247 and WO 2017/091905, herein incorporated by reference in their entirety.
  • nb-only TCRs can be constructed from a nb domain with no additional sequence engineering within the framework and constant regions of the b chain. These nb-only svd- TCRs express stably on the cell surface of mammalian cells, including T cells. They bind pMHC probes selectively and appear to trigger T cells in much the same manner as full TCRs. Moreover, they function in tandem as CAR and TCR bifunctional proteins. Such nb-only domains provide tools and components for next-generation engineered T cell therapeutics and shed light on the mechanism that dictate signaling sensitivity of TCRs and CARs.
  • single variable domain T cell receptor or “svd-TCR” refer to the variable domain of a T cell receptor capable of specifically binding to an epitope in the absence of a second TCR variable domain.
  • an svd-TCR comprising a nb variable domain is capable of binding to an epitope independent of and/or in the absence of a Va variable domain
  • an svd-TCR comprising a Va variable domain is capable of binding to an epitope independent of and/or in the absence of a nb variable domain.
  • Illustrative epitopes recognized by svd-TCRs include peptide:MHC complexes (pMHC complexes).
  • an “epitope” recognized by an svd-TCR is not a superantigen.
  • Superantigens are a class of antigen that cause non-specific activation of T-cells resulting in polyclonal T-cell activation and massive cytokine release. They are produced by some pathogenic viruses and bacteria, potentially as a defense mechanism against the immune system. Binding of SAgs to the TCR is by a different mechanism than classic TCR recognition of pMHCs and is independent of the TCR CDR3 sequences of the variable domains.
  • the terms “comprising,” “having,” “including” and “containing,” and grammatical variations thereof, are inclusive or open-ended and do not exclude additional, unrecited elements and/or method steps.
  • the term “consisting essentially of when used herein in connection with a composition, use or method, denotes that additional elements and/or method steps may be present, but that these additions do not materially affect the manner in which the recited composition, method or use functions.
  • the term “consisting of when used herein in connection with a composition, use or method excludes the presence of additional elements and/or method steps.
  • composition, use or method described herein as comprising certain elements and/or steps may also, in certain embodiments consist essentially of those elements and/or steps, and in other embodiments consist of those elements and/or steps, whether or not these embodiments are specifically referred to.
  • a use or method described herein as comprising certain elements and/or steps may also, in certain embodiments consist essentially of those elements and/or steps, and in other embodiments consist of those elements and/or steps, whether or not these embodiments are specifically referred to.
  • a reference to an element by the indefinite article “a” does not exclude the possibility that more than one of the elements is present, unless the context clearly requires that there be one and only one of the elements.
  • the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise.
  • the use of the word “a” or “an” when used herein in conjunction with the term “comprising” may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one” and “one or more than one”.
  • the term “plurality” as used herein means more than one, for example, two or more, three or more, four or more, and the like.
  • the term “about” refers to an approximately +/-10% variation from a given value. It is to be understood that such a variation is always included in any given value provided herein, whether or not it is specifically referred to.
  • range format various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6.
  • a range such as 95-99% identity includes something with 95%, 96%, 97%, 98% or 99% identity, and includes subranges such as 96-99%, 96- 98%, 96-97%, 97-99%, 97-98% and 98-99% identity. This applies regardless of the breadth of the range.
  • polypeptide is a chain of amino acid residues, including peptides and protein chains.
  • a polypeptide may include amino acid polymers in which one or more of the amino acid residues is an artificial chemical analogue of a corresponding naturally occurring amino acid, or is a completely artificial amino acid with no obvious natural analogue as well as to naturally occurring amino acid polymers.
  • nucleic acid means oligomers of bases typically linked by a sugar-phosphate backbone, such as oligonucleotides or polynucleotides, and to DNA or R A of genomic or synthetic origin which can be single-or double-stranded, and represent a sense or antisense strand.
  • nucleic acid, polynucleotide and nucleotide also specifically include nucleic acids composed of bases other than the five biologically occurring bases (i.e., adenine, guanine, thymine, cytosine and uracil), and also include nucleic acids having non-natural backbone structures.
  • bases other than the five biologically occurring bases i.e., adenine, guanine, thymine, cytosine and uracil
  • nucleic acids having non-natural backbone structures Unless otherwise indicated, a particular nucleic acid sequence of this invention encompasses complementary sequences, in addition to the sequence explicitly indicated.
  • sequence identity refers to an exact nucleotide-to- nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively.
  • techniques for determining sequence identity include determining the nucleotide sequence of a polynucleotide and/or determining the amino acid sequence encoded thereby and comparing these sequences to a second nucleotide or amino acid sequence.
  • Two or more sequences can be compared by determining their “percent identity.”
  • the percent identity of two sequences, whether nucleic acid or amino acid sequences is the number of exact matches between two aligned sequences divided by the length of the shorter sequences and multiplied by 100. Percent identity may also be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul, Proc. Natl. Acad. Sci. USA 87:2264-2268 (1990) and as discussed in Altschul, et al., J. Mol. Biol.
  • the BLAST program defines identity as the number of identical aligned symbols (generally nucleotides or amino acids), divided by the total number of symbols in the shorter of the two sequences. The program may be used to determine percent identity over the entire length of the proteins being compared. Default parameters are provided to optimize searches with short query sequences in, for example, with the blastp program. Ranges of desired degrees of sequence identity are approximately 80% to 100% and integer values . Typically, the percent identities between a disclosed sequence and a claimed sequence are at least 80%, at least 85%, at least 90%, at least 95%, or at least 98%.
  • nucleic acid vector refers to at least one of a plasmid, bacteriophage, cosmid, artificial chromosome, expression vector, or any other nucleic acid vector.
  • vectors may be used, or that the above vectors may be modified in order to combine sequences as desired.
  • vectors may be modified by inserting additional origins of replication, or replacing origins of replication, introducing expression cassettes comprising suitable promoter and termination sequences, adding one or more than one DNA binding sequence, DNA recognition site, or adding sequences encoding polypeptides as described herein, other products of interest, polypeptides of interest or proteins of interest, or a combination thereof.
  • adjacent functional components of a vector may be joined by linking sequences.
  • a “promoter” is a DNA region, typically but not exclusively 5' of the site of transcription initiation, sufficient to confer accurate transcription initiation.
  • the promoter nucleic acid typically contains regions of DNA that are involved in recognition and binding of RNA polymerase and other proteins or factors to initiate transcription.
  • a promoter is constitutively active, while in alternative embodiments, the promoter is conditionally active ( e.g ., where transcription is initiated only under certain physiological conditions). Conditionally active promoters may thus be “inducible” in the sense that expression of the coding sequence can be controlled by altering the physiological condition.
  • operably linked when used in reference to nucleic acids, refer to the linkage of nucleic acid sequences placed in functional relationships with each other.
  • an operatively linked promoter sequence, open reading frame and terminator sequence results in the accurate production of an RNA molecule.
  • operatively linked nucleic acid elements result in the transcription of an open reading frame and ultimately the production of a polypeptide (i.e., expression of the open reading frame).
  • TCRs TCRs
  • TCR Subunits TCRs
  • the engineered TCRs of the disclosure comprise an extracellular domain made up of one or more single variable domain T cell receptors (svd-TCRs), a transmembrane domain and an intracellular domain.
  • the intracellular domain comprises one or more exogenous domains.
  • TCR subunits include TCR alpha, TCR beta, CD3 zeta, CD3 delta, CD3 gamma and CD3 epsilon. Any one or more of TCR alpha, TCR beta chain, CD3 gamma, CD3 delta or CD3 epsilon, or fragments or derivative thereof, can be fused to one or more domains capable of providing a stimulatory signal of the disclosure, thereby enhancing TCR function and activity. svd-TCRs
  • a svd-TCR comprising a first TCR variable domain, the first TCR variable domain specifically binding to an antigen in the absence of a second TCR variable domain.
  • the engineered TCR contains multiple svd-TCRs.
  • the first svd-TCR is linked to a second svd-TCR, wherein the first and second svd- TCRs specifically bind peptides.
  • the peptides are bound to MHC.
  • the svd-TCR domains recognize the same peptide. In other embodiments, the svd- TCRs recognize different peptides.
  • the engineered TCR may bifunctional.
  • the term “bifunctional TCR” as described herein refers to a first antigen-binding domain, or svd-TCR, binding to a first peptide and a second antigen binding domain, or svd-TCR, binding to a second peptide, wherein the first and second peptides are not the same peptide.
  • the svd-TCR may include additional elements besides the TCR variable domain, including additional amino acid sequences, additional protein domains (covalently associated, non- covalently associated or covalently and non-covalently associated with the TCR variable domain), fusion or non-covalent association of the TCR variable domain with other types of macromolecules (for example polynucleotides, polysaccharides, lipids, or a combination thereof), fusion or non-covalent association of the TCR variable domain with one or more small molecules, compounds, or ligands, or a combination thereof. Any additional element, as described, may be combined provided that the TCR variable domain is configured to specifically bind the epitope in the absence of a second TCR variable domain.
  • An svd-TCR as described herein may comprise a single TCR chain ( e.g . a, b, g, or d chain), or it may comprise a single TCR variable domain (e.g. of a, b, g, or d chain). If the svd-TCR is a single TCR chain, then the TCR chain comprises a transmembrane domain, a constant (or C domain) and a variable (or V domain), and does not comprise a second TCR variable domain.
  • the svd-TCR may therefore comprise or consist of a TCR a chain, a TCR b chain, a TCR g chain or a TCR d chain.
  • the svd-TCR may be a membrane bound protein.
  • the svd-TCR may alternatively be a membrane- associated protein.
  • the engineered TCR as described herein utilizes a surrogate a chain that lacks a Va segment, which forms activation-competent TCRs complexed with the six CD3 subunits.
  • the engineered TCR as described herein functions independently of a surrogate a chain that lacks a Va segment.
  • the one or more svd- TCRs are fused to transmembrane (e.g., O ⁇ 3z and CD28) and intracellular domain proteins (e.g., O ⁇ 3z, CD28, and/or 4-1BB) that are capable of activating T cells in response to antigen.
  • the svd-TCR may be any svd-TCR or subset of svd-TCRs defined herein, including without limitation single TCR chains and fusion proteins comprising the svd-TCR.
  • the svd-TCR may be a single a TCR chain, a single b TCR chain, a single g TCR chain, or a single d TCR chain.
  • the svd-TCR may be a svd-TCR-Fc fusion or any other fusion protein defined herein.
  • the svd-TCR engages antigen using complementarity-determining regions (CDRs).
  • CDRs complementarity-determining regions
  • Each svd-TCR contains three complement determining regions (CDR1, CDR2, and CDR3).
  • the TCR variable domain can be stably expressed without the TCR transmembrane domain or TCR C domain to generate a soluble protein (Alajez et. al. J. Biomed. Biotechnol. Article ID 68091, 1-9 (2006); Laugel etal. J. Biol. Chem. 280:1882-92 (2005)).
  • the svd-TCR as described herein may be a soluble protein.
  • the svd-TCR may comprise a single TCR variable domain (i.e. the first TCR variable domain) without the transmembrane or C domains (or portions thereof).
  • the first TCR variable domain may comprise either a TCR Va domain, a TCR nb domain, a TCR Ug domain, or a TCR V5 domain. Therefore, the soluble svd-TCR may comprise the first TCR variable domain, for example, a single TCR variable a, b, g or d domain. In another example, the svd-TCR may comprise a svd-TCR (i.e. the first TCR variable domain) linked to a second svd-TCR (i.e. the second TCR variable domain) without transmembrane or C domains (or portions thereof).
  • the first TCR variable domain may comprise either a TCR Va domain, a TCR nb domain, a TCR Vy domain, or a TCR Vd domain
  • the second TCR variable domain may comprise either a TCR Va domain, a TCR nb domain, a TCR Vy domain, or a TCR V5 domain.
  • the first svd-TCR comprises a first TCR nb domain or an antigen binding fragment thereof and the second svd-TCR comprises a second TCR nb domain or an antigen binding fragment thereof.
  • the first and/or second TCR variable domain may be a human TCR variable domain.
  • the first TCR variable domain may be a non-human TCR variable domain.
  • the first and/or second TCR variable domain may be a mammalian TCR variable domain.
  • the first and/or second TCR variable domain may be a vertebrate TCR variable domain.
  • the TCR variable regions of the a and g chains are each encoded by a V and a J segment, whereas the variable region of b and d chains are each additionally encoded by a D segment.
  • V Variable
  • D Diversity
  • J Joining
  • RSSs recombination signal sequences
  • RAG- 1 and RAG-2 cause the formation of DNA hairpins at the coding ends of the joint (the coding joint) and removal of the RSSs and intervening sequence between them (the signal joint).
  • the variable regions are further diversified at the junctions by deletion of a variable number of coding end nucleotides, the random addition of nucleotides by terminal deoxynucleotidyl transferase (TdT), and palindromic nucleotides that arise due to template- mediated fill-in of the asymmetrically cleaved coding hairpins.
  • the nucleic acid sequences which encode CDR1 and CDR2 are contained within the V (a, b, g or d) gene segment and the sequence encoding CDR3 is made up from portions of V and J segments (for Va or Vy), or a portion of the V segment, the entire D segment and a portion of the J segment (for nb or Ud), but with random insertions and deletions of nucleotides at the V-J and V-D-J recombination junctions due to action of TdT and other recombination and DNA repair enzymes.
  • the recombined T-cell receptor gene comprises alternating framework (FR) and CDR sequences, as does the resulting T-cell receptor expressed therefrom (i.e. FR1-CDR1-FR2- CDR2-FR3-CDR3-FR4).
  • FR1-CDR1-FR2- CDR2-FR3-CDR3-FR4 alternating framework
  • randomized insertions and deletions may be added in or adjacent to CDR1, CDR2 and/or CDR3 (i.e.
  • additional insertions may be added using flanking sequences in recombination substrates before and/or after CDR1 , CDR2 and/or CDR3, and additional deletions may be made by deleting sequences in recombination substrates in or adjacent to CDR1, CDR2 and/or CDR3.
  • TCR nb chains were identified that specifically bind epitopes in the absence of TCR Va chains.
  • the CDR3 amino acid sequences are listed in Table 1 below.
  • the first TCR variable domain of the svd-TCR specifically binds to an epitope in the absence of a second TCR variable domain, and consists of optional N-terminal and/or C-terminal amino acid sequences (of any length or sequence) flanking a variable domain defined by FR1 -CDR1 - FR2 -CDR2 -FR3 -CDR3-FR4 regions.
  • FR1, FR2, FR3 and FR4 may be obtained from a natural Va, nb, Ug or V5 domain or encoded by natural Va, Ub, Ug or V d gene segments, but optionally include deletions or insertions of ( e.g .
  • CDR1, CDR2 and CDR3 may be obtained from a natural Va, nb, Vy or V5 domain, or encoded by natural Va, nb, Ug or V5 gene segments, but wherein one or more of CDR1, CDR2 and CDR3 independently contains an insertion (e.g. 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 amino acids) and/or a deletion (e.g.
  • the CDR1 contains an insertion or deletion of amino acids N- terminally, C-terminally or internally, wherein at least 50% (or optionally 60%, 70% or 80%) of natural CDR amino acid residues are retained.
  • the CDR2 contains an insertion or deletion of amino acids N-terminally, C-terminally or internally, wherein at least 50% (or optionally 60%, 70% or 80%) of natural CDR amino acid residues are retained.
  • the CDR3 contains an insertion or deletion of amino acids N-terminally, C-terminally or internally, wherein at least 50% (or optionally 60%, 70% or 80%) of natural CDR amino acid residues are retained. Insertions and/or deletions may be produced as a result of in vitro V(D)J recombination methods or from the in vitro action of TdT and recombination and DNA repair enzymes (e.g.
  • Insertion and/or deletion may further result from insertions and/or deletions to CDR nucleic acid sequences of the in vitro V(D)J recombination substrates.
  • the svd-TCR may further comprise a TCR constant region or portion thereof.
  • the svd-TCR may be fused to and/or complexed with additional protein domains.
  • a double stranded break in DNA may be introduced prior to in vitro use of the above recombination and DNA repair enzymes.
  • the svd-TCR may be (or may be incorporated into) a fusion protein.
  • fusion protein means a protein encoded by at least one nucleic acid coding sequence that is comprised of a fusion of two or more coding sequences from separate genes, regardless of whether the organism source of those genes is the same or different.
  • the nb domains each independently share at least 80% sequence identity to a human nb domain.
  • the nb domains each independently share at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, or at least 99% sequence identity to a human nb domain.
  • the first nb domain share at least 80% sequence identity to TRBV5-8 nb (SEQ ID NO: 30).
  • the first nb domain share at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, at least 99% sequence identity or are identical to TRBV5-8 nb (SEQ ID NO: 30).
  • the second nb domain shares at least 80% sequence identity to TRBV5-8 nb (SEQ ID NO: 30). In some embodiments of the polypeptides of the disclosure, the second nb domain share at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, at least 99% sequence identity or are identical to TRBV5-8 nb (SEQ ID NO: 30).
  • An illustrative an amino acid sequence of a TRBV5-8 nb is as follows:
  • the svd-TCR fusion protein may comprise an agent of interest or comprise a binding domain for non-covalent association with, or covalent attachment to, an agent of interest, such as a therapeutic or diagnostic agent.
  • an agent of interest such as a therapeutic or diagnostic agent.
  • a single TCR chain may be fused to an agent of interest, or a single TCR variable domain may be fused to an agent of interest.
  • the svd-TCR fusion may comprise: a diagnostic agent; an anticancer agent; a therapeutic radionuclide; a cytotoxic protein; a marker; a purification tag; an epitope; a ligand; a membrane anchor; or a combination thereof.
  • Non-limiting examples of diagnostic agents or moieties include radioisotopes and other detectable labels. Detectable labels useful for such purposes are well known in the art, and include radioactive isotopes such as 32P, 1251, and 13:1, fluorophores, chemiluminescent agents, and enzymes.
  • Non-limiting examples of cytotoxic proteins comprise toxins such as abrin, ricin, Pseudomonas exotoxin (PE; such as PE35, PE37, PE38, and PE40), diphtheria toxin (DT) and subunits thereof, botulinum toxin (e.g .
  • Toxins can be fused to a svd-TCR for use as an immunotoxin.
  • markers comprise GFP (green fluorescent protein), RFP (red fluorescent protein), CAT (chloramphenicol acetyltransferase), luciferase, GAL (beta- galactosidase), GUS (beta- glucuronidase) and the like.
  • purification tags include peptide tags ( e.g .
  • the svd- TCR may comprise or be fused to additional binding/association domain(s) (e.g.
  • the svd-TCR fusion may comprise bispecific or multispecific elements to recruit immune cells like NK or T-cells to the target cell.
  • bi-specific antibody formats There are currently over 60 different bi-specific antibody formats that have been described in the literature (see, e.g., Spiess et al. Mol Immunol. 2015 67(2 Pt A):95-106). Multispecific formats may be generated by adding antibody or TCR VH domains or other binding modalities to these scaffold or engineering in additional binding specificities into an antibody or TCR constant region.
  • the fusion protein may comprise a svd-TCR and any other protein domain or domains.
  • the svd-TCR may be incorporated into an Fc-fusion (i.e . an svd- TCR-Fc) and still retain its binding properties of recognizing specific pMHC complexes.
  • the Fc domain maybe N- or C-terminal to the svd-TCR portion.
  • the svd-TCR- Fc fusion protein allows for a robust approach to generating soluble MHC/peptide binders.
  • the svd- TCR-Fc may alternatively be membrane bound (e.g. cell surface displayed).
  • the Fc domain may provide extended half-life and/or ease of purification.
  • the svd-TCR may be or may form part of a chimeric antigen receptor (CAR).
  • CAR is a recombinant fusion protein in which a binding domain, a transmembrane domain and a signaling domain or domains are linked to create a novel receptor. Typically antibody scFvs are used as the binding domain.
  • a CAR may be created from a svd-TCR by linking a single TCR variable domain to transmembrane domain and signaling domain(s) or by linking a single TCR chain to a signaling domain or domains, for example.
  • the disclosure provides polypeptides comprising a transmembrane domain, and an intracellular domain capable of providing a stimulatory signal.
  • the engineered TCR comprises multiple intracellular domains capable of providing a stimulatory signal.
  • a “transmembrane domain”, as used herein, refers to a domain of a protein that spans membrane of the cell. Transmembrane domains typically consist predominantly of non-polar amino acids, and may traverse the lipid bilayer once or several times. Transmembrane domains usually comprise alpha helices, a configuration which maximizes internal hydrogen bonding.
  • Transmembrane domains isolated or derived from any source are envisaged as within the scope of the fusion proteins of the disclosure.
  • the transmembrane domain is one that is associated with one of the other domains of the fusion protein, or isolated or derived from the same protein as one of the other domains of the fusion protein.
  • the transmembrane domain and the second intracellular domain are from the same protein, for example a TCR complex subunit such as TCR alpha, TCR beta, CD3 delta, CD3 epsilon or CD3 gamma.
  • the extracellular domain (svd-TCR), the transmembrane domain and the second intracellular domain are from the same protein, for example a TCR complex subunit such as TCR alpha, TCR beta, CD3 delta, CD3 epsilon or CD3 gamma.
  • the extracellular domain (comprising one or more svd- TCRs), the transmembrane domain and the intracellular domain(s) are from different proteins.
  • the engineered svd-TCR comprises a CD28 transmembrane domain with a CD28, 4- IBB and 0)3z intracellular domain.
  • the transmembrane domain may be derived either from a natural or from a recombinant source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein.
  • the transmembrane domain is capable of signaling to the intracellular domain(s) whenever the TCR complex has bound to a target.
  • a transmembrane domain of particular use in this invention may include at least the transmembrane region(s) of e.g., the alpha, beta or zeta chain of the TCR, CD3 delta, CD3 epsilon or CD3 gamma, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD 16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137, CD154.
  • the transmembrane domain can be attached to the extracellular region of the fusion protein, e.g., the antigen binding domain of the TCR alpha or beta chain, via a hinge, e.g., a hinge from a human protein.
  • a hinge e.g., a hinge from a human protein.
  • the hinge can be a human immunoglobulin (Ig) hinge, e.g, an IgG4 hinge, or a CD8a hinge.
  • the hinge is isolated or derived from CD8a or CD28.
  • the CD8a hinge comprises an amino acid sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of TTTP APRPPTP AR ⁇ AS QPLSLRPEACRP AAGGAVHTRGLDF ACD (SEQ ID NO: 8).
  • the CD8a hinge comprises SEQ ID NO: 8.
  • the CD8a hinge consists essentially of SEQ ID NO: 8.
  • the CD8a hinge is encoded by a nucleotide sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of:
  • the CD8a hinge is encoded by SEQ ID NO: 9.
  • the CD28 hinge comprises an amino acid sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of CTIEVMYPPPYLDNEKSNGTHHVKGKHLCPSPLFPGPSKP (SEQ ID NO: 10). In some embodiments, the CD28 hinge comprises or consists essentially of SEQ ID NO: 10.
  • the CD28 hinge is encoded by a nucleotide sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of: TGTACCATTGAAGTTATGTATCCTCCTCCTTACCTAGACAATGAGAAGAGCAATGGAAC CATTATCCATGTGAAAGGGAAACACCTTTGTCCAAGTCCCCTATTTCCCGGACCTTCTA AGCCC (SEQ ID NO: 11). In some embodiments, the CD28 hinge is encoded by SEQ ID NO: 11.
  • the transmembrane comprises a TCR alpha transmembrane domain.
  • the TCR alpha transmembrane domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: VTGFRILLLKV AGFNLLMTLRLW (SEQ ID NO: 12).
  • the TCR alpha transmembrane domain comprises, or consists essentially of, SEQ ID NO: 12.
  • the TCR alpha transmembrane domain is encoded by a sequence of: GTGATTGGGTTCCGAATCCTCCTCCTGAAAGTGGCCGGGTTTAATCTGCTCATGACGCT GCGGCTGTGG (SEQ ID NO: 13).
  • the transmembrane comprises a TCR beta transmembrane domain.
  • the TCR beta transmembrane domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: TIL YEILLGK ATL Y A VL V S AL VL (SEQ ID NO: 14).
  • the TCR beta transmembrane domain comprises, or consists essentially of, SEQ ID NO: 14.
  • the TCR beta transmembrane domain is encoded by a sequence of ACCATCCTCTATGAGATCTTGCTAGGGAAGGCCACCTTGTATGCCGTGCTGGTCAGTGC CCTCGTGCTG (SEQ ID NO: 15).
  • the transmembrane comprises a CD3 zeta transmembrane domain.
  • the CD3 zeta transmembrane domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: LC YLLDGILFIY GVTLTALFL (SEQ ID NO: 16).
  • the CD3 zeta transmembrane domain comprises, or consists essentially of, SEQ ID NO: 16.
  • a transmembrane domain can include one or more additional amino acids adjacent to the transmembrane region, e.g., one or more amino acid associated with the extracellular region of the protein from which the transmembrane was derived (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to 15 amino acids of the extracellular region) and/or one or more additional amino acids associated with the intracellular region of the protein from which the transmembrane protein is derived (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to 15 amino acids of the intracellular region).
  • one or more amino acid associated with the extracellular region of the protein from which the transmembrane was derived e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to 15 amino acids of the extracellular region
  • additional amino acids associated with the intracellular region of the protein from which the transmembrane protein is derived e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to 15 amino acids of the intracellular region
  • 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, e.g., to minimize interactions with other members of the receptor complex.
  • the transmembrane domain may be a natural TCR transmembrane domain, a natural transmembrane domain from a heterologous membrane protein, or an artificial transmembrane domain.
  • the transmembrane domain may be a membrane anchor domain.
  • a natural or artificial transmembrane domain may comprise a hydrophobic a-helix of about 20 amino acids, often with positive charges flanking the transmembrane segment.
  • the transmembrane domain may have one transmembrane segment or more than one transmembrane segment. Prediction of transmembrane domains/segments may be made using publicly available prediction tools (e.g. TMHMM, Krogh et al.
  • Non-limiting examples of membrane anchor systems include platelet derived growth factor receptor (PDGFR) transmembrane domain, glycosylphosphatidylinositol (GPI) anchor (added post- translationally to a signal sequence) and the like.
  • PDGFR platelet derived growth factor receptor
  • GPI glycosylphosphatidylinositol
  • the disclosure provides fusion proteins comprising an intracellular domain.
  • the intracellular domain comprises one or more domains capable of providing a stimulatory signal to a transmembrane domain.
  • the intracellular domain comprises a first intracellular domain capable of providing a stimulatory signal and a second intracellular domain capable of providing a stimulatory signal.
  • the intracellular domain comprises a first, second and third intracellular domain capable of providing a stimulatory signal.
  • the intracellular domains capable of providing a stimulatory signal are selected from the group consisting of a CD28 molecule (CD28) domain, a LCK proto-oncogene, Src family tyrosine kinase (Lck) domain, a TNF receptor superfamily member 9 (4- IBB) domain, a TNF receptor superfamily member 18 (GITR) domain, a CD4 molecule (CD4) domain, a CD8a molecule (CD8a) domain, a FYN proto- oncogene, Src family tyrosine kinase (Fyn) domain, a zeta chain of T cell receptor associated protein kinase 70 (ZAP70) domain, a linker for activation of T cells (LAT) domain, lymphocyte cytosolic protein 2 (SLP76) domain, TCR alpha, TCR beta, CD3 delta, CD3 gamma and CD3 epsilon intracellular domains.
  • CD28 CD28
  • LCK proto-
  • an intracellular domain comprises at least one intracellular signaling domain.
  • An intracellular signaling domain generates a signal that promotes a function a cell, for example an immune effector function of a TCR containing cell, e.g., a TCR-expressing T-cell.
  • the intracellular domain of the fusion proteins of the disclosure includes at least one intracellular signaling domain.
  • the intracellular domains of CD3 gamma, delta or epsilon comprise signaling domains.
  • the extracellular domain, transmembrane domain and intracellular domain are isolated or derived from the same protein, for example T-cell receptor (TCR) alpha, TCR beta, CD3 delta, CD3 gamma or CD3 epsilon.
  • TCR T-cell receptor
  • intracellular domains for use in the fusion proteins of the disclosure include the cytoplasmic sequences of the TCR alpha, TCR beta, CD3 zeta, and 4- IBB, and the intracellular signaling co-receptors that act in concert to initiate signal transduction following antigen receptor engagement, as well as any derivative or variant of these sequences and any recombinant sequence that has the same functional capability.
  • the intracellular signaling domain comprises a primary intracellular signaling domain.
  • exemplary primary intracellular signaling domains include those derived from the proteins responsible for primary stimulation, or antigen dependent stimulation.
  • An intracellular signaling domain is generally responsible for activation of at least one of the normal effector functions of the immune cell in which the fusion protein has been introduced.
  • effector function refers to a specialized function of a cell. Effector function of a T-cell, for example, may be cytolytic activity or helper activity including the secretion of cytokines.
  • intracellular signaling domain refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function.
  • intracellular signaling domain While in some cases the entire intracellular signaling domain can be employed, in many cases it is not necessary to use the entire intracellular signaling domain. To the extent that a truncated portion of the intracellular signaling domain is used, such truncated portion may be used in place of the intact chain as long as it transduces the effector function signal.
  • the term intracellular signaling domain is thus meant to include any truncated portion of the intracellular signaling domain sufficient to transduce the effector function signal.
  • the intracellular domain comprises a CD3 delta intracellular domain.
  • the CD3 delta intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: GHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNKGGSRSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 17).
  • the CD3 delta intracellular domain comprises or consists essentially of, SEQ ID NO: 17.
  • the CD3 delta intracellular domain is encoded by a sequence of
  • the intracellular domain comprises a CD3 epsilon intracellular domain.
  • the CD3 epsilon intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: KNRKAKAKP VTRGAGAGGRQRGQNKERPPPVPNPD YEPIRKGQRDLY S GLN QRRIGGSRS KRSRLLHSDYMNMTPRRPGPTRKHYQPY APPRDF AA YRS (SEQ ID NO: 19).
  • the CD3 epsilon intracellular domain comprises or consists essentially of, SEQ ID NO: 19.
  • the CD3 epsilon intracellular domain is encoded by a sequence of
  • the intracellular domain comprises a CD3 gamma intracellular domain.
  • the CD3 gamma intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: GQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLRRNGGSRSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 21).
  • the CD3 gamma intracellular domain comprises, or consists essentially of, SEQ ID NO: 21.
  • the CD3 gamma intracellular domain is encoded by a sequence of
  • the intracellular domain comprises a CD3 zeta intracellular domain.
  • the CD3 zeta intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL (SEQ ID NO: 23).
  • the CD3 zeta intracellular domain comprises, or consists essentially of, SEQ ID NO: 23.
  • the intracellular domain comprises a TCR alpha intracellular domain.
  • a TCR alpha intracellular domain comprises Ser-Ser.
  • a TCR alpha intracellular domain is encoded by a sequence of TCCAGC.
  • the intracellular domain comprises a TCR beta intracellular domain.
  • the TCR beta intracellular domain comprises an amino acid sequence having at least 80% identity, at least 90% identity, or is identical to a sequence of: MAMVKRKDSR (SEQ ID NO: 24).
  • the TCR beta intracellular domain comprises, or consists essentially of SEQ ID NO: 23.
  • the TCR beta intracellular domain is encoded by a sequence of ATGGCCATGGTCAAGAGAAAGGATTCCAGA (SEQ ID NO: 25).
  • the intracellular signaling domain comprises at least one stimulatory intracellular domain.
  • the intracellular signaling domain comprises a primary intracellular signaling domain, such as a CD3 delta, CD3 gamma and CD3 epsilon intracellular domain, and one additional stimulatory intracellular domain, for example a co-stimulatory domain.
  • the intracellular signaling domain comprises a primary intracellular signaling domain, such as a CD3 delta, CD3 gamma and CD3 epsilon intracellular domain, and two additional stimulatory intracellular domains.
  • Exemplary co-stimulatory intracellular signaling domains include those derived from proteins responsible for co-stimulatory signals, or antigen independent stimulation.
  • co-stimulatory molecule refers to the cognate binding partner on a T-cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the T-cell, such as, but not limited to, proliferation.
  • Co-stimulatory molecules are cell surface molecules other than antigen receptors. Co-stimulatory molecules and their ligands are required for an efficient immune response.
  • Co-stimulatory molecules include, but are not limited to an MHC class I molecule, BTLA, a Toll ligand receptor, as well as hematopoietic cell signal transducer (DAP10), transmembrane immune signaling adaptor TYROBP (DAP 12), TNF receptor superfamily member 8 (CD30), TNF superfamily member 14 (LIGHT), TNF receptor superfamily member 4 (0X40), CD2 molecule (CD2), CD27 molecule (CD27), CDS, intercellular adhesion molecule 1 (ICAM-1), integrin subunit beta 2 (LFA-1, or CDl la), integrin subunit beta 2 (CD18), 4-1BB (CD137, TNF receptor superfamily member 9), and CD28 molecule (CD28).
  • MHC class I molecule BTLA
  • Toll ligand receptor hematopoietic cell signal transducer
  • DAP10 transmembrane immune signaling adaptor TYROBP
  • DAP 12 transmembrane immune signaling adaptor
  • a “co-stimulatory domain”, sometimes referred to as “a co-stimulatory intracellular signaling domain” can be the intracellular portion of a co-stimulatory protein.
  • a co-stimulatory domain can be a domain of a co- stimulatory protein that transduces the co-stimulatory signal.
  • a co-stimulatory protein can be represented in the following protein families: TNF receptor proteins, Immunoglobulin like proteins, cytokine receptors, integrins, signaling lymphocytic activation molecules (SLAM proteins), and activating NK cell receptors.
  • Examples of such molecules include CD27, CD28, 4-1BB (CD 137), 0X40, GITR, CD30, CD40 molecule (CD40), inducible T cell costimulator (ICOS), TNF receptor superfamily member 13C (BAFFR), TNF receptor superfamily member 14 (HVEM), lymphocyte function-associated antigen- 1 (LFA-1), CD2 molecule (CD2), CD7 molecule (CD7), LIGHT, killer cell lectin like receptor C2 (NKG2C), SLAM family member 7 (SLAMF7), killer cell lectin like receptor FI (NKp80), CD160 molecule (CD160), CD276 molecule (B7-H3), a ligand that specifically binds with CD83 molecule (CD83), CD4 molecule (CD4), and the like.
  • the co stimulatory domain can comprise the entire intracellular portion, or the entire native intracellular signaling domain, of the molecule from which it is derived, or a functional fragment thereof.
  • the stimulatory domain comprises a co-stimulatory domain.
  • the co-stimulatory domain comprises a CD28 or 4-1BB co-stimulatory domain.
  • CD28 and 4- IBB are well characterized co-stimulatory molecules required for full T cell activation and known to enhance T cell effector function.
  • CD28 and 4- IBB have been utilized in chimeric antigen receptors (CARs) to boost cytokine release, cytolytic function, and persistence over the first-generation CAR containing only the CD3 zeta signaling domain.
  • CARs chimeric antigen receptors
  • co stimulatory domains for example CD28 and 4-1BB domains
  • engineered TCR can increase T cell effector function and specifically allow co-stimulation in the absence of co-stimulatory ligand, which is typically down-regulated on the surface of tumor cells.
  • the stimulatory domain comprises a CD28 intracellular domain.
  • the CD28 intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: RSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 26).
  • the CD28 intracellular domain comprises, or consists essentially of, RSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 26).
  • a CD28 intracellular domain is encoded by a nucleotide sequence comprising: AGGAGCAAGCGGAGCAGACTGCTGCACAGCGACTACATGAACATGACCCC CCGGAGGCCTGGCCCCACCCGGAAGCACTACCAGCCCTACGCCCCTCCCA GGGATTTCGC CGCCTACCGG AGC (SEQ ID NO: 27).
  • the stimulatory domain comprises a 4- IBB intracellular domain.
  • the 4- IBB intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL (SEQ ID NO: 28).
  • the 4- IBB intracellular domain comprises, or consists essentially of, KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL (SEQ ID NO: 28).
  • a 4- IBB intracellular domain is encoded by a nucleotide sequence comprising: AAACGGGGC AGAAAGA AACT CCTGT AT AT ATT C A AAC AACC ATTT AT GAGGCC AGT AC AAACT ACT C A AGAGGAAGATGGCTGTAGCTGCCGATTT CC AGAAGAAGAAGAAGGAG GATGTGAACTG (SEQ ID NO: 29).
  • the engineered TCRs described herein comprise two or more antigen binding domains (e.g ., svd-TCRs).
  • linkers that, in some embodiments, can be used to link the antigen-binding domains described herein.
  • linker and “flexible polypeptide linker” as used in the context of linking protein domains, for example intracellular domains or domains within an scFv, refers to a peptide linker that consists of amino acids such as glycine and/or serine residues used alone or in combination, to link two domains together.
  • a linker as described herein can be used to link two svd-TCRs together.
  • linker may be used and many fusion protein linker formats are known.
  • the linker may be flexible or rigid.
  • rigid and flexible linkers are provided in Chen et al. (Adv Drug Deliv Rev. 2013; 65(10):1357-1369).
  • antigen-binding domains described herein may be linked to each other in a random or specified order.
  • antigen-binding domains described herein may be linked to each other in any orientation of N to C terminus.
  • a short oligo- or polypeptide linker for example, between 2 and 40 amino acids (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids) in length may form the linkage between the domains.
  • the linker is a peptide of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more than 30 amino acid residues.
  • Non limiting examples of amino acids found in linkers include Gly, Ser, Glu, Gin, Ala, Leu, Iso, Lys, Arg, Pro, and the like.
  • the linker is [(Gly)nlSer]n2, where nl and n2 may be any number ( e.g . nl and n2 may independently be 1, 2, 4, 5, 6, 7, 8, 9, 10 or more than 10). In some embodiments, nl is 4.
  • the flexible polypeptide linkers include, but are not limited to, GGS, GGGS (SEQ ID NO: 32), GGGGS (SEQ ID NO: 33), or GGGGS GG (SEQ ID NO: 31).
  • the linkers include multiple repeats of (Gly Ser), (Gly Ser) or (Gly Ser). Also included within the scope of the invention are linkers described in WO2012/138475 (incorporated herein by reference).
  • the linker sequence comprises a long linker (LL) sequence.
  • the long linker sequence comprises GGGGS (SEQ ID NO: 33), repeated four times.
  • a GGGGS (SEQ ID NO: 33) is used to link intracellular domains in a TCR alpha fusion protein of the disclosure.
  • the long linker sequence comprises GGGGS (SEQ ID NO: 33), repeated three times.
  • a GGGGS (SEQ ID NO: 33) is used to link intracellular domains in a TCR beta fusion protein of the disclosure.
  • the linker sequence comprises a short linker (SL) sequence.
  • the short linker sequence comprises GGGGS (SEQ ID NO: 33).
  • a glycine-serine doublet can be used as a suitable linker.
  • domains are fused directly to each other via peptide bonds without use of a linker.
  • antigen refers to a molecule that is capable of being bound specifically by an antibody, or being presented by a major histocompatibility complex and bound by a TCR, or otherwise provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both.
  • the antigen (or antigen of interest) which is specifically bound by the TCR variable domain of the svd-TCR may be any antigen.
  • the antigen may be a self antigen or a non-self antigen.
  • the antigen may be a conformational antigen or a linear antigen.
  • Non-limiting examples of the antigen include viral proteins or peptides, bacterial proteins or peptides, cancer-specific antigens, receptor extracellular domains, an epitope, a receptor binding protein, a receptor binding peptide, or any other peptide, polypeptide or protein antigen.
  • an antigen recognized by an engineered TCR of the disclosure is bound by a major histocompatibility complex (MHC).
  • MHC refers to a protein complex that binds to antigens and displays them on the cell surface for recognition by the appropriate T cell ( e.g ., via a TCR).
  • Peptides are processed and presented by cells using two pathways, the MHC class I and MHC class II pathways, both of which are envisaged as within the scope of the disclosure.
  • phagocytes such as macrophages and immature dendritic cells take up exogenous material (e.g., pathogens, proteins) by phagocytosis into phagosomes or endosomes, which fuse with lysosomes whose acidic enzymes cleave the exogenous material protein into peptides. These peptides are loaded onto MHC class II molecules, which are trafficked to the cell surface and presented to immune cells.
  • nucleated cells present cytosolic peptides. These cytosolic peptides are mostly self peptides derived from protein turnover and defective ribosomal products. However, during infection with intracellular localization (e.g.
  • the proteins degraded in the proteasome include proteins from the infectious organism or cancer, and are also loaded onto MHC class I molecules and displayed on the cell surface.
  • Class I MHC can display cancer and non-self antigens.
  • an engineered TCR of the disclosure recognizes a peptide antigen bound to MHC (pMHC), for example MHC class I or MHC class II.
  • pMHC peptide antigen bound to MHC
  • an engineered TCR of the disclosure recognizes an antigen that is not bound to MHC.
  • engineered TCRs whose antigen binding domain is derived from an ScFv, or VHH antigen binding domain can bind antigens that are not presented by MHC.
  • the antigen is a non-self antigen, for example an antigen from a virus, bacteria, fungus or eukaryotic pathogen.
  • the antigen is a self-antigen, for example a protein with a particular tissue-specific expression pattern.
  • an engineered TCR of the disclosure recognizes a peptide antigen bound to MHC (pMHC).
  • the pMHC comprises a cancer antigen.
  • the pMHC comprises a neoantigen.
  • a “neoantigen” refers to an antigen not previously recognized by the immune system. Neoantigens can arise from altered tumor proteins, or from viral proteins, for example.
  • the neoantigen comprises KRAS proto oncogene, GTPase (KRAS) G12D, KRAS G12V, p53 or a variant of phosphoinositide 3 kinase alpha (PI3K alpha).
  • the antigen comprises a viral antigen, such as a human papillomavirus (HPV) antigen.
  • the antigen comprises a testes or fetal antigen.
  • the pMHC comprises a cancer antigen.
  • the cancer antigen comprises CD19 molecule (CD19); interleukin 3 receptor subunit alpha (CD123); CD22 molecule (CD22); TNF receptor superfamily member 8 (CD30); LI cell adhesion molecule (CD171); CS-1 (also referred to as CD2 subset 1, CRACC, SLAMF7, CD319, and 19A24); C-type lectin-like molecule-1 (CLL-1 or CLECL1); CD33 molecule (CD33); epidermal growth factor receptor variant III (EGFRvIII); ganglioside G2 (GD2); ganglioside GD3 (aNeu5Ac(2-8)aNeu5Ac(2- 3)bDGalp(l-4)bDGlcp(l-l)Cer); TNF receptor family member B cell maturation (BCMA); Tn antigen ((Tn Ag) or (GalNAca-Ser/Thr)); prostate-specific membrane antigen (PSMA); Receptor tyrosine kinase
  • CD123
  • the engineered TCR comprises an antigen binding domain that has a binding affinity KD of 10 _4 M to 10 _9 M, e.g., 10 _5 M to 10 _7 M, e.g., 10 _6 M or 10 _7 M, for its target antigen.
  • the binding affinity of an antigen binding domain for an antigen can be determined by methods known in the art, e.g. by ELISA or surface plasmon resonance.
  • the antigen is a peptide bound in MHC to form a pMHC.
  • the MHC in the pMHC may be any MHC class.
  • the MHC may be MHC class I or may be MHC class II.
  • the peptide in the pMHC may be any length that will bind in the binding groove of the MHC.
  • the peptide may be 2 to 100 or more amino acids long, including a peptide of 2, 3, 4, 5, 6, ,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 54, 56, 68, 60, 62, 64, 66, 68, 70, 75, 80, 85, 90, 95, 100 amino acids.
  • the peptide may be about 8-30 amino acids long.
  • the peptide maybe about 8-10 amino acids long.
  • the peptide in the pMHC may be any sequence that binds in the binding groove of the MHC.
  • the peptides are non-covalently held in the binding groove in an extended configuration but some peptides may have portions which dangle outside the binding groove.
  • the peptide may have the amino acid sequence SLLMWITQC (SEQ ID NO: 34, a publicly known sequence).
  • the activity of chimeric or engineered TCRs can be assayed using a cell line engineered to express a reporter of TCR activity such as a luciferase reporter.
  • a reporter of TCR activity such as a luciferase reporter.
  • Exemplary cell lines include Jurkat T cells, although any suitable cell line known in the art may be used.
  • Jurkat cells expressing a luciferase reporter under the control of an NFAT promoter can be used as effector cells. Expression of luciferase by this cell line reflects TCR-mediated signaling.
  • the reporter cells can be transfected with each of the various fusion protein constructs, combinations of fusion protein constructs or controls described herein.
  • Fusion proteins in reporter cells can be confirmed by using fluorescently labeled MHC tetramers, for example Alexa Fluor 647-labeled NY-ESO-l-MHC tetramer, to detect expression of the fusion protein.
  • target cells are loaded with antigen prior to exposure to the effector cells comprising the reporter and the engineered TCR.
  • target cells can be loaded with antigen at least 12, 14, 16, 18, 20, 22 or 24 hours prior to exposure to effector cells.
  • Exemplary target cells include A375 cells, although any suitable cells known in the art may be used.
  • target cells can be loaded with serially diluted concentrations of an antigen, such as NY-ESO-1 peptide.
  • the effector cells can then be co-cultured with target cells for a suitable period of time, for example 6 hours. Luciferase is then measured by luminescence reading after co-culture. Luciferase luminescence can be normalized to maximum and minimum intensity to allow comparison of activating peptide concentrations for each TCR construct.
  • EC50 refers to the concentration of an inhibitor or agent where the response (or binding) is reduced by half.
  • EC50s of engineered TCRs of the disclosure refer to concentration of antigen where binding of the engineered TCR to the antigen is reduced by half. Binding of the antigen, or probe to the TCR can be measured by staining with labeled peptide or labeled peptide-MHC complex, for example MHC:NY-ESO-l pMHC complex conjugated with fluorophore.
  • EC50 can be obtained by nonlinear regression curve fitting of reporter signal with peptide titration. Probe binding and EC50 can be normalized to the levels of benchmark TCR without a fusion protein, e.g. NY-ESO-1 (clone 1G4).
  • an engineered TCR comprising a fusion protein has a relative EC50 of greater than or equal to 0.2, 0.3, 0.4, 0.5, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.8, 1.9 or 2.0 relative to a TCR that does not comprise a fusion protein.
  • an engineered TCR comprising a fusion protein has a relative EC50 of about 0.2-2.0, about 0.5-2.0, about 0.9-2.0, about 1.0-2.0, about 1.1-2.0, about 1.2-2.0, about 0.9-1.7, about 1.0- 1.7, or about 1.2- 1.7 relative to a TCR that does not comprise a fusion protein
  • the disclosure provides polynucleotides encoding the sequence of the engineered TCR described herein.
  • the disclosure provides at least one nucleic acid encoding the svd-TCR as defined herein.
  • the at least one nucleic acid may be a vector.
  • the vector may be an expression vector.
  • the at least one nucleic acid may comprise an expression cassette comprising a sequence encoding the svd-TCR and further comprising a promoter and terminator in operative association with the sequence encoding the svd-TCR for expression of the svd- TCR.
  • promoters which may be suitable include, but are not limited to CMV, SV40, El a, viral LTRs, heat shock promoters, viral and chimeric promoters, tetracycline or other inducible promoters.
  • Non-limiting examples of terminators which may be suitable include, but are not limited to SV40 poly (A), bovine growth hormone poly(A) or synthetic poly (A) sequences.
  • the nucleic acid is in operative association with a promoter and terminator for expression of the svd-TCR.
  • a promoter and terminator for expression of the svd-TCR include, but are not limited to CMV, SV40, El a, viral LTRs, heat shock promoters, viral and chimeric promoters, tetracycline or other inducible promoters.
  • terminators which may be suitable include, but are not limited to SV40 poly (A), bovine growth hormone poly(A) or synthetic poly (A) sequences.
  • Vectors derived from retroviruses such as the lentivirus are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene and its propagation in daughter cells.
  • Lentiviral vectors have the added advantage over vectors derived from onco- retroviruses such as murine leukemia viruses in that they can transduce non-proliferating cells, such as hepatocytes. They also have the added advantage of low immunogenicity.
  • the expression of natural or synthetic nucleic acids encoding engineered TCR is typically achieved by operably linking a nucleic acid encoding the engineered TCR or portions thereof to a promoter, and incorporating the construct into an expression vector.
  • the vectors can be suitable for replication and integration eukaryotes.
  • Typical cloning vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence.
  • the polynucleotides encoding the engineered TCR can be cloned into a number of types of vectors.
  • the polynucleotides can be cloned into a vector including, but not limited to a plasmid, a phagemid, a phage derivative, an animal virus, and a cosmid.
  • Vectors of particular interest include expression vectors, replication vectors, probe generation vectors, and sequencing vectors.
  • the expression vector may be provided to cells, such as immune cells, in the form of a viral vector. Viral vector technology is well known in the art and is described, for example, in Sambrook et al.
  • Viruses which are useful as vectors include, but are not limited to, retroviruses, adenoviruses, adeno-associated viruses, herpes viruses, and lentiviruses.
  • a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers, (e.g., WO 01/96584; WO 01/29058; and U.S. Pat. No. 6,326,193).
  • retroviruses provide a convenient platform for gene delivery systems.
  • a selected gene can be inserted into a vector and packaged in retroviral particles using techniques known in the art.
  • the recombinant virus can then be isolated and delivered to cells of the subject either in vivo or ex vivo.
  • retroviral systems are known in the art.
  • adenovirus vectors are used.
  • a number of adenovirus vectors are known in the art.
  • lentivirus vectors are used.
  • Additional promoter elements e.g., enhancers, regulate the frequency of transcriptional initiation.
  • these are located in the region 30-110 basepairs (bp) upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well.
  • the spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another.
  • tk thymidine kinase
  • the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline.
  • individual elements can function either cooperatively or independently to activate transcription.
  • a suitable promoter is the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto.
  • CMV immediate early cytomegalovirus
  • EF-la Elongation Growth Factor-la
  • constitutive promoter sequences may also be used, including, but not limited to the simian virus 40 (SV40) early promoter, mouse mammary tumor virus (MMTV), human immunodeficiency virus (HIV) long terminal repeat (LTR) promoter, MoMuLV promoter, an avian leukemia virus promoter, an Epstein-Barr virus immediate early promoter, a Rous sarcoma virus promoter, as well as human gene promoters such as, but not limited to, the actin promoter, the myosin promoter, the hemoglobin promoter, and the creatine kinase promoter. Further, the invention should not be limited to the use of constitutive promoters.
  • inducible promoters are also contemplated as part of the invention.
  • the use of an inducible promoter provides a molecular switch capable of turning on expression of the polynucleotide sequence which it is operatively linked when such expression is desired, or turning off the expression when expression is not desired.
  • inducible promoters include, but are not limited to a metallothionine promoter, a glucocorticoid promoter, a progesterone promoter, and a tetracycline promoter.
  • the expression vector to be introduced into a cell can also contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of expressing cells from the population of cells sought to be transfected or infected through viral vectors.
  • the selectable marker may be carried on a separate piece of DNA and used in a co-transfection procedure. Both selectable markers and reporter genes may be flanked with appropriate regulatory sequences to enable expression in the host cells.
  • Useful selectable markers include, for example, antibiotic-resistance genes, such as neo and the like.
  • Reporter genes are used for identifying potentially transfected or transduced cells and for evaluating the functionality of regulatory sequences.
  • a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells.
  • Suitable reporter genes may include genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et al, 2000 FEBS Letters 479: 79-82).
  • Suitable expression systems are well known and may be prepared using known techniques or obtained commercially.
  • the construct with the minimal 5' flanking region showing the highest level of expression of reporter gene is identified as the promoter.
  • Such promoter regions may be linked to a reporter gene and used to evaluate agents for the ability to modulate promoter-driven transcription.
  • the vector can be readily introduced into a host cell, e.g., mammalian, bacterial, yeast, or insect cell by any method in the art.
  • the expression vector can be transferred into a host cell by physical, chemical, or biological means.
  • 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.
  • 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).
  • 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 (ELIS As and Western blots) or by assays described herein to identify agents falling within the scope of the invention.
  • 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 (ELIS As and Western blots) or by assays described herein to identify agents falling within the scope of the invention.
  • cells comprising the polynucleotides, vectors, fusion proteins and engineered TCRs described herein.
  • a cell may be an immune cell involved in the innate or adaptive (acquired) immune system.
  • innate immune cells include phagocytic cells such as neutrophils, monocytes and macrophages, Natural Killer (NK) cells, polymophonuclear leukocytes such as neutrophils eosinophils and basophils and mononuclear cells such as monocytes, macrophages and mast cells.
  • NK Natural Killer
  • Immune cells with roles in acquired immunity include lymphocytes such as T-cells and B- cells.
  • a “T-cell” refers to a type of lymphocyte that originates from a bone marrow precursor that develops in the thymus gland.
  • T-cells which develop upon migration to the thymus, which include, helper CD4+ T-cells, cytotoxic CD8+ T cells, memory T cells, regulatory CD4+ T-cells and stem memory T-cells.
  • helper CD4+ T-cells cytotoxic CD8+ T cells
  • memory T cells memory T cells
  • regulatory CD4+ T-cells stem memory T-cells.
  • Different types of T-cells can be distinguished by the ordinarily skilled artisan based on their expression of markers. Methods of distinguishing between T-cell types will be readily apparent to the ordinarily skilled artisan.
  • the engineered immune cell comprising the TCR of the disclosure is a T cell.
  • the T cell is an effector T cell or a regulatory T cell.
  • CD3+ T cells can be isolated from PBMCs using a CD3+ T cell negative isolation kit (Miltenyi), according to manufacturer’s instructions.
  • T cells can be cultured at a density of 1 x 10 L 6 cells/mL in X-Vivo 15 media supplemented with 5% human A/B serum and 1% Pen/strep in the presence of CD3/28 Dynabeads (1:1 cell to bead ratio) and 300 Units/mL of IL-2 (Miltenyi).
  • T cells can be transduced with viral vectors, such as lentiviral vectors using methods known in the art.
  • the viral vector is transduced at a multiplicity of infection (MOI) of 5.
  • Cells can then be cultured in IL-2 or other cytokines such as combinations of IL-7/15/21 for an additional 5 days prior to enrichment.
  • MOI multiplicity of infection
  • Methods of isolating and culturing other populations of immune cells, such as B cells, or other populations of T cells will be readily apparent to the person of ordinary skill in the art. Although this method outlines a potential approach, it should be noted that these methodologies are rapidly evolving.
  • the T cells can be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575;
  • T cells of the instant disclosure are expanded and activated in vitro.
  • the T cells of the instant disclosure are expanded in vitro by contact with a surface having attached thereto an agent that stimulates a CD3/TCR complex associated signal and a ligand that stimulates a co-stimulatory molecule on the surface of the T cells.
  • T cell populations may be stimulated as described herein, such as by contact with an anti-CD3 antibody.
  • a ligand that binds the accessory molecule is used for co- stimulation of an accessory molecule on the surface of the T cells.
  • a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells.
  • an anti-CD3 antibody and an anti- CD28 antibody can be used.
  • an anti-CD28 antibody include 9.3, B-T3, XR-CD28 (Diaclone, Besan9on, France) can be used as can other methods commonly known in the art (Berg et al, Transplant Proc. 30(8):3975-3977, 1998; Haanen et al, J. Exp. Med. 190(9):13191328, 1999; Garland et al., J. Immunol Meth. 227(1 -2): 53-63, 1999).
  • the primary stimulatory signal and the co-stimulatory signal for the T cell may be provided by different protocols.
  • the agents providing each signal may be in solution or coupled to a surface. When coupled to a surface, the agents may be coupled to the same surface (i.e., in “cis” formation) or to separate surfaces (i.e., in “trans” formation). Alternatively, one agent may be coupled to a surface and the other agent in solution.
  • the agent providing the co-stimulatory signal is bound to a cell surface and the agent providing the primary activation signal is in solution or coupled to a surface. In certain embodiments, both agents can be in solution.
  • the agents may be in soluble form, and then cross-linked to a surface, such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents.
  • a surface such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents.
  • the two agents are immobilized on beads, either on the same bead, i.e., “cis,” or to separate beads, i.e., “trans.”
  • the agent providing the primary activation signal is an anti-CD3 antibody or an antigen-binding fragment thereof and the agent providing the co stimulatory signal is an anti-CD28 antibody or antigen-binding fragment thereof; and both agents are co-immobilized to the same bead in equivalent molecular amounts.
  • a 1 : 1 ratio of each antibody bound to the beads for CD4+ T cell expansion and T cell growth is used.
  • the ratio of CD3:CD28 antibody bound to the beads ranges from 100: 1 to 1 : 100 and all integer values there between. In one aspect of the present invention, more anti-CD28 antibody is bound to the particles than anti-CD3 antibody, i.e., the ratio of CD3:CD28 is less than one. In certain embodiments of the invention, the ratio of anti CD28 antibody to anti CD3 antibody bound to the beads is greater than 2: 1.
  • Ratios of particles to cells from 1 :500 to 500: 1 and any integer values in between may be used to stimulate T cells or other target cells.
  • the ratio of particles to cells may depend on particle size relative to the target cell. For example, small sized beads could only bind a few cells, while larger beads could bind many.
  • the ratio of cells to particles ranges from 1:100 to 100:1 and any integer values in-between and in further embodiments the ratio comprises 1:9 to 9:1 and any integer values in between, can also be used to stimulate T cells.
  • a ratio of 1 : 1 cells to beads is used.
  • ratios will vary depending on particle size and on cell size and type.
  • the cells such as T cells
  • the beads and the cells are subsequently separated, and then the cells are cultured.
  • the agent-coated beads and cells prior to culture, are not separated but are cultured together.
  • the beads and cells are first concentrated by application of a force, such as a magnetic force, resulting in increased ligation of cell surface markers, thereby inducing cell stimulation.
  • cell surface proteins may be ligated by allowing paramagnetic beads to which anti-CD3 and anti-CD28 are attached to contact the T cells.
  • the cells for example, CD4+ T cells
  • beads for example, DYNABEADS CD3/CD28 T paramagnetic beads at a ratio of 1:1
  • any cell concentration may be used.
  • it may be desirable to significantly decrease the volume in which particles and cells are mixed together (i.e., increase the concentration of cells), to ensure maximum contact of cells and particles. For example, in one embodiment, a concentration of about 2 billion cells/ml is used.
  • greater than 100 million cells/ml is used.
  • a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/ml is used.
  • a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/ml is used.
  • concentrations of 125 or 150 million cells/ml can be used.
  • cells that are cultured at a density of lxl 0 6 cells/mL are used.
  • the mixture may be cultured for several hours (about 3 hours) to about 14 days or any hourly integer value in between.
  • the beads and T cells are cultured together for 2-3 days.
  • Conditions appropriate for T cell culture include an appropriate media (e.g ., Minimal Essential Media or RPMI Media 1640 or, X-vivo 15, (Lonza)) that may contain factors necessary for proliferation and viability, including serum (e.g., fetal bovine or human serum), interleukin-2 (IL-2), insulin, IFN-g, IL-4, IL-7, GM-CSF, IF- 10, IF- 12, IF- 15, TGFP, and TNF-a or any other additives for the growth of cells known to the skilled artisan.
  • serum e.g., fetal bovine or human serum
  • IL-2 interleukin-2
  • insulin IFN-g, IL-4, IL-7
  • GM-CSF IF- 10, IF- 12, IF- 15, TGFP, and TNF-a or any
  • Media can include RPMI 1640, AIM-V, DMEM, MEM, a-MEM, F-12, X-Vivo 15, and X-Vivo 20, Optimizer, with added amino acids, sodium pyruvate, and vitamins, either serum-free or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones, and/or an amount of cytokine(s) sufficient for the growth and expansion of T cells.
  • the media comprises X-VIVO- 15 media supplemented with 5% human A/B serum, 1% penicillin/streptomycin (pen/strep) and 300 Units/ml of IF-2 (Miltenyi).
  • the T cells are maintained under conditions necessary to support growth, for example, an appropriate temperature (e.g., 37° C.) and atmosphere (e.g., air plus 5% C02).
  • an appropriate temperature e.g., 37° C.
  • atmosphere e.g., air plus 5% C02
  • the T cells comprising engineered TCRs of the disclosure are autologous.
  • a source of T cells is obtained from a subject.
  • Immune cells such as T cells can be obtained from a number of sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
  • any number of T cell lines available in the art may be used.
  • T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled artisan, such as FicollTM separation.
  • cells from the circulating blood of an individual are obtained by apheresis.
  • the apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets.
  • the cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps.
  • the cells are washed with phosphate buffered saline (PBS).
  • PBS phosphate buffered saline
  • the wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations.
  • a washing step may be accomplished by methods known to those in the art, such as by using a semi-automated “flow-through” centrifuge (for example, the Cobe 2991 cell processor, the Baxter CytoMate, or the Haemonetics Cell Saver 5) according to the manufacturer’s instructions.
  • a semi-automated “flow-through” centrifuge for example, the Cobe 2991 cell processor, the Baxter CytoMate, or the Haemonetics Cell Saver 5
  • the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca2+-free, Mg2+-free PBS, PlasmaLyte A, or other saline solution with or without buffer.
  • the undesirable components of the apheresis sample may be removed and the cells directly resuspended in culture media.
  • immune cells such as T cells are isolated from peripheral blood lymphocytes by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLLTM gradient or by counterflow centrifugal elutriation.
  • Specific subpopulations of immune cells, such as T cells, B cells, or CD4+ T cells can be further isolated by positive or negative selection techniques.
  • T cells are isolated by incubation with anti- CD4 -conjugated beads, for a time period sufficient for positive selection of the desired T cells.
  • Enrichment of an immune cell population, such as a T cell population, by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells.
  • One method is cell sorting and/or selection via negative magnetic immune- adherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected.
  • a monoclonal antibody cocktail typically includes antibodies to CD 14, CD20, CD lib, CD 16, HLA-DR, and CD8.
  • the concentration of cells and surface e.g . , particles such as beads
  • the cells may be incubated on a rotator for varying lengths of time at varying speeds at either 2-10° C or at room temperature.
  • T cells for stimulation can also be frozen after a washing step.
  • the freeze and subsequent thaw step provides a more uniform product by removing granulocytes and to some extent monocytes in the cell population.
  • the cells may be suspended in a freezing solution.
  • one method involves using PBS containing 20% DMSO and 8% human serum albumin, or culture media containing 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin and 7.5% DMSO, or 31.25% Plasmalyte-A, 31.25% Dextrose 5%, 0.45% NaCl, 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin, and 7.5% DMSO or other suitable cell freezing media containing for example, Hespan and PlasmaLyte A, the cells then are frozen to -80° C. at a rate of 1 ° per minute and stored in the vapor phase of a liquid nitrogen storage tank. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at -20° C. or in liquid nitrogen.
  • compositions comprising immune cells comprising the polypeptides of the disclosure and a pharmaceutically acceptable diluent, carrier or excipient.
  • Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; and preservatives.
  • Certain embodiments relate to use of the svd-TCR or the compositions disclosed herein for targeting a cell which externally presents an antigen of interest.
  • certain embodiments relate to a method of targeting a cell which externally presents an antigen of interest (e.g . a pMHC), comprising contacting the cell with the svd-TCR or a composition as disclosed herein.
  • Any cell which expresses the epitope on its cell surface may be targeted, including, for example, cancer cells, autoreactive immune cells, or the like.
  • the target cell expresses an antigen
  • the engineered TCR comprises an antigen binding domain that binds to the antigen expressed by the target cell.
  • the T cell exhibits a cytolytic effect on the target cell at an EC50 of less than 10 1 , 10 2 , or 10 3 mM peptide antigen. In some embodiments, the T cell exhibits a cytolytic effect when the target cell expresses a sparse antigen recognized by the engineered TCR.
  • the targeting may be for diagnostic purposes, screening purposes, therapeutic purposes, or any other purpose.
  • svd-TCRs which are soluble fusion proteins comprising an agent of interest, may be used to target an anticancer agent, fused as part of the svd-TCR, to cells in a subject which express a cancer-specific cell surface epitope.
  • svd-TCRs which when formatted for use as soluble fusion proteins comprising an agent of interest, may be used to specifically target a cytotoxic protein, fused as part of the svd-TCR, to undesired cells in a subject which express a cell surface epitope specific for an undesired cell.
  • the epitope may be a pMHC comprising proteolyzed fragments of bacterial or viral proteins which are being intracellularly expressed.
  • svd-TCRs which are soluble fusion proteins and comprising an agent of interest with an affinity for immune cells may be used to recruit immune cells, like NK or T-cells, to the target cell that is recognized by the svd-TCR.
  • T-cells which express svd-TCRs on their cell surface may be used to target cells recognized by the svd-TCR, for example, cancer cells, bacterial cells, virally- invaded cells and other undesired cells, for destruction by the host immune system.
  • svd- TCRs may be used in adoptive cell transfer therapy, e.g. similar to chimeric antigen receptors in T-cell based therapies. Because svd-TCRs can comprise a small modular binding domain, they have great flexibility in application as fusion proteins as compared to traditional TCRs which involve two different chains.
  • Cells may alternatively be redirected to particular organs or sites of healing or sites of inflammation, for example.
  • stem cells may be directed to organs or other microenvironments.
  • Certain embodiments relate to administering the polypeptide as disclosed herein to a subject which comprises the cell having the antigen of interest.
  • Provided herein are methods of treating a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a composition comprising immune cells comprising the engineered TCRs of the disclosure.
  • the subject in need thereof has cancer.
  • Cancer is a disease in which abnormal cells divide without control and spread to nearby tissue.
  • the cancer comprises a liquid tumor, or a solid tumor.
  • Exemplary liquid tumors include leukemias and lymphomas.
  • Exemplary solid tumors include sarcomas and carcinomas. Cancers can arise in virtually an organ in the body, including blood, bone marrow, lung, breast, colon, bone, central nervous system, pancreas, prostate and ovary.
  • the subject in need thereof has an infection.
  • Infections include viral, bacterial and fungal infections, as well as infection with eukaryotic parasites.
  • the subject in need thereof has an autoimmune disease, allergic disease, or inflammatory disease.
  • the autoimmune disease, allergic disease, or inflammatory disease is selected from the group consisting of systemic lupus erythematosus, rheumatoid arthritis, psoriatic arthritis, scleroderma, asthma, atopic dermatitis, and allergic rhinitis.
  • the autoimmune disease, allergic disease, or inflammatory disease is an organ- specific inflammatory disease.
  • the organ-specific inflammatory disease is selected from the group consisting of kidney disease and lung disease.
  • the organ-specific inflammatory disease is a disease of any other organ or group of organs in the body (for example, liver, brain, heart intestines, lymph nodes, circulatory system, stomach, spleen etc.).
  • the autoimmune disease, allergic disease, or inflammatory disease is transplant rejection.
  • the transplant rejection occurs in response to transplanted blood, bone marrow, bone, skin, heart, kidney, lung, muscle, heart or liver.
  • the transplant rejection is hyperacute rejection.
  • the transplant rejection is acute rejection.
  • the transplant rejection is chronic rejection.
  • a therapeutically effective amount of a composition such as a composition comprising engineered TCRs or a composition comprising immune cells comprising engineered TCRs, as described herein, effective to achieve a particular biological or therapeutic result.
  • a therapeutically effective amount of the composition reduces a sign or a symptom of the cancer.
  • a therapeutically effective amount of the composition reduces tumor number, volume, or size, or slows tumor growth, or a combination thereof.
  • kits and articles of manufacture comprising immune cells comprising the polypeptides described herein.
  • the kit comprises articles such as vials, syringes and instructions for use.
  • the kit comprises a polynucleotide or vector comprising a sequence encoding one or more polypeptides of the disclosure.
  • the kit comprises a plurality of immune cells comprising polypeptide as described herein.
  • the plurality of immune cells comprises a plurality of T cells.
  • nb-only TCRs can be constructed from a nb domain with no additional sequence engineering within the framework and constant regions of the b chain.
  • These nb-only svd-TCRs express stably on the surface of mammalian cells, including T cells. They bind pMHC probes selectively and appear to trigger T cells in much the same manner as full TCRs. Moreover, they function in tandem as CAR and TCR bifunctional proteins.
  • Such nb-only domains provide tools and components for next-generation engineered T cell therapeutics and shed light on the mechanisms that dictate signaling sensitivity of TCRs and CARs.
  • HEK-293T (ATTC CRL-3216), Jurkat clone E6-1 (ATCC TIB-152), T2 (ATCC CRL-1992), SUP-T1 (ATTC CRL-1942), A375 (ATTC CLR-1619) andK562 (ATTC CCL-243) cell lines were used in this study.
  • HEK-293T and A375 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.
  • Jurkat and SUP-T1 cells were maintained in RPMI supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin.
  • T2 cells were maintained in IMDM supplemented with 20% FBS and 1% penicillin/streptomycin.
  • K562 cells engineered to stably express single chain NY-ESO-1 -b2 ⁇ h-H ⁇ A-A2 trimer (Hansen et al, 2009) and GFP were generated and maintained in RPMI supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin. Cells were incubated at 37°C in 5% CO2.
  • Plasmid construction All constructs, except for the recovered nb-only pool from the HuTARGTM platform (Patent WO2017/091905), were generated by Golden Gate assembly into the pFenti backbone, which has an EFla promoter.
  • NY-ESO-1 and MAGE- A3 single-chain variable fragments (scFv) on the control CARs were obtained from in-house binder screens using the HuTARGTM platform. Sequences for the control NY-ESO-1 and MAGE- A3 TCRs were obtained from patents US8143376B2 and W02012054825A1, respectively.
  • HuTARGTM See patent WO2017/091905 for details. Briefly, HEK293 cells were engineered to contain a library of all combinations of unrearranged V, D and J segments of the b chain TCR locus. Because the host cells are constructed to contain a single loxP integration site, each cell post transfection of the library contains at most a single integrated copy of one of the roughly 1,800 combinations of V-D-J (64x2x14) gene segments, each segment flanked by a recombination signal sequence (RSS).
  • RSS recombination signal sequence
  • the RSSs When triggered to rearrange by addition of an exogenous inducer that activates RAGl expression, the RSSs mediate intramolecular site-specific recombination such that the population of cells produce a large repertoire of TEBb chains that are further subjected to selection for in- frame fusions using puromycin resistance.
  • the cells also contain a surrogate single alpha chain for pairing and surface expression.
  • Transfection Transient transfections of T-cell lines were performed using the Neon Transfection System (Thermo Fisher Scientific, Cat. No. MPK5000) according to the manufacturer’s instructions. Cells were pulsed three times at 1,500 V and a width of 30 msec. Transient transfection of HEK293T cells were performed using the Fugene HD transfection method (Promega, Cat. No. E2311) according to the manufacturer’s instructions.
  • FACS analysis 18 hours post-transfection, cells were harvested and washed three times with FACS buffer (PBS + 0.1% BSA). The cells were incubated with TCR PFl (8A3) antibody conjugated with PE-Cy7 (Life Technologies, Cat. No. 25576641), CD3 epsilon antibody conjugated with FITC, Alexa Fluor 647-Streptavidin (Jackson, Cat. No. 016-600-084)-labeled MHC Class I A*02:01 SLLMWITQV (NY-ESO), or Alexa Fluor 647-Streptavidm-labeled MHC Class I A*02:01 FLWGPRALV (MAGE- A3) for 1 hour at 4°C.
  • TCR PFl 8A3 antibody conjugated with PE-Cy7 (Life Technologies, Cat. No. 25576641)
  • CD3 epsilon antibody conjugated with FITC Alexa Fluor 647-Streptavidin (Jackson, Cat. No. 016-600-0
  • NFAT Luciferase assay NY-ESO- 1 peptide (SLLMWITQV) and MAGE- A3 peptide (FLWGPRALV) were synthesized by Genscript (Piscataway, NJ). Target peptides were serially diluted 3-fold starting at IOOmM and loaded onto 10,000 T2 cells in RPMI plus 1% BSA and 0.1% penicillin/streptomycin. Eighteen hours later, 12,000 transfected Jurkat cells resuspended in RPMI/10% FBS/0.1% penicillin/streptomycin were added to the peptide-loaded T2 cells. The co culture was incubated for 6 hours at 37°C. One-step luciferase assay system (BPS Cat. No. 60690) was used according to manufacturer’s instructions to read luminescence on a microplate luminometer at 100ms. Each experiment was done in duplicate.
  • BPS Cat. No. 60690 One-step luciferase assay system
  • PBMCs Peripheral blood mononuclear cells
  • lentivirus were obtained from Alstem. PBMCs and activated with human T-cell TransActTM according to manufacturer’s instructions in X-vivo media. For the transduction, lentivirus was added directly to the cells at MOI of 10. Transduced primary T-cells were expanded in X-vivo media with 1% human serum, 0.1% penicillin/streptomycin, 10 ng/ml IL-15, and 10 ng/ml IL-21. Cells were quiesced for 48 hours without stimulation or cytokines prior to assays.
  • Cytotoxicity and IFNY assay A375 cells were transfected with nuclear locating GFP (IncuCyte NucLight Green) and selected with puromycin. 5,000 A375 cells were seeded with IOmM of NY-ESO- 1 or MAGE-A3 peptides. After 18 hours, cells were treated with 10pg/ml of mitomycin C for 1 hour and washed three times. 5,000 transduced T-cells (adjusted for transduction percentage measured by probe staining) were added and monitored using the IncuCyte S3 live-cell analysis system (Essen Bioscience) at 37°C and 5% CO2. Images were captured every two hours for 42 hours using a 10X objective. Green area at each time point was normalized to time zero to measure loss of live target cells. Experiments were done in duplicate.
  • Homology Model We generated a 3D structure model of the nb-only constructs (Cjo-026(P) plus Cjo-005(a)) in Prime homology modeling suite (Schrodinger, 2019a) using the crystal structure of the MAGE-A3 TCR (TRAV21/TRBV5-1 family; PDBID:5BRZ) as the template. All structures were prepared using the Schrodinger Protein Preparation Wizard (Sastry et al., 2013) before further calculations.
  • the library construct encoded the human O ⁇ 3z transmembrane and cytoplasmic domains fused to the b chain to facilitate its expression in HEK293 cells, and subsequent analysis.
  • Specific pMHC-binding cells were enriched over multiple rounds and purified from the library.
  • MAGE pMHC sort a chain expression was inadvertently lost and b chains that endow specific epitope-binding in the absence of a second TCR variable domain were recovered.
  • Such nb-only clones were used as the basis of studies described below.
  • VB-onlv domains express stably and show selective pMHC binding in CAR and TCR formats
  • nb-only domains selective for either HLA-A2/NY-ESO-1 peptide or HLA- A2/MAGE-A3 peptide were recovered from the HuTARG sort and sequenced.
  • 3 and 4 unique CDR3 sequences were identified for NY-ESO-1- and MAGE- A3 -selective binders, respectively (Table 1).
  • all 7 nb idiotypes for both pMHC targets utilize the TRBV5- 8*01 segment, suggesting structural properties of this nb segment that may facilitate stability of a single domain absent its normal Va partner (see below).
  • the average CD3 loop length was 16.3 amino acids (range 12-20), ⁇ 2 amino acids longer than the average observed among a set of human TCR nb sequences.
  • TCR bEI (8A3) antibody was used to detect surface-expressing TCRb chains.
  • pMHC probes were generated by conjugating biotin-labeled, peptide-containing MHC Class I A*02:01 with fluorophore-labeled streptavidin. All idiotypes expressed stably on the cell surface with various probe-binding abilities (FIG. 7). The strongest binders, idiotype #2 for a NY-ESO-1 -targeted nb-only domain and idiotype #5 for a MAGE-A3- targeted domain, were selected for further studies.
  • TCRs and CARs were formatted as TCRs and CARs.
  • TCR format a generic alpha chain that is abundantly expressed in humans was used as a surrogate (TRAV41*01/J49*01).
  • CAR format Ub£ were linked to the a chain constant region (Ca), which in terms was fused to a CD3z transmembrane and intracellular signaling domain (first- generation CAR) or a CD28 transmembrane region and CD28 and E03z intracellular signaling domains (second-generation CAR) (FIG. 1A).
  • nb-only domains stably express as CARs and selectively bind to target probes in HEK293T cells nb-only domains also expressed in the TCR format with specificity for the pMHC target, but significantly lower binding (FIG. IB and FIG. 1C).
  • constructs were transfected into the Jurkat human T cell line. Additional CAR constructs with the nb domains linked to CD28 transmembrane region with CD28, 4- IBB and 093z intracellular signaling domains (third-generation CAR) were also tested.
  • nb-only CARs All NY-ESO-1- and MAGE- A3 -targeted nb-only CARs showed detectable probe binding in Jurkat cells. Slightly higher probe binding percentages were observed in second- and third-generation CARs compared to first-generation. However, nb-only domains in the TCR format did not bind probe for either pMHC target (FIG. ID and FIG IE).
  • TRB5-8 VB segment may encode a sequence that more readily forms a single functional binding domain
  • nb domains require more radical changes to form a thermodynamically stable structure absent the Va domain, compared to nb-85 (FIG. 2C and FIG. 2D).
  • the crystal structure of a TRBV28-encoded domain shows nearly 80% more hydrophobic surface area exposed, compared to the ⁇ b5-8-oh1n domain. Presumably such sequences have a more challenging route to formation of a stable single globular domain.
  • nb-only domains [0239] To assess whether target binding by nb-only domains can lead to functional activity, engineered Jurkat cells that expressed an NFAT-driven luciferase reporter gene were transfected with nb-only constructs. Serially diluted NY-ESO-1 and MAGE-A3 peptides were loaded onto T2 cells (HLA-A2+) 16 hours prior to co-culturing with transfected Jurkat effector cells. NFAT signal was measured by luminescence after 6 hours of co-culture. Peptide-titration curves showed that both NY- ESO-1 and MAGE- A3 nb-only CARs trigger peptide-concentration-dependent NFAT activation (FIG. 3 and Table 2).
  • First-generation CAR formats showed about two-fold less sensitivity than second- and third-generation CARs with both binders. Compared to control third-generation CARs with affinity-matured scFv binders, third-generation CARs with nb domains were ⁇ 100x (NY-ESO- 1) and ⁇ 1000x (MAGE-A3) less sensitive (FIG. 8A and FIG. 8B).
  • VP-only domains in TCR format are hindered by the Va domain
  • SUP- T1 cells were transfected with the b chains containing the nb-only domains and a TCRa surrogate chain.
  • SUP-T1 cells are derived from a lymphoma with a chromosomal inversion within the TCR a and b gene cluster that prevents surface expression of the endogenous TCR complex. Because TCR a and b are not expressed, other subunits of the TCR complex, the 4 CD3 proteins, are expressed but unable to assemble on the surface. Therefore, CD3F staining was used as a readout for expression and pairing of the transfected TCRa and TCRP constructs on the cell surface.
  • the NY-ESO-1 control TCR is expressed on the surface of SupTl cells. Moreover, the nb-only complex also are positive for CD3F staining, suggesting that the complex integrates the b and a subunits. However, only the control TCR showed probe binding, consistent with the observation in transfected Jurkat cells (FIG. 4B).
  • Bispecific VB-only domains function in CAR and TCR formats
  • T cells that recognize multiple antigens offer a prospective safeguard against this problem.
  • Bispecific receptors have been explored and developed in the context of CARs.
  • TCRs with a capacity to target two different antigens have not been reported to our knowledge. Given the small and versatile binding properties of nb-only domains, we suspected they might function in a more complicated format as a bifunctional CAR or TCR.
  • bispecific nb-only CARs targeting NY-ESO-1 and MAGE- A3 pMHCs were generated in a second-generation CAR architecture with Cb and the two nb domains connected in tandem via a (GIS)3GG flexible linker.
  • Jurkat cells transfected with these constructs showed detectable binding of both NY-ESO-1 and MAGE-A3 probes by flow cytometry (FIG. 5A).
  • bispecific CARs functioned in response to both NY-ESO-1- and MAGE- A3 -peptide-loaded T2 cells with only modest declines in their individual sensitivities (FIG. 5B, Table 4).
  • the binding domain positioned further from the membrane i.e., at the N-terminus
  • showed a slight decrease in sensitivity while the one directly attached to Ob showed no change compared to the monospecific CARs.
  • nb-only domains could function as bispecific TCRs
  • we constructed variants in both cis and trans configurations i.e., in tandem on the b chain, or with one nb domain on each chain, Ca and Cb (FIG. 5C).
  • nb fused on the TCRa chain was also expressed with a TCRb chain that lacked a nb domain (i.e., Cb only).
  • This construct showed no function in the Jurkat NFAT-luciferase reporter assay, indicating that Ub-only domains moved to the a-chain abolishes its function (FIG. 5D).
  • trans nb-only bispecific TCRs showed functional activity only against the pMHC target of the binder fused on the b-chain (FIG. 5D, Table 5).
  • Cis bispecific nb- only TCRs were generated by connecting two nb domains in tandem via a (GIS)3GG flexible linker and expressing this construct with a surrogate TCRa chain with the Va deleted.
  • GIS GIS3GG flexible linker
  • Cis nb-only domains in the other orientation with the MAGE- A3 binder at the N-terminus also showed functional activity against both target peptides, although the magnitude of the signal (Emax) with MAGE- A3 peptide was reduced.
  • the ECso in assays with peptides loaded on T2 was similar for the constructs, compared to the sensitivities of monospecific parental versions of the constructs (FIG. 5C and FIG. 4D).
  • nb-only domain constructs were transduced with lentivirus and expression was confirmed by NY-ESO-1 or MAGE- A3 probe staining (Fig 6A).
  • Transduced T cells were used in an IncuCyte cell killing assay that enables visualization of target and effector cells by microscopy at 37°C over time.
  • A375 cells that stably express nuclear locating GFP were loaded with IOmM NY-ESO-1 or MAGE-A3 peptides and co-cultured with transduced T cells at 1:1 ratios. T cell number was adjusted according to the transduction percentage measured by probe staining (FIG. 6A and FIG. 6B).
  • T cells expressing the benchmark TCR showed most potent cytotoxic activity, followed by T cells expressing the scFv-CAR, and the nb-only domain constructs in CAR and TCR formats which had similar killing activities. INFy measured in the supernatant of the co culture at 24 hours showed a similar trend (FIG. 6C).
  • K562 cells that overexpress single chain NY- ESO- 1 -P m-HLA- A2 trimer and GFP were also used as target cells in the real-time killing assay. In this situation where the antigen is presented abundantly, all 4 NY-ESO-l-targeted constructs showed similar killing activities (FIG. 12).
  • T cells expressing the MAGE-A3 benchmark TCR and scFv-CARs only showed mild cytotoxic activities while the nb-only-CAR and -TCR triggered more robust killing.
  • T cells with nb-only-CAR and -TCR also showed weak cytotoxicity toward K562 cells without any MAGE- A3 peptide loaded (FIG. 12), suggesting that these constructs likely trigger ligand-independent apoptosis of target cells. This is consistent with the high background NFAT signal observed in Jurkat cells transfected with the MAGE- A3 Ub-only-CAR and -TCR (FIG. 4D).

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Abstract

The invention relates to polypeptides having at least two antigen-binding domains, where at least one of the antigen binding domains is a T cell receptor single-variable domain (svd-TCR). The disclosure provides T cell receptors, polynucleotides, vectors, and immune cells comprising same, and methods of using same to treat diseases or disorders in a subject.

Description

BIFUNCTIONAL SINGLE VARIABLE DOMAIN T CELL RECEPTORS
AND USES THEREOF
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of priority to US Provisional Patent Application Serial No. 62/885,045 filed on August 9, 2019, the contents of which are hereby incorporated by reference in their entirety.
INCORPORATION BY REFERENCE OF SEQUENCE LISTING [0002] The present application is being filed with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled A2BI010_01WO_SeqList.txt, created on August 5, 2020, and is 14 kilobytes in size. The information in electronic format of the Sequence Listing is incorporated by reference in its entirety.
BACKGROUND OF THE INVENTION
[0003] Cell therapy using T cell receptors (TCRs) and chimeric antigen receptors (CARs) represents a new wave of immunotherapies garnering considerable attention and investment. Further progress in this area of medicine depends in part on improving the functional capabilities of the engineered components.
[0004] Since tumor-selective surface proteins are extremely rare among solid tumors, drug discovery has recently begun to explore the utility of peptide-MHC complexes (pMHCs) as target opportunities for CAR-Ts and T-cells with engineered receptors or native TCRs.
[0005] pMHCs are the natural ligands for TCRs and, as such, lend themselves to targeting by TCRs and their derivatives. Class I MHC molecules consist of a molecular dimer of an a chain associated with b2 microglobulin. This dimer binds in a degenerate manner to individual short peptides while folding in the endoplasmic reticulum to create the pMHC complex. The pMHC is then transported to the membrane surface where it can be recognized by cognate T cells. If a certain binding threshold is crossed, pMHCs can trigger activation and effector function of T cells through TCRs.
[0006] TCRs are composed of a complex of eight subunits, comprising six individual polypeptides in the stoichiometry a:b:g:d:2e:2z. The a and b subunits form the central pMHC binding element, which has significant structural similarity to its relative, the antibody antigen-binding fragment (Fab). Both the a and b subunits typically contribute to binding a small region on the class I MHC ligand distal to the membrane that includes residues from the MHC molecule as well as the short peptide in the complex itself.
[0007] pMHCs afford the option to target peptides derived from proteins that reside in the cytoplasm and are otherwise inaccessible to large molecules, such as monoclonal antibodies. There remains, however, a long-felt and unmet need for TCR-based binding agents, including engineered TCRs. The present disclosure addresses these issues in the prior art.
SUMMARY OF THE INVENTION
[0008] The invention relates generally to polypeptides that comprise at least two antigen-binding domains, at least one of which is a single-variable domain TCR domain (svd-TCR). In one aspect, the disclosure provides a polypeptide, comprising, in N-terminal to C-terminal order, a first antigen binding domain, a linker, and a second antigen-binding domain, wherein either or both of the first and second antigen-binding domains comprise a single-variable domain TCR (svd-TCR). In some embodiments, the polypeptide comprises a transmembrane domain C-terminal to the second antigen binding domain. In some embodiments, the first and second antigen-binding domains each independently comprise a svd-TCR.
[0009] In some embodiments of the polypeptides of the disclosure, the first and second antigen binding domains each independently comprise a svd-TCR, wherein the svd-TCR comprises a variable domain selected from a TCR Va domain, a TCR nb domain, a TCR Vy domain, and a TCR V5 domain, or an antigen-binding fragment thereof. In some embodiments, either or both of the first and the second svd-TCRs comprises a TCR constant domain selected from a TCR Ca domain, TCR Cb domain, a TCR Cy domain, and a TCR C5 domain and/or the second antigen-binding domain comprises a TCR constant domain selected from a TCR Ca domain, TCR Cb domain, a TCR Cy domain.
[0010] In some embodiments of the polypeptides of the disclosure, the first svd-TCR comprises a first TCR nb domain or an antigen-binding fragment thereof and the second svd-TCR comprises a second TCR nb domain or an antigen-binding fragment thereof. In some embodiments, the first and second nb domains each independently comprises a human nb domain. In some embodiments, the Ub domains each independently share at least 80% sequence identity to a human Ub domain. In some embodiments, the first nb domain share at least 80% sequence identity to TRBV5-8 nb (SEQ ID NO: 30). In some embodiments, the second nb domain shares at least 80% sequence identity to TRBV5- 8 nb (SEQ ID NO: 30). In some embodiments, the second svd-TCR comprises a TCR Ob domain. [0011] In some embodiments of the polypeptides of the disclosure, the first svd-TCR specifically binds a first peptide:MHC complex comprising a first peptide. In some embodiments, the second svd- TCR specifically binds a second peptide:MHC complex comprising a second peptide. In some embodiments, the first peptide comprises a tumor antigen. In some embodiments, the second peptide comprises a tumor antigen. In some embodiments the first or the second peptide:MHC complex comprises a class I MHC. In some embodiments, the first or the second peptide:MHC complex comprises a class II MHC.
[0012] In some embodiments of the polypeptides of the disclosure, the linker comprises the amino acid sequence of SEQ ID NO: 31.
[0013] In some embodiments of the polypeptides of the disclosure, the transmembrane domain is a TCRa transmembrane domain or a TO Ib transmembrane domain. In some embodiments, the transmembrane domain is a Eϋ3z transmembrane domain or a CD28 transmembrane domain.
[0014] In some embodiments of the polypeptides of the disclosure, the polypeptides comprise, C- terminal to the transmembrane domain, one or more intracellular signaling domains. In some embodiments, the transmembrane domain comprises a CD28 transmembrane domain and wherein the one or more intracellular signaling domains comprise, in any C terminal to N terminal order, a CD28 intracellular domain, or functional fragment thereof, and a Eϋ3z intracellular domain, or functional fragment thereof. In some embodiments, the transmembrane domain comprises a CD28 transmembrane domain and wherein the one or more intracellular signaling domains comprise, in any C terminal to N terminal order, a CD28 intracellular domain, a 4- IBB intracellular domain, and a E03z intracellular domain, or functional fragments thereof.
[0015] In some embodiments of the polypeptides of the disclosure, the first svd-TCR and the second svd-TCR each independently comprise a CDR3 comprising an amino acid sequence selected from SEQ ID NOs: 1-7. In some embodiments, the first svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 2 and the second svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 7. In some embodiments, the first svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 7 and the second svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID.
[0016] The disclosure provides polynucleotides comprising a nucleic acid sequence encoding a polypeptide of the disclosure. The nucleic acid sequence is in operative association with a promoter for expression of said nucleic acid.
[0017] The disclosure provides vectors comprising polynucleotides of the disclosure.
[0018] The disclosure provides cells comprising the polypeptides of the disclosure. In some embodiments, the cell is a T cell. In some embodiments, the T cell is a T regulatory (Treg) cell. In some embodiments, the T cell is a non-regulatory T cell. In some embodiments, the cell is an NK cell. [0019] The disclosure provides pharmaceutical compositions comprising a plurality of the cells of the disclosure and a pharmaceutically acceptable carrier, diluent or excipient. In some embodiments, the pharmaceutical compositions comprise a therapeutically effective amount of the cells.
[0020] The disclosure provides methods of activating a cytotoxic signal in a target cell, comprising contacting, delivering, administering, providing, and/or supplying the cell of the disclosure to the target cell. In some embodiments, the cytotoxic signal comprises NFAT signaling. In some embodiments, the cytotoxic signal comprises release of IFNy.
[0021] The disclosure provides methods inducing tolerance in a target cell, comprising contacting, delivering, administering, providing, and/or supplying the cell of the disclosure to the target cell. [0022] The disclosure provides methods of treating and/or preventing cancer in a subject in need thereof, comprising administering to the subject a plurality of the cell of the disclosure or the pharmaceutical composition of the disclosure.
[0023] The disclosure provides kits comprising a plurality of the cell of any one of claims 28-33. In some embodiments, the kits further comprise instructions for use.
[0024] In other aspects, the disclosure provides a vectors, cells, and methods of use including methods of treating diseases or disorders, e.g., cancer.
BRIEF DESCRIPTION OF THE DRAWINGS [0025] FIG. 1 A shows a schematic of the Ub-TCR and Ub-CAR constructs used in the disclosure. [0026] FIG. IB is a series of plots that shows flow cytometry of HEK293 cells transfected with NY- ESO-1 pMHC -targeted constructs. The x-axis reflects the proportion of pMHC probes bound to the cell, and the y-axis reflects the proportion of TCR 3 chain on the cell surface.
[0027] FIG. 1C is a series of plots that shows flow cytometry of HEK293 cells transfected with MAGE- A3 pMHC-targeted constructs. The x-axis reflects the proportion of pMHC probes bound to cell, and the y-axis reflects the proportion of TCR 3 chain on the cell surface.
[0028] FIG. ID is a series of plots that shows flow cytometry of Jurkat cells transfected with NY- ESO-1 pMHC-targeted constructs. The x-axis reflects the proportion of pMHC probes bound to the cell.
[0029] FIG. IE is a series of plots that shows flow cytometry of Jurkat cells transfected with MAGE- A3 pMHC-targeted constructs. The x-axis reflects the proportion of pMHC probes bound to the cell. [0030] FIG. 2 is a series of pictures that shows homology models that use the atomic coordinates of the MAGE peptide/HLA-A2 pMHC in complex with a nb5 TCR (5BRZ). The amino acid sequences for a specific TCR representing 3 different nb family segments were threaded onto the crystal structure backbone and refined to eliminate steric clashes (see Methods). Hydrophobic patches on the space-filling surface model are labeled green; charged and neutral surfaces white. For A, C and D, a ribbon cartoon shows where Va normally binds to nb in the TCR a/b dimer. The intersection between the hydrophobic surface and the a/b contact surface was calculated and is shown in Angstroms2. [0031] FIG. 3 is a pair of plots that shows the NFAT-luciferase signal of Jurkat cells transfected with nb constructs after 6 hours of co-culture with NY-ESO-1 (left panel) or MAGE-A3 (right panel) peptide-loaded T2 cells.
[0032] FIG. 4A shows a schematic of the nb-TCR constructs used in the current disclosure.
[0033] FIG. 4B is a series of plots that show pMHC probe binding (top panel) and TCR complex formation (CD3s surface expression, bottom panel) in transfected SUP-T1 cells.
[0034] FIG. 4C is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6hrs of co-culture with NY-ESO-1 (left) or MAGE-A3 (right) peptide-loaded T2 cells.
[0035] FIG. 5A is a series of plots that show a flow cytometry of transfected Jurkat cells stained for binding to NY-ESO-1 pMHC probe (y-axis) and MAGE-A3 pMHC probe (x-axis). M refers to MAGE- A3 and N refers to NY-ESO-1. [0036] FIG. 5B is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 (left) and MAGE- A3 (right) peptide-loaded T2 cells.
[0037] FIG. 5C shows a schematic of the constructs presented in this disclosure. M refers to MAGE- A3 and N refers to NY-ESO-1.
[0038] FIG. 5D is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 (left) and MAGE- A3 (right) peptide-loaded T2 cells.
[0039] FIG. 6A is a series of plots that show primary T cells transduced with indicated constructs stained with NY-ESO-1 or MAGE- A3, as indicated.
[0040] FIG. 6B is a pair of plots that show A375 cells expressing nuclear locating GFP loaded with IOmM of NY-ESO-1 (left) or MAGE-A3 (right) peptides were co-cultured with T cells transduced with NY-ESO-1 (left) or MAGE- A3 (right) binding constructs at 1:1 ratios and imaged in IncuCyte for 42 hours. Ratio of total green fluorescent area at each time point divided by time zero value is plotted.
[0041] FIG. 6C is a plot that shows IFNy measured by the BD cytometric bead array with supernatants from the 24 hour time-point of the co-cultures in FIG. 6B.
[0042] FIG. 7 is a series of plots that show flow cytometry plots of HEK293T cells transfected with nb-only domains recovered from the HuTARG™ system. The x-axis reflects the amount of target pMHC probes bound to the cell. The y-axis reflects the amount of the TCRP chain on the cell surface. [0043] FIG. 8 A shows a schematic of the nb-only CARs in the present disclosure.
[0044] FIG. 8B is a pair of plots that show the NFAT-luciferase signal of transfected Jurkat cells after 6hrs of co-culture with NY-ESO-1 (left panel) and MAGE-A3 (right panel) peptide-loaded T2 cells. [0045] FIG. 9 is a series of plots that show flow cytometry of Jurkat cells transfected with NY-ESO- 1 or MAGE- A3 pMHC-targeted constructs. The x-axis reflects the proportion of pMHC probes bound to the cell.
[0046] FIG. 10A is a series of plots that show flow cytometry of CD3 and NY-ESOl pMHC probe binding in SUP-T1 cells.
[0047] FIG. 10B is a plot that shows the NFAT-luciferase signal of transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 peptide-loaded T2 cells.
[0048] FIG. 11 A shows a schematic of scFv-CAR and TCR constructs used in FIG. 1 IB. [0049] FIG. 1 IB is a plot that shows the NFAT-luciferase signal transfected Jurkat cells after 6 hrs of co-culture with NY-ESO-1 peptide-loaded T2 cells.
[0050] FIG. 12 is a pair of plots that show K562 cells overexpressing single chain NY-ESO-1 -b2ih- HLA-A2 trimer and GFP were co-cultured with T cells expressing NY-ESO-1 (left panel) or MAGE- A3 (right panel) targeted constructs at 1 : 1 ratios. Images were taken for 42 hours by IncuCyte. Total green fluorescent area at each time point divided by the t=0 value are plotted.
DETAILED DESCRIPTION OF THE INVENTION [0051] The appeal of bifunctional targeting molecules, coupled with packaging limitations of gene- transfer vectors such as lentiviruses and retroviruses, raise the question if TCRs can function as a single binding domain; e.g., as a nb devoid of its normal partner, the a variable domain (Va). To our knowledge, no instance of such a streamlined TCR has been reported, though shark species have a variety of novel TCRs that are distinct in form from mammalian orthologs (Criscitiello et al, 2006; Greenberg et al., 1995). If such a simplified TCR variable domain that retains binding and functional activity against pMHCs could be defined, it would potentially open a path to engineering smaller, more complex binding capabilities with svd-TCRs.
[0052] Though svd-TCRs are an attractive concept, it is not evident that such stripped-down binding domains can be derived easily from mammalian TCRs. The three-dimensional structure of TCRs reveals a complex where the TCR Va and b chains pack together, covering a large ( >200 A2) hydrophobic surface. Removal of the Va domain exposes this surface to destabilizing solvent interactions. By analogy with protein engineering efforts on antibodies conducted over the past decades, such dramatic changes in structure require significant adjustments, either by design or selection, to accommodate the single- variable domain format (Dottorini et al, 2004; Rouet et al., 2015).
[0053] The HuTARG platform is a powerful tool for engineering proteins in a mammalian system due to its ability to screen billions of antigen-binding molecules directly for function. In the present disclosure, the HuTARG platform was used to generate variable regions of the svd-TCR by using TCR-specific V, D, and J elements. In vitro V(D)J recombination was used to generate sequence diversity in the TCR nb domain while keeping the Va domain constant in a controlled fashion in mammalian cells, and over 100 million TCR-expressing cells were sorted and enriched for their ability to bind peptide in the absence of a second TCR variable domain. See patent applications WO 2009/129247 and WO 2017/091905, herein incorporated by reference in their entirety.
[0054] As disclosed herein, nb-only TCRs can be constructed from a nb domain with no additional sequence engineering within the framework and constant regions of the b chain. These nb-only svd- TCRs express stably on the cell surface of mammalian cells, including T cells. They bind pMHC probes selectively and appear to trigger T cells in much the same manner as full TCRs. Moreover, they function in tandem as CAR and TCR bifunctional proteins. Such nb-only domains provide tools and components for next-generation engineered T cell therapeutics and shed light on the mechanism that dictate signaling sensitivity of TCRs and CARs.
Definitions
[0055] As used herein, “single variable domain T cell receptor” or “svd-TCR” refer to the variable domain of a T cell receptor capable of specifically binding to an epitope in the absence of a second TCR variable domain. For example, an svd-TCR comprising a nb variable domain is capable of binding to an epitope independent of and/or in the absence of a Va variable domain, and an svd-TCR comprising a Va variable domain is capable of binding to an epitope independent of and/or in the absence of a nb variable domain. Illustrative epitopes recognized by svd-TCRs include peptide:MHC complexes (pMHC complexes).
[0056] According to the present disclosure, an “epitope” recognized by an svd-TCR is not a superantigen. Superantigens are a class of antigen that cause non-specific activation of T-cells resulting in polyclonal T-cell activation and massive cytokine release. They are produced by some pathogenic viruses and bacteria, potentially as a defense mechanism against the immune system. Binding of SAgs to the TCR is by a different mechanism than classic TCR recognition of pMHCs and is independent of the TCR CDR3 sequences of the variable domains.
[0057] As used herein, the terms “comprising,” “having,” “including” and “containing,” and grammatical variations thereof, are inclusive or open-ended and do not exclude additional, unrecited elements and/or method steps. The term “consisting essentially of when used herein in connection with a composition, use or method, denotes that additional elements and/or method steps may be present, but that these additions do not materially affect the manner in which the recited composition, method or use functions. The term “consisting of when used herein in connection with a composition, use or method, excludes the presence of additional elements and/or method steps. A composition, use or method described herein as comprising certain elements and/or steps may also, in certain embodiments consist essentially of those elements and/or steps, and in other embodiments consist of those elements and/or steps, whether or not these embodiments are specifically referred to. A use or method described herein as comprising certain elements and/or steps may also, in certain embodiments consist essentially of those elements and/or steps, and in other embodiments consist of those elements and/or steps, whether or not these embodiments are specifically referred to.
[0058] A reference to an element by the indefinite article “a” does not exclude the possibility that more than one of the elements is present, unless the context clearly requires that there be one and only one of the elements. The singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. The use of the word “a” or “an” when used herein in conjunction with the term “comprising” may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one” and “one or more than one”.
[0059] Unless indicated to be further limited, the term “plurality” as used herein means more than one, for example, two or more, three or more, four or more, and the like.
[0060] As used herein, the term “about” refers to an approximately +/-10% variation from a given value. It is to be understood that such a variation is always included in any given value provided herein, whether or not it is specifically referred to.
[0061] In this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. As another example, a range such as 95-99% identity, includes something with 95%, 96%, 97%, 98% or 99% identity, and includes subranges such as 96-99%, 96- 98%, 96-97%, 97-99%, 97-98% and 98-99% identity. This applies regardless of the breadth of the range. [0062] Unless otherwise specified, “certain embodiments”, “various embodiments”, “an embodiment” and similar terms includes the particular feature(s) described for that embodiment either alone or in combination with any other embodiment or embodiments described herein, whether or not the other embodiments are directly or indirectly referenced and regardless of whether the feature or embodiment is described in the context of a method, product, use, composition, protein, nucleic acid, at least one nucleic acid, cell, cell, kit, et cetera.
[0063] As used herein, a “polypeptide” is a chain of amino acid residues, including peptides and protein chains. A polypeptide may include amino acid polymers in which one or more of the amino acid residues is an artificial chemical analogue of a corresponding naturally occurring amino acid, or is a completely artificial amino acid with no obvious natural analogue as well as to naturally occurring amino acid polymers.
[0064] As used herein, “nucleic acid”, “nucleic acid sequence”, “nucleotide sequence”, or similar terms mean oligomers of bases typically linked by a sugar-phosphate backbone, such as oligonucleotides or polynucleotides, and to DNA or R A of genomic or synthetic origin which can be single-or double-stranded, and represent a sense or antisense strand. The terms nucleic acid, polynucleotide and nucleotide also specifically include nucleic acids composed of bases other than the five biologically occurring bases (i.e., adenine, guanine, thymine, cytosine and uracil), and also include nucleic acids having non-natural backbone structures. Unless otherwise indicated, a particular nucleic acid sequence of this invention encompasses complementary sequences, in addition to the sequence explicitly indicated.
[0065] In general, “sequence identity” or “sequence homology” refers to an exact nucleotide-to- nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Typically, techniques for determining sequence identity include determining the nucleotide sequence of a polynucleotide and/or determining the amino acid sequence encoded thereby and comparing these sequences to a second nucleotide or amino acid sequence. Two or more sequences (polynucleotide or amino acid) can be compared by determining their “percent identity.” The percent identity of two sequences, whether nucleic acid or amino acid sequences, is the number of exact matches between two aligned sequences divided by the length of the shorter sequences and multiplied by 100. Percent identity may also be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul, Proc. Natl. Acad. Sci. USA 87:2264-2268 (1990) and as discussed in Altschul, et al., J. Mol. Biol. 215:403-410 (1990); Karlin And Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5877 (1993); and Altschul et al, Nucleic Acids Res. 25:3389-3402 (1997). Briefly, the BLAST program defines identity as the number of identical aligned symbols (generally nucleotides or amino acids), divided by the total number of symbols in the shorter of the two sequences. The program may be used to determine percent identity over the entire length of the proteins being compared. Default parameters are provided to optimize searches with short query sequences in, for example, with the blastp program. Ranges of desired degrees of sequence identity are approximately 80% to 100% and integer values . Typically, the percent identities between a disclosed sequence and a claimed sequence are at least 80%, at least 85%, at least 90%, at least 95%, or at least 98%.
[0066] In this disclosure, “nucleic acid vector”, “vector” and similar terms refer to at least one of a plasmid, bacteriophage, cosmid, artificial chromosome, expression vector, or any other nucleic acid vector. Those skilled in the art, in light of the teachings of this disclosure, will understand that alternative vectors may be used, or that the above vectors may be modified in order to combine sequences as desired. For example, vectors may be modified by inserting additional origins of replication, or replacing origins of replication, introducing expression cassettes comprising suitable promoter and termination sequences, adding one or more than one DNA binding sequence, DNA recognition site, or adding sequences encoding polypeptides as described herein, other products of interest, polypeptides of interest or proteins of interest, or a combination thereof. In some embodiments adjacent functional components of a vector may be joined by linking sequences.
[0067] A “promoter” is a DNA region, typically but not exclusively 5' of the site of transcription initiation, sufficient to confer accurate transcription initiation. The promoter nucleic acid typically contains regions of DNA that are involved in recognition and binding of RNA polymerase and other proteins or factors to initiate transcription. In some embodiments, a promoter is constitutively active, while in alternative embodiments, the promoter is conditionally active ( e.g ., where transcription is initiated only under certain physiological conditions). Conditionally active promoters may thus be “inducible” in the sense that expression of the coding sequence can be controlled by altering the physiological condition.
[0068] As used herein, “operably linked”, “operatively linked”, “operative association” and similar phrases, when used in reference to nucleic acids, refer to the linkage of nucleic acid sequences placed in functional relationships with each other. For example, an operatively linked promoter sequence, open reading frame and terminator sequence results in the accurate production of an RNA molecule. In some aspects, operatively linked nucleic acid elements result in the transcription of an open reading frame and ultimately the production of a polypeptide (i.e., expression of the open reading frame). [0069] All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control. However, mention of any reference, article, publication, patent, patent publication, and patent application cited herein is not, and should not be taken as an acknowledgment, or any form of suggestion, that they constitute valid prior art or form part of the common general knowledge in any country in the world.
Engineered T cell receptors (TCRs) and TCR Subunits
[0070] In some embodiments, the engineered TCRs of the disclosure comprise an extracellular domain made up of one or more single variable domain T cell receptors (svd-TCRs), a transmembrane domain and an intracellular domain. In some embodiments, the intracellular domain comprises one or more exogenous domains.
[0071] TCR subunits include TCR alpha, TCR beta, CD3 zeta, CD3 delta, CD3 gamma and CD3 epsilon. Any one or more of TCR alpha, TCR beta chain, CD3 gamma, CD3 delta or CD3 epsilon, or fragments or derivative thereof, can be fused to one or more domains capable of providing a stimulatory signal of the disclosure, thereby enhancing TCR function and activity. svd-TCRs
[0072] Certain embodiments of present disclosure relate to a svd-TCR comprising a first TCR variable domain, the first TCR variable domain specifically binding to an antigen in the absence of a second TCR variable domain. [0073] In some embodiments, the engineered TCR contains multiple svd-TCRs. In some embodiments, the first svd-TCR is linked to a second svd-TCR, wherein the first and second svd- TCRs specifically bind peptides. In some embodiments, the peptides are bound to MHC. In some embodiments, the svd-TCR domains recognize the same peptide. In other embodiments, the svd- TCRs recognize different peptides.
[0074] The engineered TCR may bifunctional. The term “bifunctional TCR” as described herein refers to a first antigen-binding domain, or svd-TCR, binding to a first peptide and a second antigen binding domain, or svd-TCR, binding to a second peptide, wherein the first and second peptides are not the same peptide.
[0075] In some embodiments, the svd-TCR may include additional elements besides the TCR variable domain, including additional amino acid sequences, additional protein domains (covalently associated, non- covalently associated or covalently and non-covalently associated with the TCR variable domain), fusion or non-covalent association of the TCR variable domain with other types of macromolecules (for example polynucleotides, polysaccharides, lipids, or a combination thereof), fusion or non-covalent association of the TCR variable domain with one or more small molecules, compounds, or ligands, or a combination thereof. Any additional element, as described, may be combined provided that the TCR variable domain is configured to specifically bind the epitope in the absence of a second TCR variable domain.
[0076] An svd-TCR as described herein may comprise a single TCR chain ( e.g . a, b, g, or d chain), or it may comprise a single TCR variable domain (e.g. of a, b, g, or d chain). If the svd-TCR is a single TCR chain, then the TCR chain comprises a transmembrane domain, a constant (or C domain) and a variable (or V domain), and does not comprise a second TCR variable domain. The svd-TCR may therefore comprise or consist of a TCR a chain, a TCR b chain, a TCR g chain or a TCR d chain. The svd-TCR may be a membrane bound protein. The svd-TCR may alternatively be a membrane- associated protein.
[0077] In some embodiments, the engineered TCR as described herein utilizes a surrogate a chain that lacks a Va segment, which forms activation-competent TCRs complexed with the six CD3 subunits. [0078] In other embodiments, the engineered TCR as described herein functions independently of a surrogate a chain that lacks a Va segment. For example, in some embodiments the one or more svd- TCRs are fused to transmembrane (e.g., Oϋ3z and CD28) and intracellular domain proteins (e.g., Oϋ3z, CD28, and/or 4-1BB) that are capable of activating T cells in response to antigen.
[0079] In some embodiments, the svd-TCR may be any svd-TCR or subset of svd-TCRs defined herein, including without limitation single TCR chains and fusion proteins comprising the svd-TCR. For example, the svd-TCR may be a single a TCR chain, a single b TCR chain, a single g TCR chain, or a single d TCR chain. The svd-TCR may be a svd-TCR-Fc fusion or any other fusion protein defined herein.
[0080] In some embodiments, the svd-TCR engages antigen using complementarity-determining regions (CDRs). Each svd-TCR contains three complement determining regions (CDR1, CDR2, and CDR3).
[0081] It is known in the art that the TCR variable domain can be stably expressed without the TCR transmembrane domain or TCR C domain to generate a soluble protein (Alajez et. al. J. Biomed. Biotechnol. Article ID 68091, 1-9 (2006); Laugel etal. J. Biol. Chem. 280:1882-92 (2005)). Thus, the svd-TCR as described herein may be a soluble protein. For example, the svd-TCR may comprise a single TCR variable domain (i.e. the first TCR variable domain) without the transmembrane or C domains (or portions thereof). The first TCR variable domain may comprise either a TCR Va domain, a TCR nb domain, a TCR Ug domain, or a TCR V5 domain. Therefore, the soluble svd-TCR may comprise the first TCR variable domain, for example, a single TCR variable a, b, g or d domain. In another example, the svd-TCR may comprise a svd-TCR (i.e. the first TCR variable domain) linked to a second svd-TCR (i.e. the second TCR variable domain) without transmembrane or C domains (or portions thereof). The first TCR variable domain may comprise either a TCR Va domain, a TCR nb domain, a TCR Vy domain, or a TCR Vd domain, and the second TCR variable domain may comprise either a TCR Va domain, a TCR nb domain, a TCR Vy domain, or a TCR V5 domain.
[0082] In some embodiments, the first svd-TCR comprises a first TCR nb domain or an antigen binding fragment thereof and the second svd-TCR comprises a second TCR nb domain or an antigen binding fragment thereof. [0083] The first and/or second TCR variable domain may be a human TCR variable domain. Alternatively, the first TCR variable domain may be a non-human TCR variable domain. The first and/or second TCR variable domain may be a mammalian TCR variable domain. The first and/or second TCR variable domain may be a vertebrate TCR variable domain.
[0084] In humans, the TCR variable regions of the a and g chains are each encoded by a V and a J segment, whereas the variable region of b and d chains are each additionally encoded by a D segment. There are multiple Variable (V), Diversity (D) and Joining (J) gene segments ( e.g . 52 nb gene segments, 2 ϋb gene segments and 13 1b gene segments) (Janeway et al. (eds.), Immunobiology: The Immune System in Health and Disease. (5th ed., 2001), Figure 4.13) which can be recombined in different V(D)J arrangements using the enzymes RAG-1 and RAG-2, which recognize recombination signal sequences (RSSs) adjacent to the coding sequences of the V, D and J gene segments. The RSSs consist of conserved heptamers and nonamers separated by spacers of 12 or 23 bp. The RSSs are found at the 3 ‘ side of each V segment, on both the 5' and 3' sides of each D segment, and at the 5' of each J segment. During recombination, RAG- 1 and RAG-2 cause the formation of DNA hairpins at the coding ends of the joint (the coding joint) and removal of the RSSs and intervening sequence between them (the signal joint). The variable regions are further diversified at the junctions by deletion of a variable number of coding end nucleotides, the random addition of nucleotides by terminal deoxynucleotidyl transferase (TdT), and palindromic nucleotides that arise due to template- mediated fill-in of the asymmetrically cleaved coding hairpins.
[0085] International Patent Publication No. W02009/129247 A2, incorporated by reference in its entirety, discloses the HuTARG system, which utilizes V(D)J recombination to generate de novo antibodies in vitro. This system was used to generate the variable regions of the svd-TCR as in WO2017/091905A1, incorporated herein by reference in its entirety, by using TCR-specific V, D and J elements. In natural in vivo systems, the nucleic acid sequences which encode CDR1 and CDR2 are contained within the V (a, b, g or d) gene segment and the sequence encoding CDR3 is made up from portions of V and J segments (for Va or Vy), or a portion of the V segment, the entire D segment and a portion of the J segment (for nb or Ud), but with random insertions and deletions of nucleotides at the V-J and V-D-J recombination junctions due to action of TdT and other recombination and DNA repair enzymes. The recombined T-cell receptor gene comprises alternating framework (FR) and CDR sequences, as does the resulting T-cell receptor expressed therefrom (i.e. FR1-CDR1-FR2- CDR2-FR3-CDR3-FR4). Using in vitro V(D)J recombination (i.e. V-J or V-D-J recombination), randomized insertions and deletions may be added in or adjacent to CDR1, CDR2 and/or CDR3 (i.e. not just CDR3), additional insertions may be added using flanking sequences in recombination substrates before and/or after CDR1 , CDR2 and/or CDR3, and additional deletions may be made by deleting sequences in recombination substrates in or adjacent to CDR1, CDR2 and/or CDR3.
[0086] In some embodiments, TCR nb chains were identified that specifically bind epitopes in the absence of TCR Va chains. The CDR3 amino acid sequences are listed in Table 1 below.
Table 1. CDR3 amino acid sequences of identified Ub domains
Figure imgf000018_0001
[0087] In some embodiments, the first TCR variable domain of the svd-TCR specifically binds to an epitope in the absence of a second TCR variable domain, and consists of optional N-terminal and/or C-terminal amino acid sequences (of any length or sequence) flanking a variable domain defined by FR1 -CDR1 - FR2 -CDR2 -FR3 -CDR3-FR4 regions. FR1, FR2, FR3 and FR4 may be obtained from a natural Va, nb, Ug or V5 domain or encoded by natural Va, Ub, Ug or V d gene segments, but optionally include deletions or insertions of ( e.g . 0, 1, 2, 3, 4, 5 or more than 5 amino acids) amino acids independently at one or more of the C-terminus of FR1 , the N-terminus of FR2, the C-terminus of FR2, the N-terminus of FR3, the C-terminus of FR3 and the N-terminus of FR4. CDR1, CDR2 and CDR3 may be obtained from a natural Va, nb, Vy or V5 domain, or encoded by natural Va, nb, Ug or V5 gene segments, but wherein one or more of CDR1, CDR2 and CDR3 independently contains an insertion (e.g. 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 amino acids) and/or a deletion (e.g. 0, 1, 2, 3, 4, 5 or more than 5 amino acids) at the C-terminus, the N- terminus or anywhere within the CDR sequence. In some embodiments, the CDR1 contains an insertion or deletion of amino acids N- terminally, C-terminally or internally, wherein at least 50% (or optionally 60%, 70% or 80%) of natural CDR amino acid residues are retained. In some embodiments, the CDR2 contains an insertion or deletion of amino acids N-terminally, C-terminally or internally, wherein at least 50% (or optionally 60%, 70% or 80%) of natural CDR amino acid residues are retained. In some embodiments, the CDR3 contains an insertion or deletion of amino acids N-terminally, C-terminally or internally, wherein at least 50% (or optionally 60%, 70% or 80%) of natural CDR amino acid residues are retained. Insertions and/or deletions may be produced as a result of in vitro V(D)J recombination methods or from the in vitro action of TdT and recombination and DNA repair enzymes (e.g. one or more of Artemis nuclease, NDA-dependent protein kinase (DNA-PK), X-ray repair cross complementing protein 4 (XRCC4), DNA ligase IV, non-homologous end-joining factor 1 (NHEJl), PAXX, and DNA polymerases l and m). Insertion and/or deletion (which includes substitution) may further result from insertions and/or deletions to CDR nucleic acid sequences of the in vitro V(D)J recombination substrates. The svd-TCR may further comprise a TCR constant region or portion thereof. The svd-TCR may be fused to and/or complexed with additional protein domains. A double stranded break in DNA may be introduced prior to in vitro use of the above recombination and DNA repair enzymes. The svd-TCR may be (or may be incorporated into) a fusion protein. As used herein, the term “fusion protein” means a protein encoded by at least one nucleic acid coding sequence that is comprised of a fusion of two or more coding sequences from separate genes, regardless of whether the organism source of those genes is the same or different. [0088] In some embodiments of the polypeptides of the disclosure, the nb domains each independently share at least 80% sequence identity to a human nb domain. In some embodiments of the polypeptides of the disclosure, the nb domains each independently share at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, or at least 99% sequence identity to a human nb domain. In some embodiments of the polypeptides of the disclosure, the first nb domain share at least 80% sequence identity to TRBV5-8 nb (SEQ ID NO: 30). In some embodiments of the polypeptides of the disclosure, the first nb domain share at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, at least 99% sequence identity or are identical to TRBV5-8 nb (SEQ ID NO: 30). In some embodiments of the polypeptides of the disclosure, the second nb domain shares at least 80% sequence identity to TRBV5-8 nb (SEQ ID NO: 30). In some embodiments of the polypeptides of the disclosure, the second nb domain share at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, at least 99% sequence identity or are identical to TRBV5-8 nb (SEQ ID NO: 30). An illustrative an amino acid sequence of a TRBV5-8 nb is as follows:
MGPRLLF WALLCLLGT GPVEAGVTQ SPTHLIKTRGQQ ATLRC SPI S GHTS VYWYQQ ALGLG LQFLLWYDEGEERNRGNFPPRF S GRQFPNY S SELNVNALELED S AL YLC AS SL (SEQ ID NO: 30).
[0089] In certain embodiments, the svd-TCR fusion protein may comprise an agent of interest or comprise a binding domain for non-covalent association with, or covalent attachment to, an agent of interest, such as a therapeutic or diagnostic agent. For example, but without limitation, a single TCR chain may be fused to an agent of interest, or a single TCR variable domain may be fused to an agent of interest. Without limitation, the svd-TCR fusion may comprise: a diagnostic agent; an anticancer agent; a therapeutic radionuclide; a cytotoxic protein; a marker; a purification tag; an epitope; a ligand; a membrane anchor; or a combination thereof. Non-limiting examples of diagnostic agents or moieties include radioisotopes and other detectable labels. Detectable labels useful for such purposes are well known in the art, and include radioactive isotopes such as 32P, 1251, and 13:1, fluorophores, chemiluminescent agents, and enzymes. Non-limiting examples of cytotoxic proteins comprise toxins such as abrin, ricin, Pseudomonas exotoxin (PE; such as PE35, PE37, PE38, and PE40), diphtheria toxin (DT) and subunits thereof, botulinum toxin ( e.g . botulinum toxin A through F), or modified toxins thereof, or other toxic agents that directly or indirectly inhibit cell growth or kill cells as well as other proteins that once internalized are toxic to the cell. Toxins can be fused to a svd-TCR for use as an immunotoxin. Non-limiting examples of markers comprise GFP (green fluorescent protein), RFP (red fluorescent protein), CAT (chloramphenicol acetyltransferase), luciferase, GAL (beta- galactosidase), GUS (beta- glucuronidase) and the like. Non- limiting examples of purification tags include peptide tags ( e.g . FLAG, V5 and the like), polyhistidine tags, glutathione S-transferase (GST) tags, maltose binding protein (MBP) tags, calmodulin binding peptide tags, intein-chitin binding domains, streptavidin/biotin- based tags, and the like (see, e.g., Kimple et al., Overview of Affinity Tags for Protein Purification. Current protocols in protein science / editorial board, John E Coligan et al. 2013;73:Unit-9.9.doi: 10.1002/0471 140864.ps0909s73). In some embodiments, the svd- TCR may comprise or be fused to additional binding/association domain(s) (e.g. ligands, epitopes and the like). For example, the svd-TCR fusion may comprise bispecific or multispecific elements to recruit immune cells like NK or T-cells to the target cell. There are currently over 60 different bi-specific antibody formats that have been described in the literature (see, e.g., Spiess et al. Mol Immunol. 2015 67(2 Pt A):95-106). Multispecific formats may be generated by adding antibody or TCR VH domains or other binding modalities to these scaffold or engineering in additional binding specificities into an antibody or TCR constant region.
[0090] In embodiments where the svd-TCR is incorporated into a fusion protein, the fusion protein may comprise a svd-TCR and any other protein domain or domains. In some embodiments, for example, but without limitation, the svd-TCR may be incorporated into an Fc-fusion ( i.e . an svd- TCR-Fc) and still retain its binding properties of recognizing specific pMHC complexes. The Fc domain maybe N- or C-terminal to the svd-TCR portion. Among other advantages/uses, the svd-TCR- Fc fusion protein allows for a robust approach to generating soluble MHC/peptide binders. The svd- TCR-Fc may alternatively be membrane bound (e.g. cell surface displayed). In some embodiments, the Fc domain may provide extended half-life and/or ease of purification.
[0091] The svd-TCR may be or may form part of a chimeric antigen receptor (CAR). A CAR is a recombinant fusion protein in which a binding domain, a transmembrane domain and a signaling domain or domains are linked to create a novel receptor. Typically antibody scFvs are used as the binding domain. A CAR may be created from a svd-TCR by linking a single TCR variable domain to transmembrane domain and signaling domain(s) or by linking a single TCR chain to a signaling domain or domains, for example.
Transmembrane Domains
[0092] The disclosure provides polypeptides comprising a transmembrane domain, and an intracellular domain capable of providing a stimulatory signal. In some embodiments, the engineered TCR comprises multiple intracellular domains capable of providing a stimulatory signal.
[0093] A “transmembrane domain”, as used herein, refers to a domain of a protein that spans membrane of the cell. Transmembrane domains typically consist predominantly of non-polar amino acids, and may traverse the lipid bilayer once or several times. Transmembrane domains usually comprise alpha helices, a configuration which maximizes internal hydrogen bonding.
[0094] Transmembrane domains isolated or derived from any source are envisaged as within the scope of the fusion proteins of the disclosure.
[0095] In some embodiments, the transmembrane domain is one that is associated with one of the other domains of the fusion protein, or isolated or derived from the same protein as one of the other domains of the fusion protein. In some embodiments, the transmembrane domain and the second intracellular domain are from the same protein, for example a TCR complex subunit such as TCR alpha, TCR beta, CD3 delta, CD3 epsilon or CD3 gamma. In some embodiments, the extracellular domain (svd-TCR), the transmembrane domain and the second intracellular domain are from the same protein, for example a TCR complex subunit such as TCR alpha, TCR beta, CD3 delta, CD3 epsilon or CD3 gamma. In other embodiments, the extracellular domain (comprising one or more svd- TCRs), the transmembrane domain and the intracellular domain(s) are from different proteins. For example, in some embodiments the engineered svd-TCR comprises a CD28 transmembrane domain with a CD28, 4- IBB and 0)3z intracellular domain.
[0096] The transmembrane domain may be derived either from a natural or from a recombinant source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein.
[0097] In some embodiments, the transmembrane domain is capable of signaling to the intracellular domain(s) whenever the TCR complex has bound to a target. A transmembrane domain of particular use in this invention may include at least the transmembrane region(s) of e.g., the alpha, beta or zeta chain of the TCR, CD3 delta, CD3 epsilon or CD3 gamma, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD 16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137, CD154.
[0098] In some embodiments, the transmembrane domain can be attached to the extracellular region of the fusion protein, e.g., the antigen binding domain of the TCR alpha or beta chain, via a hinge, e.g., a hinge from a human protein. For example, in one embodiment, the hinge can be a human immunoglobulin (Ig) hinge, e.g, an IgG4 hinge, or a CD8a hinge.
[0099] In some embodiments, the hinge is isolated or derived from CD8a or CD28. In some embodiments, the CD8a hinge comprises an amino acid sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of TTTP APRPPTP ARΉ AS QPLSLRPEACRP AAGGAVHTRGLDF ACD (SEQ ID NO: 8). In some embodiments, the CD8a hinge comprises SEQ ID NO: 8. In some embodiments, the CD8a hinge consists essentially of SEQ ID NO: 8. In some embodiments, the CD8a hinge is encoded by a nucleotide sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of:
ACCACGACGCCAGCGCCGCGACCACCAACACCGGCGCCCACCATCGCGTCGCAGCCCC TGTCCCTGCGCCCAGAGGCGTGCCGGCCAGCGGCGGGGGGCGCAGTGCACACGAGGG GGCTGGACTTCGCCTGTGAT (SEQ ID NO: 9). In some embodiments, the CD8a hinge is encoded by SEQ ID NO: 9.
[0100] In some embodiments, the CD28 hinge comprises an amino acid sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of CTIEVMYPPPYLDNEKSNGTHHVKGKHLCPSPLFPGPSKP (SEQ ID NO: 10). In some embodiments, the CD28 hinge comprises or consists essentially of SEQ ID NO: 10. In some embodiments, the CD28 hinge is encoded by a nucleotide sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to a sequence of: TGTACCATTGAAGTTATGTATCCTCCTCCTTACCTAGACAATGAGAAGAGCAATGGAAC CATTATCCATGTGAAAGGGAAACACCTTTGTCCAAGTCCCCTATTTCCCGGACCTTCTA AGCCC (SEQ ID NO: 11). In some embodiments, the CD28 hinge is encoded by SEQ ID NO: 11.
[0101] In some embodiments, the transmembrane comprises a TCR alpha transmembrane domain. In some embodiments, the TCR alpha transmembrane domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: VTGFRILLLKV AGFNLLMTLRLW (SEQ ID NO: 12). In some embodiments, the TCR alpha transmembrane domain comprises, or consists essentially of, SEQ ID NO: 12. In some embodiments, the TCR alpha transmembrane domain is encoded by a sequence of: GTGATTGGGTTCCGAATCCTCCTCCTGAAAGTGGCCGGGTTTAATCTGCTCATGACGCT GCGGCTGTGG (SEQ ID NO: 13).
[0102] In some embodiments, the transmembrane comprises a TCR beta transmembrane domain. In some embodiments, the TCR beta transmembrane domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: TIL YEILLGK ATL Y A VL V S AL VL (SEQ ID NO: 14). In some embodiments, the TCR beta transmembrane domain comprises, or consists essentially of, SEQ ID NO: 14. In some embodiments, the TCR beta transmembrane domain is encoded by a sequence of ACCATCCTCTATGAGATCTTGCTAGGGAAGGCCACCTTGTATGCCGTGCTGGTCAGTGC CCTCGTGCTG (SEQ ID NO: 15).
[0103] In some embodiments, the transmembrane comprises a CD3 zeta transmembrane domain. In some embodiments, the CD3 zeta transmembrane domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: LC YLLDGILFIY GVTLTALFL (SEQ ID NO: 16). In some embodiments, the CD3 zeta transmembrane domain comprises, or consists essentially of, SEQ ID NO: 16.
[0104] A transmembrane domain can include one or more additional amino acids adjacent to the transmembrane region, e.g., one or more amino acid associated with the extracellular region of the protein from which the transmembrane was derived (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to 15 amino acids of the extracellular region) and/or one or more additional amino acids associated with the intracellular region of the protein from which the transmembrane protein is derived (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or up to 15 amino acids of the intracellular region). [0105] In some embodiments, 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, e.g., to minimize interactions with other members of the receptor complex.
[0106] When present, the transmembrane domain may be a natural TCR transmembrane domain, a natural transmembrane domain from a heterologous membrane protein, or an artificial transmembrane domain. The transmembrane domain may be a membrane anchor domain. Without limitation, a natural or artificial transmembrane domain may comprise a hydrophobic a-helix of about 20 amino acids, often with positive charges flanking the transmembrane segment. The transmembrane domain may have one transmembrane segment or more than one transmembrane segment. Prediction of transmembrane domains/segments may be made using publicly available prediction tools (e.g. TMHMM, Krogh et al. Journal of Molecular Biology 2001 ; 305(3):567-580; or TMpred, Hofmann & Stoffel Biol. Chem. Hoppe-Seyler 1993; 347: 166). Non-limiting examples of membrane anchor systems include platelet derived growth factor receptor (PDGFR) transmembrane domain, glycosylphosphatidylinositol (GPI) anchor (added post- translationally to a signal sequence) and the like.
Intracellular Domain
[0107] The disclosure provides fusion proteins comprising an intracellular domain. An “intracellular domain,” as the term is used herein, refers to an intracellular portion of a protein.
[0108] In some embodiments, the intracellular domain comprises one or more domains capable of providing a stimulatory signal to a transmembrane domain. In some embodiments, the intracellular domain comprises a first intracellular domain capable of providing a stimulatory signal and a second intracellular domain capable of providing a stimulatory signal. In other embodiments, the intracellular domain comprises a first, second and third intracellular domain capable of providing a stimulatory signal. The intracellular domains capable of providing a stimulatory signal are selected from the group consisting of a CD28 molecule (CD28) domain, a LCK proto-oncogene, Src family tyrosine kinase (Lck) domain, a TNF receptor superfamily member 9 (4- IBB) domain, a TNF receptor superfamily member 18 (GITR) domain, a CD4 molecule (CD4) domain, a CD8a molecule (CD8a) domain, a FYN proto- oncogene, Src family tyrosine kinase (Fyn) domain, a zeta chain of T cell receptor associated protein kinase 70 (ZAP70) domain, a linker for activation of T cells (LAT) domain, lymphocyte cytosolic protein 2 (SLP76) domain, TCR alpha, TCR beta, CD3 delta, CD3 gamma and CD3 epsilon intracellular domains.
[0109] In some embodiments, an intracellular domain comprises at least one intracellular signaling domain. An intracellular signaling domain generates a signal that promotes a function a cell, for example an immune effector function of a TCR containing cell, e.g., a TCR-expressing T-cell. In some embodiments, the intracellular domain of the fusion proteins of the disclosure includes at least one intracellular signaling domain. For example, the intracellular domains of CD3 gamma, delta or epsilon comprise signaling domains.
[0110] In some embodiments, the extracellular domain, transmembrane domain and intracellular domain are isolated or derived from the same protein, for example T-cell receptor (TCR) alpha, TCR beta, CD3 delta, CD3 gamma or CD3 epsilon.
[0111] Examples of intracellular domains for use in the fusion proteins of the disclosure include the cytoplasmic sequences of the TCR alpha, TCR beta, CD3 zeta, and 4- IBB, and the intracellular signaling co-receptors that act in concert to initiate signal transduction following antigen receptor engagement, as well as any derivative or variant of these sequences and any recombinant sequence that has the same functional capability.
[0112] In some embodiments, the intracellular signaling domain comprises a primary intracellular signaling domain. Exemplary primary intracellular signaling domains include those derived from the proteins responsible for primary stimulation, or antigen dependent stimulation.
[0113] An intracellular signaling domain is generally responsible for activation of at least one of the normal effector functions of the immune cell in which the fusion protein has been introduced. The term “effector function” refers to a specialized function of a cell. Effector function of a T-cell, for example, may be cytolytic activity or helper activity including the secretion of cytokines. Thus the term “intracellular signaling domain” refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function.
[0114] While in some cases the entire intracellular signaling domain can be employed, in many cases it is not necessary to use the entire intracellular signaling domain. To the extent that a truncated portion of the intracellular signaling domain is used, such truncated portion may be used in place of the intact chain as long as it transduces the effector function signal. The term intracellular signaling domain is thus meant to include any truncated portion of the intracellular signaling domain sufficient to transduce the effector function signal.
[0115] In some embodiments, the intracellular domain comprises a CD3 delta intracellular domain. In some embodiments, the CD3 delta intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: GHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNKGGSRSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 17). In some embodiments, the CD3 delta intracellular domain comprises or consists essentially of, SEQ ID NO: 17. In some embodiments, the CD3 delta intracellular domain is encoded by a sequence of
1 ggacatgaga ctggaaggct gtctggggct gccgacacac aagctctgtt gaggaatgac
61 caggtctatc agcccctccg agatcgagat gatgctcagt acagccacct tggaggaaac
121 tgggctcgga acaagggcgg aagcaggagc aagcggagca gactgctgca cagcgactac
181 atgaacatga ccccccggag gcctggcccc acccggaagc actaccagcc ctacgcccct
241 cccagggatt tcgccgccta ccggagcta (SEQ ID NO: 18)
[0116] In some embodiments, the intracellular domain comprises a CD3 epsilon intracellular domain. In some embodiments, the CD3 epsilon intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: KNRKAKAKP VTRGAGAGGRQRGQNKERPPPVPNPD YEPIRKGQRDLY S GLN QRRIGGSRS KRSRLLHSDYMNMTPRRPGPTRKHYQPY APPRDF AA YRS (SEQ ID NO: 19). In some embodiments, the CD3 epsilon intracellular domain comprises or consists essentially of, SEQ ID NO: 19. In some embodiments, the CD3 epsilon intracellular domain is encoded by a sequence of
1 aagaatagaa aggccaaggc caagcctgtg acacgaggag cgggtgctgg cggcaggcaa
61 aggggacaaa acaaggagag gccaccacct gttcccaacc cagactatga gcccatccgg
121 aaaggccagc gggacctgta ttctggcctg aatcagcgca gaatcggcgg aagcaggagc
181 aagcggagca gactgctgca cagcgactac atgaacatga ccccccggag gcctggcccc
241 acccggaagc actaccagcc ctacgcccct cccagggatt tcgccgccta ccggagctag
(SEQ ID NO: 20) [0117] In some embodiments, the intracellular domain comprises a CD3 gamma intracellular domain. In some embodiments, the CD3 gamma intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: GQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLRRNGGSRSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 21). In some embodiments, the CD3 gamma intracellular domain comprises, or consists essentially of, SEQ ID NO: 21. In some embodiments, the CD3 gamma intracellular domain is encoded by a sequence of
1 ggacaggatg gagttcgcca gtcgagagct tcagacaagc agactctgtt gcccaatgac
61 cagctctacc agcccctcaa ggatcgagaa gatgaccagt acagccacct tcaaggaaac
121 cagttgagga ggaatggcgg aagcaggagc aagcggagca gactgctgca cagcgactac
181 atgaacatga ccccccggag gcctggcccc acccggaagc actaccagcc ctacgcccct
241 cccagggatt tcgccgccta ccggagctag (SEQ ID NO: 22).
[0118] In some embodiments, the intracellular domain comprises a CD3 zeta intracellular domain. In some embodiments, the CD3 zeta intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL (SEQ ID NO: 23). In some embodiments, the CD3 zeta intracellular domain comprises, or consists essentially of, SEQ ID NO: 23.
[0119] In some embodiments, the intracellular domain comprises a TCR alpha intracellular domain. In some embodiments, a TCR alpha intracellular domain comprises Ser-Ser. In some embodiments, a TCR alpha intracellular domain is encoded by a sequence of TCCAGC.
[0120] In some embodiments, the intracellular domain comprises a TCR beta intracellular domain. In some embodiments, the TCR beta intracellular domain comprises an amino acid sequence having at least 80% identity, at least 90% identity, or is identical to a sequence of: MAMVKRKDSR (SEQ ID NO: 24). In some embodiments, the TCR beta intracellular domain comprises, or consists essentially of SEQ ID NO: 23. In some embodiments, the TCR beta intracellular domain is encoded by a sequence of ATGGCCATGGTCAAGAGAAAGGATTCCAGA (SEQ ID NO: 25). [0121] In some embodiments, the intracellular signaling domain comprises at least one stimulatory intracellular domain. In some embodiments, the intracellular signaling domain comprises a primary intracellular signaling domain, such as a CD3 delta, CD3 gamma and CD3 epsilon intracellular domain, and one additional stimulatory intracellular domain, for example a co-stimulatory domain. In some embodiments, the intracellular signaling domain comprises a primary intracellular signaling domain, such as a CD3 delta, CD3 gamma and CD3 epsilon intracellular domain, and two additional stimulatory intracellular domains.
[0122] Exemplary co-stimulatory intracellular signaling domains include those derived from proteins responsible for co-stimulatory signals, or antigen independent stimulation.
[0123] The term “co-stimulatory molecule” refers to the cognate binding partner on a T-cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the T-cell, such as, but not limited to, proliferation. Co-stimulatory molecules are cell surface molecules other than antigen receptors. Co-stimulatory molecules and their ligands are required for an efficient immune response. Co-stimulatory molecules include, but are not limited to an MHC class I molecule, BTLA, a Toll ligand receptor, as well as hematopoietic cell signal transducer (DAP10), transmembrane immune signaling adaptor TYROBP (DAP 12), TNF receptor superfamily member 8 (CD30), TNF superfamily member 14 (LIGHT), TNF receptor superfamily member 4 (0X40), CD2 molecule (CD2), CD27 molecule (CD27), CDS, intercellular adhesion molecule 1 (ICAM-1), integrin subunit beta 2 (LFA-1, or CDl la), integrin subunit beta 2 (CD18), 4-1BB (CD137, TNF receptor superfamily member 9), and CD28 molecule (CD28).
[0124] A “co-stimulatory domain”, sometimes referred to as “a co-stimulatory intracellular signaling domain” can be the intracellular portion of a co-stimulatory protein. A co-stimulatory domain can be a domain of a co- stimulatory protein that transduces the co-stimulatory signal. A co-stimulatory protein can be represented in the following protein families: TNF receptor proteins, Immunoglobulin like proteins, cytokine receptors, integrins, signaling lymphocytic activation molecules (SLAM proteins), and activating NK cell receptors. Examples of such molecules include CD27, CD28, 4-1BB (CD 137), 0X40, GITR, CD30, CD40 molecule (CD40), inducible T cell costimulator (ICOS), TNF receptor superfamily member 13C (BAFFR), TNF receptor superfamily member 14 (HVEM), lymphocyte function-associated antigen- 1 (LFA-1), CD2 molecule (CD2), CD7 molecule (CD7), LIGHT, killer cell lectin like receptor C2 (NKG2C), SLAM family member 7 (SLAMF7), killer cell lectin like receptor FI (NKp80), CD160 molecule (CD160), CD276 molecule (B7-H3), a ligand that specifically binds with CD83 molecule (CD83), CD4 molecule (CD4), and the like. The co stimulatory domain can comprise the entire intracellular portion, or the entire native intracellular signaling domain, of the molecule from which it is derived, or a functional fragment thereof.
[0125] In some embodiments, the stimulatory domain comprises a co-stimulatory domain. In some embodiments, the co-stimulatory domain comprises a CD28 or 4-1BB co-stimulatory domain. CD28 and 4- IBB are well characterized co-stimulatory molecules required for full T cell activation and known to enhance T cell effector function. For example, CD28 and 4- IBB have been utilized in chimeric antigen receptors (CARs) to boost cytokine release, cytolytic function, and persistence over the first-generation CAR containing only the CD3 zeta signaling domain. Likewise, inclusion of co stimulatory domains, for example CD28 and 4-1BB domains, in engineered TCR can increase T cell effector function and specifically allow co-stimulation in the absence of co-stimulatory ligand, which is typically down-regulated on the surface of tumor cells.
In some embodiments, the stimulatory domain comprises a CD28 intracellular domain. In some embodiments, the CD28 intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: RSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 26). In some embodiments, the CD28 intracellular domain comprises, or consists essentially of, RSKRSRLLHSD YMNMTPRRPGPTRKHY QP Y APPRDF AA YRS (SEQ ID NO: 26). In some embodiments, a CD28 intracellular domain is encoded by a nucleotide sequence comprising: AGGAGCAAGCGGAGCAGACTGCTGCACAGCGACTACATGAACATGACCCC CCGGAGGCCTGGCCCCACCCGGAAGCACTACCAGCCCTACGCCCCTCCCA GGGATTTCGC CGCCTACCGG AGC (SEQ ID NO: 27).
[0126] In some embodiments, the stimulatory domain comprises a 4- IBB intracellular domain. In some embodiments, the 4- IBB intracellular domain comprises an amino acid sequence having at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity or is identical to a sequence of: KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL (SEQ ID NO: 28). In some embodiments, the 4- IBB intracellular domain comprises, or consists essentially of, KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL (SEQ ID NO: 28). In some embodiments, a 4- IBB intracellular domain is encoded by a nucleotide sequence comprising: AAACGGGGC AGAAAGA AACT CCTGT AT AT ATT C A AAC AACC ATTT AT GAGGCC AGT AC AAACT ACT C A AGAGGAAGATGGCTGTAGCTGCCGATTT CC AGAAGAAGAAGAAGGAG GATGTGAACTG (SEQ ID NO: 29).
Linkers
[0127] In some embodiments, the engineered TCRs described herein comprise two or more antigen binding domains ( e.g ., svd-TCRs). Provided herein are linkers that, in some embodiments, can be used to link the antigen-binding domains described herein.
[0128] The terms “linker” and “flexible polypeptide linker” as used in the context of linking protein domains, for example intracellular domains or domains within an scFv, refers to a peptide linker that consists of amino acids such as glycine and/or serine residues used alone or in combination, to link two domains together. For example, a linker as described herein can be used to link two svd-TCRs together.
[0129] Any linker may be used and many fusion protein linker formats are known. For example, the linker may be flexible or rigid. Non-limiting examples of rigid and flexible linkers are provided in Chen et al. (Adv Drug Deliv Rev. 2013; 65(10):1357-1369).
[0130] The antigen-binding domains described herein may be linked to each other in a random or specified order.
[0131] The antigen-binding domains described herein may be linked to each other in any orientation of N to C terminus.
[0132] Optionally, a short oligo- or polypeptide linker, for example, between 2 and 40 amino acids (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids) in length may form the linkage between the domains. [0133] In some embodiments, the linker is a peptide of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more than 30 amino acid residues. Non limiting examples of amino acids found in linkers include Gly, Ser, Glu, Gin, Ala, Leu, Iso, Lys, Arg, Pro, and the like. In some embodiments, the linker is [(Gly)nlSer]n2, where nl and n2 may be any number ( e.g . nl and n2 may independently be 1, 2, 4, 5, 6, 7, 8, 9, 10 or more than 10). In some embodiments, nl is 4.
[0134] In some embodiments, the flexible polypeptide linker is a Gly/Ser linker and comprises the amino acid sequence (Gly-Gly-Ser), (Gly-Gly-Gly-Ser) (SEQ ID NO: 32), or (Gly-Gly-Gly-Gly-Ser) (SEQ ID NO: 33) which can be repeated n times, where n is a positive integer equal to or greater than 1. For example, n=l, n=2, n=3, n=4, n=5, n=6, n=7, n=8, n=9 and n=10. In some embodiments, the flexible polypeptide linkers include, but are not limited to, GGS, GGGS (SEQ ID NO: 32), GGGGS (SEQ ID NO: 33), or GGGGS GG (SEQ ID NO: 31).
[0135] In some embodiments, the linkers include multiple repeats of (Gly Ser), (Gly Ser) or (Gly Ser). Also included within the scope of the invention are linkers described in WO2012/138475 (incorporated herein by reference).
[0136] In some embodiments, the linker sequence comprises a long linker (LL) sequence. In some embodiments, the long linker sequence comprises GGGGS (SEQ ID NO: 33), repeated four times. In some embodiments, a GGGGS (SEQ ID NO: 33) is used to link intracellular domains in a TCR alpha fusion protein of the disclosure.
[0137] In some embodiments, the long linker sequence comprises GGGGS (SEQ ID NO: 33), repeated three times. In some embodiments, a GGGGS (SEQ ID NO: 33) is used to link intracellular domains in a TCR beta fusion protein of the disclosure.
[0138] In some embodiments, the linker sequence comprises a short linker (SL) sequence. In some embodiments, the short linker sequence comprises GGGGS (SEQ ID NO: 33).
[0139] In some embodiments, a glycine-serine doublet can be used as a suitable linker.
[0140] In some embodiments, domains are fused directly to each other via peptide bonds without use of a linker.
Antigens
[0141] The disclosure described engineered TCRs, comprising one or more variable domains capable of recognizing an antigen.
[0142] The term “antigen” refers to a molecule that is capable of being bound specifically by an antibody, or being presented by a major histocompatibility complex and bound by a TCR, or otherwise provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both.
[0143] The antigen (or antigen of interest) which is specifically bound by the TCR variable domain of the svd-TCR may be any antigen. The antigen may be a self antigen or a non-self antigen. The antigen may be a conformational antigen or a linear antigen. Non-limiting examples of the antigen include viral proteins or peptides, bacterial proteins or peptides, cancer-specific antigens, receptor extracellular domains, an epitope, a receptor binding protein, a receptor binding peptide, or any other peptide, polypeptide or protein antigen.
[0144] In some embodiments, an antigen recognized by an engineered TCR of the disclosure is bound by a major histocompatibility complex (MHC). As used herein, “MHC” refers to a protein complex that binds to antigens and displays them on the cell surface for recognition by the appropriate T cell ( e.g ., via a TCR). Peptides are processed and presented by cells using two pathways, the MHC class I and MHC class II pathways, both of which are envisaged as within the scope of the disclosure. In MHC class II, phagocytes such as macrophages and immature dendritic cells take up exogenous material (e.g., pathogens, proteins) by phagocytosis into phagosomes or endosomes, which fuse with lysosomes whose acidic enzymes cleave the exogenous material protein into peptides. These peptides are loaded onto MHC class II molecules, which are trafficked to the cell surface and presented to immune cells. In MHC class I, nucleated cells present cytosolic peptides. These cytosolic peptides are mostly self peptides derived from protein turnover and defective ribosomal products. However, during infection with intracellular localization (e.g. by a virus or other microorganism), or a cancerous transformation, the proteins degraded in the proteasome include proteins from the infectious organism or cancer, and are also loaded onto MHC class I molecules and displayed on the cell surface. Thus, in some conditions Class I MHC can display cancer and non-self antigens.
[0145] In some embodiments, an engineered TCR of the disclosure recognizes a peptide antigen bound to MHC (pMHC), for example MHC class I or MHC class II.
[0146] In some embodiments, an engineered TCR of the disclosure recognizes an antigen that is not bound to MHC. For example, engineered TCRs whose antigen binding domain is derived from an ScFv, or VHH antigen binding domain can bind antigens that are not presented by MHC. [0147] In some embodiments, the antigen is a non-self antigen, for example an antigen from a virus, bacteria, fungus or eukaryotic pathogen.
[0148] In some embodiments, the antigen is a self-antigen, for example a protein with a particular tissue-specific expression pattern.
[0149] In some embodiments, an engineered TCR of the disclosure recognizes a peptide antigen bound to MHC (pMHC). In some embodiments, the pMHC comprises a cancer antigen. In some embodiments, the pMHC comprises a neoantigen. As used herein, a “neoantigen” refers to an antigen not previously recognized by the immune system. Neoantigens can arise from altered tumor proteins, or from viral proteins, for example. In some embodiments, the neoantigen comprises KRAS proto oncogene, GTPase (KRAS) G12D, KRAS G12V, p53 or a variant of phosphoinositide 3 kinase alpha (PI3K alpha). In some embodiments, the antigen comprises a viral antigen, such as a human papillomavirus (HPV) antigen. In some embodiments, the antigen comprises a testes or fetal antigen. [0150] In some embodiments, the pMHC comprises a cancer antigen. In some embodiments, the cancer antigen comprises CD19 molecule (CD19); interleukin 3 receptor subunit alpha (CD123); CD22 molecule (CD22); TNF receptor superfamily member 8 (CD30); LI cell adhesion molecule (CD171); CS-1 (also referred to as CD2 subset 1, CRACC, SLAMF7, CD319, and 19A24); C-type lectin-like molecule-1 (CLL-1 or CLECL1); CD33 molecule (CD33); epidermal growth factor receptor variant III (EGFRvIII); ganglioside G2 (GD2); ganglioside GD3 (aNeu5Ac(2-8)aNeu5Ac(2- 3)bDGalp(l-4)bDGlcp(l-l)Cer); TNF receptor family member B cell maturation (BCMA); Tn antigen ((Tn Ag) or (GalNAca-Ser/Thr)); prostate-specific membrane antigen (PSMA); Receptor tyrosine kinase-like orphan receptor 1 (ROR1); Fms-Like Tyrosine Kinase 3 (FLT3); Tumor- associated glycoprotein 72 (TAG72); CD38 molecule (CD38); CD44v6; Carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276 molecule); KIT proto-oncogene, receptor tyrosine kinase (KIT, or CD 117); Interleukin- 13 receptor subunit alpha-2 (IL-13Ra2 or CD213A2); Mesothelin; Interleukin 11 receptor alpha (IL-1 IRa); prostate stem cell antigen (PSCA); Protease Serine 21 (Testisin or PRSS21); vascular endothelial growth factor receptor 2 (VEGFR2); Lewis(Y) antigen; CD24 molecule (CD24); Platelet-derived growth factor receptor beta (PDGFR- beta); Stage-specific embryonic antigen-4 (SSEA-4); membrane spanning 4-domains A1 (CD20); Folate receptor alpha; Receptor tyrosine-protein kinase ERBB2 (Her2/neu); Mucin 1, cell surface associated (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); Prostase; prostatic acid phosphatase (PAP); elongation factor 2 mutated (ELF2M); Ephrin B2; fibroblast activation protein alpha (FAP); insulin-like growth factor 1 receptor (IGF-I receptor), carbonic anhydrase IX (CAIX); Proteasome (Prosome, Macropain) Subunit, Beta Type, 9 (LMP2); glycoprotein 100 (gplOO); oncogene fusion protein consisting of breakpoint cluster region (BCR) and Abelson murine leukemia viral oncogene homolog 1 (Abl) (bcr-abl); tyrosinase; ephrin type-A receptor 2 (EphA2); Fucosyl GM1; sialyl Lewis adhesion molecule (sLe); gangboside GM3 (aNeu5Ac(2-3)bDG alp(l-4)bDGlcp(l-l)Cer); transglutaminase 5 (TGS5); high molecular weight- melanoma-associated antigen (HMWMAA); o-acetyl-GD2 gangboside (OAcGD2); Folate receptor beta; tumor endothelial marker 1 (TEM1/CD248); tumor endothelial marker 7-related (TEM7R); claudin 6 (CLDN6); thyroid stimulating hormone receptor (TSHR); G protein-coupled receptor class C group 5, member D (GPRC5D); chromosome X open reading frame 61 (CXORF61); adhesion G protein- coupled receptor E5 (CD97); V-set pre-B cell surrogate light chain 1 (CD179a); anaplastic lymphoma kinase (ALK); Polysialic acid; placenta-specific 1 (PLAC1); hexasaccharide portion of globoH glycoceramide (GloboH); mammary gland differentiation antigen (NY-BR-1); uroplakin 2 (UPK2); Hepatitis A virus cellular receptor 1 (HAVCR1); adrenoceptor beta 3 (ADRB3); pannexin 3 (PANX3); G protein-coupled receptor 20 (GPR20); lymphocyte antigen 6 complex, locus K 9 (LY6K); Olfactory receptor 51E2 (OR51E2); TCR Gamma Alternate Reading Frame Protein (TARP); Wilms tumor protein (WT1); Cancer/testis antigen 1 (NY-ESO-1); Cancer/testis antigen 2 (LAGE-la); Melanoma-associated antigen 1 (MAGE-A1); Melanoma-associated antigen 3 (MAGE- A3); ETS translocation-variant gene 6, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); X Antigen Family, Member 1 A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); melanoma cancer testis antigen-1 (MAD-CT-1); melanoma cancer testis antigen-2 (MAD-CT-2); Fos-related antigen 1; tumor protein p53 (p53); p53 mutant; prostein; survivin; telomerase; prostate carcinoma tumor antigen- 1 (PCTA-1 or Galectin 8), melanoma antigen recognized by T cells 1 (MelanA or MARTI); Rat sarcoma (Ras) mutant; human Telomerase reverse transcriptase (hTERT); sarcoma translocation breakpoints; melanoma inhibitor of apoptosis (ML-IAP); ERG (transmembrane protease, serine 2 (TMPRSS2) ETS fusion gene); N-Acetyl glucosaminyl-transferase V (NA17); paired box protein Pax-3 (PAX3); Androgen receptor; Cyclin Bl; v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN); Ras Homolog Family Member C (RhoC); Tyrosinase-related protein 2 (TRP-2); Cytochrome P450 1B1 (CYP1B1); CCCTC-Binding Factor (Zinc Finger Protein)-Like (BORIS or Brother of the Regulator of Imprinted Sites), Squamous Cell Carcinoma Antigen Recognized By T Cells 3 (SART3); Paired box protein Pax-5 (PAX5); proacrosin binding protein sp32 (OY-TES1); lymphocyte-specific protein tyrosine kinase (LCK); A kinase anchor protein 4 (AKAP-4); synovial sarcoma, X breakpoint 2 (SSX2); Receptor for Advanced Gly cation Endproducts (RAGE-1); renal ubiquitous 1 (RU1); renal ubiquitous 2 (RU2); legumain; human papilloma virus E6 (HPV E6); human papilloma virus E7 (HPV E7); intestinal carboxyl esterase; heat shock protein 70-2 mutated (mut hsp70-2); CD79a; CD79b; CD72; Leukocyte- associated immunoglobulin-like receptor 1 (LAIR1); Fc fragment of IgA receptor (FCAR or CD89); Leukocyte immunoglobulin-like receptor subfamily A member 2 (LILRA2); CD300 molecule-like family member f (CD300LF); C-type lectin domain family 12 member A (CLEC12A); bone marrow stromal cell antigen 2 (BST2); EGF-like module-containing mucin-like hormone receptor-like 2 (EMR2); lymphocyte antigen 75 (LY75); Glypican-3 (GPC3); Fc receptor-like 5 (FCRL5); or immunoglobulin lambda-like polypeptide 1 (IGLL1).
[0151] In some embodiments, the engineered TCR comprises an antigen binding domain that has a binding affinity KD of 10_4 M to 10_9M, e.g., 10_5 M to 10_7 M, e.g., 10_6 M or 10_7 M, for its target antigen. The binding affinity of an antigen binding domain for an antigen can be determined by methods known in the art, e.g. by ELISA or surface plasmon resonance.
[0152] In some embodiments, the antigen is a peptide bound in MHC to form a pMHC. The MHC in the pMHC may be any MHC class. For example, the MHC may be MHC class I or may be MHC class II. The peptide in the pMHC may be any length that will bind in the binding groove of the MHC. For example, the peptide may be 2 to 100 or more amino acids long, including a peptide of 2, 3, 4, 5, 6, ,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 54, 56, 68, 60, 62, 64, 66, 68, 70, 75, 80, 85, 90, 95, 100 amino acids. The peptide may be about 8-30 amino acids long. The peptide maybe about 8-10 amino acids long. The peptide in the pMHC may be any sequence that binds in the binding groove of the MHC. The peptides are non-covalently held in the binding groove in an extended configuration but some peptides may have portions which dangle outside the binding groove. In a non-limiting example, the peptide may have the amino acid sequence SLLMWITQC (SEQ ID NO: 34, a publicly known sequence).
Assays
[0153] Provided herein are assays that can be used to measure the activity of the engineered TCRs of the disclosure.
[0154] The activity of chimeric or engineered TCRs can be assayed using a cell line engineered to express a reporter of TCR activity such as a luciferase reporter. Exemplary cell lines include Jurkat T cells, although any suitable cell line known in the art may be used. For example, Jurkat cells expressing a luciferase reporter under the control of an NFAT promoter can be used as effector cells. Expression of luciferase by this cell line reflects TCR-mediated signaling.
[0155] The reporter cells can be transfected with each of the various fusion protein constructs, combinations of fusion protein constructs or controls described herein.
[0156] Expression of the fusion proteins in reporter cells can be confirmed by using fluorescently labeled MHC tetramers, for example Alexa Fluor 647-labeled NY-ESO-l-MHC tetramer, to detect expression of the fusion protein.
[0157] To assay the activity of engineered TCRs, target cells are loaded with antigen prior to exposure to the effector cells comprising the reporter and the engineered TCR. For example, target cells can be loaded with antigen at least 12, 14, 16, 18, 20, 22 or 24 hours prior to exposure to effector cells. Exemplary target cells include A375 cells, although any suitable cells known in the art may be used. In some cases, target cells can be loaded with serially diluted concentrations of an antigen, such as NY-ESO-1 peptide. The effector cells can then be co-cultured with target cells for a suitable period of time, for example 6 hours. Luciferase is then measured by luminescence reading after co-culture. Luciferase luminescence can be normalized to maximum and minimum intensity to allow comparison of activating peptide concentrations for each TCR construct.
[0158] Provided herein are methods of determining the relative EC50 of engineered TCRs of the disclosure. As used herein, “EC50” refers to the concentration of an inhibitor or agent where the response (or binding) is reduced by half. EC50s of engineered TCRs of the disclosure refer to concentration of antigen where binding of the engineered TCR to the antigen is reduced by half. Binding of the antigen, or probe to the TCR can be measured by staining with labeled peptide or labeled peptide-MHC complex, for example MHC:NY-ESO-l pMHC complex conjugated with fluorophore. EC50 can be obtained by nonlinear regression curve fitting of reporter signal with peptide titration. Probe binding and EC50 can be normalized to the levels of benchmark TCR without a fusion protein, e.g. NY-ESO-1 (clone 1G4).
[0159] In some embodiments, an engineered TCR comprising a fusion protein has a relative EC50 of greater than or equal to 0.2, 0.3, 0.4, 0.5, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.8, 1.9 or 2.0 relative to a TCR that does not comprise a fusion protein.
[0160] In some embodiments, an engineered TCR comprising a fusion protein has a relative EC50 of about 0.2-2.0, about 0.5-2.0, about 0.9-2.0, about 1.0-2.0, about 1.1-2.0, about 1.2-2.0, about 0.9-1.7, about 1.0- 1.7, or about 1.2- 1.7 relative to a TCR that does not comprise a fusion protein
Polynucleotides
[0161] The disclosure provides polynucleotides encoding the sequence of the engineered TCR described herein.
[0162] The disclosure provides at least one nucleic acid encoding the svd-TCR as defined herein. The at least one nucleic acid may be a vector. The vector may be an expression vector. The at least one nucleic acid may comprise an expression cassette comprising a sequence encoding the svd-TCR and further comprising a promoter and terminator in operative association with the sequence encoding the svd-TCR for expression of the svd- TCR. Non-limiting examples of promoters which may be suitable include, but are not limited to CMV, SV40, El a, viral LTRs, heat shock promoters, viral and chimeric promoters, tetracycline or other inducible promoters. Non-limiting examples of terminators which may be suitable include, but are not limited to SV40 poly (A), bovine growth hormone poly(A) or synthetic poly (A) sequences.
[0163] In some embodiments, the nucleic acid is in operative association with a promoter and terminator for expression of the svd-TCR. Non-limiting examples of mammalian promoters which may be suitable include, but are not limited to CMV, SV40, El a, viral LTRs, heat shock promoters, viral and chimeric promoters, tetracycline or other inducible promoters. Non-limiting examples of terminators which may be suitable include, but are not limited to SV40 poly (A), bovine growth hormone poly(A) or synthetic poly (A) sequences. [0164] Vectors derived from retroviruses such as the lentivirus are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene and its propagation in daughter cells. Lentiviral vectors have the added advantage over vectors derived from onco- retroviruses such as murine leukemia viruses in that they can transduce non-proliferating cells, such as hepatocytes. They also have the added advantage of low immunogenicity.
[0165] The expression of natural or synthetic nucleic acids encoding engineered TCR is typically achieved by operably linking a nucleic acid encoding the engineered TCR or portions thereof to a promoter, and incorporating the construct into an expression vector. The vectors can be suitable for replication and integration eukaryotes. Typical cloning vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence.
[0166] The polynucleotides encoding the engineered TCR can be cloned into a number of types of vectors. For example, the polynucleotides can be cloned into a vector including, but not limited to a plasmid, a phagemid, a phage derivative, an animal virus, and a cosmid. Vectors of particular interest include expression vectors, replication vectors, probe generation vectors, and sequencing vectors. [0167] Further, the expression vector may be provided to cells, such as immune cells, in the form of a viral vector. Viral vector technology is well known in the art and is described, for example, in Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York), and in other virology and molecular biology manuals. Viruses, which are useful as vectors include, but are not limited to, retroviruses, adenoviruses, adeno-associated viruses, herpes viruses, and lentiviruses. In general, a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers, (e.g., WO 01/96584; WO 01/29058; and U.S. Pat. No. 6,326,193).
[0168] A number of viral based systems have been developed for gene transfer into mammalian cells. For example, retroviruses provide a convenient platform for gene delivery systems. A selected gene can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant virus can then be isolated and delivered to cells of the subject either in vivo or ex vivo. A number of retroviral systems are known in the art. In some embodiments, adenovirus vectors are used. A number of adenovirus vectors are known in the art. In one embodiment, lentivirus vectors are used.
[0169] Additional promoter elements, e.g., enhancers, regulate the frequency of transcriptional initiation. Typically, these are located in the region 30-110 basepairs (bp) upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well. The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the thymidine kinase (tk) promoter, the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline. Depending on the promoter, it appears that individual elements can function either cooperatively or independently to activate transcription.
[0170] One example of a suitable promoter is the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto. Another example of a suitable promoter is Elongation Growth Factor-la (EF-la). However, other constitutive promoter sequences may also be used, including, but not limited to the simian virus 40 (SV40) early promoter, mouse mammary tumor virus (MMTV), human immunodeficiency virus (HIV) long terminal repeat (LTR) promoter, MoMuLV promoter, an avian leukemia virus promoter, an Epstein-Barr virus immediate early promoter, a Rous sarcoma virus promoter, as well as human gene promoters such as, but not limited to, the actin promoter, the myosin promoter, the hemoglobin promoter, and the creatine kinase promoter. Further, the invention should not be limited to the use of constitutive promoters. Inducible promoters are also contemplated as part of the invention. The use of an inducible promoter provides a molecular switch capable of turning on expression of the polynucleotide sequence which it is operatively linked when such expression is desired, or turning off the expression when expression is not desired. Examples of inducible promoters include, but are not limited to a metallothionine promoter, a glucocorticoid promoter, a progesterone promoter, and a tetracycline promoter.
[0171] In order to assess the expression of a fusion protein, the expression vector to be introduced into a cell can also contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of expressing cells from the population of cells sought to be transfected or infected through viral vectors. In other aspects, the selectable marker may be carried on a separate piece of DNA and used in a co-transfection procedure. Both selectable markers and reporter genes may be flanked with appropriate regulatory sequences to enable expression in the host cells. Useful selectable markers include, for example, antibiotic-resistance genes, such as neo and the like.
[0172] Reporter genes are used for identifying potentially transfected or transduced cells and for evaluating the functionality of regulatory sequences. In general, a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells. Suitable reporter genes may include genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et al, 2000 FEBS Letters 479: 79-82). Suitable expression systems are well known and may be prepared using known techniques or obtained commercially. In general, the construct with the minimal 5' flanking region showing the highest level of expression of reporter gene is identified as the promoter. Such promoter regions may be linked to a reporter gene and used to evaluate agents for the ability to modulate promoter-driven transcription.
[0173] Methods of introducing and expressing genes into a cell are known in the art. In the context of an expression vector, the vector can be readily introduced into a host cell, e.g., mammalian, bacterial, yeast, or insect cell by any method in the art. For example, the expression vector can be transferred into a host cell by physical, chemical, or biological means.
[0174] 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.
[0175] 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.
[0176] 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).
[0177] Regardless of the method used to introduce exogenous nucleic acids into a host cell or otherwise expose a cell to the inhibitor of the present invention, 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 (ELIS As and Western blots) or by assays described herein to identify agents falling within the scope of the invention.
Cells
[0178] Provided herein are cells comprising the polynucleotides, vectors, fusion proteins and engineered TCRs described herein.
[0179] As described herein, a cell may be an immune cell involved in the innate or adaptive (acquired) immune system. Exemplary innate immune cells include phagocytic cells such as neutrophils, monocytes and macrophages, Natural Killer (NK) cells, polymophonuclear leukocytes such as neutrophils eosinophils and basophils and mononuclear cells such as monocytes, macrophages and mast cells. Immune cells with roles in acquired immunity include lymphocytes such as T-cells and B- cells.
[0180] As used herein, a “T-cell” refers to a type of lymphocyte that originates from a bone marrow precursor that develops in the thymus gland. There are several distinct types of T-cells which develop upon migration to the thymus, which include, helper CD4+ T-cells, cytotoxic CD8+ T cells, memory T cells, regulatory CD4+ T-cells and stem memory T-cells. Different types of T-cells can be distinguished by the ordinarily skilled artisan based on their expression of markers. Methods of distinguishing between T-cell types will be readily apparent to the ordinarily skilled artisan. [0181] In some embodiments, the engineered immune cell comprising the TCR of the disclosure is a T cell. In some embodiments, the T cell is an effector T cell or a regulatory T cell.
[0182] Methods transforming populations of immune cells, such as T cells, with the vectors of the instant disclosure will be readily apparent to the person of ordinary skill in the art. For example, CD3+ T cells can be isolated from PBMCs using a CD3+ T cell negative isolation kit (Miltenyi), according to manufacturer’s instructions. T cells can be cultured at a density of 1 x 10L6 cells/mL in X-Vivo 15 media supplemented with 5% human A/B serum and 1% Pen/strep in the presence of CD3/28 Dynabeads (1:1 cell to bead ratio) and 300 Units/mL of IL-2 (Miltenyi). After 2 days, T cells can be transduced with viral vectors, such as lentiviral vectors using methods known in the art. In some embodiments, the viral vector is transduced at a multiplicity of infection (MOI) of 5. Cells can then be cultured in IL-2 or other cytokines such as combinations of IL-7/15/21 for an additional 5 days prior to enrichment. Methods of isolating and culturing other populations of immune cells, such as B cells, or other populations of T cells, will be readily apparent to the person of ordinary skill in the art. Although this method outlines a potential approach, it should be noted that these methodologies are rapidly evolving. For example excellent viral transduction of peripheral blood mononuclear cells can be achieved after 5 days of growth to generate a >99% CD3+ highly transduced cell population. [0183] Methods of activating and culturing populations of T cells comprising the engineered TCRs, fusion proteins or vectors encoding the fusion proteins of the instant disclosure, will be readily apparent to the person of ordinary skill in the art.
[0184] Whether prior to or after genetic modification of T cells to express an engineered TCR, the T cells can be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575;
7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041, 10040846; and U.S. Pat. Appl. Pub. No. 2006/0121005.
[0185] In some embodiments, T cells of the instant disclosure are expanded and activated in vitro. Generally, the T cells of the instant disclosure are expanded in vitro by contact with a surface having attached thereto an agent that stimulates a CD3/TCR complex associated signal and a ligand that stimulates a co-stimulatory molecule on the surface of the T cells. In particular, T cell populations may be stimulated as described herein, such as by contact with an anti-CD3 antibody. For co- stimulation of an accessory molecule on the surface of the T cells, a ligand that binds the accessory molecule is used. For example, a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells. To stimulate proliferation of either CD4+ T cells or CD8+ T cells, an anti-CD3 antibody and an anti- CD28 antibody can be used. Examples of an anti-CD28 antibody include 9.3, B-T3, XR-CD28 (Diaclone, Besan9on, France) can be used as can other methods commonly known in the art (Berg et al, Transplant Proc. 30(8):3975-3977, 1998; Haanen et al, J. Exp. Med. 190(9):13191328, 1999; Garland et al., J. Immunol Meth. 227(1 -2): 53-63, 1999).
[0186] In some embodiments, the primary stimulatory signal and the co-stimulatory signal for the T cell may be provided by different protocols. For example, the agents providing each signal may be in solution or coupled to a surface. When coupled to a surface, the agents may be coupled to the same surface (i.e., in “cis” formation) or to separate surfaces (i.e., in “trans” formation). Alternatively, one agent may be coupled to a surface and the other agent in solution. In some embodiments, the agent providing the co-stimulatory signal is bound to a cell surface and the agent providing the primary activation signal is in solution or coupled to a surface. In certain embodiments, both agents can be in solution. In another embodiment, the agents may be in soluble form, and then cross-linked to a surface, such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents. In this regard, see for example, U.S. Patent Application Publication Nos. 20040101519 and 20060034810 for artificial antigen presenting cells (aAPCs) that are contemplated for use in activating and expanding T cells in the present invention.
[0187] In some embodiments, the two agents are immobilized on beads, either on the same bead, i.e., “cis,” or to separate beads, i.e., “trans.” Byway of example, the agent providing the primary activation signal is an anti-CD3 antibody or an antigen-binding fragment thereof and the agent providing the co stimulatory signal is an anti-CD28 antibody or antigen-binding fragment thereof; and both agents are co-immobilized to the same bead in equivalent molecular amounts. In one embodiment, a 1 : 1 ratio of each antibody bound to the beads for CD4+ T cell expansion and T cell growth is used. In some embodiments, the ratio of CD3:CD28 antibody bound to the beads ranges from 100: 1 to 1 : 100 and all integer values there between. In one aspect of the present invention, more anti-CD28 antibody is bound to the particles than anti-CD3 antibody, i.e., the ratio of CD3:CD28 is less than one. In certain embodiments of the invention, the ratio of anti CD28 antibody to anti CD3 antibody bound to the beads is greater than 2: 1.
[0188] Ratios of particles to cells from 1 :500 to 500: 1 and any integer values in between may be used to stimulate T cells or other target cells. As those of ordinary skill in the art can readily appreciate, the ratio of particles to cells may depend on particle size relative to the target cell. For example, small sized beads could only bind a few cells, while larger beads could bind many. In certain embodiments the ratio of cells to particles ranges from 1:100 to 100:1 and any integer values in-between and in further embodiments the ratio comprises 1:9 to 9:1 and any integer values in between, can also be used to stimulate T cells. In some embodiments, a ratio of 1 : 1 cells to beads is used. One of skill in the art will appreciate that a variety of other ratios may be suitable for use in the present invention. In particular, ratios will vary depending on particle size and on cell size and type.
[0189] In further embodiments of the present invention, the cells, such as T cells, are combined with agent-coated beads, the beads and the cells are subsequently separated, and then the cells are cultured. In an alternative embodiment, prior to culture, the agent-coated beads and cells are not separated but are cultured together. In a further embodiment, the beads and cells are first concentrated by application of a force, such as a magnetic force, resulting in increased ligation of cell surface markers, thereby inducing cell stimulation.
[0190] By way of example, cell surface proteins may be ligated by allowing paramagnetic beads to which anti-CD3 and anti-CD28 are attached to contact the T cells. In one embodiment the cells (for example, CD4+ T cells) and beads (for example, DYNABEADS CD3/CD28 T paramagnetic beads at a ratio of 1:1) are combined in a buffer. Again, those of ordinary skill in the art can readily appreciate any cell concentration may be used. In certain embodiments, it may be desirable to significantly decrease the volume in which particles and cells are mixed together (i.e., increase the concentration of cells), to ensure maximum contact of cells and particles. For example, in one embodiment, a concentration of about 2 billion cells/ml is used. In another embodiment, greater than 100 million cells/ml is used. In a further embodiment, a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/ml is used. In yet another embodiment, a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/ml is used. In further embodiments, concentrations of 125 or 150 million cells/ml can be used. In some embodiments, cells that are cultured at a density of lxl 06 cells/mL are used.
[0191] In some embodiments, the mixture may be cultured for several hours (about 3 hours) to about 14 days or any hourly integer value in between. In another embodiment, the beads and T cells are cultured together for 2-3 days. Conditions appropriate for T cell culture include an appropriate media ( e.g ., Minimal Essential Media or RPMI Media 1640 or, X-vivo 15, (Lonza)) that may contain factors necessary for proliferation and viability, including serum (e.g., fetal bovine or human serum), interleukin-2 (IL-2), insulin, IFN-g, IL-4, IL-7, GM-CSF, IF- 10, IF- 12, IF- 15, TGFP, and TNF-a or any other additives for the growth of cells known to the skilled artisan. Other additives for the growth of cells include, but are not limited to, surfactant, plasmanate, and reducing agents such as N-acetyl- cysteine and 2-mercaptoethanol. Media can include RPMI 1640, AIM-V, DMEM, MEM, a-MEM, F-12, X-Vivo 15, and X-Vivo 20, Optimizer, with added amino acids, sodium pyruvate, and vitamins, either serum-free or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones, and/or an amount of cytokine(s) sufficient for the growth and expansion of T cells. In some embodiments, the media comprises X-VIVO- 15 media supplemented with 5% human A/B serum, 1% penicillin/streptomycin (pen/strep) and 300 Units/ml of IF-2 (Miltenyi).
[0192] The T cells are maintained under conditions necessary to support growth, for example, an appropriate temperature (e.g., 37° C.) and atmosphere (e.g., air plus 5% C02).
[0193] In some embodiments, the T cells comprising engineered TCRs of the disclosure are autologous. Prior to expansion and genetic modification, a source of T cells is obtained from a subject. Immune cells such as T cells can be obtained from a number of sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors. In certain embodiments of the present invention, any number of T cell lines available in the art, may be used. In certain embodiments of the present invention, T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled artisan, such as Ficoll™ separation.
[0194] In some embodiments, cells from the circulating blood of an individual are obtained by apheresis. The apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets. In some embodiments, the cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps. In some embodiments, the cells are washed with phosphate buffered saline (PBS). In alternative embodiments, the wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations. As those of ordinary skill in the art would readily appreciate a washing step may be accomplished by methods known to those in the art, such as by using a semi-automated “flow-through” centrifuge (for example, the Cobe 2991 cell processor, the Baxter CytoMate, or the Haemonetics Cell Saver 5) according to the manufacturer’s instructions. After washing, the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca2+-free, Mg2+-free PBS, PlasmaLyte A, or other saline solution with or without buffer. Alternatively, the undesirable components of the apheresis sample may be removed and the cells directly resuspended in culture media.
[0195] In some embodiments, immune cells such as T cells are isolated from peripheral blood lymphocytes by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLL™ gradient or by counterflow centrifugal elutriation. Specific subpopulations of immune cells, such as T cells, B cells, or CD4+ T cells can be further isolated by positive or negative selection techniques. For example, in one embodiment, T cells are isolated by incubation with anti- CD4 -conjugated beads, for a time period sufficient for positive selection of the desired T cells. [0196] Enrichment of an immune cell population, such as a T cell population, by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells. One method is cell sorting and/or selection via negative magnetic immune- adherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected. For example, to enrich for CD4+ cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD 14, CD20, CD lib, CD 16, HLA-DR, and CD8.
[0197] For isolation of a desired population of immune cells by positive or negative selection, the concentration of cells and surface ( e.g . , particles such as beads) can be varied. In certain embodiments, it may be desirable to significantly decrease the volume in which beads and cells are mixed together (i.e., increase the concentration of cells), to ensure maximum contact of cells and beads. [0198] In some embodiments, the cells may be incubated on a rotator for varying lengths of time at varying speeds at either 2-10° C or at room temperature.
[0199] T cells for stimulation, or PBMCs from which immune cells such as T cells are isolated, can also be frozen after a washing step. Wishing not to be bound by theory, the freeze and subsequent thaw step provides a more uniform product by removing granulocytes and to some extent monocytes in the cell population. After the washing step that removes plasma and platelets, the cells may be suspended in a freezing solution. While many freezing solutions and parameters are known in the art and will be useful in this context, one method involves using PBS containing 20% DMSO and 8% human serum albumin, or culture media containing 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin and 7.5% DMSO, or 31.25% Plasmalyte-A, 31.25% Dextrose 5%, 0.45% NaCl, 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin, and 7.5% DMSO or other suitable cell freezing media containing for example, Hespan and PlasmaLyte A, the cells then are frozen to -80° C. at a rate of 1 ° per minute and stored in the vapor phase of a liquid nitrogen storage tank. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at -20° C. or in liquid nitrogen.
Pharmaceutical Compositions
[0200] The disclosure provides pharmaceutical compositions comprising immune cells comprising the polypeptides of the disclosure and a pharmaceutically acceptable diluent, carrier or excipient. [0201] Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; and preservatives.
Methods of Use
[0202] Certain embodiments relate to use of the svd-TCR or the compositions disclosed herein for targeting a cell which externally presents an antigen of interest. Similarly, certain embodiments relate to a method of targeting a cell which externally presents an antigen of interest ( e.g . a pMHC), comprising contacting the cell with the svd-TCR or a composition as disclosed herein. Any cell which expresses the epitope on its cell surface may be targeted, including, for example, cancer cells, autoreactive immune cells, or the like. For example, the target cell expresses an antigen, and the engineered TCR comprises an antigen binding domain that binds to the antigen expressed by the target cell. In some embodiments, the T cell exhibits a cytolytic effect on the target cell at an EC50 of less than 10 1, 102, or 103 mM peptide antigen. In some embodiments, the T cell exhibits a cytolytic effect when the target cell expresses a sparse antigen recognized by the engineered TCR.
[0203] The targeting may be for diagnostic purposes, screening purposes, therapeutic purposes, or any other purpose. In a non-limiting example, svd-TCRs which are soluble fusion proteins comprising an agent of interest, may be used to target an anticancer agent, fused as part of the svd-TCR, to cells in a subject which express a cancer-specific cell surface epitope. In another non-limiting example, svd-TCRs which when formatted for use as soluble fusion proteins comprising an agent of interest, may be used to specifically target a cytotoxic protein, fused as part of the svd-TCR, to undesired cells in a subject which express a cell surface epitope specific for an undesired cell. For example, which is not to be considered limiting, the epitope may be a pMHC comprising proteolyzed fragments of bacterial or viral proteins which are being intracellularly expressed. In another non-limiting example, svd-TCRs which are soluble fusion proteins and comprising an agent of interest with an affinity for immune cells may be used to recruit immune cells, like NK or T-cells, to the target cell that is recognized by the svd-TCR.
[0204] In another non-limiting example, T-cells which express svd-TCRs on their cell surface may be used to target cells recognized by the svd-TCR, for example, cancer cells, bacterial cells, virally- invaded cells and other undesired cells, for destruction by the host immune system. Accordingly, svd- TCRs may used in adoptive cell transfer therapy, e.g. similar to chimeric antigen receptors in T-cell based therapies. Because svd-TCRs can comprise a small modular binding domain, they have great flexibility in application as fusion proteins as compared to traditional TCRs which involve two different chains.
[0205] Cells may alternatively be redirected to particular organs or sites of healing or sites of inflammation, for example. In a non-limiting example, stem cells may be directed to organs or other microenvironments.
[0206] Certain embodiments relate to administering the polypeptide as disclosed herein to a subject which comprises the cell having the antigen of interest. [0207] Provided herein are methods of treating a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a composition comprising immune cells comprising the engineered TCRs of the disclosure.
[0208] In some embodiments, the subject in need thereof has cancer. Cancer is a disease in which abnormal cells divide without control and spread to nearby tissue. In some embodiments, the cancer comprises a liquid tumor, or a solid tumor. Exemplary liquid tumors include leukemias and lymphomas. Exemplary solid tumors include sarcomas and carcinomas. Cancers can arise in virtually an organ in the body, including blood, bone marrow, lung, breast, colon, bone, central nervous system, pancreas, prostate and ovary.
[0209] In some embodiments, the subject in need thereof has an infection. Infections include viral, bacterial and fungal infections, as well as infection with eukaryotic parasites.
[0210] In some embodiments, the subject in need thereof has an autoimmune disease, allergic disease, or inflammatory disease.
[0211] In some embodiments, the autoimmune disease, allergic disease, or inflammatory disease is selected from the group consisting of systemic lupus erythematosus, rheumatoid arthritis, psoriatic arthritis, scleroderma, asthma, atopic dermatitis, and allergic rhinitis.
[0212] In some embodiments, the autoimmune disease, allergic disease, or inflammatory disease is an organ- specific inflammatory disease.
[0213] In some embodiments, the organ-specific inflammatory disease is selected from the group consisting of kidney disease and lung disease. In some embodiments, the organ- specific inflammatory disease is a disease of any other organ or group of organs in the body (for example, liver, brain, heart intestines, lymph nodes, circulatory system, stomach, spleen etc.).
[0214] In some embodiments, the autoimmune disease, allergic disease, or inflammatory disease is transplant rejection. In some embodiments, the transplant rejection occurs in response to transplanted blood, bone marrow, bone, skin, heart, kidney, lung, muscle, heart or liver. In some embodiments, the transplant rejection is hyperacute rejection. In some embodiments, the transplant rejection is acute rejection. In some embodiments, the transplant rejection is chronic rejection.
[0215] The term “effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a composition, such as a composition comprising engineered TCRs or a composition comprising immune cells comprising engineered TCRs, as described herein, effective to achieve a particular biological or therapeutic result. In a subject with cancer, a therapeutically effective amount of the composition reduces a sign or a symptom of the cancer. For example, a therapeutically effective amount of the composition reduces tumor number, volume, or size, or slows tumor growth, or a combination thereof.
Kits and Articles of Manufacture
[0216] The disclosure provides kits and articles of manufacture comprising immune cells comprising the polypeptides described herein. In some embodiments, the kit comprises articles such as vials, syringes and instructions for use.
[0217] In some embodiments, the kit comprises a polynucleotide or vector comprising a sequence encoding one or more polypeptides of the disclosure.
[0218] In some embodiments, the kit comprises a plurality of immune cells comprising polypeptide as described herein. In some embodiments, the plurality of immune cells comprises a plurality of T cells.
[0219] The present description sets forth exemplary configurations, methods, parameters, and the like. It should be recognized, however, that such description is not intended as a limitation on the scope of the present disclosure, but is instead provided as a description of exemplary embodiments.
EXAMPLES
Example 1
[0220] Here we demonstrate that nb-only TCRs can be constructed from a nb domain with no additional sequence engineering within the framework and constant regions of the b chain. These nb-only svd-TCRs express stably on the surface of mammalian cells, including T cells. They bind pMHC probes selectively and appear to trigger T cells in much the same manner as full TCRs. Moreover, they function in tandem as CAR and TCR bifunctional proteins. Such nb-only domains provide tools and components for next-generation engineered T cell therapeutics and shed light on the mechanisms that dictate signaling sensitivity of TCRs and CARs.
Materials and Methods [0221] Cell culture: HEK-293T (ATTC CRL-3216), Jurkat clone E6-1 (ATCC TIB-152), T2 (ATCC CRL-1992), SUP-T1 (ATTC CRL-1942), A375 (ATTC CLR-1619) andK562 (ATTC CCL-243) cell lines were used in this study. HEK-293T and A375 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Jurkat and SUP-T1 cells were maintained in RPMI supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin. T2 cells were maintained in IMDM supplemented with 20% FBS and 1% penicillin/streptomycin. K562 cells engineered to stably express single chain NY-ESO-1 -b2ΐh-HίA-A2 trimer (Hansen et al, 2009) and GFP were generated and maintained in RPMI supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin. Cells were incubated at 37°C in 5% CO2.
[0222] Plasmid construction: All constructs, except for the recovered nb-only pool from the HuTARG™ platform (Patent WO2017/091905), were generated by Golden Gate assembly into the pFenti backbone, which has an EFla promoter. NY-ESO-1 and MAGE- A3 single-chain variable fragments (scFv) on the control CARs were obtained from in-house binder screens using the HuTARG™ platform. Sequences for the control NY-ESO-1 and MAGE- A3 TCRs were obtained from patents US8143376B2 and W02012054825A1, respectively.
[0223] HuTARG™: See patent WO2017/091905 for details. Briefly, HEK293 cells were engineered to contain a library of all combinations of unrearranged V, D and J segments of the b chain TCR locus. Because the host cells are constructed to contain a single loxP integration site, each cell post transfection of the library contains at most a single integrated copy of one of the roughly 1,800 combinations of V-D-J (64x2x14) gene segments, each segment flanked by a recombination signal sequence (RSS). When triggered to rearrange by addition of an exogenous inducer that activates RAGl expression, the RSSs mediate intramolecular site-specific recombination such that the population of cells produce a large repertoire of TEBb chains that are further subjected to selection for in- frame fusions using puromycin resistance. The cells also contain a surrogate single alpha chain for pairing and surface expression.
[0224] Transfection: Transient transfections of T-cell lines were performed using the Neon Transfection System (Thermo Fisher Scientific, Cat. No. MPK5000) according to the manufacturer’s instructions. Cells were pulsed three times at 1,500 V and a width of 30 msec. Transient transfection of HEK293T cells were performed using the Fugene HD transfection method (Promega, Cat. No. E2311) according to the manufacturer’s instructions.
[0225] FACS analysis: 18 hours post-transfection, cells were harvested and washed three times with FACS buffer (PBS + 0.1% BSA). The cells were incubated with TCR PFl (8A3) antibody conjugated with PE-Cy7 (Life Technologies, Cat. No. 25576641), CD3 epsilon antibody conjugated with FITC, Alexa Fluor 647-Streptavidin (Jackson, Cat. No. 016-600-084)-labeled MHC Class I A*02:01 SLLMWITQV (NY-ESO), or Alexa Fluor 647-Streptavidm-labeled MHC Class I A*02:01 FLWGPRALV (MAGE- A3) for 1 hour at 4°C. Cells were then washed twice, stained with DAPI or the near-IR dead cell stain kit reagents (Thermo Fisher, Cat. No. L34976), and resuspended in FACS buffer for flow cytometer analysis. Data acquisition used the BD Canto instrument and software. Data were analyzed using Flowjo software.
[0226] NFAT Luciferase assay: NY-ESO- 1 peptide (SLLMWITQV) and MAGE- A3 peptide (FLWGPRALV) were synthesized by Genscript (Piscataway, NJ). Target peptides were serially diluted 3-fold starting at IOOmM and loaded onto 10,000 T2 cells in RPMI plus 1% BSA and 0.1% penicillin/streptomycin. Eighteen hours later, 12,000 transfected Jurkat cells resuspended in RPMI/10% FBS/0.1% penicillin/streptomycin were added to the peptide-loaded T2 cells. The co culture was incubated for 6 hours at 37°C. One-step luciferase assay system (BPS Cat. No. 60690) was used according to manufacturer’s instructions to read luminescence on a microplate luminometer at 100ms. Each experiment was done in duplicate.
[0227] Primary T-cell transduction and activation: Peripheral blood mononuclear cells (PBMCs) and lentivirus were obtained from Alstem. PBMCs and activated with human T-cell TransAct™ according to manufacturer’s instructions in X-vivo media. For the transduction, lentivirus was added directly to the cells at MOI of 10. Transduced primary T-cells were expanded in X-vivo media with 1% human serum, 0.1% penicillin/streptomycin, 10 ng/ml IL-15, and 10 ng/ml IL-21. Cells were quiesced for 48 hours without stimulation or cytokines prior to assays.
[0228] Cytotoxicity and IFNY assay: A375 cells were transfected with nuclear locating GFP (IncuCyte NucLight Green) and selected with puromycin. 5,000 A375 cells were seeded with IOmM of NY-ESO- 1 or MAGE-A3 peptides. After 18 hours, cells were treated with 10pg/ml of mitomycin C for 1 hour and washed three times. 5,000 transduced T-cells (adjusted for transduction percentage measured by probe staining) were added and monitored using the IncuCyte S3 live-cell analysis system (Essen Bioscience) at 37°C and 5% CO2. Images were captured every two hours for 42 hours using a 10X objective. Green area at each time point was normalized to time zero to measure loss of live target cells. Experiments were done in duplicate.
[0229] Supernatants were harvested from the 24 hour time-point of the cytotoxicity assay co-culture. INFy levels were measured using the BD Cytometric bead array system according to manufacturer’s instruction.
[0230] Statistical analysis: For all data comparisons, the Student’s t test was performed using GraphPad Prism software. EC50 values were obtained by fitting the peptide concentration-dependent NFAT-Luciferase readout by nonlinear regression.
[0231] Homology Model: We generated a 3D structure model of the nb-only constructs (Cjo-026(P) plus Cjo-005(a)) in Prime homology modeling suite (Schrodinger, 2019a) using the crystal structure of the MAGE-A3 TCR (TRAV21/TRBV5-1 family; PDBID:5BRZ) as the template. All structures were prepared using the Schrodinger Protein Preparation Wizard (Sastry et al., 2013) before further calculations.
[0232] Molecular Dynamics Simulation: The system was solvated using the Desmond System Builder. Sodium ions were added to neutralize the system. The OPLS3e force field (Schrodinger, 2019a; Harder, 2016) was utilized for all calculations. The system equilibrated using the relaxation protocol as implemented in the Schrodinger package (Schrodinger, 2019a). Molecular Dynamics simulations were performed in the NPT ensemble at 300K and 1 atm pressure using Desmond (D.E. Shaw Research, 2019; Schrodinger, 2019b). The reversible reference system propagation algorithm (RESPA) multiple time step approach was used with a time step of 2 ps and long-ranged electrostatic interactions were computed every 6 ps (Tuckerman et al, 1992). Van der Waals and short range electrostatic interactions were cut off at 9 A “and smooth particle mesh Ewald (PME) (Essmann et al, 1995) method was employed for calculation of long range electrostatic interactions. The temperature was controlled using a Nose-Hoover chain thermostat (Martyna et al, 1992) and the pressure was controlled using the Martyna-Tobias-Klein (Martyna etal, 1994) barostat. Three simulations of 100 ns each were performed using the last frame as the initial coordinates on a Quadro P5000 GPU card with coordinates saved every 1.2 ps for subsequent analysis. [0233] Hydrophobic patch calculation: Hydrophobic patches on the surface of the homology model and crystal structures were calculated and visualized using the Protein Surface Analysis tool as implemented in Bioluminate (Schrodinger, 2019c; Sankar, 2018).
Results
Identification of Ub-only pMHC binding domains
[0234] To identify peptide-specific pMHC-binding molecules, in vitro V(D)J recombination was used to generate sequence diversity in the TCR nb domain while keeping the Va constant in a controlled fashion in HEK293 cells (see patent W02017/091905 for details about the HuTARG™ platform used to generate the TCR diversity). Over 100 million TCR-expressing cells were sorted for TCRs specific to the HLA-A*02-01 allele in complex with NY-ESO-1 peptide (SLLMWITQV) or MAGE-A3 peptide (FLWGPRALV) using pMHC multivalent probes. Note that C-terminal to the Ca/b domains, the library construct encoded the human Oϋ3z transmembrane and cytoplasmic domains fused to the b chain to facilitate its expression in HEK293 cells, and subsequent analysis. Specific pMHC-binding cells were enriched over multiple rounds and purified from the library. For the MAGE pMHC sort, a chain expression was inadvertently lost and b chains that endow specific epitope-binding in the absence of a second TCR variable domain were recovered. Such nb-only clones were used as the basis of studies described below.
VB-onlv domains express stably and show selective pMHC binding in CAR and TCR formats [0235] Several clones of nb-only domains selective for either HLA-A2/NY-ESO-1 peptide or HLA- A2/MAGE-A3 peptide were recovered from the HuTARG sort and sequenced. Among these, 3 and 4 unique CDR3 sequences were identified for NY-ESO-1- and MAGE- A3 -selective binders, respectively (Table 1). Interestingly, all 7 nb idiotypes for both pMHC targets utilize the TRBV5- 8*01 segment, suggesting structural properties of this nb segment that may facilitate stability of a single domain absent its normal Va partner (see below). Furthermore, the average CD3 loop length was 16.3 amino acids (range 12-20), ~2 amino acids longer than the average observed among a set of human TCR nb sequences. These idiotypes were characterized for their ability to express in HEK293T cells and bind pMHC targets by flow cytometry. TCR bEI (8A3) antibody was used to detect surface-expressing TCRb chains. pMHC probes were generated by conjugating biotin-labeled, peptide-containing MHC Class I A*02:01 with fluorophore-labeled streptavidin. All idiotypes expressed stably on the cell surface with various probe-binding abilities (FIG. 7). The strongest binders, idiotype #2 for a NY-ESO-1 -targeted nb-only domain and idiotype #5 for a MAGE-A3- targeted domain, were selected for further studies.
[0236] To assess the specificity and versatility of these nb-only domains, the NY-ESO-1- and MAGE- A3 -binding idiotypes (#2 and #5, respectively) were formatted as TCRs and CARs. For the TCR format, a generic alpha chain that is abundantly expressed in humans was used as a surrogate (TRAV41*01/J49*01). For the CAR format, Ub£ were linked to the a chain constant region (Ca), which in terms was fused to a CD3z transmembrane and intracellular signaling domain (first- generation CAR) or a CD28 transmembrane region and CD28 and E03z intracellular signaling domains (second-generation CAR) (FIG. 1A). For comparison we used the previously reported NY- ESO-1 -targeted TCR clone 1G4 and MAGE- A3 -targeted mouse TCR, as well as CARs with scFvs derived from reformatted antibody surface display (HuTARG™) libraries. These constructs were transfected into HEK293T cells to assess expression and binding specificity by flow cytometry. Mixtures of 7 off-target pMHCs were used to generate negative-control probe. Flow cytometry data showed that both NY-ESO-1- and MAGE- A3 -targeted nb-only domains stably express as CARs and selectively bind to target probes in HEK293T cells nb-only domains also expressed in the TCR format with specificity for the pMHC target, but significantly lower binding (FIG. IB and FIG. 1C). [0237] To examine nb-only domain expression and function in a more natural setting, the constructs were transfected into the Jurkat human T cell line. Additional CAR constructs with the nb domains linked to CD28 transmembrane region with CD28, 4- IBB and 093z intracellular signaling domains (third-generation CAR) were also tested. All NY-ESO-1- and MAGE- A3 -targeted nb-only CARs showed detectable probe binding in Jurkat cells. Slightly higher probe binding percentages were observed in second- and third-generation CARs compared to first-generation. However, nb-only domains in the TCR format did not bind probe for either pMHC target (FIG. ID and FIG IE).
The TRB5-8 VB segment may encode a sequence that more readily forms a single functional binding domain
[0238] Based on the crystal structure of a nb-5 TCR complexed with MAGE-A3 pMHC, we modeled one of the MAGE- A3 Ub-only domains described here and the results matched the expectation that some adjustments to the polypeptide backbone are required (FIG. 2A) (Raman et al, 2016). A molecular dynamics simulation of the TRB5-8 nb-only structure revealed that the interface with Va is at least partly covered by collapse of the CDR3 loop over its hydrophobic surface to accommodate the loss of Va (FIG. 2B). In addition, modeling two other TCRs that contain V segments from other families, suggests that at least some other nb domains require more radical changes to form a thermodynamically stable structure absent the Va domain, compared to nb-85 (FIG. 2C and FIG. 2D). Specifically, the crystal structure of a TRBV28-encoded domain shows nearly 80% more hydrophobic surface area exposed, compared to the \ b5-8-oh1n domain. Presumably such sequences have a more challenging route to formation of a stable single globular domain.
VB-only domains in CAR formats are functionally active
[0239] To assess whether target binding by nb-only domains can lead to functional activity, engineered Jurkat cells that expressed an NFAT-driven luciferase reporter gene were transfected with nb-only constructs. Serially diluted NY-ESO-1 and MAGE-A3 peptides were loaded onto T2 cells (HLA-A2+) 16 hours prior to co-culturing with transfected Jurkat effector cells. NFAT signal was measured by luminescence after 6 hours of co-culture. Peptide-titration curves showed that both NY- ESO-1 and MAGE- A3 nb-only CARs trigger peptide-concentration-dependent NFAT activation (FIG. 3 and Table 2). First-generation CAR formats showed about two-fold less sensitivity than second- and third-generation CARs with both binders. Compared to control third-generation CARs with affinity-matured scFv binders, third-generation CARs with nb domains were ~100x (NY-ESO- 1) and ~1000x (MAGE-A3) less sensitive (FIG. 8A and FIG. 8B).
Table 2. ECso in Jurkat/T2 assay
Figure imgf000057_0001
Figure imgf000058_0001
[0240] To identify the minimal module that is required for epitope binding of nb-only CAR constructs, CAR vectors were generated where the CP domain is replaced with a CD8 hinge (FIG. 8A). Peptide-concentration-dependent NFAT signal was observed with these constructs with only modest decrease in sensitivity, indicating that CP is not necessary for the nb-only binding ability (FIG. 8B). Cells transfected with nb-only domains in TCR formats did not signal, consistent with the lack of probe binding observed in these cells.
VP-only domains in TCR format are hindered by the Va domain
[0241] To further examine surface expression and full TCR complex formation in T cell lines, SUP- T1 cells were transfected with the b chains containing the nb-only domains and a TCRa surrogate chain. SUP-T1 cells are derived from a lymphoma with a chromosomal inversion within the TCR a and b gene cluster that prevents surface expression of the endogenous TCR complex. Because TCR a and b are not expressed, other subunits of the TCR complex, the 4 CD3 proteins, are expressed but unable to assemble on the surface. Therefore, CD3F staining was used as a readout for expression and pairing of the transfected TCRa and TCRP constructs on the cell surface. As previously reported, the NY-ESO-1 control TCR is expressed on the surface of SupTl cells. Moreover, the nb-only complex also are positive for CD3F staining, suggesting that the complex integrates the b and a subunits. However, only the control TCR showed probe binding, consistent with the observation in transfected Jurkat cells (FIG. 4B).
[0242] Because we observed pMHC probe binding of nb-only domains in CAR formats but not as a TCR complex, we hypothesized that the TCR Va may hinder the nb-only domains’ ability to bind targets. To test this hypothesis, the Va domain of the a chain was deleted and co-expressed with nb chains in SUP-T1 cells. These cells showed probe binding, confirming that the Va indeed hinders epitope binding of nb-only domains (FIG. 4A and FIG. 4B). Furthermore, Jurkat cells transfected with the P and Va-deficient chains revealed T2/peptide-dependent activation, demonstrating that the nb-only domains function in TCRs when their normal Va partner is removed (FIG. 4C and Table 3). Despite functional activity, probe binding was not observed by flow cytometry in transfected Jurkat cells (FIG. 9), suggesting that the NFAT reporter system is more sensitive than probe binding as we have observed previously (data not shown).
Table 3. ECso in Jurkat/T2 Assay
Figure imgf000059_0001
[0243] Attempts to trim the Ca domain further resulted in complete loss of probe binding of the modified TCRs in SUP-T1 cells and corresponding loss of functional activity in Jurkat cells (FIG. 10A and FIG. 10B). This result implies that an intact Ca domain is necessary to form a proper surrogate, and a minimal a polypeptide with only a transmembrane domain is not compatible with nb-only domain function, probably because of inefficient TCR complex formation absent the Ca domain, likely caused in part by exposed hydrophobic surfaces at the Ca/b interface.
Comparison of signaling sensitivities of VB-only domains in CAR and TCR formats [0244] Our system permits direct comparison of the same ligand-binding domains on a CAR and TCR. Interestingly, the sensitivity of the two formats were similar, which suggests that the ligand binding domain — its affinity and geometry — is the main determinant of sensitivity rather than the details of the signaling mechanism that differ between the CAR and TCR. This observation is consistent with studies where we grafted scFv against the same pMHC targets onto the control NY- ESO-1 TCR, modified to accept the scFvs by removing the Va and b domains. These hybrid TCRs have sensitivities in Jurkat signaling assays that are nearly identical to the CARs from which they are derived, nearly lOOx right-shifted compared to the parental TCR (FIG. 11A and FIG. 1 IB).
Bispecific VB-only domains function in CAR and TCR formats
[0245] Recent clinical trials have revealed that current adoptive T-cell therapy is susceptible to antigen escape by tumor cells. T cells that recognize multiple antigens offer a prospective safeguard against this problem. Bispecific receptors have been explored and developed in the context of CARs. However, TCRs with a capacity to target two different antigens have not been reported to our knowledge. Given the small and versatile binding properties of nb-only domains, we suspected they might function in a more complicated format as a bifunctional CAR or TCR.
[0246] To test this idea, bispecific nb-only CARs targeting NY-ESO-1 and MAGE- A3 pMHCs were generated in a second-generation CAR architecture with Cb and the two nb domains connected in tandem via a (GIS)3GG flexible linker. Jurkat cells transfected with these constructs showed detectable binding of both NY-ESO-1 and MAGE-A3 probes by flow cytometry (FIG. 5A). Consistently, in the NFAT-luciferase reporter assay, bispecific CARs functioned in response to both NY-ESO-1- and MAGE- A3 -peptide-loaded T2 cells with only modest declines in their individual sensitivities (FIG. 5B, Table 4). The binding domain positioned further from the membrane (i.e., at the N-terminus) showed a slight decrease in sensitivity while the one directly attached to Ob showed no change compared to the monospecific CARs.
Table 4: ECso in Jurkat/T2 assay
Figure imgf000060_0001
[0247] To examine if nb-only domains could function as bispecific TCRs, we constructed variants in both cis and trans configurations (i.e., in tandem on the b chain, or with one nb domain on each chain, Ca and Cb (FIG. 5C). As a control, nb fused on the TCRa chain was also expressed with a TCRb chain that lacked a nb domain (i.e., Cb only). This construct showed no function in the Jurkat NFAT-luciferase reporter assay, indicating that Ub-only domains moved to the a-chain abolishes its function (FIG. 5D). Therefore, the trans nb-only bispecific TCRs showed functional activity only against the pMHC target of the binder fused on the b-chain (FIG. 5D, Table 5). Cis bispecific nb- only TCRs were generated by connecting two nb domains in tandem via a (GIS)3GG flexible linker and expressing this construct with a surrogate TCRa chain with the Va deleted. To our surprise, bifunctional cis nb-only TCRs with NY-ESO-1 binder on the N-terminus followed by MAGE-A3 binder N-terminal to Ob showed both NY-ESO-1 and MAGE- A3 peptide-dependent signaling in Jurkat cells (FIG. 5D). Cis nb-only domains in the other orientation with the MAGE- A3 binder at the N-terminus also showed functional activity against both target peptides, although the magnitude of the signal (Emax) with MAGE- A3 peptide was reduced. The ECso in assays with peptides loaded on T2 was similar for the constructs, compared to the sensitivities of monospecific parental versions of the constructs (FIG. 5C and FIG. 4D). We also tested if there was interaction detectable at a functional level between the two pMHC ligands when supplied to Jurkat cell expressing bispecific constructs. Nothing beyond a potentially additive effect was observed using the analytical methods of Bliss and Loewe independence (data not shown)
Table 5: ECso in Jurkat/T2 assay
Figure imgf000061_0001
Primary T cells expressing VB-only constructs have cytotoxic activity
[0248] To evaluate the effect of nb-only domain constructs on T cell activity, primary T cells were transduced with lentivirus and expression was confirmed by NY-ESO-1 or MAGE- A3 probe staining (Fig 6A). Transduced T cells were used in an IncuCyte cell killing assay that enables visualization of target and effector cells by microscopy at 37°C over time. A375 cells that stably express nuclear locating GFP were loaded with IOmM NY-ESO-1 or MAGE-A3 peptides and co-cultured with transduced T cells at 1:1 ratios. T cell number was adjusted according to the transduction percentage measured by probe staining (FIG. 6A and FIG. 6B). [0249] For NY-ESO-1 binders, T cells expressing the benchmark TCR showed most potent cytotoxic activity, followed by T cells expressing the scFv-CAR, and the nb-only domain constructs in CAR and TCR formats which had similar killing activities. INFy measured in the supernatant of the co culture at 24 hours showed a similar trend (FIG. 6C). K562 cells that overexpress single chain NY- ESO- 1 -P m-HLA- A2 trimer and GFP were also used as target cells in the real-time killing assay. In this situation where the antigen is presented abundantly, all 4 NY-ESO-l-targeted constructs showed similar killing activities (FIG. 12).
[0250] T cells expressing the MAGE-A3 benchmark TCR and scFv-CARs only showed mild cytotoxic activities while the nb-only-CAR and -TCR triggered more robust killing. However, T cells with nb-only-CAR and -TCR also showed weak cytotoxicity toward K562 cells without any MAGE- A3 peptide loaded (FIG. 12), suggesting that these constructs likely trigger ligand-independent apoptosis of target cells. This is consistent with the high background NFAT signal observed in Jurkat cells transfected with the MAGE- A3 Ub-only-CAR and -TCR (FIG. 4D).

Claims

CLAIMS What is claimed is:
1. A polypeptide, comprising, in N-terminal to C-terminal order, a first antigen-binding domain, a linker, and a second antigen-binding domain, wherein either or both of the first and second antigen-binding domains comprise a single-variable domain TCR (svd-TCR).
2. The polypeptide of claim 1, wherein the polypeptide comprises a transmembrane domain C- terminal to the second antigen-binding domain.
3. The polypeptide of claim 2, wherein the first and second antigen-binding domains each independently comprise a svd-TCR, wherein the svd-TCR comprises a variable domain selected from a TCR Va domain, a TCR nb domain, a TCR Vy domain, and a TCR V5 domain, or an antigen-binding fragment thereof.
4. The polypeptide of claim 3, wherein either or both of the first and the second svd-TCRs comprises a TCR constant domain selected from a TCR Ca domain, TCR CP domain, a TCR Cy domain, and a TCR C5 domain and/or the second antigen-binding domain comprises a TCR constant domain selected from a TCR Ca domain, TCR CP domain, a TCR Cy domain.
5. The polypeptide of claim 3, wherein the first svd-TCR comprises a first TCR nb domain or an antigen-binding fragment thereof and the second svd-TCR comprises a second TCR nb domain or an antigen-binding fragment thereof.
6. The polypeptide of claim 5, wherein the first and second nb domains each independently comprise a human VP domain.
7. The polypeptide of claim 5, wherein the nb domains each independently share at least 80% sequence identity to a human VP domain.
8. The polypeptide of claim 5, wherein the first nb domain share at least 80% sequence identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to TRBV5-8 Ub (SEQ ID NO: 30).
9. The polypeptide of claim 5, wherein the second nb domain shares at least 80% sequence identity, at least 90% identity, at least 95% identity, at least 99% identity or is identical to TRBV5-8 nb (SEQ ID NO: 30).
10. The polypeptide of claim 5, wherein the second svd-TCR comprises a TCR Ob domain.
11. The polypeptide of claim 3, wherein the first svd-TCR specifically binds a first peptide:MHC complex comprising a first peptide.
12. The polypeptide of claim 3 or claim 11, wherein the second svd-TCR specifically binds a second peptide:MHC complex comprising a second peptide.
13. The polypeptide of claim 11, wherein the first peptide comprises a tumor antigen.
14. The polypeptide of claim 12, wherein the second peptide comprises a tumor antigen.
15. The polypeptide of claim 11 or 12, wherein the first or the second peptide:MHC complex comprises a class I MHC.
16. The polypeptide of claim 11 or 12, wherein the first or the second peptide:MHC complex comprises a class II MHC.
17. The polypeptide of claim of any one of claims 1-16, wherein the linker comprises the amino acid sequence of SEQ ID NO: 31.
18. The polypeptide of any one of claims claim 2-17, wherein the transmembrane domain is a TCRa transmembrane domain or a TOTIb transmembrane domain.
19. The polypeptide of any one of claims 2-17, wherein the transmembrane domain is a E03z transmembrane domain or a CD28 transmembrane domain.
20. The polypeptide of any one of claims 2-19, wherein the polypeptide comprises, C-terminal to the transmembrane domain, one or more intracellular signaling domains.
21. The polypeptide of claim 20, wherein the transmembrane domain comprises a CD28 transmembrane domain and wherein the one or more intracellular signaling domains comprise, in any C terminal to N terminal order, a CD28 intracellular domain, or functional fragment thereof, and a E03z intracellular domain, or functional fragment thereof.
22. The polypeptide of claim 20, wherein the transmembrane domain comprises a CD28 transmembrane domain and wherein the one or more intracellular signaling domains comprise, in any C terminal to N terminal order, a CD28 intracellular domain, a 4- IBB intracellular domain, and a Oϋ3z intracellular domain, or functional fragments thereof.
23. The polypeptide of any one of claims claim 3-7 or 10-22, wherein the first svd-TCR and the second svd-TCR each independently comprise a CDR3 comprising an amino acid sequence selected from SEQ ID NOs: 1-7.
24. The polypeptide of any one of claims 3-7 or 10-22, wherein the first svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 2 and the second svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 7.
25. The polypeptide of any one of claims 3-7 or 10-22, wherein the first svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 7 and the second svd-TCR comprises a CDR3 comprising the amino acid sequence of SEQ ID NO: 2.
26. A polynucleotide comprising a nucleic acid sequence encoding the polypeptide of any one of claims 2-25, operatively linked to a promoter.
27. A vector comprising the polynucleotide of claim 26.
28. A cell comprising the polynucleotide of claim 26.
29. A cell comprising the polypeptide of any one of claims 1-25.
30. The cell of claim 28 or claim 29, wherein the cell is a T cell.
31. The cell of claim 30, wherein the T cell is a T regulatory (Treg) cell.
32. The cell of claim 30, wherein the T cell is a non-regulatory T cell.
33. The cell of claim 28 or claim 29, wherein the cell is an NK cell.
34. A pharmaceutical composition, comprising a plurality of the cell of any one of claims 28-33 and a pharmaceutically acceptable carrier, diluent or excipient.
35. The pharmaceutical composition of claim 34, comprising a therapeutically effective amount of the cell of any one of claims 28-33.
36. A method of activating a cytotoxic signal in a target cell, comprising contacting, delivering, administering, providing, and/or supplying the cell of claim 32 or claim 33 to the target cell.
37. The method of claim 36, wherein the cytotoxic signal comprises NFAT signaling.
38. The method of claim 36, wherein the cytotoxic signal comprises release of IFNy.
39. A method of inducing tolerance in a target cell, comprising contacting, delivering, administering, providing, and/or supplying the cell of claim 31 to the target cell.
40. A method of treating and/or preventing cancer in a subject in need thereof, comprising administering to the subject a plurality of the cell of any one of claims 30-33.
41. A method of treating and/or preventing cancer in a subject in need thereof, comprising administering to the subject the pharmaceutical composition of claim 34 or 35.
42. A kit comprising a plurality of the cell of any one of claims 28-33 or the pharmaceutical composition of claim 34 or 35.
43. The kit of claim 42, further comprising instructions for use.
44. A method of making an immune an immune cell, comprising: a. providing a plurality of immune cells; and b. transforming the immune cells with the vector of claim 27.
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