T-cell receptors (TCRS)

Abstract

The present disclosure provides methods for identifying T-cell receptors (TCRs) from sequencing data, and TCR sequences identified using the methods. The methods can comprise identifying a TCR alpha chain, a TCR beta chain, a TCR gamma chain, or a TCR delta chain from the sequencing data, and then identifying the corresponding paired chain. The "de novo" method can comprise the identification of statistically associated TCR chain sequences by assessing patients' antigenic status and / or HLA alleles. In the "bait" method, a TCR chain sequence of a TCR known to have some degree of antigen reactivity can be used to search for related sequences in the large database. Resulting sequences may or may not exhibit statistical enrichments that can be detected using the "de novo" approach. Various pairing methods are provided. Identified paired TCR chains can be used for preparing various therapies including cell-based therapies.

Description

WSGR Docket No.: 50401-789.601T-CELL RECEPTORS (TCRS)CROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 688,114, filed on August 28, 2024, U.S. Provisional Application No. 63 / 692,917, filed on September 10, 2024, and U.S. Provisional Application No. 63 / 745,602, filed on January 15, 2025, each of which is incorporated herein by reference in its entirety.BACKGROUND OF THE INVENTION

[0002] The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analyzing the TCR repertoire may help to gain a better understanding of the immune system features and of the etiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire. Despite recent advances in repertoire sequencing methods, the characterization of TCR repertoires has been limited by access to large, real-world patient cohorts with genomic, TCR, and clinical profiling.SUMMARY OF THE INVENTION

[0003] Provided herein is a T cell comprising a T cell receptor (TCR) or a recombinant nucleic acid encoding the TCR comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 7. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 7. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta chain variable region sequences listed in Table 7. In some embodiments, the TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has anWSGR Docket No.: 50401-789.601 amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 7; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha chain variable region sequences listed in Table 7. In some embodiments, the TCR binds an epitope from HPV comprising an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A02:01 allele. In some embodiments, the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-B07:02, HLA- C07:02 allele, and / or HLA-A03:01 allele. In some embodiments, TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A01 :01, HLA- B08:01 allele, and / or HLA-C07:01 allele. In some embodiments, the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A03 :01, HLA- C07:02 allele, and / or HLA-C 07:01 allele.

[0004] Provided herein is a soluble T cell receptor (TCR) comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 7. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 7. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 7. In some embodiments, the soluble TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 7; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7. In some embodiments, the TCR alpha chain construct comprises a variable region havingWSGR Docket No.: 50401-789.601 at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 7. In some embodiments, the soluble TCR binds an epitope from HPV comprising an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A02:01 allele. In some embodiments, the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-B07:02, HLA-C07:02 allele, and / or HLA-A03:01 allele. In some embodiments, soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A01 :01, HLA-B08:01 allele, and / or HLA-C07:01 allele. In some embodiments, the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A03:01, HLA-C07:02 allele, and / or HLA-C07: 01 allele.

[0005] Provided herein is a T cell comprising a T cell receptor (TCR) or a recombinant nucleic acid encoding the TCR comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 8. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 8. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 8. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 8. In some embodiments, the TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 8; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 8. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 8. In some embodiments, the TCR binds an epitope from human RAS comprising a mutation G12D. In some embodiments, the TCR binds to aWSGR Docket No.: 50401-789.601 complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-C08:02 allele. In some embodiments, the TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-B07:02, HLA-C07:02 allele, and / or HLA-A03:01 allele.

[0006] Disclosed herein is a soluble T cell receptor (TCR) comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 8. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 8. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 8. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 8. In some embodiments, the soluble TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 8; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 8. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 8. In some embodiments, the soluble TCR binds an epitope from human RAS comprising a mutation G12D. In some embodiments, the soluble TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-C08:02 allele. In some embodiments, the soluble TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-B07:02, HLA-C07:02 allele, and / or HLA-A03:01 allele.

[0007] Provided herein is a pharmaceutical composition comprising a T cell comprising a T cell receptor (TCR), the TCR, or a nucleic acid encoding the TCR, and a pharmaceutically acceptable carrier, wherein the TCR comprises a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consistingWSGR Docket No.: 50401-789.601 of TCR beta chain CDR3 sequences listed in Table 7 or Table 8, wherein the pharmaceutical composition is suitable for being administered into a subj ect in need thereof. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 7 or Table 8. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7 or Table 8. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 7 or Table 8. In some embodiments, the TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 7 or Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7 or Table 8; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7 or Table 8. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 7 or Table 8. In some embodiments, the pharmaceutical composition is for use in treating an immune disease or cancer.

[0008] Provided herein is a use of the pharmaceutical composition of any one of the embodiments disclosed herein, for treating an immune disease or cancer.

[0009] Provided herein is a method of treating a subject having a disease or condition, comprising administering to the subject the pharmaceutical composition of any one of the embodiments disclosed herein.

[0010] Provided herein is a method of treating a subject with cancer comprising administering to the subject the pharmaceutical composition any one of the embodiments disclosed herein.

[0011] Provided herein is an expression vector comprising a nucleic acid sequence encoding a T cell receptor (TCR) comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 7 or Table 8. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chainWSGR Docket No.: 50401-789.601CDR1 sequences listed in Table 7 or Table 8. In some embodiments, the TCRbeta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7 or Table 8. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 7 or Table 8. In some embodiments, the TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7 or Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7 or Table 8; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7 or Table 8. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 7 or Table 8.INCORPORATION BY REFERENCE

[0012] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.BRIEF DESCRIPTION OF THE DRAWINGS

[0013] The novel features of the present disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which:

[0014] FIG. 1A depicts a schematic example of the de novo method of identifying T-cell receptors (TCRs) from a plurality of libraries of TCR chain sequences.

[0015] FIG. IB depicts a schematic example of the bait method of identifying TCR chains from a plurality of libraries of TCR chain sequences.

[0016] FIG. 2 depicts the results of the de novo method for identifying statistically associated TCR chain sequences for a particular condition.WSGR Docket No.: 50401-789.601

[0017] FIG. 3A depicts the results of the bait method for identifying statistically associated TCR chain sequences for a particular condition.

[0018] FIG. 3B depicts sequence logo plots for identified neighbors of each bait (e.g., the known reference TCR chain sequence(s)) to determine if particular amino acids are enriched in any CDR3 position relative to the bait sequence.

[0019] FIG. 4 depicts an association study using bulk TCR-Seq to identify candidate antigenspecific TCR chains.

[0020] FIG. 5A depicts sample counts for HPV-relevant cancers.

[0021] FIG. 5B depicts sample counts for KRAS-relevant cancers.

[0022] FIG. 6 depicts a method of identifying alpha and beta chains enriched in patient populations of interest.

[0023] FIG. 7A depicts the Fisher exact tests of association of one TCR chain by condition and by allele.

[0024] FIG. 7B depicts a plot of alpha and beta chains enriched in patient populations of interest that were identified by statistical association.

[0025] FIG. 8A depicts the number of highest-tier candidate chains by across HPV and mutant KRAS targets.

[0026] FIG. 8B depicts the plotting and identification of dozens of candidate TCR alpha chains for KRAS-G12D including the highest-tier candidate chains.

[0027] FIG. 9A depicts crystal structures of Ros9a and Ros9d TCRs in complex with HLA- C*08:02 / KRAS-G12D 9mer. See Sim et al. 2020. High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D. PNAS 117(23): 12826-12835.

[0028] FIG. 9B depicts the distribution of TCR-pMHC affinities. Data are obtained from http : / / atlas . wenglab . org /

[0029] FIG. 9C depicts T Cell Receptor Alpha Variable (TRAV) genes, T Cell Receptor Alpha Joining (TRAJ) genes, CDR3a amino acid sequences, T Cell Receptor Beta Variable (TRBV) genes, T Cell Receptor Beta Joining (TRBJ) genes, CDR3P amino acid sequences, and Kds in nM of the Ros9 family of TCRs. Dots indicate amino acids matching those of the sequences in the first row of the table. Dashes indicate gaps relative to the sequences in the first row. Long dashes indicate the same V / J genes as the first row.

[0030] FIG. 10A depicts a method of identifying paired TCR chains for candidate alpha and beta chains using an enrichment analysis.

[0031] FIG. 10B depicts a method of identifying paired TCR chains for candidate alpha and beta chains using publicly available single-cell TCR-Seq (scTCR).WSGR Docket No.: 50401-789.601

[0032] FIG. 11 depicts TRAV genes, TRAJ genes, CDR3a amino acid sequences, TRBV genes, TRBJ genes, CDR3P amino acid sequences, and As in nM of the Ros9 family of TCR and selected new candidate TCR chains from the analysis and a portion of the Ros9a, Ros9d crystal structures. Dots indicate amino acids matching those of the sequences in the first row of the table. Dashes indicate gaps relative to the sequences in the first row. Long dashes indicate the same V / J genes as the first row.

[0033] FIG. 12A depicts the plotting and identification of candidate TCR alpha chains for HPV including the highest-tier candidate chains.

[0034] FIG. 12B depicts scTCR data coming from patients with HPV+ HNSC tumors. Dots indicate amino acids matching those of the sequences in the first row of the table. Dashes indicate gaps relative to the sequences in the first row. Long dashes indicate the same V / J genes as the first row.

[0035] FIG. 12C depicts scTCR samples collected from HPV+ HNSC tumors.

[0036] FIG. 13A depicts a comparison of paired chains by condition identified using an enrichment analysis versus both the enrichment analysis and scTCR.

[0037] FIG. 13B depicts the number of candidate alpha-beta pairings by condition identified by the de novo method.

[0038] FIG. 14A depicts a method of validating candidate TCRs using surface plasmon resonance (SPR).

[0039] FIG. 14B depicts a method of validating candidate TCRs using cell lines.

[0040] FIG. 15A depicts the plotting and identification of candidate TCR beta chains for HPV using the “bait” method.

[0041] FIG. 15B depicts sequences of NCI TCR chains and close neighbors discovered from the "bait” method.

[0042] FIG. 15C depicts Binding affinities of NCI TCR chains and close neighbors measured by SPR.

[0043] FIG. 16A depicts number of HPV+ and HPV- samples from patients with cervical squamous cell carcinoma (CESC) and head and neck squamous cell carcinoma (HNSCC).

[0044] FIG. 16B depicts identification of two TCR alpha chains with significant enrichment in HPV+ tumors.

[0045] FIG. 16C depicts allele association for the enriched TCR alpha chains.

[0046] FIG. 16D depicts the number of samples and number of public TCR chains for KRAS p.G12D, KRAS pG12C, KRAS p.G12V, and HPV.

[0047] FIG. 16E depicts analysis of the identified TCR alpha chains in published scTCR datasets.WSGR Docket No.: 50401-789.601

[0048] FIG. 16F depicts analysis of metadata for patient samples with cells containing the identified TCR alpha chain.

[0049] FIG. 16G depicts the clustering of candidate paired TCR beta chains using TCRdist (distance threshold=25).

[0050] FIG. 16H depicts pairing analyses of the identified TCR alpha chain with both enrichment database and scTCR database.

[0051] FIG. 161 depicts analysis of TCR beta chains identified with the scTCR approach and enrichment approach by comparing to randomly generated TRV6-51 / TRAJ9 CDR3 from SONIA, a software tool for TCR beta chain selection (Sethna et al., PLoS Computational Biology, 2020).

[0052] FIG. 17A depicts pairing analysis of top HPV TCR alpha chains after filtering for chains with odds ratio greater than five.

[0053] FIG. 17B depicts allele association of two HPV TCR alpha chains identified.

[0054] FIG. 17C depicts unbiased clustering of the candidate TCR beta chains using TCRdist.

[0055] FIG. 17D depicts analysis of metadata for patient samples with cells containing the identified TCR beta chain.

[0056] FIG. 17E depicts cytotoxicity kill curves for TCR-transduced donor T cells plated at a 1 : 1 ratio with CaSki cells.

[0057] FIG. 17F depicts fraction of cells binding HPV E7 / A*02:01 multimer transduced with identified TCRs.

[0058] FIG. 18A depicts pGen analysis of identified TCR chains compared to published antigenspecific chains.

[0059] FIG. 18B depicts CDR3 length analysis of identified TCR chains compared to published antigen-specific chains.

[0060] FIG. 18C depicts non-templated insertion analysis of identified TCR chains compared to published antigen-specific chains.

[0061] FIG. 18D depicts correlation between CDR3 length, non-template CDR3 length, and pGen.

[0062] FIG. 18E depicts measurement of allele frequencies.

[0063] FIG. 18F depicts the observed p-values as a function of detection events for the different alleles.

[0064] FIG. 18G depicts the number of TCR chains observed as a function of detection events for the different alleles.

[0065] FIG. 18H depicts the number of significant TCR chains observed as a function of detection events for the different alleles.WSGR Docket No.: 50401-789.601

[0066] FIG. 19A depicts an exemplary schematic of how antigen-associated TCR chains can be identified using the multimodal dataset. To determine the significance of a given TCR chain, its occurrences are counted in antigen-positive and antigen-negative samples and compared against the counts of all other TCR chains in the respective populations.

[0067] FIG. 19B depicts histogram showing the distribution of TCR chain counts recovered per patient across the full multimodal dataset.

[0068] FIG. 19C depicts odds ratios and p-values for TCR chains according to their association with HPV status. Odds ratios exceeding the plot range are shown as 100. Labels show the top 3 TCR chains by p-value plus one closely related variant chain.

[0069] FIG. 19D depicts Fisher’s exact test p-values for HLA allele association for four strongly HPV-associated TCR chains. Statistical test is based on a 2x2 contingency table comparing counts of the given TCR chain vs. all other TCR chains for patients that are positive and negative for the candidate allele. Associations are calculated over the HPV+ population only. Asterisks: Bonferroni-adjusted p-value <0.05.

[0070] FIG. 19E depicts count of patient samples per cancer type.

[0071] FIG. 19F depicts mean count of RNA-Seq-derived TCR chains per patient by cancer type. Outlier values (for thymic cancer) are shown with text labels.

[0072] FIG. 19G depicts count of HPV-positive and HPV-negative patients for each of the six HPV-associated cancer types in the multimodal dataset.

[0073] FIG. 19H depicts distribution of CDR3 lengths for all unique TCR chains in the multimodal dataset vs. the HPV-associated TCR chains recovered in Table 14.

[0074] FIG. 20A depicts scatterplot wherein each point corresponds to a candidate mate chain for one of the 31 HPV-associated TCR chains that were recovered. X-axis value is the Fisher’s exact test p-value for association between the candidate mate chain and the initial HPV-associated TCR chain as calculated over the HPV+ population. Y-axis value is Fisher’s exact test p-value for association between the candidate mate chain and HPV status as calculated over the population of six HPV-associated cancer types. Mates in boxes are shown in FIG. 20C.

[0075] FIG. 20B depicts number of curated single cell TCR-Seq samples for each cancer type or control population.

[0076] FIG. 20C depicts sequence information for candidate mates of TCRa_595244 found according to enrichment pairing (top) or analysis of scTCR-Seq data (bottom).

[0077] FIG. 20D depicts counts of TCR chains exactly matching TCRa_45061 in previously published samples sequenced from six patients with HPV+ head and neck cancer. Samples were derived from tumor or metastatic lymph node and were sorted according to PD1 -positivity or multimer positivity. Values in parentheses reflect counts of close variants of TCRa_45061 (r<15).WSGR Docket No.: 50401-789.601

[0078] FIG. 20E depicts luminescence fold change for NF AT -reporter Jurkats co-cultured with HLA-engineered cells transfected with HPV RNA (El, E6 or E7 mRNA) for TCR family T13-1.

[0079] FIG. 20F depicts X-ray structure for TCRa_45061 :Eberhardt_3 complexed with HPV E2 epitope QVDYYGLYY and HLA-A*01 :01 with a zoom-in on the binding interface (2.2 angstrom resolution).

[0080] FIG. 20G depicts cell killing curves for HPV El / HLA-A*02:01 TCRs HPV4 and HPV5. Effector cells were TCR-transfected healthy donor T cells, and target cells were the HPV+ Caski cell line. Cells were plated at a 1 : 1 effectortarget ratio.

[0081] FIG. 20H depicts surface plasmon resonance (SPR) sensorgram for TCRa_45061 :Eberhardt_3 to HPV E2 QVDYYGLYY / A*01 :01.

[0082] FIG. 21 A depicts scatter plot showing odds ratio and Fisher’s exact text p-values for TCR clusters according to their enrichment in HPV-associated cancer types vs. non-HPV-associated cancer types. Given the larger number of clusters with overlapping membership, only the most significant cluster is plotted per TCR chain. Shading reflects hit status (FDR<0.1; OR>2). Shapes reflect cluster radius values and are open or filled for alpha and beta TCR chains, respectively.

[0083] FIG. 21B depicts waterfall chart showing the number of similarity groups that meet the significance criteria (OR >2; FDR<0.1) at each increasing tier of TCRdist3 radius.

[0084] FIG. 21C depicts overview of significant TCR chains that were previously characterized or deployed clinically.

[0085] FIG. 21D depicts CDR3P sequence logo for the similarity group containing TCRb_4186850 and X-ray structure of the corresponding TCR:pMHC interface. Logo letter heights are proportional to frequencies and positions are marked with respect to the start of the TCRP chain.

[0086] FIG. 21E depicts bar plot showing the number of similarity groups associated with each HLA-I allele according to confidence level. Confidence was based on manual inspection and considered odds ratio, p-value, and population frequency of the allele.

[0087] FIG. 21F depicts luminescence fold change for NF AT -reporter Jurkats co-cultured with HLA-engineered A375s (HLA-A*01 :01 or HLA-A*11 :01) transfected with HPV RNA (El, E6, or E7) for TCR families T01, T02, and TI L Fold change is relative to untransfected target cells + effector cells.

[0088] FIG. 21G depicts cytotoxicity kill curves for TCR-transduced healthy donor T cells plated at a 5: 1 ratio with CaSki cells.

[0089] FIG. 21H depicts proportion of TCR chains with 0 neighbors, 1 neighbor, 2 neighbors and so on. Area of the rectangles equals the proportion of TCR chains. Results are shown according to chain (alpha or beta) and cluster radius (5, 10, and 20).WSGR Docket No.: 50401-789.601

[0090] FIG. 211 depicts schematic representing the process by which overlapping significant clusters were merged into similarity groups. Similarity groups may draw from clusters that were defined with different radius values, and possible for similarity groups to comprise a single TCR chain.

[0091] FIG. 21 J depicts bar plot showing the number of similarity groups assigned to an HLA-I allele, an HLA-II allele, both, or neither according to a simple Bonferroni significance cutoff 0.05 / (# HLA-I alleles + # HLA-II alleles). To conduct allele inference at the similarity group level, counts were summed across all TCR chains in each similarity group.

[0092] FIG. 21K depicts bar plot showing the proportion of samples in scTCRdb that correspond to HPV-associated cancer types, non-HPV-associated cancer types, and non-cancer samples. Rates are shown for the overall database and for the subset of samples that contain matches for one of 197 HLA-I-associated similarity groups. Values for matches are shown two ways - one requiring exact match and one allowing approximate match (TCRdist radius <=15).

[0093] FIG. 21L depicts histogram showing distribution of p-values for statistical chain pairing as conducted for the 197 HLA-I-associated similarity groups. Values reflect Fisher’s exact test conducted on chain X vs. chain Y in the antigen-positive population (patients with an HPV- associated cancer type). Chains “X” and “Y” may correspond to single TCR chains and / or to clusters. The dotted line corresponds to an ad hoc definition for outlier p-values.

[0094] FIG. 21M depicts an upset plot showing how many TCR families had pairing inference supported by a single line of evidence or multiple lines of evidence, “single-cell / statistical match”: single-cell hit (any sample) matches a statistical pairing hit, “strong statistical pairing”: Statistical pairing hit with outlier p-value (p<le-l 1), “HPV-relevant single-cell pairing”: single-cell hit from a potentially relevant sample, defined as any head and neck, cervical, or anal tumor, plus any normal tissue from cervix or oropharynx, “denovo match”: Statistical pairing hit that was also a member of an antigen-associated similarity group.

[0095] FIG. 21N depicts comparison of the pairing confidence scores of TCRs validated and those that did not (DNV).

[0096] FIG. 22A depicts bar plot showing the number of similarity groups for each major KRAS mutation.

[0097] FIG. 22B depicts scatter plot showing odds ratio and Fisher’s exact text p-values for TCR clusters according to their enrichment in KRAS-mutant samples vs. KRAS-wildtype samples. Significant clusters (OR<2 and FDR>0.1) are coded according to the relevant KRAS mutation. Only the most significant cluster is plotted per TCR chain.

[0098] FIG. 22C depicts overview of matches to previously published KRAS TCRs. Functional avidities and clinical activity are indicated, where known.WSGR Docket No.: 50401-789.601

[0099] FIG. 22D depicts functional avidity of G12V / HLA-A*03:01 TCRs.

[0100] FIG. 22E depicts scatter plot of binding affinity and functional avidity for sequencesimilar KRAS G12D HLA-C*08:02 TCRs. Four TCRs correspond to the Tran et al publication. The remainder represents multimodal dataset-derived chains that were statistically significant according to the analysis or that were otherwise highly sequence-similar to the Tran et al TCRs (termed “bait” sequences).

[0101] FIG. 22F depicts count of patients with each of eight major KRAS mutations in each cancer type in the multimodal dataset.

[0102] FIG. 22G depicts waterfall plot showing net gain in observed similarity groups as analysis incorporated clusters with progressively larger TCRdist3 radius values.

[0103] FIG. 22H depicts a pairing confidence scoring system based on KRAS mutations or variants.

[0104] FIG. 221 depicts count of similarity groups associated with KRAS mutations.

[0105] FIG. 23A depicts functional avidity of identified KRAS TCRs: T18-1 and T18-5.

[0106] FIG. 23B depicts killing of NCI-H441 cells over time with T18-1 or T18-5 TCRs transduced into T cells compared to irrelevant TCR transduced T cells.

[0107] FIG. 23C depicts level of secreted IFNy upon co-culturing with NCI-H441 tumor cells with T18-1, T18-5, or irrelevant TCR transduced T cells.

[0108] FIG. 24A depicts killing of NCI-H441 cells over time with T18-1 or T18-5 TCRs transduced into T cells compared to irrelevant TCR transduced T cells or NCI A03 mTCR transduced T cells.

[0109] FIG. 24B depicts level of secreted IFNy upon co-culturing with NCI-H441 tumor cells with T18-1, T18-5, NCI A01 mTCR, or irrelevant TCR transduced T cells.

[0110] FIG. 25A depicts killing of NCI-H441 cells over time with T18-1 or T18-5 TCRs transduced into T cells compared to irrelevant TCR transduced T cells or TCR from Bear et. al. transduced T cells.

[0111] FIG. 25B depicts level of secreted IFNy upon co-culturing with NCI-H441 tumor cells with T18-1, T18-5, TCR from Bear et. al., or irrelevant TCR transduced T cells.

[0112] FIG. 26 depicts a bar plot showing the number of similarity groups associated with each HLA-I allele. In cases where a similarity group was associated with multiple alleles, as commonly occurs for alleles in strong linkage disequilibrium (e.g. HLA-B*07:02 and HLA-C*07:02), only the strongest allele by p-value is shown.

[0113] FIG. 27 depicts an overview of how antigen-associated TCR chains can be identified using the multimodal dataset. To determine the significance of a given TCR chain, its occurrences wereWSGR Docket No.: 50401-789.601 counted in antigen-positive and antigen-negative samples and compared against the counts of all other TCR chains in the respective populations.

[0114] FIG. 28 depicts the number of curated scTCR-Seq samples for each cancer type or control population.

[0115] FIG. 29 depicts the allele assignment for each TCR as a function of total TCR observations (x-axis) and condition odds ratio (y-axis).

[0116] FIG. 30 depicts epitope mapping for validated HPV-specific TCRs.

[0117] FIG. 31 depicts stacked bar plot showing the number of similarity groups that were assigned to each common KRAS mutation (G12C, G12D, and G12V) and each HLA allele. Asterisks mark mutation-allele combinations that were experimentally confirmed to present antigen.

[0118] FIG. 32 depicts stacked bar plot showing allele assignments relevant for additional KRAS mutations that were analyzed for HLA-I association only.

[0119] FIG. 33 depicts mean CDR3 hamming distance for a random pair of sequences in the same cluster according to chain (alpha and beta) and cluster radius (5, 10, and 20).

[0120] FIG. 34 shows the chain pairing inference and experimental validation for HPV TCRs.

[0121] FIG. 35 shows the experimentally tested HPV-associated TCRs.

[0122] FIG. 36 shows the sequence information of TCRs in FIGs. 19, 21C, and 22C.DETAILED DESCRIPTIONIntroduction

[0123] The present disclosure provides therapeutically relevant T-cell receptor (TCR) sequences identified from sequencing data, drawing upon two different methods. Both methods can depend on access to a database that includes bulk (or single-cell) TCR sequencing data from a large number of cancer patient tumor biopsies, where each patient / tumor can have an associated metadata (such cancer type / subtype, mutation profile, gene expression, HPV status, etc.). Utilizing an extensive plurality of patient libraries encompassing bulk TCR chain sequencing data from diverse cancer patient tumor biopsies, each enriched with relevant metadata, methodology provided herein can provide a need in the field for identifying useful TCR chain sequences directly from sequencing data.

[0124] The “de novo” method can comprise the identification of statistically associated TCR chain sequences by assessing patients’ antigenic status and / or HLA alleles. For example, patients that do / don’t harbor an antigen or interest (e.g. HPV infection status or the presence / absence of a specific KRAS mutation) and patients that do / don’t express a specific HLA allele of interest can be identified and sub-grouped. Based on these criteria, whether a specific TCR chain sequence appears to be statistically associated with an antigen and / or HLA allele can be queried. Such TCRWSGR Docket No.: 50401-789.601 chains can be antigen-specific and can potentially be used as therapeutic molecules “as-is” or with further sequence optimization.

[0125] In the “bait” method, a TCR known to have some degree of antigen reactivity can be used to search for related sequences in the large database. Resulting sequences may or may not exhibit statistical enrichments that can be detected using the “de novo” approach. Thus, the “bait” approach may be able to detect rarer TCR chains that lack sufficient counts to reach statistical significance.

[0126] To bolster the efficacy for the system, various additional methods can be performed before and / or after identifying one or more TCR chain sequence hits. For example, chain pairing can be performed since the results identify single chains (e.g., alpha, beta, gamma, or delta). There can be several approaches to find pairs for hits. If the hit is identified using the “bait” method, the corresponding chain of the bait TCR chain can be used to identify the corresponding pair of the hit to form the potential TCR pair. Auxiliary single-cell TCR (scTCR) sequencing databases can be used to see if they include the hit sequence or a close sequence neighbor thereof. Alternatively, alpha-beta sequences that frequently co-occur in the same patients in the original large bulk sequencing libraries can be identified.

[0127] In some cases, clustering can be performed. Rather than conducting the “de novo” analysis at the level of discrete TCR chains, it may be possible to first cluster the TCR chain sequences using a relevant similarity metric. This may improve the statistical power of the approach, especially for TCR chains that harbor rarer sequence motifs.

[0128] Motif-based triage can be performed. For example, hits from the “bait” and / or “de novo” methods may reveal sequence motifs such as residues that are conserved at certain positions. In this scenario, hits that conform to the overall motif may be considered as preferred candidates.

[0129] Generation probabilities can be performed. For example, the likelihood for a given TCR chain to be generated by thymic selection can be approximated using published techniques. For example, to correct for the effect of thymic selection, a correction factor can be estimated. In some cases, a sequence-specific factor for each individual is learned. In some cases, all observed sequences passing thymic selection can be assumed. The correction factor can be a normalization factor accounting for the fact that just a fraction of sequences passes thymic selection. The correction factor can be determined for each VJ-combination. For example, the correction factor can be correction factor Q where the following factorized model for Q captures the main features of selection:where can be a CDR3 region, V and J can be a V and J gene choices, ( , V,J~) can be a full TCRWSGR Docket No.: 50401-789.601 chain sequence, (ai, . . ., a ) can be the amino acid sequence of the CDR3, and L is its length. The factors qL, qi;L(a), and qvj denote selective pressures on the CDR3 length, its composition, and the associated VJ identities, respectively. (Pogorelyy et al. Elife. 2018; Elhanati et al. PNAS. 2014). Hits that are less probable may imply stronger selective forces to promote their frequency. Therefore, TCR chains with low generation probabilities may be considered as preferred candidates.

[0130] Iterative analysis can be performed. For example, hits from the “de novo” analysis may be further used as starting sequences for the “bait” approach. “De novo” hits with marginal statistical significance may be rescued based on sequence similarity with a known TCR (e.g., a “bait”) or concordance with a known motif.

[0131] Chain fishing can be performed. For example, even if a known / putative alpha-beta pairing is available, additional potential partners for a given chain can be searched for using chain pairing approaches listed above (e.g., the single-cell approach and the database correlation approach). This can generate additional alpha-beta TCRs for consideration.

[0132] Continuous variables can be performed. For example, statistical analysis for the “de novo” method may not require that the antigen be strictly present / absent. Enrichment criteria can be devised for continuous variables, such as the expression of an antigenic gene (e.g., MAGEA4).

[0133] Antigen-agnostic analyses can be performed. For example, the “de novo” method may not require the presence of an explicit antigen but may search for TCR chains enriched in a certain group of patients (e.g., a cancer subtype), possibly using healthy donors as controls. In these cases, additional analyses or experiments may be carried out to determine the antigen specificity of “hits”.

[0134] The methods and systems described herein are not limited to identifying alpha-beta TCRs and can be used to discover gamma-delta TCRs as well as BCRs and antibodies.

[0135] The methods and systems described herein are not limited to applications related to cancer and can be extended to discover TCRs relevant for infectious disease and autoimmunity.Definitions

[0136] To facilitate an understanding of the present disclosure, a number of terms and phrases are defined below. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.

[0137] The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example,WSGR Docket No.: 50401-789.601“about” can mean within 1 or more than 1 standard deviation, per the practice in the art. Alternatively, “about” can mean a range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 5 -fold, and more preferably within 2- fold, of a value. Where particular values are described in the application and claims, unless otherwise stated the term “about” meaning within an acceptable error range for the particular value should be assumed.

[0138] An “antigen” refers to a substance (e.g., a foreign substance to the body) that can induce an immune response. The antigen can be a protein or fragment thereof that is encoded by a gene in a pathogen.

[0139] An “epitope” is the collective features of a molecule (e.g., a peptide’s charge and primary, secondary and tertiary structure) that together form a site recognized by another molecule (e.g., an immunoglobulin, T-cell receptor, HLA molecule, or chimeric antigen receptor). For example, an epitope can be a set of amino acid residues involved in recognition by a particular immunoglobulin; a Major Histocompatibility Complex (MHC) receptor; or in the context of T cells, those residues recognized by a T-cell receptor protein and / or a chimeric antigen receptor. Epitopes can be prepared by isolation from a natural source, or they can be synthesized according to standard protocols in the art. Synthetic epitopes can comprise artificial amino acid residues, amino acid mimetics, (such as D isomers of naturally-occurring L amino acid residues or non- naturally-occurring amino acid residues). Throughout this disclosure, epitopes can be referred to in some cases as peptides or peptide epitopes. In certain embodiments, there is a limitation on the length of a peptide of the present disclosure. The embodiment that is length-limited occurs when the protein or peptide comprising an epitope described herein comprises a region (i.e., a contiguous series of amino acid residues) having 100% identity with a native sequence. In order to avoid the definition of epitope from reading, e.g., on whole natural molecules, there is a limitation on the length of any region that has 100% identity with a native peptide sequence. Thus, for a peptide comprising an epitope described herein and a region with 100% identity with a native peptide sequence, the region with 100% identity to a native sequence generally has a length of: less than or equal to 600 amino acid residues, less than or equal to 500 amino acid residues, less than or equal to 400 amino acid residues, less than or equal to 250 amino acid residues, less than or equal to 100 amino acid residues, less than or equal to 85 amino acid residues, less than or equal to 75 amino acid residues, less than or equal to 65 amino acid residues, and less than or equal to 50 amino acid residues. In certain embodiments, an “epitope” described herein is comprised by a peptide having a region with less than 51 amino acid residues that has 100% identity to a native peptide sequence, in any increment down to 5 amino acid residues; for example 50, 49, 48, 47,WSGR Docket No.: 50401-789.60146, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acid residues. An epitope of a protein such as a tumor antigen can comprise a continuous or discontinuous portion of the protein and can be between 5 and 100, 5 and 50, 8 and 30, or 10 and 25 amino acids in length, for example, the epitope may be 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2021, 22, 23, 24 or 25 amino acids in length.

[0140] A “T-cell receptor” (“TCR”) refers to a molecule, whether natural or partly or wholly synthetically produced that recognizes an antigen bound to a major histocompatibility complex (MHC) molecule. The TCR can be soluble or expressed on the surface of T lymphocytes (e.g., T cells). The ability of a T cells to recognize an antigen associated with various diseases (e.g., infectious diseases such as malaria) or infectious organisms is conferred by its TCR, which is made up of both an alpha (a) chain and a beta (P) chain or a gamma (y) and a delta (5) chain. The proteins which make up these chains are encoded by DNA, which employs a unique mechanism for generating the tremendous diversity of the TCR. This multi-subunit immune recognition receptor associates with the CD3 complex and binds peptides presented by the MHC class I and II proteins on the surface of antigen-presenting cells (APCs). Binding of a TCR to a peptide on an APC is a central event in T cell activation. In the current disclosure, a and a in the context of TCR can be used interchangeably to denote alpha chain, and b and P can be used interchangeably to denote beta chain.

[0141] The terms “complementarity determining region,” and “CDR,” synonymous with “hypervariable region” or “HVR,” are known in the art to refer to non-contiguous sequences of amino acids within TCR variable regions, which confer specificity and / or binding affinity to an MHC-peptide complex. In general, there are three CDRs in each alpha chain variable region (CDR-H1, CDR-H2, CDR-H3) and three CDRs in each beta chain variable region (CDR-L1, CDR-L2, CDR-L3). “Framework regions” and “FR” are known in the art to refer to the non-CDR portions of the variable regions of the alpha and beta chains. In general, there are four FRs in each full-length alpha chain variable region (FR-H1, FR-H2, FR-H3, and FR-H4), and four FRs in each full-length beta chain variable region (FR-L1, FR-L2, FR-L3, and FR-L4).

[0142] The term “variable region” or “variable domain” refers to the domain of a TCR alpha, beta, gamma, or delta chain, that is involved in binding the TCR to antigen-MHC complexes. The variable domains of the alpha chain and beta chain (Va and VP, respectively), and the gamma chain and delta chain (Vy and V5, respectively) of a native TCR generally have similar structures, with each domain comprising four conserved framework regions (FRs) and three CDRs. A single Va or VP domain, or Vy or V5 domain, may be sufficient to confer binding specificity to a peptide- MHC complex.WSGR Docket No.: 50401-789.601

[0143] Also provided herein are TCR fragments, including antigen-binding fragments. In some embodiments, the TCR is an antigen-binding portion thereof, such as a variant of a full-length TCR not containing the transmembrane and / or cytoplasmic region(s) thereof, which may be referred to as a full soluble TCR. In some embodiments, the TCR is a dimeric TCR (dTCR). In some embodiments, the TCR is a single-chain TCR (scTCR), such as a scTCR having a structure as described in PCT patent publication numbers W02003 / 020763, W02004 / 033685, or WO201 1 / 044186. In certain embodiments, the TCR is a single-chain TCR fragment comprising an alpha chain variable region linked to a beta chain variable region, such as a scTv. In some embodiments, a scTv is also referred to as a scFv. A single-chain Tv or scTv refers in some aspects TCR fragments that comprise the variable alpha or gamma chain (Va or Vy) and variable beta or delta chain (VP or V5) domains of a TCR, wherein these domains are present in a single polypeptide chain. Generally, the Tv polypeptide further comprises a polypeptide linker between the Va and VP domains or Vy and V5 domains which enables the scTv to form the desired structure for antigen binding. A diabody refers in some aspects to TCR fragments with two antigen-binding sites, which fragments comprise a Va connected to a VP in the same polypeptide chain (Va-VP) or a Vy connected to a V5 in the same polypeptide chain (Vy-V5). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigenbinding sites. Exemplary diabodies are described more fully in, for example, EP404097 and WO93 111161. Fv refers in some aspects to a TCR fragment which contains a complete peptide- MHC complex recognition and peptide-MHC complex binding site. This region consists of a dimer of one TCRa chain and one TCRP chain or one TCRy chain and one TCR5 chain in tight, non-covalent association. It is in this configuration that the three CDRs of each variable domain interact to define a peptide-MHC complex binding site on the surface of the Va-VP dimer or Vy- V5 dimer. Collectively, a combination of one or more of the CDRs from each of the Va-VP chains or Vy-V5 chains confers peptide-MHC complex binding specificity to the TCR. For example, it would be understood that, for example, the CDRa3 and CDRP3 or CDRy3 and CDR53 could be sufficient to confer antigen-binding specificity to a TCR when transferred to Va and VP chains or Vy-V5 chains of a recipient selected TCR or antigen-binding fragment thereof and this combination of CDRs can be tested for binding, affinity, etc. Furthermore, although the two domains of a Tv fragment (Va and VP or Vy and V5 ), are coded for by separate genes, they can be joined using recombinant methods by a synthetic linker that enables them to be made as a single protein chain in which the Va and VP or Vy and V5 chain regions pair to form monovalent molecules (known as single chain Tv (scTv). Such scTvs are also intended to be encompassed within the peptide-MHC complex binding portion of a TCR.WSGR Docket No.: 50401-789.601

[0144] The term “cancer neoantigen” or “neoantigen” or “neoepitope” can refer to antigens that are not encoded in a normal, non-mutated host genome. A neoantigen can relate to an antigen including one or more amino acid modifications compared to the parental antigen. For example, a neoantigen may be a tumor-associated neoantigen, wherein the term “tumor-associated neoantigen” can include a peptide or protein including amino acid modifications due to tumorspecific mutations. In some instances, a neoantigen represents either oncogenic viral proteins or abnormal proteins that arise as a consequence of somatic mutations. For example, a neoantigen can arise by the disruption of cellular mechanisms through the activity of viral proteins. Another example can be an exposure of a carcinogenic compound, which in some cases can lead to a somatic mutation. This somatic mutation can ultimately lead to the formation of a tumor / cancer. A neoantigen can be a class of tumor antigens which arise from tumor-specific changes in proteins. Neoantigens encompass, but are not limited to, tumor antigens which arise from, for example, a substitution in a protein sequence, a frame shift mutation, a fusion polypeptide, an in-frame deletion, an insertion, and expression of an endogenous retroviral polypeptide. A neoepitope can be an epitope that is not present in a reference, such as a non-diseased cell, e.g., a non-cancerous cell or a germline cell, but is found in a diseased cell, e.g., a cancer cell. This includes situations where a corresponding epitope is found in a normal non-diseased cell or a germline cell but, due to one or more mutations in a diseased cell, e.g., a cancer cell, the sequence of the epitope is changed so as to result in the neoepitope.

[0145] A “TCR epitope” refers in some aspects to a portion of an antigen or other macromolecule capable of forming a binding interaction with the variable region binding pocket of a TCR. In some aspects, a TCR epitope refers to a portion of a peptide-MHC complex capable of forming a binding interaction with the variable region binding pocket of a TCR. Such binding interactions can be manifested as an intermolecular contact with one or more amino acid residues of one or more CDRs. Peptide-MHC complex binding can involve, for example, a CDR3, a CDR3 pair, or in some instances, interactions of up to all six CDRs of the Va and VP chains or Vy or V5 chains. An epitope can be a linear peptide sequence (e.g., “continuous”) or can be composed of noncontiguous amino acid sequences (e.g., “conformational” or “discontinuous”). A TCR can recognize one or more amino acid sequences. Therefore, an epitope can define more than one distinct amino acid sequence. In some aspects, a TCR can recognize one or more amino acid sequences or epitopes in the context of an MHC. Epitopes recognized by TCRs can be determined by peptide mapping and sequence analysis techniques well known to one of skill in the art. Binding interactions are manifested as intermolecular contacts with one or more amino acid residues of a CDR. A TCR epitope can be an antigenic determinant in a molecule such as an antigen, e.g., to a part in or fragment of the molecule that is recognized by the immune system, for example, that isWSGR Docket No.: 50401-789.601 recognized by a T cell, in particular when presented in the context of MHC molecules. A TCR epitope of a protein such as a tumor antigen can comprise a continuous or discontinuous portion of the protein and can be between 5 and 100, 5 and 50, 8 and 30, or 10 and 25 amino acids in length, for example, the epitope may be 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 21, 22, 23, 24 or 25 amino acids in length.

[0146] The term “binding” refers to a direct association between two molecules, due to, for example, covalent, electrostatic, hydrophobic, and ionic and / or hydrogen-bond interactions under physiological conditions, and includes interactions such as salt bridges and water bridges, as well as any other conventional means of binding.

[0147] In some embodiments, reference to a TCR with “specific binding” refers to a situation in which a TCR will not show any significant binding to molecules other than the peptide-MHC complex containing the epitope recognized by the TCR. The term is also applicable where for example, an antigen binding domain is specific for a particular epitope which is carried by a number of peptide-MHC complexes, in which case the selected TCR or peptide-MHC complex binding fragment thereof carrying the peptide-MHC complex binding domain will be able to bind to the various peptide-MHC complexes carrying the epitope. The terms “preferentially binds” or “specifically binds” mean that the TCRs or fragments thereof bind to an epitope with greater affinity than it binds unrelated amino acid sequences, and, if cross-reactive to other polypeptides containing the epitope, are not toxic at the levels at which they are formulated for administration to human use. In one aspect, such affinity is at least 1-fold greater, at least 2-fold greater, at least 3-fold greater, at least 4-fold greater, at least 5-fold greater, at least 6-fold greater, at least 7-fold greater, at least 8-fold greater, at least 9-fold greater, 10-fold greater, at least 20-fold greater, at least 30-fold greater, at least 40-fold greater, at least 50-fold greater, at least 60-fold greater, at least 70-fold greater, at least 80-fold greater, at least 90-fold greater, at least 100-fold greater, or at least 1000-fold greater than the affinity of the TCR or fragment thereof for unrelated amino acid sequences.

[0148] The term “affinity” refers to a measure of the strength of binding between two members of a binding pair (e.g., a human leukocyte antigen (HLA)-binding peptide and a class I or II HLA, or a peptide-HLA complex and a T cell receptor (TCR)). Affinity can be expressed as an equilibrium constant of the reversible binding of two agents and can be expressed as KD, KA, Koff or Kon. KD refers to the dissociation constant between two members of a binding pair and has units of molarity. KA refers to the affinity constant between two members of a binding pair is the inverse of the dissociation constant. Affinity may be determined experimentally, for example by surface plasmon resonance (SPR) using commercially available Biacore SPR units. Koff refers to the off-rate constant of two members of a binding pair, (e.g., the off-rate constant of an HLA-WSGR Docket No.: 50401-789.601 binding peptide and a class I or II HLA, or a peptide-HLA complex and a TCR). Kon refers to the on-rate constant of two members of a binding pair, (e.g., the on-rate constant of an HLA-binding peptide and a class I or II HLA, or a peptide-HLA complex and a TCR). Affinity of a binding protein to a ligand such as affinity of a TCR for an epitope can be, for example, from about 100 nanomolar (nM) to about 0.1 nM, from about 100 nM to about 1 picomolar (pM), or from about 100 nM to about 1 femtomolar (fM).

[0149] The term “avidity” refers to the resistance of a complex of two or more agents to dissociation after dilution.

[0150] Any binding data results described herein may be expressed in terms of the dissociation constant KD or the “IC50.” Affinity may also be expressed as the inhibitory concentration 50 (IC50), or the concentration at which 50% of a first member of a binding pair (e.g., a peptide) is displaced. Likewise, ln(IC50) refers to the natural log of the IC50. For example, an IC50 may be the concentration of a tested peptide in a binding assay at which 50% inhibition of binding of a labeled reference peptide is observed. Given the conditions in which the assays are run (e.g., limiting HLA protein concentrations and / or labeled reference peptide concentrations), these values can approximate KD values. Assays for determining binding are well known in the art and are described in detail, for example, in PCT publications WO 94 / 20127 and WO 94 / 03205, and other publications such as Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); and Sette, et al., Mol. Immunol. 31 :813 (1994). Alternatively, binding can be expressed relative to binding by a reference standard peptide. Binding can also be determined using other assay systems including those using: live cells (e.g., Ceppellini et al., Nature 339:392 (1989); Christnick et al., Nature 352:67 (1991); Busch et al., Int. Immunol. 2:443 (1990); Hill et al., J. Immunol. 147: 189 (1991); del Guercio et al., J. Immunol. 154:685 (1995)), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol. 21 :2069 (1991)), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890 (1994); Marshall et al., J. Immunol. 152:4946 (1994)), ELISA systems (e.g., Reay et al., EMBO J. 11 :2829 (1992)), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem. 268: 15425 (1993)); high flux soluble phase assays (Hammer et al., J. Exp. Med. 180:2353 (1994)), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476 (1990); Schumacher et al., Cell 62:563 (1990); Townsend et al., Cell 62:285 (1990); Parker et al., J. Immunol. 149:1896 (1992)).

[0151] “Major Histocompatibility Complex” or “MHC” is a cluster of genes or the protein products thereof that plays a role in control of the cellular interactions responsible for physiologic immune responses. The terms “major histocompatibility complex” and the abbreviation “MHC” can include any class of MHC molecule, such as MHC class I and MHC class II molecules, and relate to a complex of genes which occurs in all vertebrates. In humans, the MHC complex is alsoWSGR Docket No.: 50401-789.601 known as the human leukocyte antigen (HLA) complex. Thus, a “Human Leukocyte Antigen” or “HLA” refers to a human Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., Immunology, 8TH Ed., Lange Publishing, Los Altos, Calif. (1994). For a detailed description of the MHC and HLA complexes, see, Paul, Fundamental Immunology, 3rd Ed., Raven Press, New York (1993).

[0152] The major histocompatibility complex in the genome comprises the genetic region whose gene products expressed on the cell surface are important for binding and presenting endogenous and / or foreign antigens and thus for regulating immunological processes. MHC proteins or molecules are important for signaling between lymphocytes and antigen-presenting cells or diseased cells in immune reactions. MHC proteins or molecules bind peptides and present them for recognition by T-cell receptors. The proteins encoded by the MHC can be expressed on the surface of cells and display both self-antigens (peptide fragments from the cell itself) and nonself-antigens (e.g., fragments of invading microorganisms) to a T-cell. MHC binding peptides can result from the proteolytic cleavage of protein antigens and represent potential lymphocyte epitopes, (e.g., T cell epitope and B cell epitope). MHCs can transport the peptides to the cell surface and present them there to specific cells, such as cytotoxic T-lymphocytes, T-helper cells, or B cells. The MHC region can be divided into three subgroups, class I, class II, and class III. MHC class I proteins can contain an a-chain and p2-microglobulin (not part of the MHC encoded by chromosome 15). They can present antigen fragments to cytotoxic T-cells. MHC class II proteins can contain a- and P-chains and they can present antigen fragments to T-helper cells. MHC class III region can encode for other immune components, such as complement components and cytokines. The MHC can be both polygenic (there are several MHC class I and MHC class II genes) and polymorphic (there are multiple alleles of each gene).

[0153] The term “motif’ refers to a pattern of residues in an amino acid sequence of defined length, for example, a peptide of less than about 15 amino acid residues in length, or less than about 13 amino acid residues in length, for example, from about 8 to about 13 amino acid residues (e.g., about 8, about 9, about 10, about 11, about 12, or about 13) for a class I HLA motif and from about 6 to about 25 amino acid residues (e.g., about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, or about 25) for a class II HLA motif, which is recognized by a particular HLA molecule. Motifs are typically different for each HLA protein encoded by a given human HLA allele. These motifs differ in their pattern of the primary and secondary anchor residues. In some embodiments, an MHC class I motif identifies a peptide of 7, 8 9, 10, 11, 12 or 13 amino acid residues in length. In some embodiments, an MHC class II motif identifies a peptide of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 amino acid residues in length. A “cross-reactiveWSGR Docket No.: 50401-789.601 binding” peptide refers to a peptide that binds to more than one member of a class of a binding pair members (e.g., a peptide bound by both a class I HLA molecule and a class II HLA molecule).

[0154] An “immune cell” refers to a cell that plays a role in the immune response. Immune cells are of hematopoietic origin, and include lymphocytes, such as B cells and T cells; natural killer cells; myeloid cells, such as monocytes, macrophages, eosinophils, mast cells, basophils, and granulocytes.

[0155] The terms “polynucleotide,” “nucleotide,” “nucleotide sequence,” “nucleic acid,” and “oligonucleotide” are used interchangeably. They can refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three dimensional structure, and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), short interfering RNA (siRNA), shorthairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. Polynucleotides can include nonstandard nucleotides, such as nucleotide analogs or modified nucleotides. In some embodiments, nonstandard nucleotides can stabilize hybrid formation. In some embodiments, nonstandard nucleotides can destabilize hybrid formation. In some embodiments, nonstandard nucleotides can enhance hybridization specificity. In some embodiments, nonstandard nucleotides can reduce hybridization specificity. Examples of nonstandard nucleotide modifications include 2’ O-Me, 2’ O-allyl, 2’ O-propargyl, 2’ O-alkyl, 2’ fluoro, 2’ arabino, 2’ xylo, 2’ fluoro arabino, phosphorothioate, phosphorodithioate, phosphoroamidates, 2’ Amino, 5-alkyl-substituted pyrimidine, 3’ deoxyguanosine, 5 -halo- substituted pyrimidine, alkyl-substituted purine, halo- substituted purine, bicyclic nucleotides, 2’MOE, PNA molecules, LNA-molecules, LNA-like molecules, diaminopurine, S2T, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1 -methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3 -methylcytosine, 5-methylcytosine, N6-adenine, 7-methyl guanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5’- methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio- D46-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-WSGR Docket No.: 50401-789.601 thiocytosine, 5- methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5 -methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxy acetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2- carboxypropyl) uracil, (acp3)w, 2,6-diaminopurine, and derivatives thereof. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.

[0156] The term “complementarity” refers to the ability of a nucleic acid to form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non- traditional types. A percent complementarity can indicate the percentage of residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary, respectively). “Perfectly complementary” can mean that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. “Substantially complementary” refers to a degree of complementarity that is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or can refer to two nucleic acids that hybridize under stringent conditions. Sequence identity, such as for the purpose of assessing percent complementarity, may be measured by any suitable alignment algorithm, including but not limited to the Needleman- Wunsch algorithm (e.g., the EMBOSS Needle aligner available at www.ebi.ac.uk / Tools / psa / emboss_needle / nucleotide.html, optionally with default settings), the BLAST algorithm (see e.g., the BLAST alignment tool available at blast.ncbi.nlm.nih.gov / Blast.cgi, optionally with default settings), or the Smith-Waterman algorithm. Optimal alignment may be assessed using any suitable parameters of a chosen algorithm, including default parameters.

[0157] The terms “polypeptide” and “protein” are used interchangeably to refer to a polymer of amino acid residues, and are not limited to a minimum length. For example, a polypeptide can comprise at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 peptides or amino acids. Examples of polypeptides include, but are not limited to, amino acid chains, proteins, peptides, hormones, polypeptide saccharides, lipids, glycolipids, phospholipids, antibodies, enzymes, kinases, receptors, transcription factors, and ligands. Polypeptides, including the provided TCRs and TCR chains and other peptides, e.g., linkers and binding peptides, may include amino acid residues including natural and / or non-natural amino acid residues. The terms also include postexpression modifications of the polypeptide, for example, glycosylation, sialylation, acetylation, phosphorylation, and the like. In some aspects, the polypeptides may contain modifications withWSGR Docket No.: 50401-789.601 respect to a native or natural sequence, as long as the protein maintains the desired activity. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through mutations of hosts which produce the proteins or errors due to PCR amplification.

[0158] As used herein, the twenty conventional amino acids and their abbreviations known to one skilled in the art follow conventional usage. Stereoisomers (e.g., D-amino acids) of the twenty conventional amino acids, unnatural amino acids such as a-, a-disubstituted amino acids, N-alkyl amino acids, lactic acid, and other unconventional amino acids may also be suitable components for polypeptides of the present invention. Examples of unconventional amino acids include: 4- hydroxyproline, y-carboxyglutamate, s-N,N,N-trimethyllysine, s-N-acetyllysine, O- phosphoserine, N-acetyl serine, N-formylmethionine, 3 -methylhistidine, 5-hydroxylysine, o-N- methylarginine, and other similar amino acids and imino acids (e.g., 4-hydroxyproline). In the polypeptide notation used herein, the left hand direction is the amino terminal direction and the right hand direction is the carboxy-terminal direction, in accordance with standard usage and convention. Percent (%) sequence identity with respect to a reference polypeptide sequence (or nucleic acid sequence) is the percentage of amino acid residues (or nucleotides in case of nucleic acid sequence) in a candidate sequence that are identical with the amino acid residues (or nucleotides) in the reference polypeptide sequence (or nucleic acid sequence), after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, however, % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, Calif., or may be compiled from the source code. The ALIGN-2 program should be compiled for use on a UNIX operating system, including digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary. In situations where ALIGN-2 is employed for amino acid sequence comparisons, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises aWSGR Docket No.: 50401-789.601 certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows: 100 times the fraction X / Y, where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A. Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described in the immediately preceding paragraph using the ALIGN-2 computer program.

[0159] The term “pharmaceutically acceptable” refers to a generally non-toxic, inert, and / or physiologically compatible composition or component of a composition. A “pharmaceutical excipient” or “excipient” comprises a material such as an adjuvant, a carrier, pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like. A “pharmaceutical excipient” is an excipient which is pharmaceutically acceptable.

[0160] The terms “identical” or percent “identity” in the context of two or more nucleic acids or polypeptides, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned (introducing gaps, if necessary) for maximum correspondence, not considering any conservative amino acid substitutions as part of the sequence identity. The percent identity can be measured using sequence comparison software or algorithms or by visual inspection. Various algorithms and software that can be used to obtain alignments of amino acid or nucleotide sequences are well- known in the art. These include, but are not limited to, BLAST, ALIGN, Megalign, BestFit, GCG Wisconsin Package, and variations thereof. In some embodiments, two nucleic acids or polypeptides described herein are substantially identical, meaning they have at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, and in some embodiments at least 95%, at least 96%, at least 97%, at least 98%, at least 99% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm or by visual inspection. In some embodiments, identity exists over a region of the sequences that is at least about 10, at least about 20, at least about 40-60 residues, at least about 60-80 residues in length or any integral value there between. In some embodiments, identity exists over a longer region than 60-80 residues, such as at least about 80-100 residues, and in some embodiments the sequences are substantially identical over the full length of the sequences being compared, such as an amino acid sequence of a peptide or a coding region of a nucleotide sequence.WSGR Docket No.: 50401-789.601

[0161] The term “subject” refers to any animal (e.g., a mammal), including, but not limited to, humans, non-human primates, canines, felines, rodents, and the like, which is to be the recipient of a particular treatment. Typically, the terms “subject” and “patient” are used interchangeably herein in reference to a human subject.

[0162] The terms “effective amount” or “therapeutically effective amount” or “therapeutic effect” refer to an amount of a therapeutic effective to “treat” a disease or disorder in a subject or mammal. The therapeutically effective amount of a drug has a therapeutic effect and as such can prevent the development of a disease or disorder; slow down the development of a disease or disorder; slow down the progression of a disease or disorder; relieve to some extent one or more of the symptoms associated with a disease or disorder; reduce morbidity and mortality; improve quality of life; or a combination of such effects.

[0163] The terms “treating” or “treatment” or “to treat” or “alleviating” or “to alleviate” refer to therapeutic measures that cure, slow down, lessen symptoms of, and / or halt progression of a diagnosed pathologic condition or disorder. Thus, those in need of treatment include those already with the disorder. In some cases, treating may refer to reducing, or ameliorating a disorder and / or symptoms associated therewith (e.g., a neoplasia or tumor or infectious agent or an autoimmune disease). “Treating” can refer to administration of the therapy to a subject after the onset, or suspected onset, of a disease (e.g., cancer or infection by an infectious agent or an autoimmune disease). “Treating” includes the concepts of “alleviating”, which refers to lessening the frequency of occurrence or recurrence, or the severity, of any symptoms or other ill effects related to the disease and / or the side effects associated with therapy. The term “treating” may also encompass the concept of “managing” which refers to reducing the severity of a disease or disorder in a patient, e.g., extending the life or prolonging the survivability of a patient with the disease, or delaying its recurrence, e.g., lengthening the period of remission in a patient who had suffered from the disease. It is appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition, or symptoms associated therewith be completely eliminated.

[0164] The terms “prevent” or “prevention” refer to prophylactic or preventative measures that slow down the development of a targeted pathologic condition or disorder. Thus, those in need of prevention include those prone to have the disorder or those in whom the disorder is to be prevented.

[0165] A “reference” can be used to correlate and / or compare the results obtained in the methods of the present disclosure from a diseased specimen. Typically, a “reference” may be obtained on the basis of one or more normal specimens, in particular specimens which are not affected by a disease, either obtained from an individual or one or more different individuals (e.g., healthyWSGR Docket No.: 50401-789.601 individuals), such as individuals of the same species. A “reference” can be determined empirically by testing a sufficiently large number of normal specimens.

[0166] The term “Ros9 family of TCRs,” as used herein, refers to the known TCRs that recognize KRAS G12D 9-mer presented by C*08:02 identified in Tran et al. 2016. T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer. New England Journal of Medicine 375:2255-2262; Leidner et al. 2022. Neoantigen T-Cell Receptor Gene Therapy in Pancreatic Cancer. New England Journal of Medicine 386: 2112-2119; and Sim et al. 2020. High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D. PNAS 117(23): 12826-12835. The Ros9 family of TCRs can include Ros9a, Ros9b, Ros9c, and Ros9d.Methods of Identifying T-Cell Receptors (TCRs)

[0167] The present disclosure provides methods for discovering therapeutically relevant TCRs. The methods provided herein can depend on access to a database that includes bulk (or singlecell) TCR sequencing data from a large number of cancer patient tumor biopsies. Each patient / tumor can have an associated metadata (such cancer type / subtype, mutation profile, gene expression, HPV status, etc.).

[0168] In some cases, the methods are “de novo” methods, where patients that harbor or do not harbor an antigen or interest (e.g., HPV infection status or the presence / absence of a specific KRAS mutation) and patients that express or do not express a specific HLA allele of interest can be identified. Based on these criteria, whether a specific TCR chain sequence appears to be statistically associated with an antigen and / or HLA allele can be queried. Such TCR chains can be antigen-specific and can potentially be used as therapeutic molecules “as-is” or with further sequence optimization.

[0169] FIG. 1A depicts a schematic example of the de novo method of identifying T-cell receptors (TCRs) from a plurality of libraries of TCR chain sequences. First, a plurality of libraries of TCR chain sequences can be sub-grouped libraries with and without a particular condition or set of conditions, (e.g., antigen expression, mutation profile, and / or HLA allele expression). The first image depicts the result of sub-grouping a plurality of libraries of TCR chain sequences into “Subgroup A” and “Sub-group B.” Second, TCR alpha and / or beta chain sequences statistically associated with the condition or set of conditions are identified. The graph plots the -log 10 of the p value of the condition against the -loglO of the p value of the allele to display statistically associated TCR chains. Third, and optionally, paired alpha / beta TCRs can be identified.

[0170] In some cases, the methods are “bait” methods. The “bait” method can start with a TCR known to have some degree of antigen reactivity. Related sequences in the large database can then be searched for. Resulting sequences may or may not exhibit statistical enrichments that may haveWSGR Docket No.: 50401-789.601 been detected using the “de novo” approach. Thus, the “bait” approach may be able to detect rarer TCRs that lack sufficient counts to reach statistical significance.

[0171] FIG. IB depicts a schematic example of the bait method of identifying TCRs from a plurality of libraries of TCR chain sequences. First, TCR chain sequence(s) validated experimentally or from literature can be obtained. The image depicts TCR chain sequences validated experimentally or from literature. Second, similar sequences in a plurality of libraries of TCR chain sequences can be searched for. The image depicts an example sequence alignment of a plurality of libraries of TCR chain sequences with respect to the reference TCR chain sequence (e.g., alpha or beta chain from the reference TCR) validated experimentally or from literature. Third, TCR alpha and / or beta chain sequences statistically associated with the condition or set of conditions are identified. The graph plots the -log 10 of the p value of the condition against the - loglO of the p value of the allele to display statistically associated TCR chains. Third, and optionally CDR3’s of the identified TCR chain sequences can be analyzed to obtain conserved amino acids in CDR3. The image is a sequence logo which is a graphical representation of the sequence conservation of nucleotides or amino acids. The image is a result of analyzing CDR3’s for conserved amino acids. Fourth, and optionally paired alpha / beta TCRs can be identified.De novo methods of identifying TCRs

[0172] The present disclosure provides a method of identifying therapeutically relevant T-cell receptor (TCR) sequences. The method can comprise providing a plurality of libraries of TCR chain sequences. The plurality of libraries of TCR chain sequences can have a first plurality of libraries of TCR chain sequences from a first sub-group of at least 10 subjects (e.g., cancer patients) and a second plurality of libraries of TCR chain sequences from a second sub-group of at least 10 subjects. In some cases, the first sub-group or the second sub-group can comprise at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 80, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects. Each library of TCR chain sequences from a subject of the first sub-group of at least 10 subjects can be from a single subject. Each library of TCR chain sequences from a subject of the second sub-group of at least 10 subjects can be from a single subject. Each of the subjects of the first sub-group of at least 10 subjects can have the same disease or condition. Each of the subjects of the second sub-group of at least 10 subjects may not have the same disease or condition as the first sub-group of at least 10 subjects. Each of the subjects of the first sub-group of at least 10WSGR Docket No.: 50401-789.601 subjects can have the same antigen profile. Each of the subjects of the second sub-group of at least 10 subjects may not have the same antigen profile as the first sub-group of at least 10 subjects. Each of the subjects of the first sub-group of at least 10 subjects can express a major histocompatibility complex (MHC) encoded by a same human leukocyte antigen (EILA) allele. The HL A allele can be a class I HLA allele or a class II HL A allele. Each of the subjects of the second sub-group of at least 10 subjects may not express an MHC encoded by the same HLA allele as the first sub-group of at least 10 subjects. In some cases, each of the subjects of the first sub-group of at least 10 subjects can have the same disease or condition, the same antigen profile, and can express the MHC encoded by the same HLA allele. In some cases, each of the subjects of the second sub-group of at least 10 subjects may not have the same disease or condition, the same antigen profile, and may not express the MHC encoded by the same HLA allele. In some cases, the method can comprise providing a plurality of libraries of TCR chain sequences having a first plurality of libraries of TCR chain sequences from a first sub-group of at least 10 subjects and a second plurality of libraries of TCR chain sequences from a second sub-group of at least 10 subjects, where: (i) each of the subjects of the first sub-group of at least 10 subjects has the same disease or condition, and each of the subjects of the second sub-group of at least 10 subjects does not have the same disease or condition as the first sub-group of at least 10 subjects; (ii) each of the subjects of the first sub-group of at least 10 subjects has the same antigen profile, and each of the subjects of the second sub-group of at least 10 subjects does not have the same antigen profile as the first sub-group of at least 10 subjects; and / or (iii) each of the subjects of the first sub-group of at least 10 subjects express a major histocompatibility complex (MHC) encoded by a same human leukocyte antigen (HLA) allele, and each of the subjects of the second sub-group of at least 10 subjects do not express an MHC encoded by the same HLA allele as the first sub-group of at least 10 subjects.

[0173] The method can further comprise identifying one or more TCR chain sequences based on an analysis of TCR chain sequences in the plurality of libraries of TCR sequences. The analysis can comprise comparing a frequency of one or more TCR chain sequences from the first subgroup to a frequency of the same one or more TCR chain sequences from the second sub-group. The frequency of one or more TCR chain sequences from the first sub-group can be the number of subjects of the first sub-group with the one or more TCR chain sequences over the total number of unique TCR chain sequences of the first sub-group. The frequency of the same one or more TCR chain sequences from the second sub-group can be the number of subjects of the second subgroup with the same one or more TCR chain sequence over the total number of unique TCR chain sequences of the second sub-group. The total number of unique TCR chain sequences of the firstWSGR Docket No.: 50401-789.601 sub-group or the second sub-group may comprise unique TCR chain sequences that are counted twice or more if the unique TCR chain sequences appear in two or more different subjects.

[0174] The method can further comprise determining a statistical significance of a difference in a frequency of a TCR chain sequence of the one or more TCR chain sequences from the first subgroup of at least 10 subjects to a frequency of the same TCR chain sequence of the one or more TCR chain sequences from the second sub-group of subjects based on the comparison described herein. A potentially therapeutic TCR chain sequence can be identified from the one or more TCR chain sequences obtained from the first sub-group of at least 10 subjects.

[0175] In some cases, determining a statistical significance may not comprise directly comparing the frequency of a TCR chain sequence of the one or more TCR chain sequences from the first sub-group of at least 10 subjects to a frequency of the same TCR chain sequence of the one or more TCR chain sequences from the second sub-group of subjects. For example, when determining a statistical significance of a difference in a frequency of a TCR chain sequence of the one or more TCR chain sequences from the first sub-group of at least 10 subjects to a frequency of the same TCR chain sequence of the one or more TCR chain sequences from the second subgroup of subjects, four counts can be calculated, including counts of the candidate TCR chain of interest in the first sub-group, the total counts of all unique TCR chains in the first sub-group, counts of the candidate TCR chain of interest in the second sub-group, and the total counts of all unique TCR chains in the second sub-group. The total number of unique TCR chain sequences of the first sub-group or the second sub-group may comprise unique TCR chain sequences that are counted twice or more if the unique TCR chain sequences appear in two or more different subjects. The method can further comprise determining a statistical significance of a difference in a frequency of a TCR chain sequence of the one or more TCR chain sequences from the first sub-group of at least 10 subjects to a frequency of the same TCR chain sequence of the one or more TCR chain sequences from the second sub-group of subjects based on the calculated counts described herein.

[0176] Statistical significance refers to a mathematical tool used in hypothesis testing to determine whether a particular result is beyond the realm of random chance. This concept is applied primarily when comparing two or more sets of data or testing the effect of certain variables within an experiment. The threshold of significance, often denoted by the p-value, is commonly set at 0.05, although this can be adjusted based on the circumstances or preferences of the researcher. If the calculated p-value falls below this threshold, it indicates that the likelihood of obtaining the observed data (or something more extreme) by mere chance is low, thereby suggesting that the observed results are statistically significant. This in turn provides evidenceWSGR Docket No.: 50401-789.601 supporting the alternative hypothesis, or the assumption that some form of relationship exists between the variables being studied.

[0177] For example, statistical significance can be determined by the Fisher’s exact test, a statistical significance test used primarily in the analysis of small sample sizes. This test is employed when the numbers are too small for a Chi-square test to be applicable, to determine whether there are nonrandom associations between two categorical variables. An essential feature of the Fisher’s exact test is that it does not assume an equal distribution of probabilities for all possible outcomes, making it especially useful for studies with unequal, or 'non-standard', sample sizes. It calculates the exact probability of a specific distribution of outcomes, rather than approximating a probability based on a distribution, thus offering increased precision and reliability when dealing with small data sets. Some alternative tests to Fisher's exact test include the Chi-Square test, the Yates Correction test for continuity, or the Likelihood Ratio test.

[0178] FIG. 6 depicts a method of identifying TCR chains enriched in patient populations of interest and examples of the statistical analysis. First, all chains present in at least 5 patients (in some cases, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10 or more patients) was identified. Second, for each TCR chain, a Fisher’s exact test is used to determine whether that TCR chain is over-represented in the HPV+ population. The table gives the input values for the Fisher’s exact test. Third, for each TCR chain, a Fisher’s exact test is used to determine whether that TCR chain is over-represented in any population defined by HLA class I alleles. The table give input values for the Fisher’s exact test. The results of the method are depicted by the two populations of circles- TCR chains from HPV+ patients and TCR chains from HPV- patients. Each circle represents an observation meaning 1 TCR chain in 1 patient. Dark circles represent TCR chains of interest. Light circles represent other TCR chains. Outline shade indicates Patient ID.

[0179] The method can further comprise selecting a TCR chain sequence of the first sub-group of at least 10 subjects that has a statistically significant difference in frequency to the frequency of the same TCR chain sequence in the second sub-group of subjects as described herein. The statistically significant difference in the frequency can be a p-value of at most 0.1. In some cases, the statistically significant difference in the frequency can be a p-value of at most 0.1, at most 0.01, at most 0.001, at most 0.0001, at most 0.00001, at most 0.000001, at most 0.0000001, at most 0.00000001, at most 0.000000001, at most 0.0000000001, at most 0.00000000001, at most 0.000000000001, at most 0.0000000000001, at most 0.00000000000001, at most 0.000000000000001, at most 0.0000000000000001, at most 0.00000000000000001 or less. The TCR chain sequence can be present at a higher frequency in the first sub-group of at least 10 subjects relative to the frequency of the same TCR chain sequence in the second sub-group ofWSGR Docket No.: 50401-789.601 subjects. The TCR chain sequence can be present in at least 5 subjects from the first sub-group of at least 10 subjects. In some cases, the TCR chain sequence can be present in at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects from the first sub-group of at least 10 subjects.

[0180] In some cases, the method of identifying therapeutically relevant T-cell receptor (TCR) chain sequences can comprise (a) providing a plurality of libraries of TCR chain sequences having a first plurality of libraries of TCR chain sequences from a first sub-group of at least 10 subjects and a second plurality of libraries of TCR chain sequences from a second sub-group of at least 10 subjects, wherein each library of TCR chain sequences from a subject of the first sub-group of at least 10 subjects is from a single subject and each library of TCR chain sequences from a subject of the second sub-group of at least 10 subjects is from a single subject; wherein: each of the subjects of the first sub-group of at least 10 subjects has the same disease or condition, and each of the subjects of the second sub-group of at least 10 subjects does not have the same disease or condition as the first sub-group of at least 10 subjects; each of the subjects of the first sub-group of at least 10 subjects has the same antigen profile, and each of the subjects of the second subgroup of at least 10 subjects does not have the same antigen profile as the first sub-group of at least 10 subjects; and / or each of the subjects of the first sub-group of at least 10 subjects express a major histocompatibility complex (MHC) encoded by a same human leukocyte antigen (HLA) allele, and each of the subjects of the second sub-group of at least 10 subjects do not express an MHC encoded by the same HLA allele as the first sub-group of at least 10 subjects; (b) identifying one or more TCR chain sequences based on an analysis of TCR chain sequences in the plurality of libraries of TCR chain sequences, wherein the analysis comprises comparing a frequency of one or more TCR chain sequences from the first sub-group to a frequency of the same one or more TCR chain sequences from the second sub-group , wherein the frequency of one or more TCR chain sequences from the first sub-group is the number of subjects of the first sub-group with the one or more TCR chain sequences over the total number of unique TCR chain sequences of the first sub-group, and the frequency of the same one or more TCR chain sequences from the second sub-group is the number of subjects of the second sub-group with the same one or more TCR chain sequence over the total number of unique TCR chain sequences of the second sub-group;WSGR Docket No.: 50401-789.601(c) determining a statistical significance of a difference in a frequency of a TCR chain sequence of the one or more TCR chain sequences from the first sub-group of at least 10 subjects to a frequency of the same TCR chain sequence of the one or more TCR chain sequences from the second sub-group of subjects based on the comparing in (b), thereby identifying a potentially therapeutic TCR chain sequence from the one or more TCR chain sequences obtained from the first sub-group of at least 10 subjects; and (d) selecting a TCR chain sequence of the first subgroup of at least 10 subjects that (i) has a statistically significant difference in frequency to the frequency of the same TCR chain sequence in the second sub-group of subjects based on (c), wherein the statistically significant difference in the frequency is a p-value of at most 0.1, (ii) is present at a higher frequency in the first sub-group of at least 10 subjects relative to the frequency of the same TCR chain sequence in the second sub-group of subjects, and (iii) is a TCR chain sequence that is present in at least 5 subjects from the first sub-group of at least 10 subjects. In some cases, the TCR chain sequence can be present in at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects from the first subgroup of at least 10 subjects.

[0181] In some cases, the number of subjects of the first sub-group of at least 10 subjects with the TCR chain sequence selected over the total number of unique TCR chain sequences of the first sub-group of at least 10 subjects can have a statistically significant difference compared to the number of subjects of the second sub-group of subjects with the TCR chain sequence selected over the total number of unique TCR chain sequences of the second sub-group of subjects.

[0182] In some cases, whether the subjects have the same disease or condition, whether the subjects have the same antigen profile, and / or whether the subjects express the same MHC encoded by the same HLA allele may not be known. In such cases, the methods can further comprises, prior to identifying TCR chain sequences, identifying the first sub-group of at least 10 subjects as (i) having the same disease or condition, (ii) having the same antigen profile, (iii) expressing the MHC encoded by the same HLA allele, or (iv) the same combination thereof, and the second sub-group of subjects as (i) not having the same disease or condition as the first subgroup, (ii) not having the same antigen profile as the first sub-group, (iii) not expressing an MHC encoded by the same HLA allele as the first sub-group, or (iv) not having the same combination thereof as the first sub-group.WSGR Docket No.: 50401-789.601

[0183] The statistically significant difference in the frequency can be a p-value of at most 0.05, at most 0.001, or at most 0.0001. In some cases the p value can be at most at most 0.01, at most 0.001, at most 0.0001, at most 0.00001, at most 0.000001, at most 0.0000001, at most 0.00000001, at most 0.000000001, at most 0.0000000001, at most 0.00000000001, at most 0.000000000001, at most 0.0000000000001, at most 0.00000000000001, at most 0.000000000000001, at most 0.0000000000000001, at most 0.00000000000000001 or less. The p-value can be an adjusted p- value. The selected TCR chain sequence can be a TCR chain sequence that is present in at least 10 subjects from the first sub-group of at least 10 subjects. The selected TCR chain sequence can be a TCR chain sequence that is present in at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects from the first sub-group of at least 10 subjects.

[0184] In some cases, after selecting a candidate TCR chain sequence using the method (a)-(d) described above using the first sub-group and second sub-group separated based on one criterium (e.g., the same disease or condition, the method may be repeated using the first sub-group and the second sub-group separated based on other criteria (e.g., the HLA allele, the antigen, etc.). FIG. 4 depicts an example association study using bulk TCR-Seq to identify candidate antigen-specific TCR chains. Bulk TCR-seq data was segregated by TCR chain sequences statistically associated with and without HPV and with and without HLA-A*02:01 to produce 4 sub-groups. Dark gray figures represent patients with the query TCR chain. Light gray figures represent patients without query TCR chains. Candidate antigen-specific TCR chains can be enriched in the HPV+ HLA- A* 02:01+ subgroup.

[0185] The first sub-group of at least 10 subjects can have the same disease or condition, and the second sub-group of at least 10 subjects may not have the same disease or condition as the first sub-group. The method can further comprise repeating the method (a)-(d) described above using the plurality of libraries of TCR chain sequences from a first sub-group of at least 10 subjects that express an MHC encoded by a same HLA allele, and a second sub-group of at least 10 subjects that do not express an MHC encoded by the same HLA allele as the first sub-group.

[0186] The first sub-group of at least 10 subjects can have the same antigen profile. The second sub-group of at least 10 subjects may not have the same antigen profile as the first sub-group. The method can further comprise repeating the method (a)-(d) as described above using the pluralityWSGR Docket No.: 50401-789.601 of libraries of TCR chain sequences from a first sub-group of at least 10 subjects that express an MHC encoded by a same HL A allele, and a second sub-group of at least 10 subjects that do not express an MHC encoded by the same HLA allele as the first sub-group.

[0187] The first sub-group of at least 10 subjects can have the same disease or condition and the same antigen profile, and the second sub-group of at least 10 subjects may not have the same disease or condition as the first sub-group and may not have the same antigen profile as the first sub-group. The method can further comprise repeating the method (a)-(d) as described above using the plurality of libraries of TCR chain sequences from a first sub-group of at least 10 subjects that express an MHC encoded by a same HLA allele, and a second sub-group of at least 10 subjects that do not express an MHC encoded by the same HLA allele as the first sub-group.

[0188] The first sub-group of at least 10 subjects may express an MHC encoded by a same HLA allele, and a second sub-group of at least 10 subjects may not express an MHC encoded by the same HLA allele as the first sub-group. The method can further comprise repeating the method (a)-(d) as described above using the plurality of libraries of TCR chain sequences from a first subgroup of at least 10 subjects that have the same disease or condition, and the second sub-group of at least 10 subjects that do not have the same disease or condition as the first sub-group. The method can further comprise repeating the method (a)-(d) as described above using the plurality of libraries of TCR chain sequences from a first sub-group of at least 10 subjects that have the same antigen profile, and the second sub-group of at least 10 subjects that do not have the same antigen profile as the first sub-group.

[0189] The first sub-group of at least 10 subjects can comprise at least 100, at least 1,000, or more subjects. The first sub-group of at least 10 subjects can comprise at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 960, at least 1000, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects.

[0190] The second sub-group of at least 10 subjects can comprise at least 100, at least 1,000, or more subjects. The second sub-group of at least 10 subjects can comprise at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 960, at least 1000, at least 1040, at least 1160, at leastWSGR Docket No.: 50401-789.6011280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects.

[0191] The selected TCR chain sequence can be a TCR alpha chain sequence. The method can further comprise selecting a TCR beta chain sequence that is present at a higher frequency in the first sub-group of at least 10 subjects relative to the frequency of the same TCR beta chain sequence in the second sub-group of at least 10 subjects, and is present in at least 2 subjects (e.g., at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects) from the first sub-group of at least 10 subjects. The method can further comprise identifying a TCR beta chain sequence associated with or cognately paired to the selected TCR alpha chain. The method can further comprise (i) providing single-cell TCR sequencing data from a subject having the same disease or condition, having the same antigen profile, expressing an MHC encoded by the same HLA allele, or having the same combination thereof, (ii) determining if a TCR alpha chain sequence is present in the single-cell TCR sequencing data that is the same as or has at most 1, 2, 3, 4 or 5 amino acid differences with the selected TCR alpha chain sequence, and (iii) identifying a TCR beta chain sequence associated with or cognately paired to the selected TCR alpha chain sequence in the single-cell TCR sequencing data.

[0192] The selected TCR chain sequence can be a TCR beta chain sequence. The method can further comprise selecting a TCR alpha chain sequence that is present at a higher frequency in the first sub-group of at least 10 subjects relative to the frequency of the same TCR alpha chain sequence in the second sub-group of at least 10 subjects, and is present in at least 2 subjects (e.g., at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects) from the first sub-group of at least 10 subjects. The method can further comprise identifying a TCR alpha chain sequence associated with or cognately paired to the selected TCR beta chain. TheWSGR Docket No.: 50401-789.601 method can further comprise (i) providing a single-cell TCR sequencing data from a subject having the same disease or condition, having the same antigen profile, expressing an MHC encoded by the same HLA allele, or having the same combination thereof, (ii) determining if a TCR beta chain sequence is present in the single-cell TCR sequencing data that is the same as or has at most 1, 2, 3, 4 or 5 amino acid differences with the selected TCR beta chain sequence, and (iii) identifying a TCR alpha chain sequence associated with or cognately paired to the selected TCR beta chain sequence in the single-cell TCR sequencing data.

[0193] The method can further comprise pairing the TCR alpha chain sequence and the TCR beta chain sequence to form a paired TCR chain sequences.

[0194] The selected TCR chain sequence can be a TCR gamma chain sequence. The method can further comprise selecting a TCR delta chain sequence that is present at a higher frequency in the first sub-group of at least 10 subjects relative to the frequency of the same TCR delta chain sequence in the second sub-group of at least 10 subjects, and is present in at least 2 subjects (e.g., at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects) from the first sub-group of at least 10 subjects. The method can further comprise identifying a TCR delta chain sequence associated with or cognately paired to the selected TCR gamma chain. The method can further comprise (i) providing a single-cell TCR sequencing data from a subject having the same disease or condition, having the same antigen profile, expressing an MHC encoded by the same HLA allele, or having the same combination thereof, (ii) determining if a TCR gamma chain sequence is present in the single-cell TCR sequencing data that is the same as or has at most 1, 2, 3, 4 or 5 amino acid differences with the selected TCR gamma chain sequence, and (iii) identifying a TCR delta chain sequence associated with the selected TCR gamma chain sequence in the single-cell TCR sequencing data.

[0195] The selected TCR chain sequence can be a TCR delta chain sequence. The method can further comprise selecting a TCR gamma chain sequence that is present at a higher frequency in the first sub-group of at least 10 subjects relative to the frequency of the same TCR gamma chain sequence in the second sub-group of at least 10 subjects, and is present in at least 2 subjects (e.g., at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at leastWSGR Docket No.: 50401-789.60160, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects) from the first sub-group of at least 10 subjects. The method can further comprise identifying a TCR gamma chain sequence associated with or cognately paired to the selected TCR delta chain. The method can further comprise (i) providing a single-cell TCR sequencing data from a subject having the same disease or condition, having the same antigen profile, expressing an MHC encoded by the same HLA allele, or having the same combination thereof, (ii) determining if a TCR delta chain sequence is present in the single-cell TCR sequencing data that is the same as or has at most 1, 2, 3, 4 or 5 amino acid differences with the selected TCR delta chain sequence, and (iii) identifying a TCR gamma chain sequence associated with the selected TCR delta chain sequence in the single-cell TCR sequencing data.

[0196] The method can further comprise pairing the TCR gamma chain sequence and the TCR delta chain sequence to form a paired TCR chain sequences.

[0197] The paired TCR chain sequences may not be a cognate TCR pair.

[0198] The same condition can be HPV infection. A TCR having the paired TCR chain sequences can bind to an epitope associated with the HPV infection in complex with an HLA molecule. The first sub-group of at least 10 subjects can comprise a same HLA allele. The same antigen profile can comprise a same oncogenic driver mutation. A TCR having the paired TCR chain sequences can bind to a neoepitope comprising the same oncogenic driver mutation in complex with an HLA molecule. The first sub-group of at least 10 subjects can comprise a same HLA allele.

[0199] The same condition can comprise HPV infection. The same condition can comprise a cancer. The same condition can comprise an autoimmune disorder. The same condition can comprise an infectious disease. The same antigen profile can comprise having a same cancer mutation, a same neoantigen, a same tumor-associated antigen, or any combination thereof. The same cancer mutation can comprise KRAS-G12C, KRAS-G12D, or KRAS-G12V mutation. A TCR having the paired TCR chain sequences can bind to an epitope having a RAS mutation in complex with an HLA molecule.

[0200] The same HLA allele can comprise an allele selected from the group consisting of HLA- A:01:01, HLA-A:02:01, HLA-A:03:01, HLA-A:l l:01, HLA-A:24:02, HLA-B:07:02, HLA- B:08:01, HLA-B: 15:01, HLA-B:44:02, HLA-B:44:03, HLA-C:04:01, HLA-C:05:01, HLA- C:06:02, HLA-C:07:01, HLA-C:07:02, and HLA-C:08:02. In some embodiments, the HPV epitope comprises a sequence of SEQ ID NO: 283 or 300. In some embodiments, the RAS epitopeWSGR Docket No.: 50401-789.601 comprises a sequence of vvvgaVgvgk (SEQ ID NO: 312) or vvgaVgvgk (SEQ ID NO: 367). In some embodiments, the RAS epitope comprises a sequence of gaDgvgksal (SEQ ID NO: 368), vvvgaDgvgk (SEQ ID NO: 369) ,or vvgaDgvgk (SEQ ID NO: 370). In some embodiments, the RAS epitope comprises a sequence of vvvgaCgvgk (SEQ ID NO: 371).

[0201] Each library of TCR chain sequences can be a sequencing dataset obtained by bulk sequencing of TCR chain sequences from a subject. The subject can be a cancer patient. The subject may also include a healthy subject.

[0202] An epitope or an HLA allele that a TCR comprising the paired TCR chain sequences recognizes can be unknown.

[0203] The method can further comprise assaying a TCR comprising the paired TCR chain sequences for a binding affinity against an epitope associated with the same disease or condition or associated with the same antigen profile in complex with the same HLA allele. For example, the binding affinity can be assayed by Surface Plasmon Resonance (SPR), isothermal titration calorimetry (ITC), or florescence anisotropy.

[0204] A TCR comprising the selected TCR chain sequence can recognize an epitope from HPV E2.

[0205] A TCR comprising the selected TCR chain sequence can recognize an epitope from HPV E2 in complex with HLA-A:01 :01.

[0206] The frequency of one or more TCR chains in each library of TCR chain sequences from the first sub-group of at least 10 subjects can be at least about 2-fold, at least about 3 -fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15-fold, at least about 20-fold, at least about 25-fold, at least about 30-fold, at least about 35-fold, at least about 40-fold, at least about 45-fold, at least about 50-fold, at least about 55-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, at least about 100-fold or more the frequency of one or more TCR chains in each library of TCR chain sequences from the second sub-group of at least 10 subjects.

[0207] The statistical significance of a TCR chain sequence can be determined by a Fisher’s exact test.

[0208] The method can further comprise, prior to determining the statistical significance, grouping two or more TCR chain sequences of the one or more TCR chain sequences based on sequence identity into a grouped TCR chain sequences. The grouped TCR chain sequences can share at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more sequence identity. The variable regions of the grouped TCR chain sequences can share at least 60%, at least 65%, at least 70%, at least 75%, at least 80%,WSGR Docket No.: 50401-789.601 at least 85%, at least 90%, at least 95%, at least 99% or more sequence identity. The CDR3 sequences of the grouped TCR chain sequences can share at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more sequence identity.

[0209] The one or more TCR chain sequences can comprise two or more TCR chain sequences that have been grouped based on sequence identity. The grouped TCR chain sequences can share at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more sequence identity. The variable regions of the grouped TCR chain sequences can share at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more sequence identity. The CDR3 sequences of the grouped TCR chain sequences can share at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more sequence identity.

[0210] Selecting the TCR chain sequences can comprise selecting a plurality of TCR chain sequences. The method can further comprise aligning the plurality of TCR chain sequences to obtain conserved residues or sequence motifs.

[0211] The method can further comprise analyzing the likelihood of the selected TCR chain sequence to be generated by thymic selection. For example to correct for the effect of thymic selection, a correction factor can be estimated. In some cases, a sequence-specific factor for each individual is learned. In some cases, all observed sequences passing thymic selection can be assumed. The correction factor can be a normalization factor accounting for the fact that just a fraction of sequences pass thymic selection. The correction factor can be determined for each VJ- combination. For example, the correction factor can be correction factor Q where the following factorized model for Q captures the main features of selection:where f can be a CDR3 region, V and J can be a V and J gene choices, (f, V,J~) can be a full TCR chain sequence, (ai, . . ., a ) can be the amino acid sequence of the CDR3, and L is its length. The factors qL, qi;L(a), and qvj denote selective pressures on the CDR3 length, its composition, and the associated VJ identities, respectively.

[0212] The first sub-group of at least 10 subjects can have the same antigen profile as the second sub-group of at least 10 subjects. The first sub-group of at least 10 subjects may express a protein with a same antigen or RNA encoding the protein with a same antigen at a higher level than the expression of the protein with a same antigen or RNA encoding the protein with a same antigen in the second sub-group of at least 10 subjects. The same antigen can comprise a mutation.WSGR Docket No.: 50401-789.601

[0213] The first sub-group of at least 10 subjects may have the same disease or condition and the second sub-group of at least 10 subjects may not have the same disease or condition.

[0214] An alternative method of the “de novo” methods can comprise analyzing differential target antigen expression in two different groups of subjects (having a TCR chain or not having a TCR chain) given an arbitrary TCR chain sequence. The arbitrary TCR chain sequence can be selected based on its presence in at least five subjects. For example, the method can comprise providing a plurality of libraries of TCR chain sequences from at least 10 subjects. Each library of TCR chain sequences can be from a single subject. The method can further comprise selecting a TCR chain sequence that is present in at least 5 subjects from the at least 10 subjects. In some cases, the TCR chain sequence can be present in at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects from the first subgroup of at least 10 subjects. The method can further comprise, based on the TCR chain sequence selected, subgrouping the plurality of libraries of TCR chain sequences into a first plurality of libraries of TCR chain sequences from a first subgroup of subjects and a second plurality of libraries of TCR chain sequences from a second subgroup of subjects. The first plurality of libraries of TCR chain sequences from the first sub-group of subjects may comprise the TCR chain sequence selected, and the second plurality of libraries of TCR chain sequences from the second sub-group of subjects may not comprise the TCR chain sequence selected. The method can further comprise determining whether the first sub-group of subjects and the second sub-group of subjects may have differential expression level of an antigen.

[0215] Determining described herein can comprise analyzing sequencing data of the first subgroup and the second sub-group. The first sub-group of subjects and the second sub-group of subjects can have differential expression level of the antigen. The antigen can have a probability of being recognized by the TCR chain sequence selected when being presented by an MHC. The antigen described herein can be a neoantigen. The antigen can be a tumor associated antigen. The antigen may or may not contain a mutation.Bait method of identifying TCRs

[0216] The method of identifying therapeutically relevant T-cell receptor (TCR) sequences can comprise providing a reference TCR chain sequence and libraries of TCR chain sequences from a population of subjects. Each library can be from a single subject of the population of subjects.WSGR Docket No.: 50401-789.601The method can further comprise analyzing one or more TCR chain sequences of the libraries of TCR chain sequences to determine sequence similarity between the one or more TCR chain sequences and the reference TCR chain sequence. The reference TCR chain sequence can be from a known antigen-specific TCR. The method can further comprise identifying one or more TCR chain sequences from the libraries of TCR chain sequences that have a sequence similarity with the reference TCR chain sequence. An identified TCR chain sequence can have a same amino acid sequence encoded by the V-gene as the reference TCR chain sequence, and no more than three amino acid variations in a CDR3 sequence compared to a CDR3 sequence of the reference TCR chain sequence. The amino acid variations can comprise amino acids substitutions, deletions and / or insertions.

[0217] The reference TCR chain can comprise a reference TCR alpha chain sequence and a reference TCR beta chain sequence from the known antigen-specific TCR. Analyzing one or more TCR chain sequences can comprise analyzing each TCR alpha chain sequence (or TCR gamma chain sequence) and each TCR beta chain sequence (or TCR delta chain sequence) separately.

[0218] Analyzing one or more TCR chain sequences can comprise analyzing each TCR alpha chain sequence of the libraries of TCR chain sequences to determine sequence similarity between each TCR alpha chain sequence (or TCR gamma chain sequence) and a reference TCR alpha chain sequence (or a reference TCR gamma chain sequence).

[0219] The method can further comprise analyzing each TCR beta chain sequence (or TCR delta chain sequence) of the libraries of TCR chain sequences to determine sequence similarity between each TCR beta chain sequence (or TCR delta chain sequence) and a reference TCR beta chain sequence paired natively with the reference TCR alpha chain sequence (or TCR delta chain sequence paired natively with the reference TCR gamma chain sequence).

[0220] The method can further comprise, for each TCR chain of the one or more TCR chain sequences identified, determining whether the TCR chain is likely to be restricted by an HLA allele by conducting a statistical test assessing whether a frequency of the TCR chain in a first subgroup of the population of subjects positive for the HLA allele is different from a frequency of the TCR chain in a second subgroup of the population of subjects negative for the HLA allele. The p-value for the statistical test can be at most 0.1. In some cases, the p value can be at most 0.1, at most 0.01, at most 0.001, at most 0.0001, at most 0.00001, at most 0.000001, at most 0.0000001, at most 0.00000001, at most 0.000000001, at most 0.0000000001, at most 0.00000000001, at most 0.000000000001, at most 0.0000000000001, at most 0.00000000000001, at most 0.000000000000001, at most 0.0000000000000001, at most 0.00000000000000001 or less.WSGR Docket No.: 50401-789.601

[0221] The p-value can be at most 0.01. The p-value can be at most 0.001. The p-value can be at most 0.0001.

[0222] The method can further comprise determining the likelihood of identified TCR chain sequence specificity to the same pMHC complex as the reference TCR chain sequence. Determining the likelihood can comprise aligning a CDR3 sequence of the identified TCR chain sequences to the CDR3 sequence of the reference TCR chain sequence. A TCR comprising the reference TCR chain sequence may recognize HLA-A*02-presented epitopes, HLA-A*11- presented epitopes, HLA-A*03-presented epitopes, or HLA-C*08-presented epitopes. The identified TCR chain sequence can be a potentially therapeutic TCR chain sequence if the HLA allele is the same allele recognized by the reference TCR chain sequence. The HLA allele recognized by the identified TCR chain sequence and the reference TCR chain sequence can be selected from the group consisting of HLA-A*02, HLA-A*11, HLA-A*03, and HLA-C*08.

[0223] A TCR comprising the reference TCR chain sequence can be specific for an epitope from HPV E7.

[0224] A TCR comprising the identified TCR chain sequence can be specific for an epitope of HPV E7, wherein the epitope comprises a sequence set forth in SEQ ID NO: 283 or 300.

[0225] A TCR comprising the identified TCR chain sequence can be specific for the epitope from HPV E7 in complex with HLA-A*02.

[0226] A TCR comprising the reference TCR chain sequence can be specific for an epitope from KRAS-G12C.

[0227] A TCR comprising the reference TCR chain sequence can be specific for the epitope from KRAS-G12C in complex with HLA- A* 11.

[0228] A TCR comprising the identified TCR chain sequence can be specific for the epitope from KRAS-G12C in complex with HL- A* 11.

[0229] A TCR comprising the reference TCR chain sequence can be specific for an epitope from KRAS-G12D.

[0230] A TCR comprising the reference TCR chain sequence can be specific for the epitope from KRAS-G12D in complex with HLA-A*03, HLA-A*11, or HLA-C*08.

[0231] A TCR comprising the identified TCR chain sequence can be specific for the epitope from KRAS-G12D in complex with HLA-A*03, HLA-A*11, or HLA-C*08.

[0232] A TCR comprising the reference TCR chain sequence can be specific for an epitope from KRAS-G12V.

[0233] A TCR comprising the reference TCR chain sequence can be specific for the epitope from KRAS-G12V in complex with HLA-A*03 or HLA-A* 11.WSGR Docket No.: 50401-789.601

[0234] A TCR comprising the identified TCR chain sequence can be specific for the epitope from KRAS-G12V in complex with HLA-A*03 or HLA-A*11. A TCR comprising the identified TCR chain sequence can be specific for the epitope from KRAS-G12V in complex with HLA-B* 15:01.

[0235] The method can further comprise analyzing the likelihood for the identified TCR chain to be generated by thymic selection. For example to correct for the effect of thymic selection, a correction factor can be estimated. In some cases, a sequence-specific factor for each individual is learned. In some cases, all observed sequences passing thymic selection can be assumed. The correction factor can be a normalization factor accounting for the fact that just a fraction of sequences pass thymic selection. The correction factor can be determined for each VJ- combination. For example, the correction factor can be correction factor Q where the following factorized model for Q captures the main features of selection:where can be a CDR3 region, V and J can be a V and J gene choices, ( , V, ) can be a full TCR chain sequence, (ai, . . ., ar) can be the amino acid sequence of the CDR3, and L is its length. The factors qL, qi;L(a), and qvj denote selective pressures on the CDR3 length, its composition, and the associated VJ identities, respectively.

[0236] The reference TCR chain sequence can be a TCR chain sequence selected by the method described, for example, the de novo or bait methods described herein.

[0237] The present disclosure also provides methods of making the TCRs identified herein or cells comprising the TCRs identified. The method of making a TCR can comprise preparing a TCR comprising a TCR chain sequence selected according to the methods described herein. The method of making a cell comprising the identified TCR can comprise delivering a TCR sequence comprising a TCR chain sequence selected according to the methods described herein or a nucleic acid sequence encoding the TCR chain into the cell.

[0238] The method of making a TCR can comprise preparing a TCR comprising a TCR chain sequence identified according to the methods described herein and the reference TCR chain sequence.

[0239] The identified TCR chain can be used to prepare a pharmaceutical composition. The pharmaceutical composition can comprise a TCR chain comprising a TCR chain sequence selected according to the method described, and a pharmaceutically acceptable carrier.

[0240] TCRs comprising the TCR chains identified by the methods described herein can recognize epitopes in complex with an MHC molecule. The MHC molecules described herein can be encoded by a class I HLA allele, and / or a class II HLA allele.Identification of B-cell receptors or antibodiesWSGR Docket No.: 50401-789.601

[0241] The methods (e.g., de novo or bait methods) described herein are not limited to identifying alpha-beta TCRs or gamma-delta TCRs and can be used to identify B-cell receptors (BCRs) and antibodies. For example, the method of identifying therapeutically relevant BCR or antibody sequences can comprise providing a plurality of libraries of BCR or antibody sequences having a first plurality of libraries of BCR or antibody sequences from a first sub-group of at least 10 subjects and a second plurality of libraries of BCR or antibody sequences from a second sub-group of at least 10 subjects. Each library of BCR or antibody sequences from a subject of the first subgroup of at least 10 subjects can be from a single subject and each library of BCR or antibody sequences from a subject of the second sub-group of at least 10 subjects can be from a single subject. In some cases, each of the subjects of the first sub-group of at least 10 subjects can have the same disease or condition, and each of the subjects of the second sub-group of at least 10 subjects may not have the same disease or condition as the first sub-group of at least 10 subjects. In some cases, each of the subjects of the first sub-group of at least 10 subjects can have the same antigen profile, and each of the subjects of the second sub-group of at least 10 subjects may not have the same antigen profile as the first sub-group of at least 10 subjects. The method can further comprise identifying one or more BCR or antibody sequences based on an analysis of BCR or antibody sequences in the plurality of libraries of BCR or antibody sequences. The analysis can comprise comparing a frequency of one or more BCR or antibody sequences from the first subgroup to a frequency of the same one or more BCR or antibody sequences from the second subgroup. The frequency of one or more BCR or antibody sequences from the first sub-group can be the number of subjects of the first sub-group with the one or more BCR or antibody sequences over the total number of unique BCR or antibody sequences of the first sub-group, and the frequency of the same one or more BCR or antibody sequences from the second sub-group can be the number of subjects of the second sub-group with the same one or more BCR or antibody sequence over the total number of unique BCR or antibody sequences of the second sub-group. The method can further comprise determining a statistical significance of a difference in a frequency of a BCR or antibody sequence of the one or more BCR or antibody sequences from the first sub-group of at least 10 subjects to a frequency of the same BCR or antibody sequence of the one or more BCR or antibody sequences from the second sub-group of subjects based on the comparison of the frequency above, thereby identifying a potentially therapeutic BCR or antibody sequence from the one or more BCR or antibody sequences obtained from the first sub-group of at least 10 subjects. The method can further comprise selecting a BCR or antibody sequence of the first sub-group of at least 10 subjects that has a statistically significant difference in frequency to the frequency of the same BCR or antibody sequence in the second sub-group of subjects based on the statistical significance, where the statistically significant difference in the frequency can beWSGR Docket No.: 50401-789.601 a p-value of at most 0.1. The method can further comprise selecting a BCR or antibody sequence of the first sub-group of at least 10 subjects that is present at a higher frequency in the first subgroup of at least 10 subjects relative to the frequency of the same BCR or antibody sequence in the second sub-group of subjects. The method can further comprise selecting a BCR or antibody sequence of the first sub-group of at least 10 subjects that is a BCR or antibody sequence that is present in at least 2 subjects (e.g., at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects) from the first sub-group of at least 10 subjects.

[0242] The selected BCR or antibody sequence can be a heavy chain sequence. The method can further comprise selecting a light chain sequence that is present at a higher frequency in the first sub-group of at least 10 subjects relative to the frequency of the same light chain sequence in the second sub-group of at least 10 subjects, and is present in at least 2 subjects (e.g., at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120, at least 140, at least 160, at least 180, at least 200, at least 240, at least 280, at least 320, at least 360, at least 400, at least 480, at least 560, at least 640, at least 720, at least 800, at least 920, at least 1040, at least 1160, at least 1280, at least 1400, at least 1600, at least 1800, at least 2000, at least 2200, at least 2400, at least 2800, at least 3200, at least 3600, at least 4000, at least 4400, at least 5000 or more subjects) from the first sub-group of at least 10 subjects. The method can further comprise identifying a light chain sequence associated with or cognately paired to the selected heavy chain. The method can further comprise (i) providing single-cell BCR or antibody sequencing data from a subject having the same disease or condition and / or having the same antigen profile, (ii) determining if a heavy chain sequence is present in the single-cell BCR or antibody sequencing data that is the same as or has at most 1, 2, 3, 4 or 5 amino acid differences with the selected heavy chain sequence, and (iii) identifying a light chain sequence associated with or cognately paired to the selected heavy chain sequence in the single-cell BCR or antibody sequencing data. The same methods can be used to pair a heavy chain sequence to a selected light chain sequence.T Cell ReceptorsWSGR Docket No.: 50401-789.601

[0243] Provided herein are T cell receptors (TCRs) and recombinant nucleic acids encoding the same identified by a method disclosed herein. In some embodiments, a TCR or a recombinant nucleic acid encoding the TCR is identified by a de novo method disclosed herein. In some embodiments, a TCR or a recombinant nucleic acid encoding the TCR is identified by a bait method disclosed herein. In some aspects, provided herein is an identified TCR or a recombinant nucleic acid encoding the TCR comprising a TCR beta construct and a TCR alpha chain construct that recognizes epitopes (e.g., epitope from human RAS or HPV) in complex with a human MHC.

[0244] The ability of T cells to recognize antigens associated with infectious organisms or cancers is conferred by its TCR, which is made up of both an alpha (a) chain and a beta (P) chain or a gamma (y) and a delta (5) chain. The proteins which make up these chains are encoded by DNA, which employs a unique mechanism for generating the diversity of the TCR. This multisubunit immune recognition receptor can associate with the CD3 complex and bind peptides presented by the MHC class I and II proteins on the surface of antigen-presenting cells (APCs). The first signal in activation of T cells can be provided by binding of the T-cell receptor to a short peptide presented by the MHC on another cell. This ensures that only a T cell with a TCR specific to that peptide is activated. The partner cell is usually an antigen-presenting cell such as a professional antigen-presenting cell, usually a dendritic cell in the case of naive responses, although B-cells and macrophages can be important APCs. Binding of a TCR to the antigenic peptide on the APC can be a central event in T cell activation, which occurs at an immunological synapse at the point of contact between the T cell and the APC.

[0245] Each TCR can comprise variable complementarity determining regions (CDRs), as well as framework regions (FRs) and a constant region. The TCR described herein may be in soluble form. The TCR described herein may not comprise a constant region. The TCR described herein may comprise a functional fragment of a full-length TCR. The TCR described herein may comprise the variable region of the alpha chain or beta chain only. The amino acid sequence of the third complementarity-determining region (CDR3) loops of the alpha (or a) and beta (or P) chain variable domains largely determines the sequence diversity of aP T cells arising from recombination between variable (VP), diversity (DP), and joining (JP) gene segments in the P chain locus, and between analogous Va and Ja gene segments in the a chain locus, respectively. The existence of multiple such gene segments in the TCR a and P chain loci allows for a large number of distinct CDR3 sequences to be encoded. Independent addition and deletion of nucleotides at the VP-DP, Dp-jp, and Va-Ja junctions during the process of TCR gene rearrangement further increases CDR3 sequence diversity. In this respect, immunocompetence is reflected in the diversity of TCRs. The y5 TCR is distinctive from the aP TCR in that it encodes a receptor that interacts closely with the innate immune system. TCRyS, is expressed early inWSGR Docket No.: 50401-789.601 development, has specialized anatomical distribution, has unique pathogen and small-molecule specificities, and has a broad spectrum of innate and adaptive cellular interactions. Early in ontogeny, as the restricted subsets of TCRyS cells populate various tissues prenatally, a biased pattern of TCRy V and J segment expression is established.

[0246] TCRs can bind to a peptide: MHC complex. In some cases, the TCR can bind to an MHC peptide complex comprising an epitope from an antigen or candidate antigen described herein. In some cases, the TCR can bind to an MHC peptide complex comprising an epitope of protein encoded by the genome of a cancer cell. The binding of the TCR complex and the epitope bound with the MHC molecule (e.g., MHC class I or MHC class II) can trigger signal transduction pathways that lead to regulation of immune responses against the antigenic peptide. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of 1 pM to 1 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 500 nM, 250 nM, 150 nM, 100 nM, 50 nM, 25 nM or 10 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 500 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 250 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 150 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 100 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 50 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 25 nM. In some embodiments, the TCR disclosed herein binds to an MHC-peptide complex with a KD or an IC50 of less than 10 nM.

[0247] In some embodiments, the TCR sequence is comprised of human sequences. In some embodiments, the TCR sequence is comprised of non-human animal sequences that have been humanized using any method of humanization known in the art. The TCRs disclosed herein can be engineered TCRs. In some embodiments, the TCR is a soluble TCR.

[0248] In some aspects, provided herein is a TCR or a recombinant nucleic acid comprising a sequence encoding thereof. In some embodiments, a TCR or a recombinant nucleic acid disclosed herein comprises a sequence encoding thereof comprises a TCR beta chain construct. In some embodiments, a TCR or a recombinant nucleic acid disclosed herein comprises a sequence encoding thereof comprises a TCR alpha chain construct.

[0249] The TCRs identified can bind to various peptide-MHC complexes. In some embodiments, the TCR binds to an MHC:HPV peptide complex, wherein the HPV peptide comprises a sequence of SEQ ID NO: 283 or 300. In some embodiments, the TCR binds to an MHC:RAS peptideWSGR Docket No.: 50401-789.601 complex, wherein the RAS peptide comprises a sequence of vvvgaVgvgk (SEQ ID NO: 312) or vvgaVgvgk (SEQ ID NO: 367). In some embodiments, the TCR binds to an MHC:RAS peptide complex, wherein the RAS peptide comprises a sequence of gaDgvgksal (SEQ ID NO: 368), vvvgaDgvgk (SEQ ID NO: 369) ,or vvgaDgvgk (SEQ ID NO: 370). In some embodiments, the TCR binds to an MHC:RAS peptide complex, wherein the RAS peptide comprises a sequence of vvvgaCgvgk (SEQ ID NO: 371). In some embodiments, the epitope sequences recognized by an identified TCR may to unknown.

[0250] In some embodiments, the TCR beta chain construct comprises a complementarity determining region 3 (CDR3), wherein the CDR3 has an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 5 or Table 7. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 3 (CDR3), wherein the CDR3 has an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 5 or Table 7. In some embodiments, TCR comprises a TCR alpha chain having a TCR alpha variable region, wherein the TCR alpha variable region is derived from a V gene segment selected from the group consisting of TRAV3, TRAV21, and TRAV1-2, and a J gene segment selected from the group consisting of TRAJ41, TRAJ36, TRAJ9, and TRAJ33. In some embodiments, TCR comprises a TCR beta chain having a TCR beta variable region, wherein the TCR beta variable region is derived from a V gene segment selected from the group consisting of TRBV12-5, TRBV27, TRBV6-5, and TRBV12-3, and a J gene segment selected from the group consisting of TRBJ1-1, TRBJ2-7, TRBJ2-2, TRBJ1-2, TRBJ2-2, and TRBJ2-1. Sequences of TRAV, TRAJ, TRBV, and TRBJ described herein can be obtained from UniProt.

[0251] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 14. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 14. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises aWSGR Docket No.: 50401-789.601 complementarity determining region 2 (CDR2) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-5, TRBJ1-1, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 52. n some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 52. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 1. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 1. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV3, TRAJ41, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence setWSGR Docket No.: 50401-789.601 forth in SEQ ID NO: 51. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 51. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A02:01 allele.

[0252] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 14. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 14. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 52. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 52. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 2. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 2. In some embodiments, the TCR alpha chainWSGR Docket No.: 50401-789.601 construct comprises a complementarity determining region 1 (CDR1) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV3, TRAJ41, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 51. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 53. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A02:01 allele.

[0253] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 15. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 15. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequenceWSGR Docket No.: 50401-789.601 set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-5, TRBJ1-7, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 54. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 54. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 1. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 1. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV3, TRAJ41, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at leastWSGR Docket No.: 50401-789.60196%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 51. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 51. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A02:01 allele.

[0254] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 15. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 15. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-5, TRBJ1-7, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 54. n some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 54. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 2. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has anWSGR Docket No.: 50401-789.601 amino acid sequence set forth in SEQ ID NO: 2. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV3, TRAJ41, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 53. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 53. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A02:01 allele.

[0255] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 16. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 16. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct further comprises aWSGR Docket No.: 50401-789.601 complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-5, TRBJ1-7, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 56. n some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 56. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 3. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 3. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV3, TRAJ41, or combination thereof. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV3, TRAJ41, or a combination thereof. In some embodiments, the TCR alphaWSGR Docket No.: 50401-789.601 chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 55. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 55. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A02:01 allele.

[0256] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 17. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 17. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-5, TRBJ1-7, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 57. n some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 57. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atWSGR Docket No.: 50401-789.601 least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 1. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 1. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV3, TRAJ41, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 51. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 51. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A02:01 allele.

[0257] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 18. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 18. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at leastWSGR Docket No.: 50401-789.60190%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 103. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-5, TRBJ1-7, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 59. n some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 59. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 4. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 4. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 100. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV3. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 101. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 101. In someWSGR Docket No.: 50401-789.601 embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV3, TRAJ41, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 58. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 58. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A02:01 allele.

[0258] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 19. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 19. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV27. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV27. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:107. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 107. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV27, TRBJ2-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 61. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 61. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%,WSGR Docket No.: 50401-789.601 at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 5. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 5. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ36, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 60. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 60. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A03:01 allele, HLA-B07:02 allele, HLA-C07:02 allele, or a combination thereof.

[0259] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 19. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 19. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV27. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1WSGR Docket No.: 50401-789.601 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV27. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:107. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 107. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV27, TRBJ2-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 61. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 61. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 6. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 6. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequenceWSGR Docket No.: 50401-789.601 set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ36, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 62. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 62. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A03:01 allele, HLA-B07:02 allele, HLA-C07:02 allele, or a combination thereof.

[0260] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 20. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 20. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV27. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV27. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:107. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 107. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV27, TRBJ2-7, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 63. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 63. In someWSGR Docket No.: 50401-789.601 embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 5. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 5. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ36, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 60. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 60. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A03:01 allele, HLA-B07:02 allele, HLA-C07:02 allele, or a combination thereof.

[0261] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 21. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 21. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV6-5. In some embodiments, the TCR beta chainWSGR Docket No.: 50401-789.601 construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV6-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 65. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 65. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 7. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 7. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprisesWSGR Docket No.: 50401-789.601 a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ9, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 64. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 64. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A01 :01 allele, HLA-B08:01 allele, HLA-C07:01 allele, or a combination thereof.

[0262] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 21. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 21. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV6-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 65. n some embodiments, the TCR beta chain constructWSGR Docket No.: 50401-789.601 comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 65. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 8. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 8. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ9, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 66. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 66. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A01 :01 allele, HLA-B08:01 allele, HLA-C07:01 allele, or a combination thereof.

[0263] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 22. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 22. In some embodiments, the TCR beta chain construct comprises a complementarityWSGR Docket No.: 50401-789.601 determining region 1 (CDR1) derived from TRAV6-5. In some embodiments, the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV6-5. In some embodiments, the TCRbeta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV6-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 68. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 68. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 9. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 9. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence setWSGR Docket No.: 50401-789.601 forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ9, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 67. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 67. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A01 :01 allele, HLA-B08:01 allele, HLA-C07:01 allele, or a combination thereof.

[0264] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 23. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 23. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV6-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acidWSGR Docket No.: 50401-789.601 sequence set forth in SEQ ID NO: 69. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 69. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 9. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 9. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ9, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 67. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 67. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A01 :01 allele, HLA-B08:01 allele, HLA-C07:01 allele, or a combination thereof.

[0265] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 24. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO:WSGR Docket No.: 50401-789.60124. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV6-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 71. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 71. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 10. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 10. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at leastWSGR Docket No.: 50401-789.60185%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ9, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 70. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 70. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A01 :01 allele, HLA-B08:01 allele, HLA-C07:01 allele, or a combination thereof.

[0266] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 25. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 25. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV6-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%,WSGR Docket No.: 50401-789.601 at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 72. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 72. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 10. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 10. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ9, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 70. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 70. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A01 :01 allele, HLA-B08:01 allele, HLA-C07:01 allele, or a combination thereof.

[0267] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequenceWSGR Docket No.: 50401-789.601 of SEQ ID NO: 22. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 22. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 106. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV6-5. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 108. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV6-5, TRBJ1-2, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 68. n some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 68. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 10. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 10. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 104. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV21. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2),WSGR Docket No.: 50401-789.601 wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 105. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 105. some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV21, TRAJ9, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 70. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 70. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A01 :01 allele, HLA-B08:01 allele, HLA-C07:01 allele, or a combination thereof.

[0268] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 26. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 26. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-3. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 111. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 111. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-3. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 112. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 112. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-3, TRBJ2-1, or combination thereof. In someWSGR Docket No.: 50401-789.601 embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 74. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 74. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 11. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 11. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV1-2. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 109. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 109. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV1-2. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 110. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 110. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV1- 2, TRAJ33, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 73. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 73. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A03:01 allele, HLA- C07:02 allele, HLA-C07:01 allele, or a combination thereof.

[0269] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises aWSGR Docket No.: 50401-789.601CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 26. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 26. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-3. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 111. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 111. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-3. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 112. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 112. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-3, TRBJ2-1, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 74. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 74. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 12. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 12. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV1-2. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 109. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 109. In some embodiments, the TCRWSGR Docket No.: 50401-789.601 alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV1-2. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 110. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 110. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV1- 2, TRAJ33, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 75. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 75. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to an epitope from HPV in complex with a human MHC encoded by an HLA-A03:01 allele, HLA- C07:02 allele, HLA-C07:01 allele, or a combination thereof.

[0270] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 26. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 26. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV12-3. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 111. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 111. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV12-3. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 112. In some embodiments, the TCR beta chain construct further comprisesWSGR Docket No.: 50401-789.601 a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 112. In some embodiments, the TCR beta chain construct comprises a variable region derived from TRAV12-3, TRBJ2-1, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 74. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 74. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 13. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 13. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV1-2. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 109. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 109. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV1-2. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 110. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 110. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV1- 2, TRAJ33, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 76. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 76. In some embodiments, the TCR binds to an epitope from HPV. In some embodiments, the epitope from HPV comprises an amino acid sequence set forth in SEQ ID NO: 133. In some embodiments, the TCR binds to anWSGR Docket No.: 50401-789.601 epitope from HPV in complex with a human MHC encoded by an HLA-A03:01 allele, HLA- C07:02 allele, HLA-C07:01 allele, or a combination thereof.

[0271] In some embodiments, the TCR beta chain construct comprises a complementarity determining region 3 (CDR3), wherein the CDR3 has an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 6 or Table 8. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 3 (CDR3), wherein the CDR3 has an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 6 or Table 8. In some embodiments, TCR comprises a TCR alpha chain having a TCR alpha variable region, wherein the TCR alpha variable region is derived from a V gene segment selected from the group consisting of TRAV4, and TRAV8-4, and a J gene segment selected from the group consisting of TRAJ15, and TRAJ21. In some embodiments, TCR comprises a TCR beta chain having a TCR beta variable region, wherein the TCR beta variable region is derived from a V gene segment selected from the group consisting of TRBV5-6, TRBV7-2, TRBV27, TRBV29-1, TRBV7-9, and TRBV20-1, and a J gene segment selected from the group consisting of TRBJ1-6, TRBJ1-3, TRBJ1-2, TRBJ1-4, TRBJ2-2, TRBJ1- 1, and TRBJ1-4. Sequences of TRAV, TRAJ, TRBV, and TRBJ described herein can be obtained from UniProt.

[0272] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 41. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 41. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:116. In some embodiments, the TCR beta chain construct further comprises a complementarityWSGR Docket No.: 50401-789.601 determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 78. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 78. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 27. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 27. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 77. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 77. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.WSGR Docket No.: 50401-789.601

[0273] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 42. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 42. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:116. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 28. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 28. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprisesWSGR Docket No.: 50401-789.601 a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 79. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 79. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0274] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 41. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 41. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:WSGR Docket No.: 50401-789.601116. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 78. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 78. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 28. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 28. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 79. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 79. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. InWSGR Docket No.: 50401-789.601 some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0275] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 42. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 42. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:116. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 29. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 29. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at leastWSGR Docket No.: 50401-789.60185%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 81. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 81. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0276] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 42. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 42. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2WSGR Docket No.: 50401-789.601 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 30. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 30. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 82. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 82. In some embodiments, the TCR binds to a mutated epitope from human RAS. In someWSGR Docket No.: 50401-789.601 embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0277] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 42. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 42. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:116. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 31. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 31. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1),WSGR Docket No.: 50401-789.601 wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 83. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 83. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0278] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 42. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 42. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chainWSGR Docket No.: 50401-789.601 construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 32. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 32. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 84. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ IDWSGR Docket No.: 50401-789.601NO: 84. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0279] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 41. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 41. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:115. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 115. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV5-6. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO:116. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 116. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV5-6, TRBJ1-6, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 78. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 78. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 31. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 31. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, theWSGR Docket No.: 50401-789.601TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 83. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 83. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0280] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 43. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 43 In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV7-2. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 117. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 117. In some embodiments, the TCR beta chain construct comprises a complementarityWSGR Docket No.: 50401-789.601 determining region 2 (CDR2) derived from TRAV7-2. In some embodiments, the TCRbeta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 118. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 118. In some embodiments, the TCRbeta chain construct comprises a variable region derived from TRAV7-2, TRBJ1-3, or combination thereof. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 86. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 86. In some embodiments, a TCR alpha chain construct comprises a CDR3 having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence forth in SEQ ID NO: 33. In some embodiments, the TCR alpha chain construct comprises a CDR3, wherein the CDR3 has an amino acid sequence set forth in SEQ ID NO: 33. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 113. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) derived from TRAV4. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence set forth in SEQ ID NO: 114. In some embodiments, the TCR alpha chain construct comprises a variable region derived from TRAV4, TRAJ15, or a combination thereof. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 85. In some embodiments, the TCR alphaWSGR Docket No.: 50401-789.601 chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 85. In some embodiments, the TCR binds to a mutated epitope from human RAS. In some embodiments, the mutated epitope from human RAS is characterized by a G12D mutation. In some embodiments, the TCR binds to a mutated epitope from human RAS in complex with a human MHC encoded by an HLA-C08:02 allele.

[0281] In some embodiments, a TCR beta chain construct comprises a complementarity determining region 3 (CDR3). In some embodiments, the TCR beta chain construct comprises a CDR3, wherein the CDR3 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence of SEQ ID NO: 43. In some embodiments, the CDR3 has an amino acid sequence of SEQ ID NO: 43 In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) derived from TRAV7-2. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 117. In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 117. In some embodiments, the TCR beta chain construct comprises a complementarity...

Claims

1. WSGR Docket No.: 50401-789.601CLAIMSWhat is claimed is:

1. A T cell comprising a T cell receptor (TCR) or a recombinant nucleic acid encoding the TCR comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 7.

2. The T cell of claim 1, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 7.

3. The T cell of claim 1 or 2, wherein the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7.

4. The T cell of any one of claims 1-3, wherein the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta chain variable region sequences listed in Table 7.

5. The T cell of any one of claims 1-4, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 7; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7.

6. The T cell of claim 5, wherein the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha chain variable region sequences listed in Table 7.

7. The T cell of any one of claims 1-6, wherein the TCR binds an epitope from HPV comprising an amino acid sequence set forth in SEQ ID NO: 133.WSGR Docket No.: 50401-789.6018. The T cell of any one of claims 1-7, wherein the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A02:01 allele.

9. The T cell of any one of claims 1-7, wherein the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-B07:02, HLA- C07:02 allele, and / or HLA-A03:01 allele.

10. The T cell of any one of claims 1-7, wherein TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A01 :01, HLA- B08:01 allele, and / or HLA-C07:01 allele.

11. The T cell of any one of claims 1-7, wherein the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A03 :01, HLA- C07:02 allele, and / or HLA-C07:01 allele.

12. The T cell of any one of claims 1-6, wherein the TCR binds an epitope from HPV comprising an amino acid sequence set forth in SEQ ID NOs: 283 or 300.

13. The T cell of claim 12, wherein the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HL A- Al 1 :01, HLA-A24:02, HLA- A03:01, or HLA-A02:01.

14. The T cell of claim 12, wherein the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-B07:02 / HLA-C07:02 allele or HLA-B08:01 / HLA-C07:01 allele.

15. The T cell of claim 12, wherein the TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A01 :01 allele.

16. A soluble T cell receptor (TCR) comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 7.

17. The soluble TCR of claim 16, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 7.

18. The soluble TCR of claim 16 or 17, wherein the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7.

19. The soluble TCR of any one of claims 16-18, wherein the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identityWSGR Docket No.: 50401-789.601 to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 7.

20. The soluble TCR of any one of claims 16-19, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 7; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7.

21. The soluble TCR of claim 16, wherein the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 7.

22. The soluble TCR of any one of claims 16-21, wherein the soluble TCR binds an epitope from HPV comprising an amino acid sequence set forth in SEQ ID NO: 133.

23. The soluble TCR of any one of claims 16-22, wherein the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A02:01 allele.

24. The soluble TCR of any one of claims 16-22, wherein the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-B07:02, HLA-C07:02 allele, and / or HLA-A03:01 allele.

25. The soluble TCR of any one of claims 16-22, wherein soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA- A01 :01, HLA-B08:01 allele, and / or HLA-C07:01 allele.

26. The soluble TCR of any one of claims 16-22, wherein the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A03:01, HLA-C07:02 allele, and / or HLA-C07:01 allele.

27. The soluble TCR of any one of claims 16-21, wherein the soluble TCR binds an epitope from HPV comprising an amino acid sequence set forth in SEQ ID NOs: 283 or 300.

28. The soluble TCR of claim 27, wherein the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HL A- Al 1 :01, HLA- A24:02, HLA-A03:01, or HLA-A02:01.WSGR Docket No.: 50401-789.60129. The soluble TCR of claim 27, wherein the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-B07:02 / HLA- C07:02 allele or HLA-B08:01 / HLA-C07:01 allele.

30. The soluble TCR of claim 27, wherein the soluble TCR binds to a complex comprising (i) the epitope from HPV and (ii) an MHC protein encoded by an HLA-A01 :01 allele.

31. A T cell comprising a T cell receptor (TCR) or a recombinant nucleic acid encoding the TCR comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 8.

32. The T cell of claim 31, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 8.

33. The T cell of claim 31 or 32, wherein the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 8.

34. The T cell of any one of claims 31-33, wherein the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 8.

35. The T cell of any one of claims 31-34, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 8; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 8.

36. The T cell of claim 35, wherein the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 8.WSGR Docket No.: 50401-789.60137. The T cell of any one of claims 31-36, wherein the TCR binds an epitope from human RAS comprising a mutation G12D.

38. The T cell of claim 37, wherein the TCR binds an epitope from human RAS comprising a sequence of gaDgvgksal (SEQ ID NO: 368), vvvgaDgvgk (SEQ ID NO: 369) ,or vvgaDgvgk (SEQ ID NO: 370).

39. The T cell of any one of claims 31-38, wherein the TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-C08:02 allele.

40. The T cell of any one of claims 31-38, wherein the TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-B07:02, HLA-C07:02 allele, and / or HLA-A03:01 allele.

41. The T cell of any one of claims 31-36, wherein the TCR binds an epitope from human RAS comprising a sequence of vvvgaVgvgk (SEQ ID NO: 312) or vvgaVgvgk (SEQ ID NO: 367).

42. The T cell of any one of claims 31-36, wherein the TCR binds an epitope from human RAS comprising a mutation G12V.

43. The T cell of claim 42, wherein the TCR binds an epitope from human RAS comprising a sequence of vvvgaVgvgk (SEQ ID NO: 312).

44. The T cell of claim 42 or 43, wherein the TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12V and (ii) an MHC protein encoded by an HLA-A03 :01 allele.

45. The T cell of any one of claims 31-36, wherein the TCR binds an epitope from human RAS comprising a mutation G12C.

46. The T cell of claim 45, wherein the TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12C and (ii) an MHC protein encoded by an HLA-B 15:01 allele.

47. A soluble T cell receptor (TCR) comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 8.

48. The soluble TCR of claim 47, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 8.

49. The soluble TCR of claim 47 or 48, wherein the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has anWSGR Docket No.: 50401-789.601 amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 8.

50. The soluble TCR of any one of claims 47-49, wherein the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 8.

51. The soluble TCR of any one of claims 47-50, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 8; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 8.

52. The soluble TCR of claim 51, wherein the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 8.

53. The soluble TCR of any one of claims 47-52, wherein the soluble TCR binds an epitope from human RAS comprising a mutation G12D.

54. The soluble TCR of any one of claims 47-53, wherein the soluble TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-C08:02 allele.

55. The soluble TCR of any one of claims 47-53, wherein the soluble TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12D and (ii) an MHC protein encoded by an HLA-B07:02, HLA-C07:02 allele, and / or HLA-A03:01 allele.

56. The soluble TCR of any one of claims 47-52, wherein the soluble TCR binds an epitope from human RAS comprising a mutation G12V.

57. The soluble TCR of claim 56, wherein the soluble TCR binds an epitope from human RAS comprising a sequence of SEQ ID NO: 312.WSGR Docket No.: 50401-789.60158. The soluble TCR of claim 56 or 57, wherein the soluble TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12V and (ii) an MHC protein encoded by an HLA-A03:01 allele.

59. The soluble TCR of any one of claims 47-52, wherein the soluble TCR binds an epitope from human RAS comprising a mutation G12C.

60. The soluble TCR of claim 59, wherein the soluble TCR binds to a complex comprising (i) the epitope from human RAS comprising the mutation G12C and (ii) an MHC protein encoded by an HLA-B 15:01 allele.

61. A pharmaceutical composition comprising a T cell comprising a T cell receptor (TCR), the TCR, or a nucleic acid encoding the TCR, and a pharmaceutically acceptable carrier, wherein the TCR comprises a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 7 or Table 8, wherein the pharmaceutical composition is suitable for being administered into a subject in need thereof.

62. The pharmaceutical composition of claim 61, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 7 or Table 8.

63. The pharmaceutical composition of claim 61 or 62, wherein the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7 or Table 8.

64. The pharmaceutical composition of any one of claims 61-63, wherein the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 7 or Table 8.

65. The pharmaceutical composition of any one of claims 61-64, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR1 sequences listed in Table 7 or Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7 or Table 8; andWSGR Docket No.: 50401-789.601 the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7 or Table 8.

66. The pharmaceutical composition of claim 65, wherein the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 7 or Table 8.

67. The pharmaceutical composition of any one of claims 61-66, for use in treating an immune disease or cancer.

68. Use of the pharmaceutical composition of any one of claims 61-66, for treating an immune disease or cancer.

69. A method of treating a subject having a disease or condition, comprising administering to the subject the pharmaceutical composition of any one of claims 61-66.

70. A method of treating a subject with cancer comprising administering to the subject the pharmaceutical composition any one of claims 61-66.

71. An expression vector comprising a nucleic acid sequence encoding a T cell receptor (TCR) comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from the group consisting of TCR beta chain CDR3 sequences listed in Table 7 or Table 8.

72. The expression vector of claim 71, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1), wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR beta chain CDR1 sequences listed in Table 7 or Table 8.

73. The expression vector of claim 71 or 72, wherein the TCR beta chain construct further comprises a complementarity determining region 2 (CDR2), wherein the CDR2 has an amino acid sequence selected from the group consisting of TCR beta chain CDR2 sequences listed in Table 7 or Table 8.

74. The expression vector of any one of claims 71-73, wherein the TCR beta chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR beta variable region sequences listed in Table 7 or Table 8.

75. The expression vector of any one of claims 71-74, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3,WSGR Docket No.: 50401-789.601 wherein the CDR1 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7 or Table 8; the CDR2 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR2 sequences listed in Table 7 or Table 8; and the CDR3 has an amino acid sequence selected from the group consisting of TCR alpha chain CDR3 sequences listed in Table 7 or Table 8.

76. The expression vector of claim 75, wherein the TCR alpha chain construct comprises a variable region having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to an amino acid sequence selected from the group consisting of TCR alpha variable region sequences listed in Table 7 or Table 8.

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