HIGH AFFINITY ENGINEERED T-CELL RECEPTORS TARGETING CMV

INFECTED CELLS

[0001] This application claims the benefit of United States Provisional Patent Application No. 62/804,642, filed February 12, 2019, the entirety of which is incorporated herein by reference.

[0002] This invention was made with government support under Grant No. F32 GM111018 awarded by the National Institutes of Health and Grant No. DGEI610403 awarded by the National Science Foundation The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

L Field of the Invention

[0003] The present invention relates generally to the field of medicine. More particularly, it concerns high affinity engineered T-cell receptors for detecting and targeting CMV infected cells.

2, Description of Related Art

[0004] Antibodies represent a large and growing class of successful therapeutics, by- virtue of their abilities to tightly bind antigens that are secreted or expressed on a target cell surface. The structurally analogous T-cell receptor (TCR) provides access to a much wider array of intracellular and extracellular antigens that are presented on a cell surface as proteolyzed peptides in complex with major histocompatibility complex (MHC). Like antibodies, TCR binding sites are formed by six complementarity determining regions (CDRs), three on the alpha variable domain and three on the beta variable domain with the CDR3 loops dominating TCR-peptide interactions (Rossjohn et ai, 2015). When a peptide-MHC complex is recognized by the TCR expressed on a T cell, TCR activation, cytokine release, and cell killing can follow.

[0005] There is considerable interest in using TCRs as therapeutics and reagents to monitor the presence of disease-related peptides. Engineered TCRs can be used in adoptive T- ceil therapies to re-direct patient T cells to recognize a chosen target (Harris and Kranz, 2016), while soluble TCRs can be used as antibody-like reagents to bind specific peptide MHC complexes presented on a cell surface (Oates et al, 2015). Proof-of-concept for these approaches has been demonstrated with TCRs targeting the immunodominant Gag epitope SL9 from HIV. When transduced into patient T cells, high affinity TCRs were able to control viral replication (Varela-Rohena et al, 2008). When expressed as a soluble TCR linked to a CD3- specific single-chain antibody, the chimeric protein was able to redirect polyclonal CD 8 T cells to kill CD4 T cells harboring reactivated HIV (Yang et al, 2016).

[0006] Viral infection by cytomegalovirus (CMV) is also controlled by cytotoxic T cells in healthy individuals but causes disease in the very young, very old, and immunocompromised, with no vaccine candidate nearing licensure (P! oik in and Boppana, 2018). CMV-specific cytotoxic T cells primarily target peptides from the pp65 tegument protein, with the immune-dominant peptide residing between residues 495-503 (sequence NLVPMVATV (SEQ ID NO: 41), hereafter called NLV) (Wills et al , 1996; Saulquin et al, 2000) in complex with HLA-A2* 02:01 (hereafter called A2), the most common allele in North America. Adoptive transfer of NLV- specific T cells is sufficient to control infection in allogeneic hematopoietic stem cell transplantation patients with CMV infection (Feuchtinger et al, 2010). Notably, NLV is presented on the infected cell surface early after infection, prior to de novo protein synthesis and in the presence of therapeutics blocking viral replication (Riddell et al, 1991).

[0007] Identification of a validated, CMV-specific peptide-MHC complex suggests opportunities to monitor NLV-presenting cells, if an appropriate peptide-specific TCR is available. While hundreds of TCRs can recognize an immunodominant peptide, the NLV/A2 response is dominated by“public” clones whose CDR3a and/ or CDR3|3 sequences are shared among unrelated individuals (Trautmann et al, 2005; Wang et al, 2012). One of these, RA14, emerged as the dominant clone after rounds of immunosuppression and viral reactivation in a rheumatoid arthritis patient with asymptomatic CMV infection (Trautmann et al, 2005). The RA14 CDR3a contains the two most common public features observed in NLV -reactive TCRs: CDR3a sequence xnGNQF (where xn indicates a variable number of residues), observed in 14% of all sequences across multiple donors and CDR3p sequence SxnTGxnYGY, observed in 13% of all sequences (Wang et al, 2012). The RA14 TCR has been crystallized in complex with its ligand NLV/A2, revealing a typical TCR-pMHC binding interface characterized by high structural complementarity for the entire peptide (Trautmann et al , 2009). [0008] While RA14 appears to be an excellent candidate to monitor NLV/A2 presence and may be suitable for adoptive therapy applications, there are several limitations to using TCRs as soluble, antibody-like reagents. First, TCR-ligand binding affinities are much weaker than antibodies: RAH has been reported to have a 6-30 mM equilibrium affinity for NLV/A2 (Gras et al 2009; Gakamsky et ah, 2007), whereas antibody -ligand affinities are typically >1000-fold stronger (1-10 nM Kd). Second, despite considerable effort, soluble expression of TCRs continues to present challenges, with no generally successful strategies identified.

[0009] To address these shortcomings, TCRs have been engineered for increased stability, expression level, and affinity. This has been achieved using a single-chain format and yeast display (Shusta et al. , 1999; Holler et al, 2000; Shusta et ah, 2000), but engineering of each unique TCR appears required to enable incorporation of properly folded protein into these formats (Aggen et ah, 2011). Phage display of the TCR extracellular regions with a stabilizing di-sulfide bond in between the constant domains (Boulter el ah, 2003) has also been used to identify several very high affinity human TCR variants (Varela-Rohena et ah, 2008; Li et al , 2005; Liddy et al.. 2012). While successful, phage display lacks the eukaryotic protein folding machinery', which is likely required to allow' expression of a greater range of TCRs and is not compatible with efficient F AC S-based selection strategies. To produce soluble protein, single- chain or extracellular two-chain TCRs are most commonly refolded from bacterial inclusion bodies with varying levels of success (Aggen el ah, 2011). Some TCR sequences are amenable to soluble expression in bacteria with chaperone co-expression (Wulfing and Pluckthun, 1994; Maynard et al, 2005; Gunnarsen et al. , 2013), in yeast (Shusta et ah, 1999), or in mammalian cells (Mosquera el al, 2005, Walseng et ah, 2015; Foss et al 2016) but these represent only a fraction of TCRs of interest. Taken together, considerable effort is required to convert a TCR into a recombinant protein that can be used in biochemical assays or therapeutic methods.

SUMMARY OF THE INVENTION

[0010] In a first embodiment, there is provided an engineered T-cell receptor (TCR) comprising an alpha chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 1-7 and/or a beta chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 8- 17. In some aspects, the engineered TCR is HLA-A2 restricted. In further aspects, the engineered TCR is HLA-A2* 02:01 restricted. In other aspects, the engineered TCR specifically recognizes a peptide comprising an amino acid sequence of NLVPMVAT V (SEQ ID NO: 41) in complex with HLA-A2*02:0I . In certain aspects, the engineered TCR comprises an alpha chain CDR3 having the amino acid sequence of SEQ ID NO: 2 and a beta chain CDR3 having the amino acid sequence of SEQ ID NO: 15. In several aspects, the engineered TCR comprises an alpha chain variable region having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequence of any one of SEQ ID NOs: 18-24 and/or a beta chain variable region having at least 90% identity to the amino acid sequence of any one of SEQ ID NOs: 25-34.

[0011] In still further aspects, the engineered TCR comprises an alpha chain of any one of SEQ ID NOs: 18-24 and/or a beta chain of any one of SEQ ID NOs: 25-34. In specific aspects, the engineered TCR comprises an alpha chain of SEQ ID NO: 19 and a beta chain of SEQ ID NO: 32. In another aspect, the engineered TCR is further defined as a soluble TCR, wherein the soluble TCR does not comprise a transmembrane domain. In some aspects, the soluble TCR is linked to a CD3-specific antibody. In certain aspects, an extracellular domain of the TCR is fused to an antibody Fc domain. In several aspects, the alpha chain of the TCR extracellular domain is fused to the antibody Fc domain. In some particular aspects, the Fc domain is a human or mouse Fc domain. In another aspect, the engineered TCR further comprises an antibody hinge region.

[0012] In yet still further aspects, the engineered CAR is further defined as a chimeric antigen receptor. In another aspect, the engineered TCR further comprises a detectable label. In some aspects, the engineered TCR is covalently bound to a therapeutic agent. In some specific aspects, the therapeutic agent is an immunotoxin or a chemotherapeutic agent.

[0013] In an embodiment of the present disclosure, there is provided an engineered T- cel! receptor (TCR) comprising an alpha chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 1-7 or 60-61 and/or a beta chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 8-17 or 62-63.

[0014] In some aspects, the engineered TCR is FILA-A2 restricted, such as HLA- .42*02:01 restricted. In particular aspects, the engineered TCR specifically recognizes a peptide comprising an amino acid sequence of NLVPMVATV (SEQ ID NO: 41) in complex with HLA-A2*02:01.

[0015] In certain aspects, the engineered TCR comprises an alpha chain CDR3 having the amino acid sequence of SEQ ID NO: 2 and a beta chain CDR3 having the amino acid sequence of SEQ ID NO: 15. In some aspects, the engineered TCR comprises an alpha chain CDR3 having the amino acid sequence of SEQ ID NO: 60 and a beta chain CDR3 having the amino acid sequence of SEQ ID NO: 62. In particular aspects, the engineered TCR comprises an alpha chain CDR3 having the amino acid sequence of SEQ ID NO: 61 and a beta chain CDR3 having the amino acid sequence of SEQ ID NO: 63.

[0016] In some aspects, the engineered TCR comprises an alpha chain CDR1 of Table 1A-2 or Table 1C. In specific aspects, the engineered TCR comprises an alpha chain CDR1; CDR2 and CDR3 of Table 1 C. In further aspects, the engineered TCR comprises a beta chain CDR1; CDR2 and CDR3 of Table ID. For example, the engineered TCR may comprise an alpha chain CDR1 ; CDR2 and CDR3 of Table 1C; and a beta chain CDR1 ; CDR2 and CDR3 of Table ID.

[0017] In certain aspects, the engineered TCR comprises an alpha chain variable region having at least 90% (e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the amino acid sequence of any one of those in Table 1C and/or a beta chain variable region having at least 90% (e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the amino acid sequence of any one of those in Table ID. In particular aspects, the engineered TCR comprises an alpha chain of any one of those in Table 1C and/or a beta chain of any one of those in Table I D. In one specific aspect, the engineered TCR comprises an alpha chain of SEQ ID NO: 19 and a beta chain of SEQ ID NO: 32.

[0018] In some aspects, the engineered TCR is further defined as a soluble TCR, wherein the soluble TCR does not comprise a transmembrane domain. In further aspects, the soluble TCR is linked to a CD3-specific antibody. In some aspects, an extracellular domain of the TCR is fused to an antibody Fc domain. For example, the alpha chain of the TCR extracellular domain may be fused to the antibody Fc domain. The Fc domain may be a human or mouse Fc domain. In additional aspects, the TCR further comprises an antibody hinge region.

[0019] In certain aspects, the Fc domain exhibits reduced binding a viral Fc receptor (vFcR) relative to a wt Fc. In some aspects, the vFcR comprises CMV gp34 and/or gp68. In particular aspects, the vFcR is able to bind to human FcRIIIa and/or FcRn. In specific aspects, the Fc domain comprises one or more substitutions relative to wt Fc domain selected from a substitution at S337, K334; G341 , E345; T350; K338; H268; E294 and Q31 1. In some aspects, the Fc domain comprises substitutions selected from: (a) S337; (b) S337 and G341; (c) S337; E345; and T350; (d) K334; and K338; (e) S337 and T350; (f) H268; and K334; and (g) H268; E294; Q311; and K334. In certain aspects, the Fc domain comprises one or more substitutions relative to wt Fc domain selected from S337F; K334E; G341E; E345K, T35QI; K338I; H268L; E294K and Q311L, wherein the engineered Fc domain exhibits reduced binding a viral Fc receptor (vFcR) relative to a wt Fc. In some aspects, the Fc domain comprises substitutions selected from: (a) S337F; (b) S337F and G341E; (c) S337F; E345K; and T350I; (d) K334E; and K338I; (e) S337F and T350I; (f) H268L; and K334E; and (g) H268L; E294K; Q311 L; and K334E. In specific aspects, the Fc domain comprises wherein the antibody Fc domain comprises one or more substitution selected from M252Y; S254T and T256E. In some aspects, the engineered antibody Fc domain comprises the following substitutions M252Y, S254T and T256E.

[0020] In some aspects, the engineered TCR is further defined as a chimeric antigen receptor.

[0021] In additional aspects, the TCR further comprises a detectable label. In some aspects, the engineered TCR is covalently hound to a therapeutic agent, such as an immunotoxin or a chemotherapeutic agent.

[0022] A further embodiment provides a polynucleotide encoding the engineered TCR of the present embodiment and aspects thereof (e.g , an engineered T-cell receptor (TCR) comprising an alpha chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 1-7 or 60-61 and/or a beta chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 8-17 or 62-63).

[0023] Also provided herein is an expression vector encoding the engineered TCR of the present embodiment and aspects thereof (e.g., an engineered T-cell receptor (TCR) comprising an alpha chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 1-7 or 60-61 and/or a beta chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 8-17 or 62-63). In some aspects, the sequence encoding the TC is under the control of a promoter. The expression vector may be a viral vector, such as a retroviral vector. In other aspects, the expression vector is an episomal vector. In additional aspects, the vector further encodes a linker domain. The linker domain may be positioned between the alpha chain and beta chain. In some aspects, the linker domain comprises one or more cleavage sites, such as a Furin cleavage site (e.g., RRKR) and/or a P2A cleavage site. In certain aspects, the one or more cleavage sites are separated by a spacer, such as SGSG or GSG.

[0024] Another embodiment provides a cell engineered to express the TCR of the present embodiment and aspects thereof (e.g., an engineered T-cell receptor (TCR) comprising an alpha chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 1-7 or 60- 61 and/or a beta chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 8- 17 or 62-63). In some aspects, the cell is a T cell, NK cell, invariant NK cell, NKT cell, mesenchymal stem cell (MSC), or induced pluripotent stem (iPS) cell. In particular aspects, the cell is an immune cell. The cell may be isolated from an umbilical cord. In particular aspects, the T cell is a CD8 ⁺ T cell, CD4+ T cell, or gd T cell. In some aspects, the T cell is a regulatory T cell (Treg).

[0025] A further embodiment provide a method for engineering the cell of the present embodiments or aspects thereof comprising contacting said immune cell with the TCR of the present embodiment and aspects thereof (e.g., an engineered T-cell receptor (TCR) comprising an alpha chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 1-7 or 60- 61 and/or a beta chain CDR3 having the amino acid sequence of any one of SEQ ID NOs: 8- 17 or 62-63) or the expression vector of the present embodiments or aspects thereof. In some aspects, the immune cell is a T cell, peripheral blood lymphocyte, NK cell, invariant NK cell, or NKT cell. In additional aspects, contacting is further defined as transfecting or transducing. In some aspects, transfecting comprises electroporating RNA encoding the TCR of the present embodiments into the immune cell. In further aspects, the method further comprises generating viral supernatant from the expression vector of the present embodiments prior to transducing the immune cell. In some aspects, the immune cell is a stimulated lymphocyte, such as a human lymphocyte. In particular aspects, stimulating comprises contacting the immune cell with or incubating the immune cell in QKT3 and/or IL-2. In additional aspects, the method further comprises sorting the immune cells to isolate TCR engineered T cells. In some aspects, the method further comprising performing T cell cloning by serial dilution. In certain aspects, the method further comprises expansion of the T cell clone by the rapid expansion protocol.

[0026] In another embodiment there is provided a polynucleotide encoding the engineered TCR of any of the embodiments and aspects described above. [0027] Still a further embodiment of the invention provides a cell engineered to express the TCR of any of the embodiments and aspects described above. In some aspects, the cell is a T cell, NK cell, invariant NK cell, NKT cell, mesenchymal stem cell (MSC), or induced pluripotent stem (iPS) cell. In certain aspects, the cell is an immune cell. In another aspect, the cell is isolated from an umbilical cord. In several aspects, the T cell is a CD8 ⁺ T cell, CD4+ T cell, or gd T cell. In other aspects, the T cell is a regulatory T cell (Treg).

[0028] In still yet a further embodiment, there is provided a method for engineering the cell of any of the embodiments and aspects described above, comprising contacting said immune cell with the TCR of any of the embodiments and aspects described above or the expression vector of any of the embodiments and aspects described above. In certain aspects, the immune cell is a T cell, peripheral blood lymphocyte, NK cell, invariant NK cell, or NKT cell. In another aspect, contacting is further defined as transfecting or transducing. In some aspects, transfecting comprises electroporating RNA encoding the TCR of any of the embodiments and aspects described above into the immune cell. In additional aspects, the method further comprises generating viral supernatant from the expression vector of the embodiments and aspects described above prior to transducing the immune cell.

[0029] In further aspects, the immune cell is a stimulated lymphocyte. In some aspects, the stimulated lymphocyte is a human lymphocyte. In several aspects, stimulating comprises contacting the immune cell with or incubating the immune ceil in OKT3 and/or IL-2, In additional aspects, the method further comprises sorting the immune cells to isolate TCR engineered T cells. In still further aspects, the method also comprises performing T cell cloning by serial dilution. In another aspects, the method further comprises expansion of the T cell clone by the rapid expansion protocol.

[0030] Yet a further embodiment provides use of a therapeutically effective amount of NLV/A2 TCR-specific cells according to any of the embodiments and aspects described above for the treatment of a disease or disorder in a patient. In certain aspects, the NLV/A2 TCR- specific ceils are T cells

[0031] Still a further embodiment of the invention provides use of a therapeutically effective amount of a soluble TCR according to any of the embodiments and aspects described above for the treatment of a disease or disorder in a patient. [0032] In yet still a further embodiment of the invention there is provided a method of treating a disease or disorder in a subject in need thereof, monitoring disease progression in a subject, or monitoring vaccine efficacy in a subject, the method comprising administering an effective amount of the TCR-engineered cells of any of the embodiments and aspects described above or a soluble TCR according to any of the embodiments and aspects described above to the subject. In certain aspects, the subject has been identified as having an HLA-A2* 02:01 allele. In some aspects, the TCR-engineered cell is a T cell or peripheral blood lymphocyte. In additional aspects, the T cell is a CDS ^· T cell, CD4 ⁺ T cell, or Treg. In specific aspects, the cell is autologous. In other aspects, the cell is allogeneic. In certain aspects, the disease is a cancer. In a particular aspect, the cancer is a glioblastoma. In some aspects, an NLV peptide has been delivered to cells of the cancer. In several aspects, the subject is a human. In additional aspects, the cells are administered to the subject intravenously, intraperitoneally, or intratumorally. In certain aspects, the method further comprises administering a second anticancer therapy. In some aspects, the second anticancer therapy is a chemotherapy, immunotherapy, surgery, radiotherapy, or biotherapy. In certain aspects, the immunotherapy is an immune checkpoint inhibitor. In another aspect, the immune checkpoint inhibitor inhibits an immune checkpoint protein or ligand thereof selected from the group consisting of CTLA- 4, PD-L PD-Ll, PD-L2, LAG-3, BTLA, B7H3, B7H4, TIM3, KIR, or adenosine A2a receptor (A2aR). In several aspects, the immune checkpoint inhibitor inhibits PD-1 or CTLA-4. In some aspects, the patient has been determined to have a cancer with a reactivated CMV infection.

[0033] Still a further embodiment provides a method of detecting NLV/A2 complexes on cells, the method comprising contacting the cells with a soluble TCR of any one of claims 11-16 and 18 and detecting binding of the soluble TCR to the cells. In certain aspects, the soluble TCR comprises a mouse Fc domain. In some aspects, the cells are peptide-pulsed antigen presenting cells. In other aspects, the antigen presenting cells have been pulsed with a peptide comprising an amino acid sequence of NLVPMVATV (SEQ ID NO: 41 ).

[0034] Yet still a further embodiment provides an immunoglobulin fusion complex comprising: (i) an aTCR variable domain fused to a first antibody Fc domain, wherein aTCR variable domain is bound to a pTCR variable domain by a disulfide bond; or (ii) a pTCR variable domain fused to a first antibody Fc domain, wherein PTCR variable domain is bound to an aTCR variable domain by a disulfide bond, wherein the aTCR variable domain and the bTOI variable domain comprise amino acid substitutions that block N-linked glycosylation. In some aspects, the first antibody Fc domain is bound to a second antibody Fc domain by a disulfide bond. In certain aspects, the second antibody Fc domain is fused to an antibody heavy chain variable domain that is bound to an antibody light chain by a disulfide bond. In several aspects, the complex further comprises two immunoglobulin fusion complexes that are bound by disulfide bonds between the Fc domains. In some aspects, the second Fc domain is fused to a targeting moiety. In certain aspects, the targeting moiety is an antibody VH/VL domain. In another aspect, the targeting moiety binds to immune effector ceils. In some aspects, the targeting moiety binds to CD3. In further aspects, the aTCR variable domain is bound to a b1 ^' CR variable domain by two disulfide bonds. In certain aspects, the aTCR variable domain and the [JTCR variable domain comprise N to Q amino acid substitutions that block N-linked glycosylation. In other aspects, the aTCR variable domain and the |3TCR variable domain specifically bind to a peptide in complex with 1 11. A. In some specific aspects, the HLA is HLA-A2. In certain aspects, the peptide in complex with HLA is a cancer protein peptide, an autoimmune peptide or an infectious disease peptide. In another aspect, the peptide is a CMV peptide. In some particular aspects, the CDR3 dom ains of the TCR variable domains are those recited in the first embodiment described above.

[0035] In yet a further embodiment, there is provided a method of producing a TCR complex comprising (a) expressing one or more nucleic acid molecules in a mammalian cell encoding: (i) an aTCR variable domain fused to a first antibody Fc domain, wherein aTCR variable domain is bound to a PTCR variable domain by a disulfide bond; or (ii) a PTCR variable domain fused to a first antibody Fc domain, wherein TCR variable domain is bound to an aTCR variable domain by a disulfide bond, wherein the aTCR variable domain and the pTCR variable domain comprise amino acid substitutions that block N-linked glycosylation; and (b) collecting or purifying the TCR complex. In some aspects, the mammalian cell is CHO cell. Also provided herein is a TCR complex produced by the present methods.

[0036] Further provided herein is an engineered antibody Fc domain comprising one or more substitutions relative to wt Fc domain selected from a substitution at S337; K334; G341; E345; T350; K338; H268; E294 and Q31 1, wherein the engineered Fc domain exhibits reduced binding a viral Fc receptor (vFcR) relative to a wt Fc. In some aspects, the Fe domain comprises substitutions selected from: (a) S337; (b) S337 and G341 ; (c) S337; E345; and T350; (d) K334; and K338; (e) S337 and T350, (f) 1 1268. and K334; and (g) 1 1268; E294; Q311; and K334. In certain aspects, the Fc domain comprises one or more substitutions relative to wt Fc domain selected from S337F; K334E; G341E; E345K; T350I; K338I; H268L; E294K and Q311L, wherein the engineered Fc domain exhibits reduced binding a viral Fc receptor (vFcR) relative to a wt Fc. In certain aspects, the Fc domain comprises substitutions selected from: (a) S337F; (b) S337F and G341E; (c) S337F, E345K; and T350I; (d) K334E; and K338I; (e) S337F and T350I; (f) H268L; and K334E; and (g) ! 12081.; E294K; Q311L; and K334E. In some aspects, the vFcR comprises CMV gp34 and/or gp68. For example, the vFcR may be CMV gp34. In particular aspects, the engineered Fc domain is able to bind to human FcRIIIa and/or FcRn. In some aspects, the engineered Fc domain comprises a CHI, CH2 and CH3 domain at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, or 95% identical to a human IgGl CHI, CH2 and CH3. In some aspects, the engineered Fc domain is an IgGl Fc domain or an IgG2 Fc domain. In some aspects, the engineered Fc domain is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, or 95% identical to any one of SEQ ID NOs: 53-60. In additional aspects, the method Fc domain further comprises one or more substitutions selected from M252; S254 and T256. In some aspects, the Fc domain further comprises a substitution at M252; S254 and T256. In certain aspects, the Fc domain further comprises one or more substitution selected from M252Y; S254T and T256E. In some aspects, the Fc domain further comprises the following substitutions M252Y; S254T and T256E. In some aspects, the Fc domain further comprises an antibody variable domain or a TCR variable domain. The engineered Fc domain may be fused or conjugated to antibody variable domains or TCR variable domains that bind to a target of interest, such as a viral protein or a viral peptide bound to HLA. In some aspects, the target of interest is a CMV protein or a CMV peptide bound to HLA. In particular aspects, the engineered Fc domain is fused or conjugated to TCR variable domains that bind to NLVPMVATV (SEQ ID NO: 41) in complex with HLA-A2* 02:01. Also provided herein is nucleic acid molecule encoding an engineered antibody Fc domain of the present embodiments and aspects thereof. Further provided herein is host cell expressing a nucleic acid molecule of the present embodiments. For example, the cell is a CHO cell.

[0037] Another embodiment provides a method of targeting a CMV infected cell comprising contacting the cell with molecule that binds to a CMV polypeptide or a CMV peptide bound to HLA, wherein the molecule is fused or conjugated to an engineered antibody Fc domain comprising one or more substitutions relative to i Fc domain selected from a substitution at S337; K334; G341; E345; T350; K338; H268; E294; Q311; M252; S254; and T256, wherein the engineered Fc domain exhibits reduced binding a viral Fc receptor (vFcR) relative to a wt Fc. In some aspects, the engineered antibody Fc domain comprises one or more substitution selected from M252Y; S254T and T256E. In certain aspects, the engineered antibody Fc domain comprises the following substitutions M252Y, S254T and T256E. In some aspects, the engineered antibody Fc domain is a domain in accordance with the present embodiments or aspects thereof.

[0038] As used herein,“essentially free,” in terms of a specified component, is used herein to mean that none of the specified component has been purposefully formulated into a composition and/or is present only as a contaminant or in trace amounts. The total amount of the specified component resulting from any unintended contamination of a composition is preferably below 0.01%. Most preferred is a composition in which no amount of the specified component can be detected with standard analytical methods.

[0039] As used herein in the specification and claims,“a” or“an” may mean one or more. As used herein in the specification and claims, when used in conjunction with the word “comprising”, the words“a” or“an” may mean one or more than one. As used herein, in the specification and claim,“another” or“a further” may mean at least a second or more.

[0040] As used herein in the specification and claims, the term“about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.

[0041] Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating certain embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0042] The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein. [0043] FIGS. 1A-1C: The NLV-specific human TCR RA14 displays on the surface of CHO-Kl cells. (FIG. 1 A) The RAM variable and constant regions were cloned in-frame with the mouse/human Ig heavy leader sequence (LS), a T2A peptide for cleavage, and the PDGFR transmembrane region (TM) with either the alpha (a/b-TM) or the beta chain (b/a-TM) in the first position. The cassettes were then cloned into a pcDNA3 mammalian expression vector. (FIG. IB) Display of functional RAM TCR was detected with a dual-stain approach, with an anti-Vp6-5 antibody -PE conjugate detecting expression of the TCR beta chain, and a peptide/ A2 tetramer conjugated to APC used to assess ligand binding. (FIG. 1C) Plasmids encoding the TCR in both chain orientations and with the wild- type (WT) or engineered disulfide (ds) constant regions were transfected, stained two days later, and assayed for APC and PE signal via flow cytometry'. Rainbow dots depict staining using a tetramer with the specific NLV peptide, while grey dots depict staining with a tetramer containing a control peptide from HCV. Control transfections without plasmid and with a plasmid lacking the alpha chain are also shown.

[0044] FIGS. 2A-23B: Structural interactions between RAM CDR3 loops and NLV peptide/ A2. The crystal structure of the RAM TCR complexed with NLV/A2 (PDB 3GSN) was used to guide library design. The A2 surface is shown in grey space-fill, the NLV peptide surface in pink space-fill and the RAM structure in purple ribbon. The residues comprising the CDR3a (SEQ ID NO: 39) (FIG. 2A) and CDR3P (SEQ ID NO: 40) loops (FIG. 2B) are listed (IMGT definition), with those targeted for mutagenesis highlighted in red in the text and in the structure. Boxed residues form direct pMHC contacts in the wild-type crystal as analyzed by (Gras el al, 2009)

[0045] FIGS. 3A-3D: RAM variants with improved tetramer binding can be isolated by CHO display. The TCR display cassette optimized in FIG. 1 was mutagenized into two libraries following the strategy in FIG. 2, and cloned into a pPy vector to allow episomal maintenance (see U.S. Patent No. 7,919,270). The CDR3a (FIG. 3 A) and C ⁽⁾ R3p (FIG. 3B) libraries were separately transfected into CHO-T cells, stained and sorted over three rounds to enrich for improved tetramer binding. Untransfected cells and cells displaying Fab hulB7 (Nguyen et al. , 2015) are shown as controls. The gate drawn is representative of the sorting gate used in round three, with the percentage of cells falling into the gate noted in red to facilitate comparisons. Individual clones from the round three sorts of the CDR3a (FIG. 3C) and CDR3p (FIG. 3D) libraries were re-transfected, stained, and checked for improved specific tetramer binding compared to the wild-type sequence. Specific tetramer binding refers to the ratio of the AF647 signal (tetramer binding) to the PE signal (anti-TC display) calculated on a per-cell basis. The median fluorescence intensity for this new variable was normalized to the wild-type. Variants selected for further characterization are indicated by an asterisk (*). In this initial screening experiment there were no replicate transfections, therefore no error bars are indicated.

[0046] FIGS. 4A-4B: Combining selected CDR3 variants further improves NLV/A2 tetramer staining and activation (FIG. 4A) The wild-type and improved alpha-chain variants (al and a2) were cloned in combination with the wild-type and improved beta-chain variants (bnΐ, bU4, pV7, b¥8) in the display format and expressed in CHG-T cells. After two days, cells were stained and analyzed by flow cytometry, with specific tetramer binding quantified as in Figure 3. The standard deviation is shown for combinations that were tested multiple times (FIG. 4B) Activation of human Jurkat T cells expressing RA14 and selected variants was measured by CD69 upregulation. Transfected cells were co-cultured with peptide-pulsed human T2 antigen-presenting cells. After 24 hours, TCR-positive cells (NLV-tetramer-binding and nb-positive) were further monitored for CD69 upregulation using anti-CD69- FITC antibody. Data shows the average and standard deviation of three independent experiments. ANOVA was used to compare tetramer MFI for each clone combination (****p<0.()01).

[0047] FIGS. 5A-5C: Engineered RA14 TCR2ds~huFc variants show increased affinity for NLV/A2. (FIG. 5A) TCR2ds-huFc formats of each variant were purified by protein A and size-exclusion chromatography to isolate only the intact protein. Protein purity was evaluated by non-reduced and reduced 4-20% gradient SDS-PAGE gel (3 pg protein per lane). (FIG. 5B) The tetramer binding activities of purified RA14 variants were compared by ELISA. Plates w^ere coated with NLV/A2 tetramer, followed by TCR2ds-huFc and goat-anti-human Fc-HRP. Data shown are the average and range of duplicate series for a representative experiment; this was repeated several times with similar results. (FIG. 5C) The binding kinetics were measured by SPR. Each TCR2ds-huFc variant was immobilized on a CMS chip at 2000- 5000 RUs, after which monomeric NLV/A2 was injected at six concentrations between 3.9- 500 nM. An in-line blank flow cell was used to assess background binding. Peptide specificity was evaluated with injections of monomeric PICV/ A2 at the maximum concentration used for NLV/A2 for each variant. All injections were performed in duplicate; shown are the data and fits with the kinetics reported in Table2. [0048] FIGS. 6A-6D: Equilibrium binding affinity of RAH and variants for NLV/ A2. The wild-type RAH TCR2ds-huFc fusion and variants were immobilized on a CMS chip at 2000-5000 RUs before injecting monomeric NLV/ A2 at concentrations ranging from 7.9 to 500 nM at a flowrate of 30 ul/min. The observed equilibrium response values were plotted against concentration using BIAevaluation 3 0 software. The equilibrium affinity Kd 'as calculated using least-squares fit to the data, assuming a 1 : 1 stoichiometry; numerical values listed in Table 2. No binding was observed with the control HCV7 A2 monomer at the highest concentrations used for each variant (shown in FIG. 7).

[0049] FIGS. 7A-7D: Expression and stability of the wild-type RA 14 TCR as a soluble Fc fusion protein. (FIG. 7A) Several iterations of the TCR-Fc fusion protein were designed. In all scaffolds, the TCR a chain was fused to a human IgGl hinge and Fc. Open circles represent native glycosylation sites. Additional modifications include a second disulfide bond (ds, green) in the TCR2ds-huFc format and the removal of predicted N-linked glycosylation sites (Agly, blue crosses) in the TCR2dsAgly-huFc format. (FIG. 7B) The purity of each protein A purified design w'as evaluated via reducing and non-reducing 4-20% gradient SDS-PAGE, with 3 pg loaded per lane. (FIG. 7C) Protein homogeneity was analyzed by size exclusion chromatography. The arrow indicates the major peak collected for experiments using a glycosylated scaffold. Triangles indicate elution volumes for molecular weight standards: thyroglobulin with a 669 kDa size eluted at 8.65 ml; ferritin 440 kDa at 10.45 ml; aldolase 158 kDa at 12.77 ml; conalbumin 75 kDa at 14.32 ml; ovalbumin 44 kDa at 15.27 ml; carbonic anhydrase 29 kDa at 16.68 ml. Representative data are shown for each design. (FIG. 7D) The melting temperature of each design was analyzed by differential scanning fluorimetry. An average value for two separate normalized curves shown for each scaffold, from a representative experiment. For FIG. 7C and FIG. 7D, dotted black lines correspond to the TCR- Fc scaffold, the dashed green lines correspond to the TCR2ds-huFc scaffold, and the solid blue lines are used for the TCR2dsAgiy-huFc scaffold.

[0050] FIGS. 8A-8B: ELISA shows no impact of TCR2ds-huFc de-glycosylation on pMHC binding. The tetramer binding activities of RA14 variants genetically deglycosylated (TCR2dsAgiy-huFc) versus unmodified (TCR2ds-huFc) were compared by ELISA. Plates were coated with NLV/A2 tetramer at 1 pg/mL, followed by serially diluted TCR2ds-huFc or TCR2dsAgly-huFc and 1 : 1000 goat-anti-human Fc-HRP. Data shown are the average and range of duplicate series, the experiment was repeated several times with similar results. No coat and an irrelevant peptide (HCV/A2 tetramer) controls were performed in parallel and showed no binding.

[0051] FIGS. 9A-9C: High affinity TCR-mFc proteins bind peptide-pulsed antigen presenting cells. (FIG. 9A) The wild-type (WT) RAM and improved variants were expressed as TCR2ds-mFc proteins with mouse IgG2a hinge and Fc domains to reduce binding to human Fc receptors expressed on T2 cells. SDS-PAGE was used to confirm protein purity (3 pg per lane). (FIG. 9B) Human T2 antigen presenting cells were pulsed overnight with 100 mM NLV or HCV peptide and stained with l mM TCR2ds-mFc and 1 :500 anti-mouse Fc-AF647 before flow cytometric analysis. This experiment was performed twice with similar results. (FIG. 9C) Human T2 antigen presenting cells were pulsed overnight with NLA ⁷ at 0, 0.5, 1, 5, 10, 25, 50, 100, 250, and 500 m M NLV or HCV peptide at 500 mM and stained with 1 mM aV2.pV8 in the TCR2dsAgiy-mFe format and 1 :500 anti-mouse Fc-AF647 before flow cytometric analysis. This experiment was performed twice with similar results. Binding was significant over signals observed for HCV pulsed T2 cells to NLV peptide concentrations as low as 0.5 mM.

[0052] FIGS. 10A-10C: Genetic de-glycosylation of TCR2ds-huFc fusion proteins yields monodisperse protein. The purity of TCR2dsAgly-huFc (solid lines) and TCR2ds-huFc (dashed lines) proteins for affinity matured RAM variants w'as analyzed by size exclusion chromatography. Protein A purified protein was injected (100 pg in 100 m!) onto a Superdex S200 column on an Akta FPLC. Triangles indicate elution volumes for the molecular weight standards: thyrog!obulin with a 669 kDa size eluted at 8.65 ml; ferritin 440 kDa atl0.45 ml; aldolase 158 kDa at 12,77 ml; conalbumin 75 kDa at 14.32 ml; ovalbumin 44 kDa at 15.27 ml; carbonic anhydrase 29 kDa at 16.68 ml. Representative data are shown for each TCR variant in each format.

[0053] FIG. 11 : Schematic representation of improved RAM TCR variant, 341 (SEQ ID NO: 52) having the transmembrane linker on the alpha chain and eliminating the predicted glycosylation sites with N-^Q amino acid substitutions.

[0054] FIG. 12: FACS comparison of a2b8 and 341 against the corresponding wild- type RA .

[0055] FIG. 13: Graphical representation of enhancement in binding/expression (AF647/PE) shown in FIG. 12. [0056] FIG. 14A-C: Expression and purification of the human Qb.lA12 TCR as a TCR-human Fc fusion protein from CHO cells. Human Ob 1 A12 was isolated from a patient with multiple sclerosis. The protein was expressed as a TCR-human Fc fusion in CHO cells. In these constructs, the a chain was fused to human Fc. Both constant chains but not the variable domains were glycosylated. A, SDS-PAGE protein gel. Light chain (b): 30 kDa Heavy Chain (oFc): 51 kDa. B, Size exclusion chromatography using an S200 column on an Akta FPLC shows homogenous product. Molecular weight markers suggest size is similar to that expected for a glycosylated protein (-160 kDa plus sugars). C, ELISA demonstrates specific binding of the purified Ob.1 A12 TCR-Fc protein to its corresponding peptide-MHC complex. Plates were coated with 85-99MBP/ DRB1 * I 501 protein or MHC with the control peptide CLIP, CLIP/ DRB1 * 1501 (both obtained from the NIH tetramer facility), purified TCR added and detected with goat anti-human Fe-FIRP.

[0057] FIG. 15: Sequence changes in the CDRs conferring improved pp65/ A2 binding affinity to the RA14 TCR. Positions indicated by arrows are of greatest interest; no changes were identified outside these regions.

[0058] FIG. 16A-C: Selected variants show excellent expression characteristics and improved pp65/ A2 affinity. Selected TCR variants were expressed in CHO cells as TCR- mouse Fc fusion proteins and purified by protein A chromatography. A, SDS-PAGE gel shows protein purity and mono-dispersity, as well as the expected molecular weights under non reducing (-150 kDa) and reducing conditions (-50 and 25 kDa bands). B, Protein monodispersity was evaluated using analytical size exclusion chromatography with an S200 Superdex column on an Akta FPLC (30 itg each protein was injected, except 100 pg was used for the a2b8 TCR-mFc). C, An ELISA in which dilutions of the purified TCR-Fc proteins were used for coating, followed by monomeric pp65/A2 and streptavidin-HRP for detection shows that selected variants exhibit affinity increases, as measured by the TCR-Fc concentration resulting in 50% of the maximum ELISA signal. Controls include uncoated wells and an irrelevant peptide/ A2 complex

[0059] FIG. 17: Binding kinetics for selected TCR-Fc variants with the pp65/A2 ligand. SEC-purified TCR-Fc was immobilized on CMS chips at -500 RU. The monomeric pp65/ A2 was injected at concentrations ranging from 0.1 - 500 nM. The control pMHC complex, the GIL peptide from HCV complexed with the A2 MHC, was injected at the highest concentration, 500 nM. Binding kinetics were determined using a 1 : 1 Langmuir fit. Experiments performed on a BIAcore XI 00 SPR instrument.

[0060] FIG. 18: Increased TCR affinity resnits in increased selectivity of binding to pp65 peptide-pulsed antigen presenting cells. Selected TCR variants were expressed in CHQ ceils as TCR-mouse Fc fusion proteins and purified. These were then used to stain human T2 antigen presenting cells which were pulsed with 100 mM pp65 or control HCV peptide and detected with anti-mouse Fc (F(ab)2-AF647 in the presence of Fc block. The observed population mean fluorescence shift correlates with the TCR affinity.

[0061] FIG. 19: Engineered TCR sequences activate T cells in the presence of pp65~peptide~pidsed antigen presenting cells. Selected RAM TCR sequences were expressed with the five described N-to-Q substitutions that eliminate N-l inked glycosylation sites on the surface of human Jurkat cells as well as native TCR transmembrane and intracellular sequences. These cells were co-cultured w/ human T2 antigen presenting cells pulsed with NLV (pp65) or KLV (control flu) peptides and the resulting T cell activation monitored by CD69 upregulation & flow cytometry.

[0062] FIG. 20A-I): The vFcyRs gp34 and tgp68 were expressed in CHO cells and pnrified. Receptors were cloned from the AD169/GFP bacterial artificial chromosomal DNA, appended with strep and FLAG tags, and expressed transiently in CHO cells. A, After purification on a streptactin column, 4 pg of reduced (R) and non-reduced (NR) protein was analyzed by SDS-PAGE. Each protein appeared as a single band and at approximately the correct size (66 kDa for glycosylated tgp68 and 68 kDa for glycosylated gp34). B and C, Protein monodispersity was assessed with size exclusion chromatography (SEC) using a Superdex200 column on an Akta FPLC and D, observed molecular weights for these glycosylated proteins estimated using the elution volumes of proteins with known sizes on the same S200 column.

[0063] FIG. 21A-C: Competition E LISAs indicate that gp34 and FcyRIIlA have overlapping epitopes and gp68 and FcRn have overlapping epitopes. A) Human IgGl (purple shape was coated on high-binding plates. Receptor alone or mixed with competitor was added to plates and detected with anti-FLAG-HRP. B) Human IgGl was coated on ELISA plates, and then a dilution series of FL AG-tagged FcRn was added and detected with anti- FLAG-HRP (negative control). Competition was performed by mixing each competitor (gp34, tgp68, or excess IgGl) at 0.5 pg/ml (6.7 nM) with FcRn prior to addition to the plate. C) Human IgGl was coated on ELISA plates, and then a dilution series of FL AG-tagged FcyRIIIA was added and detected with anti-FLAG-HRP (negative control). Competition was performed by mixing each competitor (gp34, tgp68, or excess IgGl) at 0.2 pg/ml (0.3 nM) with FcyRIIIA prior to addition to the plate.

[0064] FIG. 22A-B: Receptor binding data for the gp68 Fe escape variant YTE. The YTE antibody changes (M252Y, S254T, T256E (Dall'Acqua etal. 2006) eliminate binding to the gp68 vFc receptor while actually increasing binding to the hist FcRn. Binding demonstrated using flow cytometry' with yeast expressing the wild-type or YTE human IgGl Fc as an Aga-2 fusion protein. Ceils were then stained with an anti-human Fe-AF647 to monitor Fc display level and one of the four Fe receptors plus fluorescent detection (FcRn, FcgRIIIa, gp34 or gp68). Note, gp34 and gp68 bind Fc with nanomolar affinities while the host receptors bind with micromolar affinities; FcR binding w'as monitored at low pH to increase binding affinity. YTE is known to slightly reduce binding to FcgRIIIa.

[0065] FIG. 23A-B: Antibody Fc sequences that lack of binding to gp34 but retain binding to FcRn. A, sequence alignment from Kabat residues 220 to 353 of human IgGl . B, list of selected amino acid changes using Kabat numbering scheme.

[0066] FIG. 24: Receptor binding data for selected gp34 Fc escape variants. Variants selected by yeast display were analyzed for binding to gp34, human FcRn and human FcgRIIIa by flow cytometry. Yeast expressing the wild-type or selected human IgGl Fc variants as an Aga-2 fusion protein w'ere stained with each Fe receptor individually (FcRn, FcgRIIIa, gp34) followed by fluorescent detection. FcRn binding w'as monitored at low pH to increase binding affinity.

[0067] FIG. 25A-C: Expression of the OT-II TCR-Fc in CHO cells followed by protein A chromatography purification. A, SDS-PAGE gel, B, size exclusion chromatography and C, ELISA with purified TCR-Fc protein.

[0068] FIG. 26A-C: DO11.10 and variants bind KJ1-26 as scTCR-Fc fusion proteins. Proteins were produced in CHO cells as scTCR-Fc fnsion proteins nsing the VP-linker-Va format and purified using protein A chromatography. A, Protein purity and size was assessed by SDS-PAGE under reducing and non-reducing conditions. B, Analytical SEC was used to assess the polydispersity of the purified protein preparations following seven days storage at 4°C using an S200 column. Shown are traces for DOl l-Fc, 176-Fc, 817-Fc and the control 172.10-Fc. C, Binding to the KJ1 -26 clonotypic antibody was assessed by ELISA. Purified scTCR-Fc proteins were titrated on KJI-26 coated and blocked. Shown are DOl l-Fc (circles), 176-Fc (squares), 817-Fc (triangles) and the 172.10-Fc control (inverted triangles). Shown are the mean and std dev for duplicates; data are representative of three replicate experiments

[0069] FIG. 27A-C: DOl l ami variants detect OVA/l-Ad on A20 antigen presenting cells as scTCR-Fc fusion proteins. A, Murine A20 cells were pulsed overnight with 100 mM QVA323-339 peptide or an equivalent volume of DMSO before staining with 0.5 mM of each TCR-Fc fusion variant and detection with anti-human Fc (AF-647) in the presence of Fc block. Shown are histograms resulting from staining with only the secondary antibody; the 172.10-Fc control, DOl l-Fc, 176-Fc and 817-Fc. For all conditions, background staining to A20 ceils without peptide pulsing are shown (hollow' traces). B, The scTCR-Fc dissociation rates from peptide-pulsed cells were measured using flow cytometry'. Cells were stained as above, with 10 pg/ ^' ml (KJI-26 added at time zero to block scTCR rebinding. Temporal data were fit to a single exponential decay to calculate cellular off-rates. C, Tabulated off-rate data and half-life data (tl/2 = ln2/ koff). Shown are the mean and std dev of replicates. Data are representative of 2-3 independent experiments. No comparisons were statistically significantly different by ANOVA.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0070] While antibodies recognize secreted and surface-bound proteins, T-cell receptors (TCRs) recognize otherwise inaccessible disease-associated intracellular proteins when presented as a processed, nonamerie peptide bound to a major histocompatibility complex (pMHC). TCRs have been primarily explored for cancer applications but could target infectious diseases, such as cytomegalovirus (CMV). However, TCRs are much more difficult to express and engineer than antibodies, and advanced methods are needed to enable their widespread use. Engineered TCRs can be used in adoptive T-cell therapies to re-direct patient T cells to recognize a chosen target, while soluble TCRs can be used as antibody-like reagents to bind specific peptide MHC complexes presented on a cell surface. [0071] Provided herein are antibody-like reagents that specifically recognize CMV- infected cells by virtue of the immunodominant pp65 peptide in complex. These reagents have an increased affinity relative to a native TCR (from ~30 micromolar to 50 nanomolar) and a novel TCR-Fc format providing for very high expression levels. These reagents have multiple potential applications. For example, therapeutic uses of the engineered TCR include targeting brain cancers (e.g., glioblastomas) where latent CMV is reactivated. Another use includes delivering the NLV peptide to cancer cells in a patient and then administering a therapeutic engineered TCR to the patient to detect the efficiency of NLV peptide delivery /display as well as re-target CMV -specific T cells. A therapeutic engineered TCR may be a bispecific molecule that binds to both NLV/A2 and to CD3, thereby re-targeting T cells to destroy virus-infected cells. In addition, the engineered TCRs may be used to monitor NLV/A2 expression on host cells, either in vitro or in vivo. This use includes monitoring NLV presentation after vaccination with novel CMV vaccines as well as detecting active infection in organ transplant recipients.

L The Present Embodiments

[0072] Soluble TCRs have considerable potential as therapeutics and reagents to monitor disease progression or vaccine efficacy. In particular, T cells recognizing the immunodominant NLV peptide from CMV are sufficient to maintain clinical latency, suggesting NLV is a useful marker to monitor disease or vaccination status. Here, variants of the human CMV-specific TCR RA14 with nanomolar affinity for the cognate NLV/A2 complex were identified by selection on the CHO cell surface. These variants retained peptide selectivity and activity when expressed on the surface of human Jurkat T cells. Moreover, high level production of homogeneous protein was observed when the TCR domains were fused to an antibody Fc domain to create an antibody-like targeting molecule. This construct specifically detected NLV/A2 complexes on the surface of human antigen presenting cells at low display levels and provides proof-of-concept for a new TCR engineering strategy.

[0073] Since TCR engineering continues to be challenging with phage and yeast display platforms, it was reasoned that TCR expression on the near-native eukaryotic membrane might offer a more straightforward approach. High levels of acti ve TCR were able to be displayed using a PDGFR transmembrane domain, modified only by inclusion of a previously described non-native disulfide bond between the TCR constant domains (Boulter et al, 2003) Specific pMHC binding activity was measured as the ratio of NLV7A2 tetramer binding to TCR display level, with the wildtype RAM showing a clear population of cells with high specific activity (FIG. 1 C). In contrast, phage or yeast display of scTCRs or paired TCR extracellular domains are restricted to well-behaved germline segments (e.g., mouse TRBV13 and human TRAV12) (Li et al., 2004; Maynard et al., 2005) or require considerable engineering to achieve display of active protein, including identification of specific mutations and co-expression of chaperones (Maynard et al., 2005; Gimnarsen el al, 2013). Even so, variants with partially suppressed stop codons have been isolated, suggesting the proteins retain toxicity (Li el al, 2005).

[0074] Eukaryotic display has been explored previously for TCR engineering. Importantly, these prior reports used completely native TCRs, with TCR extracellular, transmembrane, and intracellular signaling domains expressed on T cells (Kessels et al. , 2000; Chervin et al. , 2008; Malecek et al., 2013). In contrast, use of the PDGFR transmembrane domain fused to just one TCR chain eliminated TCR dependence on CD3 co-expression, provided selection pressure for proper TCR assembly, and allowed the use of CHO cells. An episomal plasmid allowed the more cumbersome retroviral transfection system used in the earlier studies to be avoided while maintaining TCR expression for ~2 months, and while inclusion of a 2A peptide ensured equimolar expression of the alpha and beta chains. Since most therapeutic proteins are produced in CHO cells, this system allows for selection of TCRs with characteristics that are expected to be more predictive of the soluble protein when expressed in CHO cells. Importantly, this includes glycosylation sites that may affect ligand binding (Nguyen et al., 2018) or TCR assembly (FIGS. 7A-D).

[0075] Eukaryotic display platforms have constrained library sizes due to their lower transfection efficiencies as compared to bacteria and yeast. Despite this, the three previously reported eukaryotic TCR libraries all produced interesting clones. Kessels et al. (2000) randomized seven codons in CDR3p of the flu-specific F5 TCR to generate a library of ~3xl0 ⁴ unique clones. After four rounds of fl ow cytometric sorting with labelled tetramer, they isolated a variant with physiologic affinity and newly acquired binding to an altered peptide ligand containing two residue changes. Similarly, Chervin et al. (2008) altered five codons in the mouse 2C TCR CDR3a to yield a library of ~10 ³ -10 ⁴ clones. After two rounds of flow cytometry', they isolated variant mlOO with an estimated 1,900 nM affinity, representing a 4- to-15-fold improvement over the wild-type TCR. By contrast, an even higher affinity 2C variant, m33 with a ~32 nM affinity, was isolated from a similarly designed, but larger (5xl0 ⁵ ), yeast display library (Holler et al, 2003). [0076] The libraries provided here, while still of modest size (4x10 ⁵ for CDR3a and IxlO ⁶ for CDR3 ), were larger than those previously reported for eukaryotic TCR display systems. Taking into account a -50% transfection efficiency, cell death, and dilution with blank plasmid, a single T-150 flask with adherent CHO cells can reasonably yield five-fold coverage of a 5xl0 ⁵ member library. With shaker flasks and suspension cells to facilitate scale up, a library of 10 ' should be achievable. While this remains smaller than many bacterial or yeast- display libraries, the stereotypical TCR-pMHC binding interaction in which the two CDR3 loops dominate peptide binding (Rossjohn et al, 2015), can be exploited to generate targeted mutagenesis libraries rich in higher affinity variants.

[0077] From these libraries, variants with increased on-rate and decreased off-rate were isolated (Table 2). Importantly, the changes in specific tetramer binding observed during library' screening anticipated the affinity improvements measured by SPR (FIGS. 3C-D). When the two selected chains were combined to create variant a¥2 bU8, the benefits were roughly additive, resulting in an overall -60-fold improved NLV/A2 affinity as compared with the wild- type RAM. Specificity for the NLV peptide was retained, as binding to a control HCV/A2 complex was not detected even at 500 nM (Table 2). Analysis of previously engineered TCRs indicates that affinity improvements are typically due to large decreases in off-rate and small increases in on -rate, as was observed for RAM Structurally, this has been mediated by increases in overall shape complementarity and formation of new contacts between the TCR and peptide residues, which retain the native TCR/pMHC binding angle (Sami et al, 2007; Cole et a!., 2013). For example, four residue changes in CDR3|3 of the A6 TCR formed 26 new peptide contacts that were sufficient to increase affinity for the tax/A2 complex from 3.2 mM to 4 nM (Cole et al. , 2013).

[0078] As expected based on the significantly lower affinities present in endogenous TCR repertoires, the sequences identified here have not been reported in human sequencing studies of NLV/ A2 -binding T cells (Trautmann et al. , 2005; Wang et al. , 2012). In CDR3a, two residues from the xnGNQF motif were altered: the conserved glycine was not always observed in position a: 109, while the enhanced on-rate aV2 variant replaced the canonical a:Q115 with a histidine. Regardless, these modest sequence and affinity changes support the idea that this common public CDR3a sequence is relatively optimized for NLV/A2 binding. Furthermore, the structure of the related TCR C7 (CDR3a sequence: ITGNQF) in complex with NLV/A2 demonstrates the ability of this CDR3a to preserve a similar peptide-binding interaction while making small adjustments to accommodate a different CDR3 (Yang et al, 2015). Changes to the CD ip motif SxnTGxnYGY were more dramatic despite revealing VP:G1 1 1 to be absolutely conserved in all sequences recovered in this work; notably, residue nb:01 1 1 was anticipated as crucial for binding from the initial analysis of the RA14-NLV/A2 crystal structure (Gras et al. , 2009) Among other€DR3p residues, the motif residue V|3:G115 was not always retained, but was preferentially replaced with hydrophobic residues, with five of ten clones using leucine. The other randomized CDR3 positions all showed evidence of structural plasticity, with the slow off-rate bUΈ variant preferring hydrophobic residues in all three modified positions (Table 1).

[0079] High-level expression of soluble TCR proteins continues to present challenges due to their low expression levels and weak heterodimerization properties. Common expression strategies include generation of single-chain TCRs, which typically requires identification of specific residue changes that support folding and expression in this format (Shusta et al, 2000; Aggen etal , 2011; Wulfing & Piuckthun, 1994); refolding of intact extracellular domains (van Bozel et al. , 2009), often with a modified disulfide bond supporting constant domain heterodimerization introduced at residues Ca:T84C and C :S79C (Boulter et al. , 2003); and TCR-antibody chimeras expressed in eukaryotes. For this latter approach, a variety of designs have been evaluated, including single-chain TCRs fused to a constant beta domain and then antibody heavy chain domains 1-3 (Mosquera et al, 2005), complete TCR extracellular domains appended with constant kappa domains (Gregoire et al , 1991) or an intact antibody fused to the TCR C -terminus (Lunde et al, 2010; Lebowitz et al, 1999) and simply replacing the antibody variable regions with TCR variable regions (Lunde et al , 2010)

[0080] The present approach was to use the simplest antibody-like design that supported expression of active TCR material. This strategy was guided by the desire to employ established antibody purification processes and minimize the risks of proteolysis and immunogenicity in the resulting protein. After evaluation of several designs, substitution of the antibody Fab domains with the TCR extracellular domains emerged as the best approach. Specifically, the extracellular TCR a chain was fused to the antibody Fc domain with the b chain expressed in turns. Subsequent replacement of the human Fc for the corresponding mouse Fc domains allowed for detection of NLV/A2 complexes on peptide-pulsed antigen presenting cells (FIG. 9B). [0081] Additional modifications were introduced to support proper assembly of the TCR-Fc chimera. In addition to the previously described engineered disulfide bond between the TCR constant domains (Boulter et al, 2003), the human IgGl upper and core hinge region introduced a second disulfide bond joining the TCR constant domains and two disulfide bonds stabilizing the Fc homodimer, while the free cysteine at position 85.1 was replaced with an alanine. Finally, two predicted N-linked glycosylation sites in the variable domains and three in the human constant TCR domains were eliminated by N-to-Q substitutions. Together, this allowed for production of 0.75-1 mg purified TCR2dsAgly-huFc protein from 50 mL media, matching typical antibody yields in the lab scale transient CHO cell expression system. This strategy has yielded similar production levels for three additional TCRs.

[0082] Prior attempts to replace the antibody Fab with the TCR extracellular domains 'ere less successful (Lunde el al , 2010, Ozawa et al , 2012); but these in general did not include the antibody upper hinge region to provide an additional di-sulfide bond stabilizing the alpha and beta chains and did not remove glycosylation sites then thought to increase protein solubility. Although endogenous TCRs are highly glycosylated on the T-celi surface, analysis of TCR affinity and structure are typically performed on baeterially expressed TCR protein, which is aglycosylated. The expression system developed here allows for direct comparison of identical TCR proteins with and without glycosylation at specific sites. Removal of predicted N-linked glycosylation sites dramatically increased protein homogeneity as measured by size- exclusion chromatography and SDS-PAGE (FIG. 5 A), with no negative impact on yield or thermal stability. Further investigation could provide insights into the impact of glycosylation on TCR function, as removal of glycosylation sites has been shown to increase the functional avidity of TCRs expressed on T cells (Kuball et al , 2009).

[0083] The ability of TCRs to detect pMHC on the target cell surface is inextricably linked to not just the TCR-pMHC affinity but also the peptide display level and pMHC clustering on the cell surface. Peptide display level in turn reflects several factors, including antigen expression level, proteolysis sensitivity, and peptide-MFIC affinity. For TCRs expressed with their native signaling machinery' on T ceils, an affinity of 1-5 mM seems sufficient to confer maximal signaling responses (Irving etal , 2012) while retaining the ability to respond to as few as 1-10 pMHC complexes per cell (Kageyama et al. , 1995; Sykuiev et al. , 1996) For soluble TCRs, which lack the elaborate array of coreceptors that support cellular TCR-pMHC recognition, high affinity is crucial to allow' detection of low' levels of target pMHC antigens. In this work, the ability of RA14 TCR variants to detect NLV/A2 correlated strongly with affinity for human T2 cells pulsed with 100 mM NLA ⁷ peptide (FIG. 9B). A subsequent peptide dosing experiment demonstrated that the oV2,pV8 variant could detect NLV/A2 complexes after pulsing T2 cells with as little as 0.5 mM peptide (FIG. 9C).

[0084] The sensitivity exhibited by aV2. V8 is relevant for detection in clinical settings. The NLV peptide was previously reported to present -100 molecules/cell when primary human fibroblasts were infected with an AD 169 strain that retains the ability to suppress MHC display (Makler et aL, 2010). A bivalent TCR dike antibody with a 300 nM affinity was previously shown to detect the NLV/A2 complex after infection of primary human fibroblasts with CMV, but has not been further developed (Makler et aL, 2010). The higher 50 nM affinity of the present engineered TCR suggests that the aV2 |3V8 clone could be used to track pMHC display and demonstrates the feasibility of the present TCR engineering approach. Moreover, the flow cytometer sensitivity can be increased with an enzymatic amplification step (Anikeeva et aL, 2009) or a single molecule fluorescence assay (Boss! et aL, 2013).

[0085] There is considerable interest in using TCRs to monitor the presence of disease- related peptides and a need to detect the NLV/A2 complex to support CMV diagnostics and therapeutics development. High-affinity, soluble TCRs directed at cancer antigens are currently under evaluation in the clinic as part of a bispecific molecule (Boss! et aL, 2014). As compared to cancer antigens, infectious disease-associated antigens are more likely to be unique to diseased tissue, thereby reducing the risks of toxicity

IL Engineered NLY7A2-specific TCRs

[0086] In some embodiments, provided herein are engineered antigen receptors ( e.g ., TCRs or CARs) having antigenic specificity for NLV/A2. The engineered antigen receptors may comprise an alpha chain CDR.3 having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-7 (or a sequence from Table 1C) and/or a beta chain CDR3 having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 8-17 (or a sequence from Table ID). The engineered antigen receptors may comprise an alpha chain with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity or similarity to any one of SEQ ID NOs: 18-24 (or a sequence from Table 1C) and/or a beta chain with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity or similarity to any one of SEQ ID NOs: 25-34 (or a sequence from Table ID). Also provided herein are polynucleotides encoding the alpha chain and/or beta chain of the NLV/A2-specific antigen receptors provided herein. As used herein numbering of amino acids relative to TCR sequences uses the imgt numbering system (see, the world wide web at imgt.org/IMGTrepertoire/Proteins/proteinDisplays. php?species=human&latin=Homo%20sap iens&group ^: =TRAV, incorporated herein by reference).

[0087] Exemplary antigen receptors, including CARs and recombinant TCRs, as well as methods for engineering and introducing the receptors into cells, include those described, for example, in International Patent Application Publication Nos. WG2000/14257, WO2013/126726, WO2012/129514, WO2014/031687, WO2013/166321, WO2013/071154, W02013/123061; U.S. Patent Application Publication Nos. US2002/0131960, US2013/0287748, US2013/0149337; U.S. Patent Nos. 6,451,995, 7,446, 190, 8,252,592,

8,339,645, 8,398,282, 7,446,179, 6,410,319, 7,070,995, 7,265,209, 7,354,762, 7,446, 191,

8,324,353, and 8,479,118; and European Patent Application No. EP2537416. In some aspects, the genetically engineered antigen receptors include a CAR as described in U.S. Patent No. 7,446, 190, and those described in International Patent Application Publication No. W 02014/055668.

[0088] In some embodiments, the engineered antigen receptors include recombinant T cell receptors (TCRs). A“T cell receptor” or“TCR” refers to a molecule that contains a variable a and b chains (also known as TCRa and TOIb, respectively) and that is capable of specifically binding to an antigen peptide bound to an MHC receptor. The TCRs may comprise an alpha chain CDR3 having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1 -7 (or a sequence from Table 1C) and/or a beta chain CDR3 having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 8-17 (or a sequence from Table ID). The TCRs may comprise an alpha chain with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity or similarity to any one of SEQ ID NOs: 18-24 (or a sequence from Table 1C) and/or a beta chain with at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity or similarity to any one of SEQ ID NOs: 25-34 (or a sequence from Table ID). [0089] In some embodiments, a TCR also can contain a constant domain, a transmembrane domain, and/or a short cytoplasmic tail. For example, in some aspects, each chain of the TCR can possess one N-terminal immunoglobulin variable domain, one immunoglobulin constant domain, a transmembrane region, and a short cytoplasmic tail at the

5 C-terminal end. In some embodiments, a TCR is associated with invariant proteins of the CD 3 complex involved in mediating signal transduction. Unless otherwise stated, the term“TCR” should be understood to encompass functional TCR fragments. The term also encompasses intact or full-length TCRs.

[0090] For purposes herein, reference to a TCR includes any TCR or functional0 fragment, such as an antigen-binding portion of a TCR that binds to a specific antigenic peptide bound in an MHC molecule, i.e., MHC-peptide complex. An“antigen-binding portion” or “antigen-binding fragment” of a TCR, which can be used interchangeably, refers to a molecule that lacks a portion of the structural domains of a TCR, but that binds the antigen (e.g, MHC- peptide complex) to which the full TCR binds. In some cases, an antigen-binding portion5 contains the variable domains of a TCR, such as variable a chain and variable b chain of a TCR, sufficient to form a binding site for binding to a specific MHC-peptide complex, such as generally where each chain contains three complementarity determining regions.

[0091] In some embodiments, the variable domains of the TCR chains associate to form loops, or complementarity determining regions (CDRs) analogous to immunoglobulins, which0 confer antigen recognition and determine peptide specificity by forming the binding site of the TC molecule. Typically, like immunoglobulins, the CDRs are separated by framework regions (FRs). In some embodiments, CDR3 is the main CDR responsible for recognizing processed antigen, although CDR1 of the alpha chain has also been shown to interact with the N-terminal part of the antigenic peptide, whereas CDR1 of the beta chain interacts with the C-5 terrninal part of the peptide. CDR2 is thought to recognize the MHC molecule. In some embodiments, the variable region of the b-chain can contain a further hypervariability (HV4) region.

[0092] In some embodiments, the TCR chains contain a constant domain. For example, like immunoglobulins, the extracellular portion of TCR chains (e.g., a-chain, b-chain) can0 contain two immunoglobulin domains, a variable domain (e.g ., Va or nb; typically amino acids J to 116 based on Kabat numbering (Kabat et al, "Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5 ^th ed.) at the N-terminus, and one constant domain (e.g, a-chain constant domain or Ca, typically amino acids 117 to 259 based on Kabat, b-chain constant domain or Ob, typically amino acids 117 to 295 based on Kabat) adjacent to the cell membrane. For example, in some cases, the extracellular portion of the TCR formed by the two chains contains two membrane-proximal constant domains, and two membrane-distal variable domains containing CDRs. The constant domains of the TCR contain short connecting sequences in which a cysteine residue forms a disulfide bond, making a link between the two chains. In some embodiments, a TCR may have an additional cysteine residue in each of the a and b chains such that the TCR contains two disulfide bonds in the constant domains. [0093] In some embodiments, the TCR chains can contain a transmembrane domain.

In some embodiments, the transmembrane domain is positively charged. In some cases, the TCR chains contains a cytoplasmic tail. In some cases, the structure allows the TCR to associate with other molecules like CD3. For example, a TCR containing constant domains with a transmembrane region can anchor the protein in the cell membrane and associate with invari ant subunits of the CD3 signaling apparatus or complex.

[0094] In some embodiments, the TCR may be a heterodimer of two chains a and b or it may be a single-chain TCR construct. In some embodiments, the TCR is a heterodimer containing two separate chains (a and b chains) that are linked, such as by a disulfide bond or disulfide bonds. In some embodiments, a TCR for a target antigen (e.g, NLV7A2) is identified and introduced into the cells. In some embodiments, a nucleic acid encoding the TCR can be obtained from a variety of sources. In some embodiments, the TCR is obtained from a biological source, such as from cells such as from a T-cell hybridomas. In some embodiments, the T cells can be a cultured T-cell hybridoma or clone.

Table 1A. CDR3 sequences for a chain variants.

Table 1.4-2, CDR1 sequences for a chain variants.

Table IB. CDR3 sequences for b chain variants.

Table 1C. Protein sequences for a chain variable regions. Underlined text indicates the CDR region; gray text indicates N-to-Q changes introduced for deglycosylation; gray text in the CDRs indicates a change in the CDR sequence selected during library sorting and associated wi th i ncreased afti ni ty

Table ID. Protein sequences for b chain variable regions. Underlined text indicates the CDR region; grayjext indicates N-to-Q changes introduced for deglycosylation; gray text in the

CDRs indicates a change in the CDR sequence selected during library sorting and associated with increased affinity.

A, Soluble TCRs and BiTEs

[0095] In addition, the present disclosure provides soluble TCRs. Furthermore, soluble bispecific T cell-engaging molecules (BiTEs) can be generated by linking the engineered NLV/A2-specific TCR to CD3- or CD 16-specific Fab fragments or CD3- or CD 16-specific single-chain antibodies. These bi specific molecules can bind the cell surface of a. CMV- infected cell via their TCR domain binding to the NLV/A2 complex, and the CD 3 -specific domain would crosslink the TCR. This would result in cellular activation and elimination of the target cell. Thus, these soluble bispecifie TCR constructs can be used for treating patients (e.g., transplant patients with active CMV disease or brain cancer patients) directly.

[0096] In the context of this application,“solubility” is defined as the ability of the TCR to be purified as a mono-disperse heterodimer in phosphate buffered saline (PBS) (KC1 2 7 M, KH2PO4 1.5 mM, NaCl 137 mM, and Xa.dHti 8 mM, pH 7.1 -7.5. Life Technologies, Gibco BRL) at a concentration of 1 mg/ml and for more than 90% of said TCR to remain as a mono disperse heterodimer after incubation at 25° C for 1 hour

[0097] The soluble TCR can be fused to an antibody Fc region to create an antibody - TCR chimera. For this, the antibody Fc is fused to the TCR extracellular domains. For example, the TCR a chain may be fused to the Fc and the TCR b chain may be expressed in trans. The chimera may include the antibody hinge region. The antibody Fc may be derived from a mouse or human antibody.

[0098] The soluble TCR can be used as a probe for diagnostic evaluation of peptide/MHC in cells, either in vitro or in vivo, or to direct therapeutic molecules to sites of interest in vivo. The soluble TCR molecules also could be labeled with tracers, such as a fluorescent probe or radioactive probe, and then used for diagnostic evaluation of the presentation of peptide/MHC in cells. Furthermore, the soluble TCR molecules could be linked with therapeutic molecules, such as toxin, and then directed to the sites for the treatment of infected cells.

[0099] In some embodiments, the present disclosure provides soluble TCRs, such as an engineered NLV/A2-specific TCR provided herein. Soluble TCRs may be used for investigating specific TCR-pMHC interactions or as a diagnostic tool to detect infection or response to vaccination. Soluble TCRs may have applications in staining, for example to stain cells for the presence of a particular peptide antigen presented in the context of the MI 1C Similarly, soluble TCRs can be used to deliver a therapeutic agent, for example a cytotoxic compound or an immunostimulating compound, to cells presenting a particular antigen. In some aspects, the TCR is linked to another molecule that delivers a cell in proximity to the tumor. In further aspects, the TCR delivers a toxin, a cytokine, costimulatory ligand, or inhibitor ligand and directs the molecule, ceil or compound to the target cells expressing the peptide-MHC.

[00100] In some aspects, the present disclosure provides a soluble TCR that comprises (i) all or part of a TCR a chain (e.g, SEQ ID NOs: 18-24), except the transmembrane domain thereof, and (ii) all or part of a TCR b chain (e.g., SEQ ID NOs: 25-34), except the transmembrane domain thereof, wherein (i) and (ii) each comprise a functional variable domain and at least a part of the constant domain of the TCR chain, and are linked by a disulfide bond between constant domain residues that is not present in native TCR.

[00101] In some aspects, the soluble TCR comprises a TCR a or g chain extracellular domain dimerized to a TCR b or d chain extracellular domain respectively, by means of a pair of C-terminai dimerization peptides, such as leucine zippers (International Patent Publication No. WO 99/60120, U.S. Patent No. 7,666,604).

[00102] A soluble TCR of the present disclosure may be provided in substantially pure form, or as a purified or isolated preparation. For example, it may be provided in a form which is substantially free of other proteins. [00103] The TCR of the present disclosure may alternatively or additionally be associated with ( e.g ., covalently or otherwise linked to) a therapeutic agent which may be, for example, a toxic moiety for use in cell killing, or an immunostimulating agent such as an interleukin or a cytokine. The present disclosure also provides a method for delivering a therapeutic agent to a target cell, which method comprises contacting potential target cells with a TCR under conditions to allow attachment of the TCR to the target cell, said TCR being specific for the TCR ligand and having the therapeutic agent associated therewith.

[00104] In particular, the soluble TCR can be used to deliver therapeutic agents to the location of cells presenting a particular antigen. This wOuld be useful in many situations and, in particular, against certain types of tumors A therapeutic agent could be delivered such that it would exercise its effect locally but not only on the cell it binds to. Thus, one particular strategy envisages anti-tumor molecules linked to T cell receptors specific for NLV/A2 in order to kill glioblastoma cells.

[00105] Many therapeutic agents could be employed for this use, for instance radioactive compounds, enzymes (perforin for example) or chemotherapeutic agents (cisplatin for example). To ensure that toxic effects are exercised in the desired location, the toxin could be inside a liposome linked to streptavidin so that the compound is released slowly. This will prevent damaging effects during the transport in the body and ensure that the toxin has maximum effect after binding of the TCR to the relevant antigen presenting cells. B. Chimeric Antigen Receptors

[00106] In various aspects, the antigen binding region of the TCR may be included in a chimeric antigen receptor (CAR) as the extracellular domain comprising an antigen binding region. The CAR may be transfected into cells (e.g., autologous or allogeneic ceils) that may be used in an adoptive cell transfer therapy. In some embodiments, the CAR is humanized to reduce immunogenicity (hCAR).

[00107] The CARs generally include an extracellular antigen (or ligand) binding domain linked to one or more intracellular signaling components, in some aspects via linkers and/or transrnembrane domain(s). Such molecules typically mimic or approximate a signal through a natural antigen receptor, a signal through such a receptor in combination with a costimulatory receptor, and/or a signal through a costimulatory receptor alone. In some embodiments, the CAR includes an antigen-binding portion or portions of a TCR.

[00108] The arrangement of the antigen-binding domain of a CAR may be multimeric. The hinge portion of the CAR may in some embodiments be shortened or excluded (i.e., generating a CAR that only includes an antigen binding domain, a transrnembrane region, and an intracellular signaling domain). In some embodiments, the hinge region may have the first cysteine maintained, or mutated by a proline or a serine substitution, or be truncated up to the first cysteine. In some embodiments, the hinge portion of may comprise or consist of an 8- 14 amino acid peptide (e.g., a 12 AA peptide), a portion of CD 8 a, or the IgG4 Fc. In some embodiments, the antigen binding domain may be suspended from cell surface using a domain that promotes oligomerization, such as CD8 alpha. In some embodiments, the antigen binding domain may be suspended from cell surface using a domain that is recognized by monoclonal antibody (mAh) clone 2D 3 (mAb clone 2D3 described, e.g, in Singh et al, 2008).

[00109] The endodomain or intracellular signaling domain of a CAR can generally cause or promote the activation of at least one of the normal effector functions of an immune ceil comprising the CAR. For example, the endodomain may promote an effector function of a T cell such as, e.g., cytolytic activity or helper activity including the secretion of cytokines. The effector function in a naive, memory, or memory-type T cell may include antigen-dependent proliferation. The terms“intracellular signaling domain” or“endodomain” refers to the portion of a CAR that can transduce the effector function signal and/or direct the cell to perform a specialized function. While usually the entire intracellular signaling domain may be included in a CAR, in some cases a truncated portion of an endodomain may be included. Generally, endodomains include truncated endodomains, wherein the truncated endodomain retains the ability to transduce an effector function signal in a cell.

[00110] In some embodiments, an endodomain comprises the zeta chain of the T cell receptor or any of its homologs (e.g., eta, delta, gamma, or epsilon), MB 1 chain, B29, Fc RIII, Fc RI, and combinations of signaling molecules, such as OB3z and CD28, CD27, 4- 1BB, DAP- 10, 0X40, and combinations thereof, as well as other similar molecules and fragments. Intracellular signaling portions of other members of the families of activating proteins can be used, such as FcyRIII and FcsRI. In some embodiments, an endodomain may comprise the human OB3z intracellular domain.

[00111] The antigen-specific extracellular domain and the intracellular signaling-domain are preferably linked by a transmembrane domain. Transmembrane domains that may be included in a CAR include, e.g., the human IgG4 Fc hinge and Fc regions, the human CD4 transmembrane domain, the human CD28 transmembrane domain, the transmembrane human€B3z domain, or a cysteine mutated human OB3z domain, or a transmembrane domain from a human transmembrane signaling protein such as, e.g ^· ., the CD 16 and CDS and erythropoietin receptor.

[00112] In some embodiments, the endodomain comprises a sequence encoding a costimulatory receptor such as, e.g , a modified CD28 intracellular signaling domain, or a CD28, CD27, QX-40 (CD 134), DAP 10, or 4- IBB (CD 137) costimulatory receptor. In some embodiments, both a primary' signal initiated by CD3 z, an additional signal provided by a human costimulatory receptor may be included in a CAR to more effectively activate a transformed T cells, which may help improve in vivo persistence and the therapeutic success of the adoptive immunotherapy. As noted in Table 2, the endodomain or intracellular receptor signaling domain may comprise the zeta chain of CD3 alone or in combination with an Fey RIII costimulatory signaling domains such as, e.g., CD28, CD27, DAP 10, CDI 37, 0X40, CD2, 4-1BB. In some embodiments, the endodomain comprises part or all of one or more of TCR zeta chain, CD28, CD27, OX40/CD134, 4-1BB/CD137, FccRIy, ICOS/CD278, IL- 2Rbeta/CD I22, IL-2Ralpha/CD132, DAP 10, DAP 12, and CD40. In some embodiments, 1, 2, 3, 4 or more cytoplasmic domains may be included in an endodomain. For example, in some CARs it has been observed that at least two or three signaling domains fused together can result in an additive or synergistic effect [00113J In some aspects, an isolated nucleic acid segment and expression cassette including DNA sequences that encode a CAR may be generated. A variety of vectors may be used. In some preferred embodiments, the vector may allow for delivery of the DNA encoding a CAR to immune such as T cells. CAR expression may be under the control of regulated eukaryotic promoter such as, e.g., the MNDU3 promoter, CMV promoter, EF1 alpha promoter, or Ubiquitin promoter. Also, the vector may contain a selectable marker, if for no other reason, to facilitate their manipulation in vitro. In some embodiments, the CAR can be expressed from mR A in vitro transcribed from a DNA template.

[00114] Chimeric antigen receptor molecules are recombinant and are distinguished by their ability to both bind antigen and transduce activation signals via immunoreceptor activation motifs (ITAM's) present in their cytoplasmic tails. Receptor constructs utilizing an antigen-binding moiety (for example, generated from single chain antibodies (scFv)) afford the additional advantage of being“universal” in that they can bind native antigen on the target cell surface in an HLA-independent fashion. For example, a scFv constructs may be fused to sequences coding for the intracellular portion of the CD3 complex’ s zeta chain (z), the Fc receptor gamma chain, and sky tyrosine kinase.

[00115] In some embodiments, a TCR is included in a CAR as the antigen binding domain {e.g., as a scFv region) and the CAR further comprises a hinge region, a transmembrane region, and an endodomain. Table 2. Regions that may be included in an anti-NLV/A2 targeting CAR

z-zeta; D-mutant; Note = 4-1BB is also referred to as CD 137;“+” refers to the fusion of the different regions.

III. Engineered NLV/A2-specific Cells

[00116] Antigen-specific cells can be generated by using the NLV/A2-specific TCRs provided herein. For example, the TCR or CAR sequence may be inserted into a vector (e.g., retroviral or !entiviral vector) that is introduced into host cells, such as T cells (e.g, CD4 ⁺ T cells, CD8 ⁺ T cells, gd T cells, or Tregs), NK cells, invariant NK cells, NKT cells, mesenchymal stem cells (MSCs), or induced pluripotent stem (iPS) cells to generate antigen- specific cells that can be used for adoptive cell therapy. For example, the host cells may be autologous or allogeneic cells (e.g., isolated from an umbilical cord).

[00117] Further provided herein are cells, such as T cells, NK cells, invariant NK ceils, or NKT cells, engineered to express the NLV/ A2-spedfi c TCR or CAR provided herein. These effector immune cells may express a TCR together with CDS molecules or other signaling domains linked to the TCR, which would initiate the signal transduction in these cells.

[00118] The engineered immune cell s may be constructed using any of the many well-established gene transfer methods known to those skilled in the art. In certain embodiments, the engineered cells are constructed using viral vector-based gene transfer methods to introduce nucleic acids encoding an NLV/A2-specific TCR. The viral vector-based gene transfer method may comprise a lenti viral vector, a retroviral vector, an adenoviral or an adeno-associated viral vector. In certain embodiments, the engineered cells are constructed using non-virai vector-based gene transfer methods to introduce nucleic acids encoding a NLV/A2-specific TCR or CAR The vector for the TCR may comprises the alpha chain polypeptide and the beta chain polypeptide, which may be linked by a linker domain or IRES sequence. The linker domain may comprise one or more cleavage sites, such as a Turin cleavage site and/or a P2A cleavage site, which may be separated by a spacer, such as SGSG or GSG In certain embodiments, the non-virai vector-based gene transfer method comprises a gene-editing method selected from the group consisting of a zinc -finger nuclease (ZFN), a transcription activator-like effector nuclease (TALENs), and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) nuclease. In certain embodiments, the non-virai vector-based gene editing method comprises a transfection or transformation method selected from the group consisting of lipofection, nucleofection, virosomes, liposomes, polycation or lipid: nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA.

IV. Methods of Use

[00119] As used herein, the terms“treat,”“treatment,”“treating,” and the like refer to the process of ameliorating, lessening, or otherwise mitigating the symptoms of a disease or condition in a subject by, for example, administering a therapeutic agent to the subject, or by performing a surgical, clinical, or other medical procedure on the subject.

[00120] As used herein, the terms “subject” or “patient” are used interchangeably herein to refer to an individual, e.g., a human or a non-human organism, such as a primate, a mammal, or a vertebrate.

[00121] As used herein, the terms“therapeutically effective” or“therapeutically beneficial” and the like refer to a therapeutic agent, or a surgical, clinical, or other medical procedure that ameliorates, mitigates or otherwise relieves one or more symptoms of a disease, disorder, or condition, thereby enhancing the well-being of a subject having a disease, disorder, or condition by, for example, reducing the frequency or severity of the signs or symptoms of a disease, disorder, or condition. Thus, a therapeutically effective or therapeutically beneficial cancer treatment may, for example, reduce the size of a tumor, reduce the growth rate of a tumor, reduce the likelihood of tumor dissemination or metastasis.

[00122] Provided herein are methods for treating a disease or disorder in a subject comprising administering to the subject a therapeutically effective amount of a soluble TCR of the present embodiments to a population of NLV/'A2-speeific cells, such as T ceils, NK cells, invariant NK cells, NKT ceils, MSCs, or iPS cells, produced by any of the methods provided herein. Also provided are methods of using a soluble TCR of the present embodiments to detect the presence of NL V/A2 in the surface of a cell, either in vitro or in vivo.

[00123] Provided herein are methods for treating or delaying progression of cancer in an individual comprising administering to the individual an effective amount an NLV/A2-specific T cell therapy, wherein the patient has a cancer where CMV has been reactivated. Adoptive T cell therapies with genetically engineered TCR-transduced T cells (conjugate TCR to other bioreactive proteins (e.g., anti-CD3)) are also provided herein.

[00124] Tumors for which the present treatment methods are useful include any malignant cell type expressing NLV due to reactivation of CMV, such as those found in a solid tumor or a hematological tumor. Exemplary solid tumors can include, but are not limited to, a tumor of an organ selected from the group consisting of pancreas, colon, cecum, stomach, brain, head, neck, ovary, kidney, larynx, sarcoma, lung, bladder, melanoma, prostate, and breast. Exemplary hematological tumors include tumors of the bone marrow, T or B cell malignancies, leukemias, lymphomas, blastomas, myelomas, and the like. Further examples of cancers that may be treated using the methods provided herein include, but are not limited to, brain cancer (glioblastoma), lung cancer (including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous carcinoma of the lung), cancer of the peritoneum, gastric or stomach cancer (including gastrointestinal cancer and gastrointestinal stromal cancer), pancreatic cancer, cervical cancer, ovarian cancer, liver cancer, bladder cancer, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, various types of head and neck cancer, and melanoma.

[00125] In certain embodiments, the method further comprises a step of performing lymphodepletion prior to administration of the therapeutically effective amount of the population of NL\7A2-speeifie TCR cells. In certain embodiments, the lymphodepletion comprises non-myeloablative iymphodepleting chemotherapy. In certain embodiments, the non-myeloablative Iymphodepleting chemotherapy comprises administration of cyclophosphamide and fludarabine.

[00126] In certain embodiments, the method further comprises a step of administering a T-cell growth factor that promotes the growth and activation of autologous T ceils to the subject, either concomitantly with the autologous T cells or subsequently to the autologous T cells. In certain embodiments, the T cell growth factor comprises any suitable growth factor that promotes the growth and activation of the autologous T-cells. In certain embodiments, the T cell growth factor is selected from the group consisting of interleukin (IL)- 2, IL-7, IL-I 5, and IL-12, and combinations thereof (e.g., IL-2 and IL-7, IL-2 and IL-I 5, IL-7 and IL-15, IL-2, IL-7 and IL-15, IL-12 and IL-7, IL-12 and IL-15, or IL-12 and IL-2).

[00127] In certain embodiments, the therapeutically effective amount of the population of NLV/A2-specific TCR cells produced by any of the methods provided herein is administered to the subject intravenously, intratumora!ly, or intraperitonealiy. The appropriate dosage of the cell therapy may be determined based on the type of cancer to be treated, the severity and course of the disease, the clinical condition of the individual, the individual’s clinical history and response to the treatment, and the discretion of the attending physician.

A. Combination Therapies

[00128] In certain embodiments, the compositions and methods of the present embodiments involve an antigen-specific cell population or soluble TCR in combination with at least one additional therapy. The additional therapy may be radiation therapy, surgery (e.g., lumpectomy and a mastectomy), chemotherapy, gene therapy, DNA therapy, viral therapy, RNA therapy, immunotherapy, bone marrow transplantation, nanotherapy, monoclonal antibody therapy, or a combination of the foregoing. The additional therapy may be in the form of adjuvant or neoadjuvant therapy .

[00129] In some embodiments, the additional therapy is the administration of small molecule enzymatic inhibitor or anti -metastatic agent. In some embodiments, the additional therapy is the administration of side- effect limiting agents (e.g, agents intended to lessen the occurrence and/or severity of side effects of treatment, such as anti-nausea agents, etc.). In some embodiments, the additional therapy is radiation therapy. In some embodiments, the additional therapy is surgery. In some embodiments, the additional therapy is a combination of radiation therapy and surgery. In some embodiments, the additional therapy is gamma irradiation. In some embodiments, the additional therapy is a chemotherapy such as, e.g., dacarbazine, or temozoiomide. The additional therapy may be one or more of the chemotherapeutic agents known in the art.

[00130] A T cell therapy or soluble TCR may be administered before, during, after, or in various combinations relative to an additional cancer therapy, such as immune checkpoint therapy. The administrations may be in intervals ranging from concurrently to minutes to days to weeks. In embodiments where the T cell therapy or soluble TCR is provided to a patient separately from an additional therapeutic agent, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the two compounds would still be able to exert an advantageously combined effect on the patient. In such instances, it is contemplated that one may provide a patient with the antibody therapy and the anti-cancer therapy within about 12 to 24 or 72 h of each other and, more particularly, within about 6-12 h of each other. In some situations it may be desirable to extend the time period for treatment significantly where several days (2, 3, 4, 5, 6, or 7) to several weeks (1, 2, 3, 4, 5, 6, 7, or 8) lapse between respective administrations.

[00131] Various combinations may be employed. For the example below an antigen-specific T cell therapy, peptide, or TCR is“A” and an anti -cancer therapy is“B”:

A/B/A B/A/B B/B/A A/A/B A/B/B B/A/A A/B/B/B B/A/B/B

B/B/B/A B/B/A/B A/A/B/B A/B/A/B A/B/B/A B/B/A/ A

B/A/B/A B/A/A/B A/A/A/B B/A/A/A A/B/A/A A/A/B/A [00132] Administration of any compound or therapy of the present embodiments to a patient will follow general protocols for the administration of such compounds, taking into account the toxicity, if any, of the agents. Therefore, in some embodiments there is a step of monitoring toxicity that is attributable to combination therapy.

1. Chemotherapy

[00133] A wide variety of chemotherapeutic agents may be used in accordance with the present embodiments. The term“chemotherapy” refers to the use of drugs to treat cancer. A“chemotherapeutic agent” is used to connote a compound or composition that is administered in the treatment of cancer. These agents or drugs are categorized by their mode of activity within a ceil, for example, whether and at what stage they affect the cell cycle. Alternatively, an agent may be characterized based on its ability to directly cross-link DNA, to intercalate into DNA, or to induce chromosomal and mitotic aberrations by affecting nucleic acid synthesis.

[00134] Examples of chemotherapeutic agents include alkylating agents, such as thiotepa and cyciosphosphamide; alkyl sulfonates, such as busulfan, improsulfan, and piposulfan; aziridines, such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methyl am el amines, including altretamine, tri ethyl enem el amine, trietyl enephosphoramide, triethiylenethiophosphoramide, and trimethyl olomelamine; acetogenins (especially bullataein and bullataeinone), a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8), dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancrati statin; a sarcodictyin; spongistatin; nitrogen mustards, such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, and uracil mustard; nitrosureas, such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics, such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores, aclacinomysins, actinomycin, authrarnycin, azaserine, bleomycins, cactinomycin, carabicin, carminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detombicin, 6-diazo-5-oxo-L-norleucine, doxombicin (including morpholine- doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcel! omycin, mitomycins, such as mitomycin C, mycophenolic acid, nogaiarnycin, olivomycins, peplomycin, potfiromycin, puromycin, quelarnycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, and zorubicin; anti-metabolites, such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues, such as denopterin, pteropterin, and trimetrexate; purine analogs, such as f!udarabine, 6-mercaptopurine, thiamiprine, and thioguanine; pyrimidine analogs, such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, and floxuridine; androgens, such as caiusterone, dromostanolone propionate, epitiostanol, mepitiostane, and testolactone; anti-adrenals, such as mitotane and trilostane: folic acid replenisher, such as frolinic acid, aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniiuracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids, such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenarnet; pirarubicin; !osoxantrone; podophyl!inic acid, 2-ethylhydrazide; procarbazine; PSKpolysaccharide complex; razoxane; rhizoxin; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2',2”- trich!orotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitoi; mitoiactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide, taxoids, e.g., paclitaxel and docetaxel gemcitabine; 6-thioguanine; mercaptopurine; platinum coordination complexes, such as cisplatin, oxaliplatin, and carboplatin; vinblastine, platinum, etoposide (VP- 16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000, difluorometlhylomithine (DMFO); retinoids, such as retinoic acid; capecitabine; carboplatin, procarbazine, piicomycin, gemcitabien, navelbine, famesyl-protein tansferase inhibitors, transplatinum, and pharmaceutically acceptable salts, acids, or derivatives of any of the above.

2. Radiotherapy

[00135] Other factors that cause DNA damage and have been used extensively include what are commonly known as g-rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells. Other forms of DNA damaging factors are also contemplated, such as microwaves, proton beam irradiation (U.S. Patents 5,760,395 and 4,870,287), and UV- irradiation. It is most likely that all of these factors affect a broad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes. Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens. Dosage ranges for radioisotopes vary widely, and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.

3. Immunotherapy

[00136] The skilled artisan will understand that additional immunotherapies may be used in combination or in conjunction with methods of the embodiments. In the context of cancer treatment, immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells Rituximab (RITUXAN®) is such an example. The immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell. The antibody alone may serve as an effector of therapy or it may recruit other ceils to actually affect cell killing. The antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, riein A chain, cholera toxin, pertussis toxin, etc.) and serve as a targeting agent. Alternatively, the effector may he a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target. Various effector cells include cytotoxic T cells and NK cells.

[00137] Antibody-drug conjugates have emerged as a breakthrough approach to the development of cancer therapeutics. Cancer is one of the leading causes of deaths in the world. Antibody-drug conjugates (ADCs) comprise monoclonal antibodies (MAbs) that are covalently linked to cell-killing drugs. This approach combines the high specificity of MAbs against their antigen targets with highly potent cytotoxic drags, resulting in“armed” MAbs that deliver the payload (drug) to tumor cells with enriched levels of the antigen. Targeted deliver}- of the drug also minimizes its exposure in normal tissues, resulting in decreased toxicity and improved therapeutic index. The approval of two ADC drugs, ADCETRIS® (brentuximab vedotin) in 201 1 and KADCYLA® (trastuzumab emtansine or Ί -DM 1 } in 2013 by FDA validated the approach. There are currently more than 30 ADC drag candidates in various stages of clinical trials for cancer treatment (Leal et al. , 2014). As antibody engineering and linker-payload optimization are becoming more and more mature, the discovery and development of new ADCs are increasingly dependent on the identification and validation of new targets that are suitable to this approach and the generation of targeting MAbs. Two criteria for ADC targets are upreguiated/high levels of expression in tumor cells and robust internalization.

[00138] In one aspect of immunotherapy, the tumor cell must bear some marker that is amenable to targeting, i.e., is not present on the majority of other cells. Many tumor markers exist and any of these may be suitable for targeting in the context of the present embodiments. Common tumor markers include CD20, carcinoembryonic antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, FLAP, laminin receptor, erb B, and pi 55. An alternative aspect of immunotherapy is to combine anticancer effects with immune stimulatory effects. Immune stimulating molecules also exist including: cytokines, such as IL-2, IL-4, IL-12, GM-CSF, gamma-IFN, chemokines, such as MIP-1, MCP-1, 1L-8, and growth factors, such as FLT3 ligand.

[00139] Examples of immunotherapies currently under investigation or in use are immune adjuvants, e.g., Mycobacterium bovis, Plasmodium falciparum, dinitrochlorobenzene, and aromatic compounds ( U S. Patents 5,801,005 and 5,739,169; Hui and Hashimoto, 1998; Christodoulides et ah, 1998), cytokine therapy, e.g., interferons a, b, and g, EL-1, GM-CSF, and TNF (Bukowski et at., 1998; Davidson et at., 1998; Hell strand et a!., 1998), gene therapy, e.g., TNF, EL-1, IL-2, and p53 (Qin et a!. 1998, Austin-Ward and Villaseca, 1998; U.S. Patents 5,830,880 and 5,846,945); and monoclonal antibodies, e.g., anti- CD20, anti-ganglioside GM2, and anti-p185 (Hollander, 2012; Hanibuchi et at., 1998; U.S. Patent 5,824,31 1). It is contemplated that one or more anti-cancer therapies may be employed with the antibody therapies described herein.

[00140] In some embodiments, the immunotherapy may be an immune checkpoint inhibitor. Immune checkpoints either turn up a signal (e.g., co-stimulatory molecules) or turn down a signal. Inhibitory immune checkpoints that may be targeted by immune checkpoint blockade include adenosine A2A receptor (A2AR), B7-H3 (also known as CD276), B and T lymphocyte attenuator (BTLA), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4, also known as CD152), indoleamine 2,3 -dioxygenase (IDO), killer-cell immunoglobulin (KIR), lymphocyte activation gene-3 (LAG3), programmed death 1 (PD-1), T-ce! 1 immunoglobulin domain and mucin domain 3 (TIM-3) and V-domain Ig suppressor of T cell activation (VISTA). In particular, the immune checkpoint inhibitors target the PD-1 axis and/or CTLA-4. [00141 j The immune checkpoint inhibitors may be drugs such as small molecules, recombinant forms of ligand or receptors, or, in particular, are antibodies, such as human antibodies (e.g, International Patent Publication W02015016718; Pardo!l, Nat Rev Cancer, 12(4): 252-64, 2012; both incorporated herein by reference). Known inhibitors of the immune checkpoint proteins or analogs thereof may be used, in particular chimerized, humanized or human forms of antibodies may be used. As the skilled person will know, alternative and/or equivalent names may be in use for certain antibodies mentioned in the present disclosure. Such alternative and/or equivalent names are interchangeable in the context of the present disclosure. For example, it is known that lambrolizumab is also known under the alternative and equivalent names MK-3475 and pembroiizumab.

[00142] In some embodiments, the PD-1 binding antagonist is a molecule that inhibits the binding of PD-1 to its ligand binding partners. In a specific aspect, the PD-1 ligand binding partners are PDLi and/or PDL2 In another embodiment, a PDL1 binding antagonist is a molecule that inhibits the binding of PDLI to its binding partners. In a specific aspect, PDLI binding partners are PD-1 and/or B7-1. In another embodiment, the PDL2 binding antagonist is a molecule that inhibits the binding of PDL2 to its binding partners. In a specific aspect, a PDL2 binding partner is PD- 1. The antagonist may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide. Exemplary antibodies are described in U.S. Patent Nos. US8735553, US8354509, and US8008449, all incorporated herein by reference. Other PD-1 axis antagonists for use in the methods provided herein are known in the art such as described in U.S. Patent Application No. US20140294898, US2014022021 , and US201 10008369, all incorporated herein by reference

[00143] In some embodiments, the PD-1 binding antagonist is an anti -PD-1 antibody {e.g., a human antibody, a humanized antibody, or a chimeric antibody). In some embodiments, the anti -PD-1 antibody is selected from the group consisting of nivolumab, pembroiizumab, and CT-011. In some embodiments, the PD-1 binding antagonist is an immunoadhesin {e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PDLI or PDL2 fused to a constant region {e.g., an Fc region of an immunoglobulin sequence). In some embodiments, the PD-1 binding antagonist is AMP- 224. Nivolumab, also known as MDX-1 106-04, MDX-1 106, GNG-4538, BMS-936558, and QPDIVQ ^® , is an anti- PD-1 antibody described in W02006/121 168. Pembroiizumab, also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA ^® , and SCH-900475, is an anti -PD-1 antibody described in W02009/1 14335 CT-01 1 , also known as hBAT or hBAT-1, is an anti -PD- 1 antibody described in W02009/10161 1. AMP-224, also known as B7-DCIg, is a PDL2-Fc fusion soluble receptor described in WO2010/027827 and WO201 1/066342

[00144] Another immune checkpoint that can be targeted in the methods provided herein is the cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), also known as CD 152. The complete cDNA sequence of human CTLA-4 has the Genbank accession number LI 5006. CTLA-4 is found on the surface of T cells and acts as an“off’ switch when bound to CD80 or CD86 on the surface of antigen-presenting cells. CTLA4 is a member of the immunoglobulin superfamily that is expressed on the surface of Helper T cells and transmits an inhibitor _} ' signal to T cells. CTLA4 is similar to the T-cell co-stimulatory protein, CD28, and both molecules bind to CD80 and CD86, also called B7-1 and B7-2 respectively, on antigen-presenting cells. CTLA4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal. Intracellular CTLA4 is also found in regulatory T cells and may ^¬ be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.

[00145] In some embodiments, the immune checkpoint inhibitor is an anti- CTLA-4 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.

[00146] Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art. Alternatively, art recognized anti-CTLA-4 antibodies can be used. For example, the anti -CTLA-4 antibodies disclosed in: US 8,119,129, WO 01/14424, WO 98/42752; WO 00/37504 (CP675,2Q6, also known as tremelimumab; formerly ticilimumab), U.S. Patent No. 6,207, 156; Hurwitz et al. (1998 ) Proc Natl Acad SO USA 95(17): 10067-10071; Camacho el al. (2004) J Clin Oncology > 22(145): Abstract No. 2505 (antibody CP-675206); and Mokyr et al. (1998) Cancer Res 58:5301-5304 can be used in the methods disclosed herein. The teachings of each of the aforementioned publications are hereby incorporated by reference. Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used. For example, a humanized CTLA-4 antibody is described in International Patent Application No. W02001Q14424, W02000037504, and U.S. Patent No. 8,017,1 14; all incorporated herein by reference. [00147] An exemplary anti -CTLA-4 antibody is ipilimumab (also known as lODL MDX- 010, MDX- 101, and Yervoy®) or antigen binding fragments and variants thereof (see, e.g., WO 01/14424). In other embodiments, the antibody comprises the heavy and light chain CDRs or VRs of ipilimumab. Accordingly, in one embodiment, the antibody comprises the CDRl, CDR2, and CDR3 domains of the VH region of ipilim um ab, and the CDR1, CDR2 and CDR3 domains of the VL region of ipilimumab. In another embodiment, the antibody competes for binding with and/or binds to the same epitope on CTLA-4 as the above- mentioned antibodies. In another embodiment, the antibody has at least about 90% variable region amino acid sequence identity with the above-mentioned antibodies (e.g., at least about 90%, 95%, or 99% variable region identity with ipilimumab).

[00148] Other molecules for modulating CTLA-4 include CTLA-4 ligands and receptors such as described in U.S. Patent Nos. US5844905, US5885796 and International Patent Application Nos WO1995001994 and WO1998042752; all incorporated herein by- reference, and immunoadhesins such as described in U.S. Patent No. US8329867, incorporated herein by reference.

4. Surgery

[00149] Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative, and palliative surgery ^? . Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed and may be used in conjunction with other therapies, such as the treatment of the present embodiments, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy, and/or alternative therapies. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically-controlled surgery (Mohs’ surgery).

[00150] Upon excision of part or all of cancerous cells, tissue, or tumor, a cavity may be formed in the body. Treatment may be accomplished by perfusion, direct injection, or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every- 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, or 12 months. These treatments may be of varying dosages as well. 5. Other Agents

[00151] It is contemplated that other agents may be used in combination with certain aspects of the present embodiments to improve the therapeutic efficacy of treatment. These additional agents include agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adhesion, agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers, or other biological agents. Increases in intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperproliferative effects on the neighboring hyperproliferative cell population. In other embodiments, cytostatic or differentiation agents can be used in combination with certain aspects of the present embodiments to improve the anti- hyperproliferative efficacy of the treatments. Inhibitors of cell adhesion are contemplated to improve the efficacy of the present embodiments. Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cell to apoptosis, such as the antibody c225, could be used in combination with certain aspects of the present embodiments to improve the treatment efficacy.

B. Pharmaceutical Compositions

[00152] In select embodiments, it is contemplated that a cell expressing a TCR as disclosed herein, a protein containing the variable regions of a TCR, or a DNA encoding the variable regions of a TCR of the present invention may be comprised in a composition and administered to a subject to induce a therapeutic response in the subject A therapeutic composition for pharmaceutical use in a subject may comprise a TCR composition disclosed herein, such as a soluble TCR (optionally attached to an imaging agent), and a pharmaceutically acceptable carrier.

[00153] The phrases “pharmaceutical,” “pharmaceutically acceptable,” or “pharmacologically acceptable” refers to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, such as, for example, a human, as appropriate. As used herein,“pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g, antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, such like materials and combinations thereof, as would be known to one of ordinary- skill in the art (see, for example, Remington: The Science and Practice of Pharmacy, 21st edition, Pharmaceutical Press, 2011, incorporated herein by reference). Except insofar as any conventional carrier is incompatible with the active ingredient, its use in the vaccine compositions of the present invention is contemplated.

[00154] A person having ordinary skill in the medical arts will appreciate that the actual dosage amount of a therapeutic composition administered to an animal or human patient can be determined by physical and physiological factors such as body weight, severity of condition, the type of disease being treated, previous or concurrent therapeutic interventions, idiopathy of the patient and on the route of administration. The practitioner responsible for administration will, in any event, determine the concentration of active ingredientfs) in a composition and appropriate dose(s) for the individual subject.

[00155] A therapeutic composition disclosed herein can be administered intravenously, intradermally, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostaticaly, intrapleurally, intratracheally, intranasally, intravitreaily, intravaginally, intrarectally, topically, intratum orally, intramuscularly, intraperitoneally, subcutaneously, subconjunctivally, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraoculariy, orally, topically, locally, and by inhalation, injection, infusion, continuous infusion, lavage, and localized perfusion. A therapeutic composition may also be administered to a subject via a catheter, in cremes, in lipid compositions, by ballistic particulate delivery, or by other method or any combination of the forgoing as would be known to one of ordinary skill in the art.

[00156] While any suitable carrier known to those of ordinary- skill in the art may be employed in the pharmaceutical compositions of this invention, the type of carrier will vary depending on the mode of administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g, polylactic galactide) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Patents 4,897,268 and 5,075, 109. [00157] In other embodiments, a composition comprises an immobilized or encapsulated TCR or soluble TCR disclosed herein and a support substrate. In these embodiments, a support substrate can include, but is not limited to, a lipid microsphere, a lipid nanoparticle, an ethosome, a liposome, a niosome, a phospholipid, a sphingosome, a surfactant, a transferosome, an emulsion, or a combination thereof. The formation and use of liposomes and other lipid nano- and microcarrier formulations is generally known to those of ordinary _' skill in the art, and the use of liposomes, mi croparticles, nanocapsules and the like have gained widespread use in delivery of therapeutics (e.g., U.S. Patent 5,741,516, specifically incorporated herein in its entirety by reference). Numerous methods of liposome and liposome like preparations as potential drug carriers, including encapsulation of peptides, have been reviewed (U.S. Patents 5,567,434; 5,552, 157; 5,565,213; 5,738,868 and 5,795,587, each of which is specifically incorporated in its entirety by reference)

[00158] A soluble TCR may be formulated into a composition in a neutral or salt form. Pharmaceutically acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids such as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.

[00159] In any case, the composition may comprise various antioxidants to retard oxidation of one or more component. Additionally, the prevention of the action of microorganisms can be brought about by preservatives such as various antibacterial and antifungal agents, including but not limited to parabens (e.g, methylparabens, propylparabens), chlorobutanol, phenol, sorbic acid, thimerosal or combinations thereof

[00160] Sterile injectable solutions are prepared by incorporating the active peptides in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle that contains the basic dispersion medium and/or the other ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, suspensions or emulsion, the preferred methods of preparation are vacuum-drying or freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered liquid medium thereof. The liquid medium should be suitably buffered if necessary and the liquid diluent first rendered isotonic prior to injection with sufficient saline or glucose. The preparation of highly concentrated compositions for direct injection is also contemplated, where the use of DMSO as solvent is envisioned to result in extremely rapid penetration, delivering high concentrations of the active agents to a small area.

[00161 ] The composition must be stable under the conditions of manufacture and storage, and preserved against the contaminating action of microorganisms, such as bacteria and fungi. It will be appreciated that endotoxin contamination should be kept minimally at a safe level, for example, less that 0.5 ng/mg protein.

[00162] In particular embodiments, prolonged absorption of an injectable composition can be brought about by the use in the compositions of agents delaying absorption, such as, for example, aluminum monostearate, gelatin or combinations thereof.

V. Examples

[00163] The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Materials & Methods

[00164] Display of recombinant RAM variants on the CHO cell surface. The amino acid sequences of the of the extracellular alpha and beta chains of the human TCR RA14 were obtained from the protein data bank (PDB 3GSN; Gras et al, 2009), with the constant regions including the native-PESSC and -C on the alpha and beta chain C-termini, respectively. Minor changes were introduced into this sequence: Va: l l and V|3:M2A were added to match the germline TRAV24 and TRBV6-5 sequences (IMGT), and oA78V (PDB residue 152) substitution was made to match the germline TRAC gene (UniProt). These sequences were then reverted to DNA with CHO cell optimized codons and synthesized as a gblock (IDT). These were assembled into a cassette with a murine IgH leader sequence (Smith et al. , 2009) followed by one TCR chain, a T2A cleavage site with furin cut site (bold) and GSG linker (italics; sequence: RRKRGri’GEGRG SLLT CGD VEENPGP (SEQ ID NO: 43)), then the second TCR chain fused to a PDGFR transmembrane region (FIG. 1 A) (Chng et al., 2015). The TCR chains were cloned in both orientations, alpha- T2A-heta and beta-T2A- a!pha. The constant regions were further modified to create a disulfide variant (ds) by introducing the amino acid substitutions Va:T84C, Ub:8790, and nb:€'85.1A to move the terminal disulfide to a more central position and remove a free cysteine (Boulter etal, 2003). The cassette was cloned into a pcDNA3 (Invitrogen) backbone for transient expression and moved into a pPyEBV backbone (Acyte Biotech) for semi-stable replication used during library sorting (Nguyen ei al., 2018).

[00165] CHO cell transfection for TCR display analysis. CHO-T cells (Acyte Biotech) w^ere grown in CHO-S-SFM II media (Gibco) supplemented with 2x GlutaMax and penicillin/streptomycin. For transfection, cells were spun and resuspended at a concentration of 1.5xl0 ⁶ cells/mL, with 2 mL plated per well in a 6-well plate. For each w ^? eli, 250 iiL of OptiMEM (Therm oFisher) was mixed with 10 pL of Lipofectamine 2000 (ThermoFisher) and added to another tube with 250 pL of OptiMEM and 4 pg of DNA. The solution was mixed and allowed to equilibrate for 30 minutes at room temperature, before adding the solution to the appropriate well. The next day, cells were fed an additional 1 mL of media

[00166] TCR library design and cloning. Two separate libraries w'ere generated, one targeting the CDR3a and the other targeting CDR3P with saturation mutagenesis. The targeted region was defined as the single continuous stretch of residues in each CDR3 having direct contact with the pMHC (Gras et al, 2009), as well as an additional residue on either side to confer additional loop flexibility (Va: 107-115, Ub: 108-1 15; FIGS. 2A-B). To limit library size and retain binding affinity, three residues forming hydrogen bonds with the peptide (Va: 114, Ub: 110, Ub: 114) were not randomized.

[00167] Libraries were generated using overlap PCR with degenerate codons {( ^' DR.3 a: NNS-NN S-NNS- AAC-NN S (SEQ ID NO: 44) and (T)K3b: NBS-VBC-ACC- VBC-VBC-VBC-TAC-NBS (SEQ ID NO: 45)) and Q5 hot-start master mix (NEB). The PCR insert and pPyEBV backbone were both digested with restriction enzymes flanking each targeted region (for CDR3a, Age I and Nhel for CDR3p, BamHl and Nhel, NEB), gel extracted, and desalted. For each library ~1 pg of vector was ligated with insert at a 3 : 1 (CDR3a) or 6: 1 (CDR3 ) ratio overnight using T4 ligase (NEB). The following day, ligations were desalted and transformed into fresh NEBIOb electrocompetent cells. After one hour of recovery, dilutions were plated and incubated, and colony counts used to estimate the library size. The library was grown to an ODgoo of 2 in liquid culture, which was then used to make frozen stocks and inoculate a new flask for overnight growth. Library DNA was prepared using a Maxiprep kit (Qiagen).

[00168] Tetramer preparation. Biotinylated HLA-A*0201 monomer loaded with the pp6549s-503 NLV peptide from human CMV or a control HGV peptide (Biolegend and the NIH tetramer facility') at 100 pg/rnL was combined in a 4: 1 molar ratio with streptavi din-conjugated to APC, AF647, or AF488 (ThermoFisher). Streptavidin was added slowly over 1 hour on ice to favor the formation of tetramer. Biotin (30 mM) was then added to block any unfilled biotin binding sites, and the tetramers incubated overnight at 4 °C.

[00169] Flow cytometry and analysis. Transfected CHO-K1 or CHO-T cells (~lxl0 ⁶ )were centrifuged (250 for 10 min) and resuspended in 100 pL PBS plus 2% FBS (Sigma) with 2 pg/mL NLV or HCV tetramer and a 1 :50 dilution of anti-Vp6-5-PE (Beckman Coulter). Cells were stained on ice for 1 hour, then rinsed and resuspended in 0 5 mL PBS plus 2% FBS. Samples were run on a Fortessa cytometer (BD Biosciences). A forward- and side-scatter gate was used to select live cells, with TCR-positive cells defined as having a PE signal greater than or equal to 10 ³ . To compare binding activity of TCR variants, NLV tetramer binding was normalized by TCR display level by dividing the AF647 signal by the PE signal on a per-cell basis for the TCR-positive population. All analyses were performed with FlowJo software.

[00170] Library transfection and sorting. Confluent CHO-T cells (1 or 2 T-150 flasks) were transfected as above, with quantities scaled accordingly. Library DNA was diluted 1 :4 with an inert yeast plasmid as carrier DNA (pCTCON) (Colby et al, 2004) so that each CHO cell received at most one TCR expressing pPy plasmid. Flasks were also transfected with the wild-type pPy_RA14 as a positive control and pPy__hu4D5 expressing the anti~HER2 Fab as a negative control. TWO days later, cells were scanned for TCR surface display using the anti-Vb6-5 antibody to evaluate transfection efficiency, and media replaced with half-strength selective media (CHO-S-SFM II plus 2x GlutaMax plus 150 pg/mL Hygromycin). Four or five days after transfection, ceils w ^? ere expanded and transferred into fu!l-strength selective media with 300 pg/mL hygromyein. Cells were maintained in selective media until reaching confluence in a T-150 (-2 weeks).

[00171] For sorting, ~lxl0 ⁷ live cells were centrifuged (250g, 5 min) and resuspended in OptiMEM plus 1% BSA and stained with anti-TCR nbo-5 and NLV tetramer as described above. Cells were sorted using a FACS Aria, with the sort gate drawn to collect most fluorescent -1-2% of the population, biased towards cells showing higher tetramer binding at the same TCR display level, to collect -lxlO ³ cells. The sorted cells w ^? ere expanded for -1 week, and the process repeated two times. To recover plasmid from sorted CHO cells, genomic DNA was prepared from the pooled population one week after each sort. The region of interest (CDR3a or 3b, depending on the library) was PCR-amplified using flanking primers and 500 ng template DNA. PCR product was ligated into a TOPO vector (Invitrogen/Thermo Fisher) or digested and ligated into empty pPy backbone. After transformation, 10-40 individual colonies were sequenced from each round of sorting

[00172] Expression of soluble TCR-Fc fusion proteins. To express soluble TCR-Fc fusion proteins, DNA encoding the RA14 extracellular alpha and beta chains w¾s cloned into pcDNA3.0 plasmids downstream of a human IgG heavy chain leader sequence Both the native human TCR constant domains and versions with the additional inter-chain disulfide introduced were used. The Ca domain was followed by the upper hinge sequence of human IgGl (VEPKSC (SEQ ID NO: 46)) and then the Fc domains. The native IgGl light chain cysteine was inserted at the C -terminus of€b to pair with the cysteine in the upper hinge and further stabilize the TCR constant domains. Additional modifications included the removal of five N-linked glycosylation sites predicted by NetNGlyc 1.0 Server (DTU Bioinformatics; available on the world wide web at cbs.dtu.dk/services/NetNGlyc/) by introducing a:N20Q, a:N177Q, a:N188Q, b:N65(), and b:N184z) substitutions (FIG. 5 A).

[00173] In one version, the construct consisted of alpha-T2A-beta-huIgGl hinge, CH2 and CH3 domains, in another these two chains were encoded on separate pcDNA3.0-hased plasmids, with either alpha or beta chain fused to the Fc. Both human IgGl and mouse IgG2a hinge-Fc sequences were used (Uniprot #P01857 and #P01863, respectively). Constructs containing the mouse IgG2a Fc retained the human IgGl VEPKSC before the mouse hinge-Fc sequence. Cloning was performed using Q5 hot-start polymerase (NEB) and either traditional digestion/ligation or Gibson assembly methods and confirmed by Sanger sequencing.

[00174] For large-scale expression, two T-150 flasks of adherent CHO-K1 cells (ATCC #CCL-61) were grown to confluency and transfected using the same ceil/media/reagent ratio described above for each variant. Cells w'ere grown in high-glucose DMEM (Sigma) with 10% low-IgG FBS (ThermoFisher) and no antibiotics at 37 °C with 5% CO2. Media was replaced the day after transfection and cells were transferred to a 32 °C, 5% CO2 incubator for one week. Media was harvested and loaded onto a protein A column using an FPLC (AKTAPure, GE healthcare) using 100 mM phosphate, 150 rnM NaCl, pH 7.2 and eluted with 100 mM glycine, pH 2.5. The eluate was immediately neutralized with 1M Tris, pH 8, and buffer-exchanged into PEIS, pH 7.4, using a centrifugal filter (Amicon or Centricon).

[00175] Protein biophysical characterization. Purified TCR-Fc proteins (3 pg each) were prepared in reducing or non-reducing 6x SDS loading buffer and incubated for five minutes at 80 °C or 42 °C, respectively. Samples were am on a 4-20% gradient gel (BioRad) and stained with GelCode Blue (ThermoFisher Scientific). Size exclusion chromatography was performed with 100 pg purified protein in 100 pL using a Superdex S200 column and Akta FPLC with PBS as the running buffer and Gel Filtration Calibration Kit High and Low' molecular weight standards (GE Healthcare). For affinity variants, the peak eluting at -10.5 niL containing properly assembled, bivalent TCR-Fc was collected and concentrated. To monitor thermal stability, protein was prepared at 200 pg/mL and diluted with protein thermal shift dye (ThermoFisher Scientific) following the recommended protocol. Samples were heated at 1 °C/min on a RT-PCR machine measuring fluorescence

[00176] Protein-protein binding assays. For ELISA analyses, high-protein binding plates (Costar) were coated with 1 pg/mL of NLV/A2, HCV/A2 tetramer or nothing in PBS overnight at 4 °C, before blocking with 5% milk in PBS with 0.05% Tween-20 (PBS- T) for one hour at room temperature. The plate was washed three times with PBS-T, purified TCR-Fc titrated in 1 :5 dilution steps from 10 pg/mL and incubated for one hour. After washing again, 1 : 1000 dilution of goat-anti -hum an Fc-HRP conjugate (Southern Biotech) was added to the plate for one hour. After a final wash, the plate was developed with TMB (Fisher Scientific), quenched with IN HC1, and absorbance measured at 450 nm on a Molecular Devices Spectramax. All plated volumes were 50 pL. Data were analyzed with Graphpad Prism 5.

[00177] Dynamic and equilibrium binding kinetics were obtained using a BIAcore 3000 instrument. The purified TCR-Fc was immobilized on a CM 5 sensor chip (GE Healthcare) via EDC/NHS coupling using a sodium acetate buffer at pH 4.0 for a total of 2000-5000 response units, with a blank flow cell used as the reference channel. Monomeric NLV7A2 was injected at concentrations ranging from 4 to 1000 nM at 30 pL/min for two minutes and allowed to dissociate for six minutes, which resulted in a return to baseline without regeneration. The negative control HCV/A2 monomer was injected at the highest concentration for all variants. All data was measured at 25 °C. On rate, off rate, and equilibrium affinity analyses were performed using BIAEvaluation 3 0 software and fit using the 1 : 1 Langmuir binding model. All injections were performed twice and final kinetic values reported are the average and standard deviation for the entire dataset.

[00178] Staining peptide-pulsed antigen-presenting cells. Human TAP- deficient T2 lymphoblasts (174 x CEM.T2; ATCC #CRL-1992) expressing empty HLA-A2 were cultured in IMDM media supplemented with 4 mM glutamine at 37 °C and 5% C0 ₂ The pp65 _495-503 peptide NLVPMVATV (SEQ ID NO: 41) and control HCV ₁₄ o6-i4i5 peptide KLVALGINAV (SEQ ID NO: 42) were produced by solid phase synthesis (Peptide 2.0) and dissolved in DMSO for a final peptide stock of 50 mM. T2 cells in a six-well plate (2 mL/well) containing 10 ⁶ ceils/mL were adjusted to 100 pM or the indicated peptide concentration and incubated at 37 °C. After 24 hours, 5x10 ^s cells per sample were stained on ice for one hour using 2 pM of purified TCR-mFc in PBS with 1% FBS (PBS-F) with 50 pg/mL human Fc block (BD Biosciences) in a 50 pL volume. Cells were washed twice with PBS-F and bound TCR-mFc detected with a 1 :500 dilution of goat-anti-mouse Fc-AF647 (Jackson Immunobiology) for another hour. After a final wash, cells were resuspended and assayed for AF647 signal using a flow cytometer (Fortessa, BD Biosciences)

[00179] Activation of human Jiirkat T cells expressing RA14 variants. A pcDNA3.1 -derived plasmid with a CMV promoter was modified to support transient expression of a signaling-competent TCR comprised of the RA14 variable regions and mouse constant/transmembrane regions. First, a Kozak sequence with optimal ribosome binding site (sequence: CC ACC ATG G), multiple cloning site, and stop codon followed by n Hindill site and terminal SV40 PolyA tail signal were added to pcDNB.l . Next, separate plasmids containing the TCR alpha and beta chains were cloned. The pRA14a alpha chain plasmid includes a murine alpha chain TCR signal sequence from IMGT TRAV5D-4 (amino acid sequence: MKTYAPTLFMFLWLQLDGMSQ (SEQ ID NO: 47)) in-frame with the human TCR alpha variable region, both flanked by restriction sites Ec&RI and Aflll and the murine TCR alpha constant region (TRAC*01) and alpha transmembrane domain between restriction sites Aflll and Hindill. The pRA14b beta chain plasmid w'as constructed similarly, but with the murine beta chain signal sequence from IMGT TRBV13-2 (MGSRLFF VLS SLLC SKHM (SEQ ID NO: 48)) and human variable beta domain flanked by EcoRI and Aflll sites and beta constant region (TRBC*02) and beta transmembrane domain between restriction sites Aflll and Hindill. Signal sequences were encoded by oligonucleotides, constant regions amplified from mouse DO1 1.10 hybridoma mRNA by RT-PCR. Altered RA14 variable regions were introduced by PCR amplification followed by digestion/ligation into the EcoHA and Aflll sites.

[00180] Human Jurkat T-cells, clone E6-1 (ATCC #TIB-152) were grown in RPMI 1640 media with 10% FBS and 100 units/mL penicillin-streptomycin (Sigma) and transfected as previously described (Goyarts et al., 1998). Briefly, 10 ⁶ cells per transfection were centrifuged at 250,g- for five minutes, resuspended in 5 mL OptiMEM and incubated at room temperature for eight minutes. Cells were centrifuged as before and resuspended in 400iiL OptiMEM. Cells were then mixed with 7.5 pg of each alpha and beta plasmid in a 4 mm electroporation cuvette (Fisher) and incubated for eight minutes before pulsing exponentially with 250V, 950pF, and oo W on a Biorad GenePulser. After an eight-minute recovery period, cells were rescued with 7 ml of RPMI 1640 (supplemented with 10% FBS and antibiotics) in a T-25 flask at 37°C and 5% CO2. After 18-24 hours, recombinant TCR expression was monitored by flow' cytometry , with the RAM display level monitored by the anti-TRBV6-5 antibody -PE and binding activity monitored by NLV/A2 tetramer-AF647, as described above.

[00181] The ability of transfected RAM variants to activate Jurkat cells was monitored by CD69 upregulation after incubation with peptide-pulsed T2 cells. T2 cells (10 ⁵ ) w'ere pulsed with NLV and HCV peptides at 0.1 mM for four hours. T2 cells were washed once in RPMI to remove excess peptide. Transfected Jurkat cells (10 ⁵ ) were co cultured with pulsed T2 cells at a TCR-positive effector: target ratio of 1 : 1. After 24 hours, cells were collected and incubated with 50 pg/mL human Fc block (BD Biosciences) for 10 minutes before adding an†i-TRBV6~5-PE, NLV/A2 tetramer-AF647, and anti-CD69-FITC (Biolegend; 1 mE of each antibody and 5 nM of tetramer per 50 mI_ staining volume) for one hour on ice. Cells were scanned on a Fortessa cytometer (BD Biosciences) and gated for display of RA14 variants (PE signal >500) to exclude T2 cells. All analyses were performed with Flow Jo.

Example 1 - Display of pp65 NLV-specific TCR RA14 on the CHO cell surface

[00182] To first determine the level of recombinant TCR displayed on the CHO cell surface, the truncated extracellular alpha and beta chains of the human RA14 TCR were cloned into a pcDN A3 -based plasmid with a CMV promoter, human IgH lead er sequence, one TCR chain, and T2A peptide sequence followed by the second TCR chain fused in-frame to a platelet-derived growth factor receptor (PDGFR)-derived transmembrane region (FIG. 1 A). As only the second chain is fused to the transmembrane region and chain order can impact yields (Maynard et ah, 2005), the chains were cloned in both the a/b-TM and b/a-TM orientations. Similarly, since moving the terminal inter-chain di-sulfide bond to the Ca:T84C and Cb:S79C position (IMGT numbering used throughout) and removing the free cysteine at position Cp85.1 has been reported to improve expression of soluble and phage/yeast displayed TCRs (Boulter et al. , 2003; Ho et ah, 1998), these modifications were also tested in each chain orientation.

[00183] After cloning and sequence confirmation, midi-prepped plasmid DNA was transiently transfected into CHG-T cells and TCR surface display assessed by flow cytometry' two days later. The presence of TCR on the cell surface was monitored by an antibody binding the human variable beta chain (nbό-5-PE), while NLV/A2 tetramers conjugated to APC were used to assess ligand binding activity. A tetramer presenting an unrelated peptide from hepatitis C virus (HCV1406-1415 sequence: KLVALGINAV (SEQ ID NO: 42); hereafter called HCV) complexed with A2 was used to evaluate peptide specificity (FIG. I B).

[00184] Flow cytometry showed varying expression patterns for each vector design, with the PE+/APC+ population indicative of cells binding tetramer and displaying TCR (FIG 1C). Cells transfected with empty pcDNA3 vector showed minimal binding to either reagent, while a b-TM only construct bound the nb antibody, indicating that unpaired TCR chains will not be detected by tetramer binding. By contrast, cells transfected with constructs containing both TCR chains presented a diagonal double-positive population, indicating a correlation between tetramer staining and surface display over a range of expression levels. Staining with the control HCV tetramer also showed no binding, indicating that the displayed TCRs retained peptide specificity. All samples included a population of unstained, non expressing cells, which is expected for eukaryotes with unsynchronized growth. While inclusion of the modified di-sulfide bond greatly increased the specific tetramer binding activity (tetramer binding: TCR display ratio), chain order had less impact. A small but consistent improvement was detected in specific tetramer binding activity' for the a/b-TM configuration. Accordingly, this design with the modified di-sulfide was selected for further use. Example 2 - Design of CDR3« and CDR3p libraries

[00185] Analysis of the RA14-NLV/A2 crystal structure revealed that RAH engages nearly all solvent-exposed peptide residues and forms hot spots with peptide residues P4 : Pro, P5:Met and P8:Thr (Gras et al, 2009). In the alpha chain, CDR3a:N114 forms a key hydrogen bond with P5:Met which is also present in structure of the related TCR C7 with NLV/A2 (Yang et al , 2015), which has a nearly identical CDR3a. In the beta chain, CDR3p:TI 10 forms multiple hydrogen bonds with P8:Pro. To identify high affinity RAM variants, separate CDR3a and CDR3p libraries were designed, which allowed a larger sequence space for each CDR to be probed. Three anchor residues (Va:Nl 14, nb:T1 10 and Ub:U114) were retained while four or six residues flanking these contacts were randomized to optimize the TCR-pMHC interface (FIG. 2).

[00186] To create each library, primers incorporating degenerate codons were designed to maximize amino acid diversity while keeping the theoretical library sizes (IxlO ⁶ for CDR3a, 4xl0 ⁶ for CDR3 ) near ~10 ^b , a limitation determined by mammalian cell culture volume constraints. Mutagenized cassettes were generated using overlap PCR with these primers, followed by overlap extension PCR to produce full-length inserts. These were digested and ligated into the pPyEBV vector, which allows semi-stable, selectable transfection in CHO- T cells (Nguyen et al, 2018). After transformation into E. coli , actual library sizes were estimated as 4xl0 ⁵ for the CDR3a library and IxlO ⁶ for the CDR3 library, with diversity confirmed by DNA sequencing. Example 3 - Selection of RA14 variants with improved tetramer binding

[00187] Pooled library plasmids were diluted with a 1 :4 molar ratio of carrier DNA, to ensure each cell will acquire at most one library clone, and transfected into CHO-T cells (Nguyen et ai., 2018). After two weeks of growth under antibiotic selection to eliminate cells lacking the pPy plasmid, cells were stained with AlexaFluor-647 (AF647)4abelled NLV/A2-tetramers to detect ligand binding and anti-Vp6-5-PE to detect surface TCR display. Each library was sorted by FACS to collect the 1-2% of cells with the highest ratio of tetramer binding to TCR display. After sorting, each library _' was allowed one week of recovery before being sorted again, for a total of three rounds. Comparison of the libraries at each step demonstrated enrichment of clones with high levels of tetramer binding (FIGS. 3A-B). The CDR3a and CDR3p libraries each showed a 5-10-fold increase in the number of cells falling within the gated area per round.

[00188] TCR sequences w ^? ere recovered from pooled cells after round three sorting by PCR amplifi cation from total cellular DNA, followed by re-cloning into the pPyEBV plasmid for sequencing. Analysis of 20-35 colonies revealed seven unique CDR3a and 10 unique CDR3 sequences (Tables 3A-B). The wild-type residues were largely retained at positions nb: 109 and Ub: 11 1 within the CDR3P library, while positions Ub: 112 and V|3: l 13 were highly variable. RA14 covers an unusually high percent of the exposed peptide upon binding, and in particular that the CDR3P contacts are mostly backbone-mediated, which may explain the high variation possible in these residues (Gras et al. , 2009). Finally, larger residues were frequently found in the flanking sites, which may have been preferentially enriched if they were able to introduce additional peptide contacts.

Table 3 A. Amino acid sequences of RA14 CDR3a variants isolated from round 3 sorting.

Table 3R, Amino acid sequences of RAM CDR3p variants isolated from round 3 sorting.

Example 4 - Characterization of RA14 variants with improved tetramer binding

[00189] AH identified CDR variants were transfected into fresh CHO-T cells in combination with the complementary wild-type chain and analyzed for TCR display level and tetramer binding as single clones. To compensate for TCR expression level differences, the specific tetramer binding activity (tetramer-AF647 signal/ anti-TCR-PE signal) was compared on a per cell basis for each clone. The median of this distribution was then normalized to the median value obtained for wild-type RA14 to report a fold-increase as compared to RA14 (FIGS 3C-D). A similar process was performed after staining with the control HCV tetramers, revealing that peptide restriction was retained for all selected variants. Only two CDR3a variants (aVl, aV2) showed binding similar to or improved over wild-type, with the best variant (aV2) having a 2.3-fold increase in normalized binding. In contrast, all 10 of the CDR3p variants showed significant improvements over wild-type, with 1.8- to 3.5-fold improved specific tetramer binding. The variants with the greatest specific tetramer binding activity (aVl, aV2, b¥1, bU4, bU7, and b V8) were selected for further analysis.

[00190] Next, it was determined whether the best alpha and beta variants could be combined to further improve tetramer binding, as reported in other studies (Li et al, 2005). The wild-type and selected alpha (aVl, aV2) and beta (bnΐ, b¥4, bU7, bn8) variants were combined pairwise, transfected and analyzed as before. The combinations generally showed further improved specific tetramer binding (FIG. 4A), with some variation in TCR display levels among clones. As surface display levels can be useful predictors of soluble expression yields (Shusta et al, 1999), the aV2 and bU 8 combination was selected as the lead candidate. Variant aV2 contains the Va:T108Y and Va:Q115H substitutions, while bn8 contains Vp:P108L and the frequently-observed V b : 11 13V and Vp:Gl 15L mutations (Tables 3A-B).

[00191] To better understand the impact of the selected CDR changes on TCR function, TCR activation was evaluated after transfection into human Jurkat T ceils. The native RA14 and selected aV2 and bn8 variable regions were combined with murine constant regions followed by human TCR transmembrane regions on a pcDNA-based plasmid. Mouse constant regions were used to prevent mispairing with the endogenous human TCR expressed in Jurkat cells (Cohen et al, 2006). After electroporation, Jurkat cells were co-cultured with human T2 antigen-presenting cells pre-incubated with 0.1 mM NLV or control HCV peptide and activation was measured by CD69-upregulation using flow cytometry 24 hours later (FIG. 4B). All TCRs tested showed activation in the presence of NLV but not HCV-pulsed T2 ceils. Moreover, the engineered TCRs showed significantly improved activation (2.2-2.7-fold) as compared to the wild-type RA14. Although the selection strategy was based upon TCR display levels and tetramer binding, these data suggest that features required for TCR activation were also retained (Sibener et al, 2018), which is not always the case for affinity matured TCRs.

Example 5 · Production of RA14 TCR as a soluble Fc-fusion protein

[00192] In order to fully characterize our engineered TCRs and to support future applications of high affinity NLV-binding TCRs, it was necessary to produce these as soluble proteins. TCRs are notoriously difficult to produce, with no generally successful strategies yet identified (Maynard et al, 2005 and Gunnarsen et al, 2013). Since TCRs are naturally produced by mammalian cells and since fusion of a poorly expressed protein to an antibody Fc domain generally increases expression level, increases avidity through bivalency, and provides a convenient detection handle for immunoassays, a TCR-Fc format was selected for production in CHO cells. Antibody expression plasmids were modified (Nguyen et al, 2015) to express the wild-type RA14 variable and constant domains with one chain fused to the human IgGl upper and core hinge region, followed by human Fc domains.

[00193] Several constructs were evaluated by small scale CHO expression and ELISA to compare expression level, including a one plasmid system with the two chains separated by a T2A peptide and versions with either the beta or alpha chain fused to the Fc. For these, constant TCR domains with the modified inter-chain disulfide bond were used (named TCRds-huFc; Boulter et al, 2003) in addition to a second disulfide-bond joining the base of the TCR constant domains contributed by the antibody upper hinge sequence (named TCR2ds-huFc). The highest expression levels, approaching that observed with antibodies, were obtained with a two-plasmid system in which the a-chain was fused to the Fc.

[00194] To compare RA14 and the engineered variants in the TCR2ds-huFc format, the aV2 and bU8 domains were cloned into the two-plasmid expression syste and transfected pairwise with plasmids encoding the wild-type RA14 chains to produce four variants: wild-type RA14 (WT), aV2.pWT, a\UT.bU8, and aV2.pV8. After protein A purification, size exclusion chromatography (SEC) was performed to isolate the dominant peak (eluting at -10.5 mL) containing protein with the highest tetramer binding activity and appearing to correspond to intact, bivalent protein. SDS-PAGE analysis showed similar, high levels of purity for all variants (FIG. 5A). Protein stability was compared by thermal unfolding, using differential scanning fluorimetry and using the inflection point of the first unfolding event to compare TCR domain stabilities. The bU8 changes are mildly destabilizing, inducing a >4 °C decrease in melting temperature as compared to RA14. In contrast, the <xV2 changes increase thermal stability >2 °C, and partially compensate for the presence of the less stable bU8 in the combined aU2.bU8 variant (Table 4).

Table 4. Affinity and stability of RAM TCR-Fc variants.

Example 6 Engineered variants show improved pMHC affinity as soluble TCR2ds- huFc fusion [00195] To provide an initial assessment of NLY/A2 binding, the ability of purified TCR2ds-huFc variants to bind immobilized pMHC were compared in an ELISA. The NLV or HCV tetramer was coated onto an ELISA plate, TCR2ds-huFc protein titrated and detected by anti-human-Fc-HRP (FIG. 5B). No binding was detected for any variant to the control surface, while RAM provided a clear dose-response curve on NLV tetramer coated wells, with a detection limit near 0.1 pg/mL. Both variants including the pV8 chain showed a distinct increase in binding, with the detection limit --30-fold lower than observed for the other variants. In contrast, the aU2.b\¥T showed improved detection but a much shallower slope than observed for RA14. [00196] Surface plasmon resonance was used to rigorously quantify binding of the four TCR-Fc variants to NLV/A2. SEC-purified TCR2ds-huFc was coupled to the sensor surface, with varying concentrations of NLV/A2 or HCV/A2 monomer passed over the surface. The WT RAM exhibited the slow on-rates (9.5xl0 ⁴ M N ¹ ) and fast off-rates (0.29 sec ¹ ) typical of TCRs, resulting in a calculated affinity of 3.1 mM for the bivalent TCR2ds- huFc format. This compares w ^? eli to the 6.3 mM Kd previously reported for monovalent RAM using an immobilized pMHC orientation, but is tighter than the 27.7 mM reported using immobilized TCR (Gras et al. , 2009, Gakamsky et al. , 2007) By contrast, the aV2 CDR changes affected only the on-rate, with a three-fold increase, while the b¥8 CDR changes affected only the off-rate, with a 10-fold decrease (FIG. 5C). When combined, these changes showed synergy, conferring a 50 nM affinity for aV2.pV8, a 60-fold improved affinity over RAM (Table 4). Equilibrium binding analyses yielded similar data (Table 4, FIGS. 6A-D). No variant exhibited detectable binding to the control HCV7 HLA-A2 monomer at the highest concentrations used (FIG 5C).

Example 7 - Genetic deglycosylation yields homogeneous TCR-Fc protein

[00197] The success of affinity maturation prompted efforts to further improve soluble TCR-Fc expression. Specifically, reducing SDS-PAGE showed broad bands with approximately the expected size, while SEC showed two or three distinct peaks, indicating the presence of incompletely-assembled TCR-Fc species (FIGS. 7B-C). This prompted the evaluation of two hypotheses: first, that TCR-Fc assembly was improved by stronger a-b chain interactions from the additional disulfide bond (Boulter et al, 2003), and second, that assembly was sterically inhibited by TCR glycosylation, since RAM includes several predicted N-linked glycosylation sites near chain interfaces.

[00198] To evaluate these possibilities, several constructs were compared: one with only the engineered di-sulfide bond between the constant domains (TCRds-huFc), one with an additional di-sulfide bond (TCR2ds-huFc) and one in wiiich five predicted N-linked glycosylation sites were disrupted by N-to-Q amino acid substitutions (TCR2dsAgly-huFc; FIG. 7A). SDS-PAGE analysis sho 's that genetic de-glycosylation resulted in sharper protein bands (FIG. 7B). Introduction of the additional disulfide bond eliminated the minor SEC peak eluting at -13.5 niL, while de-glycosylation of the doubly-disuifide bonded format eliminated the second minor peak at -12.5 mb, resulting in a single, monodisperse product on SEC (FIG. 7C & lOA-C). [00199] To evaluate the potential impact of these changes on protein stability, the thermal stability of each version was monitored, as above (FIG. 7D). The melting point of the RA14 TCRds-huFc increased slightly with the addition of the second disulfide bond and slightly again after deglycosylation to 68.8 ^C C (Table 4). This melting temperature is in the range of values typically reported for antibody Fab domains (67-79 °C; Nguyen et a!., 2015). It was subsequently confirmed that the SEC-purified glycosylated and genetically deglycosylated versions of each TCR2ds-Fc variant bind NLV tetramer similarly in an ELISA (FIGS. 8A-B).

Example 8 - Engineered TCR proteins stain pMHC-displaying cells

[00200] To demonstrate the potential utility of high affinity TCR-Fc fusion proteins to detect CMV-positive cells, they were used to stain peptide-pulsed antigen presenting cells. To prevent background staining due to binding between the human Fc on the TCR2ds-huFc proteins and human Fey receptors on the T2 cells, the human IgGl hinge and Fc domains were replaced with their murine IgG2a counterparts to create TCR2ds-mFc constructs, which achieved similar yields and purity as the TCR2ds-huFc format (FIG. 9A). Human T2 antigen presenting cells were incubated overnight with 100 mM purified NLV or HCV peptide, stained with 1 mM purified TCR2ds-mFc followed by anti-mouse Fc-Alexa647 and analyzed by flow cytometry. Cells incubated with the HCV control peptide showed no shift in fluorescence as compared to ceils incubated only with the anti-mouse Fc-AF647. A clear correlation in fluorescence shift with TCR affinity was observed, which increased from no detectable staining for RAM to a distinct population for aV2.pV8 (FIG. 9B). Finally, to determine the peptide detection sensitivity, the peptide dose was serially diluted before incubation with T2 cells and staining with 1 mM a2b8 TCR2dsAgly-mFc. Signals did not saturate at high peptide concentrations, as is expected for these TAP-deficient cells which upregulate MHC levels in the presence of peptide and were detectable down to 0.5 mM peptide (FIG. 9C).

Example 9 - Further improved RA14 TCR variant, 341

[00201J Using nearly the same method described above, a variant with further increased affinity due to changes in CDR1 was identified. For this library, the alpha chain was appended with the PDGFR transmembrane anchor, which allowed us to select for enhanced alpha-beta chain pairing with an anti-beta chain antibody (FIG. 11). Additionally, the five predicted glycosylation sites were eliminated with amino acid substitutions at positions Va:N20Q, Ca:N90Q, a:N109Q, V[3:N77Q and Cp:N85.6Q, since these changes improved assembly of purified TCR-Fc protein and are expected to also enhance TCR assembly when expressed on the eukaryotic ceil surface. To generate this library, four residues in CDR 1b and la of the deglycosylated a2.b8 were randomi zed using degenerate oligonucleotides (red residues in FIG. 11). Finally, instead of the KLV control peptide complexed with HLA A2, a similar peptide from influenza was used to monitor promiscuous peptide binding, here called GIL (full sequence: GILGFVFTL (SEQ ID NO: 51)), also complexed with HLA A2 Three rounds of FACS selection, performed as above, resulted in clone 341 with a single residue change at position VccN29D and 7.8-fold enhanced binding over wild-type when displayed on CHO cells (Table 5 and FIG. 12) In the same experiment, a2.b8 was 3-fold better than wild-type and clone 341 -2.5-fold better than a2.b8 (Table 5) Quantification of the flow data corresponding to FIG. 12 is shown below in Table 5 as well as in FIG. 13 Table 5. Quantification of flow data from FIG. 12 to document improved binding to the NLV/A2 tetramer of TCR variants expressed on the CHO cell surface.

[00202] None of the clones (wild-type RA14, a2.b8, nor 341) binds to the control peptide when complexed with HLA-A2. Controlling for display level, there is an absolute improvement in binding.

Example 10: Further development of sub-nanomolar TCR-Fc variants

[00203] Additional affinity maturation of pp65/HLA-A2-specific TCRs was performed. Further mutations in CDR3a, OBK3b, and CDRloc that have resulted in 300-fold improvements in affinity, down to -10 nM Kd. These variants were used to create a final “shuffled” library comprising selected mutations or wild-type residue to remove detrimental or neutral mutations and identify beneficial or synergistic mutations. This library was generated using degenerate oligonucleotides and subjected to three additional rounds of FACS sorting after expression on the CHO cell surface and staining with fluorescent pMHC- tetramer-AF647. This resulted in identification of variants 2S-16, which has an affinity of 0.6 nM, as measured by SPR (see FIGs. 15-17). This represents a 1000-fold improved affinity as compared to the wild-type RA14 and improves the complex half-life from 2.3 seconds to 39 minutes. The affinity improved variants, especially the highest affinity 2S-16 variant, show an improved ability to detect pp65~pu!sed human cells and exhibit decreased signal: noise (FIG. 18). When expressed on the surface of T cells with endogenous TCR transmembrane regions and exposed to human T2 cells pulsed with either the pp65 or a control peptide, the TCRs retain the ability to activate the T cell (FIG. 19).

Example 11: Antibody Fc variants that escape capture by CMV viral Fe receptors

(vFcR)

[00204] HCMV has evolved an impressive array of immune evasion strategies[7] that allow the vims to infect and establish latency at some point in the majority of humans. It is clear that HCMV infection stimulates a robust adaptive immune response, [8] but spread of clinical strains of HCMV is not inhibited by antibodies from seropositive individuals, [9] about 1% of seropositive mothers still transmit HCMV to their fetuses, [10] the best attempts at immunization are only -50% effective, [1 1, 12] and prophylactic IVIG administration of HCMV-specific antibodies to pregnant women have not provided particularly impressive fetal protection. [13] For example, the neutralizing anti -HCMV monoclonal antibody MSL-109 prevented hCMV infection in vitro , but not in the clinic. This antibody binds the glycoprotein gH on the surface of infected cells, but HCMV quickly became resistant to the antibody. [14]

[00205] The ability of antibodies to eliminate hCMV-infected cells and prevent ceil-to-cell spread [9] appears to be hampered by expression of viral Fc gamma receptors (vFcyRs). HCMV induces the expression of vFcyRs in infected cells, which causes capture and degradation of antibodies targeting HCMV [15] In theory, antibody-cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) should be important components of an immune response to viral infection, but data supporting this role is limited. Data suggest that previously tested antibody therapeutics such as the anti-gH MSL-109 have been negatively impacted by the immune evasion mediated by vFcyRs. [14] When vFcyRs are expressed on the infected cell’s surface, antibodies that bind exposed antigens, such as a pMHC complex or gH, are then bound by vFcyRs and internalized via bipolar bridging[15, 16] for degradation or repackaging for further evasion. [14] In HCMV strains lacking the vFcyRs gp34 and gp68, HCMV antibodies were much more potently able to bind human FcyRs and induce ADCC in vitro. [17] This immune response blunts the ability of antibodies to initiate ADCC and stimulate local immune responses.

[00206] Human Fc receptors in the FcyRI, FcyRII, and FcyRIII families all have overlapping binding sites on the human IgGl Fc hinge, while FcRn binds between CH2 and CH3. To determine whether the binding sites of the human and viral Fc receptors can be uncoupled, gp34 and gp68 proteins were first cloned and purified. The gp34 protein (residues 24-182) and a truncated version of gp68 (tgp68, residues 68-289) were expressed, purified, and characterized (FIG. 20). The genes encoding the vFcyRs were amplified from the AD169/GFP[18] BAC (with an added strep tag for purification and detection and expressed in CHO cells. After purification, both proteins are homogeneous and monodisperse. Gp34 expresses as a homodimer of ~30 kDa glycosylated monomers, while gp68 expresses as a monomer of ~68 kDa.

[00207] The human and viral Fc receptors were used in competition ELISAs to determine that gp34 competitively inhibits FcgRHIa binding while tgp68 competitively inhibits

FcRn binding (FIG. 21). These data show that gp34 likely shares a partially overlapping epitope with FcyRIII A, while gp68 likely binds near the FcRn binding site, and the two vFcyRs do not share an epitope. Prior mutagenesis studies support the conclusions that gp68 binds in the CH2- CH3 hinge. [19] [00208] Additional ELISAs evaluated binding of the Fc receptors to multiple established Fc variants. The vFcyRs were minimally impacted by mutations known to impact FcRn and FcyRIIIA binding, with the exception of YTE,[20] which improves binding to FcRn, but abolishes binding to tgp68 (FIG. 22). This indicates that the vFcyRs do not bind identical epitopes to either FcRn or FcyRIIIA. [00209] Using yeast Fc display, additional antibody Fc variants were identified that have lost the ability to bind two vFcyRs but retain native binding to the host Fey receptors, including FcgRIIIA which is required for ADCC and FcRn which mediates antibody recycling and is crucial for the long antibody half-life in serum. The human IgGl Fc region was mutagenized and screened by yeast display to identify variants with reduced binding to HCMV vFcyRs but retain binding to host FcRn and FcgRIIIa Libraries were created by error prone PCR on the CH2 domain with a 0.25 % error rate to yield a final library of I .όcIO ⁶ variants. The hinge region was excluded from mutagenesis as it includes the FcgR3 A binding site. The library was initially sorted by flow cytometry to select variants that maintain binding to FcyRIIIA. After regrowth, they were then sorted for variants which lost gp34 binding by staining with 20 nM FcyRIIIa-PE in the presence of an excess (1.5 mM) of unlabeled, purified gp34 as competitor. Selected sequences are shown in FIG. 23 and binding to viral and host Fc receptors in FIG. 24.

Example 12: Expression of additional TCR constructs in CHO cells

[00210] To demonstrate the generality of this CHO cell system for expression and engineering of TCRs, other than the RAM TCR, additional TCR constructs were studied

[00211] The Ob.1 A 12 human TCR recognizing the myelin basic protein peptide formed by residues 85-99 when presented by the class II DRBP 1501 MHC molecule was derived from a patient with relapsing-remitting multiple sclerosis (Wucherpfennig etal , 1994). Notably, as an autoimmune-associated TCR, this exhibits a very low affinity (estimated at Kd >100 mM) for its pMHC ligand. This TCR was expressed in CHO cells as a TCR-Fc fusion protein with the alpha chain fused to the human Fc domain and purified using protein A chromatography. Protein gel show's the protein purity, while size exclusion chromatography shows that the protein is monodisperse (FIG. 14).

[00212] Two classic mouse TCRs were also used as model systems. The OT-II and the DOT 1.10 mouse TCRs both bind the same ovalbumin peptide (residues 323-339) when bound by the class II MHC I-Ab (OT-II) or I- Ad (DG11.10). These T cell hybridomas, originally elicited by vaccination of mice with hen egg white ovalbumin (OVA) (White et al., 1983), are well understood model system used to study CD4+ T ceil responses (Scott et al, 1998). Class II MHCs present exogenous peptides and are thus important for infection resistance and autoimmunity. Data presented in FTGs. 26-28 demonstrate that these TCR-Fc fusion constructs produced in CHO ceils could likewise be successfully, expressed and purified and displayed the selective binding to target peptide.

[00213] All of the methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art. are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

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