EP-4739702-A1 - CONVERGENT RECOMBINATION-DERIVED HEPATOCELLULAR CARCINOMA-SPECIFIC TCRS AND APPLICATIONS THEREOF

Abstract

The T-cell receptor (TCR) plays a crucial role in the adaptive immune response by recognizing specific antigens. In the context of cancer immunotherapy, TCR sequences can be engineered to target specific tumor antigens. In this study, hepatocellular carcinoma (HCC) was modeled in mice by combining genetic alterations recurrently observed in the human disease, and identified HCC-specific TCRs using single-cell TCR-seq. TCR convergence was observed across HCC-bearing mice, indicating that TCRs specific for HCC antigens elicit the expansion of CD4 + T cells. To further elucidate the function of this HCC-specific TCR, TCR-expressing vectors were designed and built, which can be used for various in vitro and in vivo applications, including identifying the specific peptide sequence that the TCR recognizes, manufacturing TCR-engineered T cells, studying T cell function, and screening potential immunotherapies. The findings have important implications for the development of T cell-based cancer immunotherapies.

Inventors

• MAK, TAK WAH
• ZHENG, Chunxing

Assignees

• The University Of Hong Kong
• Centre for Oncology and Immunology Limited
• University Health Network

Dates

Publication Date

20260513

Application Date

20240705

Claims (17)

1. An immune protein comprising (a) a TCR β chain variable domain (TCR-β domain) comprising Complementarity Determining Regions (CDRs) having the sequences SGHSA (SEQ ID NO: 53) , FRNQAP (SEQ ID NO: 54) , and ASSLDRGQDTQY (SEQ ID NO: 55) , (b) a TCR α chain variable domain (TCR-α domain) comprising CDRs having the sequences TISGNEY (SEQ ID NO: 56) , GLQQN (SEQ ID NO: 57) , and ILRGTGGNNKLT (SEQ ID NO: 58) , or (c) both.
2. The immune protein of claim 1, wherein the immune protein comprises a T-cell receptor (TCR) , wherein the TCR comprises the TCR-β domain, the TCR-α domain, or both.
3. The immune protein of claim 1 or 2, wherein the TCR-β domain has a sequence identity of at least 75%to SEQ ID NO: 51, and wherein the TCR-α domain has a sequence identity of at least 75%to SEQ ID NO: 52.
4. The immune protein of claim 3, wherein the TCR-β domain comprises the sequence SEQ ID NO: 51, and wherein the TCR-α domain comprises the sequence SEQ ID NO: 52.
5. The immune protein of any one of claims 1-4, wherein the immune protein targets hepatocellular carcinoma (HCC) antigens.
6. A pharmaceutical composition comprising the immune protein of any one of claims 1-5 and a pharmaceutically acceptable buffer, carrier, diluent or excipient.
7. A nucleic acid encoding the immune protein of anyone of claims 1-5.
8. A vector comprising the nucleic acid of claim 7.
9. The vector of claim 8, wherein the nucleic acid comprises an expression segment comprising coding regions in the following order: a signal sequence (such as fibroin protein from silk moth (FiBL) ) , the TCR-β domain, a TCR β constant region, a furin cleavage site, a flexible linker, T2A, the TCR-α domain, and a TCR α constant region.
10. A cell expressing the immune protein of any one of claims 1-5.
11. The cell of claim 10, wherein the cell is a genetically modified T-cell.
12. A population of cells derived by expanding the cell of claim 11.
13. A pharmaceutical composition comprising the population of cells of claim 12 and a pharmaceutically acceptable buffer, carrier, diluent or excipient.
14. A method of treating a subject having a disease, disorder, or condition, the method comprising administering to the subject an effective amount of the pharmaceutical composition of claim 6 or 13.
15. The method of claim 14, wherein the subject has HCC or has been identified as being at increased risk of getting HCC.
16. The method of claim 14 or 15, wherein the population of cells were isolated from or derived from the expansion of a cell obtained from the subject having the disease, disorder, or condition prior to the introduction to the cell.
17. The method of claim 14 or 15, wherein the population of cells were isolated from, or derived from the expansion of a cell obtained from a healthy donor.

Description

CONVERGENT RECOMBINATION-DERIVED HEPATOCELLULAR CARCINOMA-SPECIFIC TCRS AND APPLICATIONS THEREOF CROSS-REFERENCE TO RELATED APPLICATIONS This application claims benefit of U.S. Provisional Application No. 63/512, 299, filed July 07, 2023. Application No. 63/512,299, filed July 07, 2023, is hereby incorporated herein by reference in its entirety. REFERENCE TO SEQUENCE LISTING The Sequence Listing XML submitted as a file named “UHK_01396_PCT_ST26, ” created on June 26, 2024, and having a size of 61, 683 bytes is hereby incorporated by reference pursuant to 37 C.F.R. § 1.834 (c) (1) . FIELD OF THE INVENTION The present invention generally relates to T-cell receptor (TCR) , More specifically, the present invention relates to discovery and applications of convergent recombination derived hepatocellular carcinoma-specific TCRs. BACKGROUND OF THE INVENTION The T-cell receptor (TCR) is a key component of the adaptive immune response, playing a crucial role in the recognition of specific antigens. The TCR is composed of two different protein chains, alpha and beta, or gamma and delta, that are linked together by disulfide bonds. The alpha and beta chains contain variable (V) , diversity (D) , and joining (J) gene segments that are rearranged during T cell development to generate a unique TCR sequence that can recognize specific antigens. This process of TCR rearrangement is known as V (D) J recombination and is mediated by the RAG1 and RAG2 proteins, which recognize recombination signal sequences (RSSs) flanking the V, D, and J gene segments. The RAG proteins cleave the DNA at the RSSs, creating double-strand breaks that are repaired by the non-homologous end joining (NHEJ) pathway. This process results in the formation of a unique TCR sequence that is specific to each T cell. TCRs on T-cells can recognize specific cancer antigens. Modified T-cells targeting HCC antigens, such as AFP, GPC3, and MAGE-A, can be employed for adoptive cellular therapy (ACT) to destroy cancer cells. Viral antigens (HBsAg) are also targets for ACT. CD8 T cells have been traditionally considered the most effective immune cells for ACT, and infusion of CD8 CAR T cells alone has shown long-term B-cell eradication. However, CD4 T cells also play a crucial role in the immune response, and they can enhance the cytolytic activities of CD8 T cells through cytokine production. Studies have shown that CD4 CAR T cells demonstrate comparable effectiveness in directly killing target tumor cells both in vitro and in vivo. While CD4 CAR T cells may exhibit slower granzyme B secretion and tumor killing at the onset, they are less prone to AICD and exhaustion compared to CD8 counterparts, which confers the CD4 compartment a relatively better persistence following antigen exposure. Ideally, the antigen chosen for a target in ACT needs to be highly expressed in tumor cells and not by essential healthy tissues. Multiple strategies can be employed to identify TCRs that specifically recognize tumor antigens. One such method is single-cell TCR sequencing (TCR-seq) , which allows for the identification and characterization of TCRs at the single-cell resolution as disclosed herein. Any discussion of documents, acts, materials, devices, articles or the like which has been included in the present specification is not to be taken as an admission that any or all of these matters form part of the prior art base or were common general knowledge in the field relevant to the present disclosure as it existed before the priority date of each claim of this application. Throughout this specification the word “comprise, ” or variations such as “comprises” or “comprising, ” will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps. SUMMARY OF THE INVENTION Disclosed are compounds, compositions, and methods that involve and can be used treat liver cancer. Disclosed are immune proteins related to or derived from T-cell receptors (TCRs) discovered to be associated with liver cancer. The disclosed immune proteins generally include and/or retain functional portions of the discovered TCRs. For example, in some forms, the immune proteins include (a) Complementarity Determining Regions (CDRs) having the sequences SGHSA (SEQ ID NO: 53) , FRNQAP (SEQ ID NO: 54) , and ASSLDRGQDTQY (SEQ ID NO: 55) , (b) CDRs having the sequences TISGNEY (SEQ ID NO: 56) , GLQQN (SEQ ID NO: 57) , and ILRGTGGNNKLT (SEQ ID NO: 58) , or (c) both. In some forms, the immune proteins include comprising (a) a TCR β chain variable domain (TCR-β domain) comprising Complementarity Determining Regions (CDRs) having the sequences SGHSA (SEQ ID NO: 53) , FRNQAP (SEQ ID NO: 54) , and ASSLDRGQDTQY (SEQ ID NO: 55) , (b) a TCR α chain variable domain (TCR-α domain) comprising CDRs having the sequences TISGNEY (SEQ ID NO: 56) , GLQQN (SEQ ID NO: 57) , and ILRGTGGN