Structural basis for T cell recognition of cancer neoantigens and implications for predicting neoepitope immunogenicity

TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions

Recognition of antigens by T cell receptors (TCRs) is a key component of adaptive immunity. Understanding the structures of these TCR interactions provides major insights into immune protection and diseases, and enables design of therapeutics, vaccines and predictive modeling algorithms. Previously, we released TCR3d, a database and resource for structures of TCRs and their recognition. Due to the growth of available structures and categories of complexes, the content of TCR3d has expanded substantially in the past 5 years. This expansion includes new tables dedicated to TCR mimic antibody complex structures, TCR-CD3 complexes and annotated Class I and II peptide-MHC complexes. Additionally, tools are available for users to calculate docking geometries for input TCR and TCR mimic complex structures. The core tables of TCR-peptide-MHC complexes have grown by 50%, and include binding affinity data for experimentally determined structures. These major content and feature updates enhance TCR3d as a resource for immunology, therapeutics and structural biology research, and enable advanced approaches for predictive TCR modeling and design. TCR3d is available at: https://tcr3d.ibbr.umd.edu.

Neoantigens in cancer immunotherapy: focusing on alternative splicing

Alternative splicing (AS) functions as a crucial program in transcriptional modulation, leading to proteomic diversity and functional alterations of proteins. These splicing actions induce various neoantigens that hold prognostic significance and contribute to various aspects of cancer progression, including immune responses against cancer. The advent of immunotherapy has remarkably revolutionized tumor therapy. In this regard, AS-derived neoantigens are potent targets for cancer vaccines and chimeric antigen receptor (CAR) T cell therapies. In this review, we outline that AS-derived neoantigens serve as promising immunotherapeutic targets and guide immunotherapy strategies. This evidence contributes to a deeper comprehension of the complexity of proteomic diversity and provides novel perspectives and techniques for precision medicine in immunotherapy. Moreover, we underscore the obstacles that are awaited to be addressed for this novel approach to become clinically applicable.

The tumor-driven antibody-mediated immune response in cancer

Immune cells in the tumor microenvironment play a crucial role in cancer prognosis and response to immunotherapy. Recent studies highlight the significance of tumor-infiltrating B cells and tertiary lymphoid structures as markers of favorable prognosis and patient-positive response to immune checkpoint blockers in some types of cancer. Although the presence of germinal center B cells and plasma cells in the tumor microenvironment has been established, determining their tumor reactivity remains challenging. The few known tumor targets range from viral proteins to self and altered self-proteins. The emergence of self-reactive antibodies in patients with cancer, involves the opposing forces of antigen-driven affinity increase and peripheral tolerance mechanisms. Here, B cell tumor antigen specificity and affinity maturation in tumor-directed immune responses in cancer are discussed.

Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity

The inherent cross-reactivity of the T cell receptor (TCR) is balanced by high specificity, which often manifests in confounding ways not easily interpretable from static structures. We show here that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen derived from mutant PIK3CA and its wild-type (WT) counterpart emerges from motions within the HLA binding groove that vary with the identity of the peptide's first primary anchor. The motions form a dynamic gate that in the complex with the WT peptide impedes a large conformational change required for TCR binding. The more rigid neoantigen is insusceptible to this limiting dynamic, and with the gate open, is able to transit its central tryptophan residue underneath the peptide backbone to the contralateral side of the HLA-A3 peptide binding groove, facilitating TCR binding. Our findings reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I complexes, with implications for resolving long-standing and often confounding questions about the determinants of T cell specificity.

Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens

T cell receptors (TCRs) that recognize cancer neoantigens are important for anti-cancer immune responses and immunotherapy. Understanding the structural basis of TCR recognition of neoantigens provides insights into their exquisite specificity and can enable design of optimized TCRs. We determined crystal structures of a human TCR in complex with NRAS Q61K and Q61R neoantigen peptides and HLA-A1 MHC, revealing the molecular underpinnings for dual recognition and specificity versus wild-type NRAS peptide. We then used multiple versions of AlphaFold to model the corresponding complex structures, given the challenge of immune recognition for such methods. Interestingly, one implementation of AlphaFold2 (TCRmodel2) was able to generate accurate models of the complexes, while AlphaFold3 also showed strong performance, although success was lower for other complexes. This study provides insights into TCR recognition of a shared cancer neoantigen, as well as the utility and practical considerations for using AlphaFold to model TCR-peptide-MHC complexes.

LAIR1-mediated resistance of hepatocellular carcinoma cells to T cells through a GSK-3β/β-catenin/MYC/PD-L1 pathway

BACKGROUND

An increasing number of studies have reported the involvement of oncogenes in the regulation of the immune system. LAIR1 is an immunosuppressive molecule and its role in immune-related diseases has been mainly reported. To date, it is unclear whether LAIR1 in tumor cells is involved in immune regulation. Therefore, the aim of this study was to investigate the role of LAIR1 in the immune microenvironment of hepatocellular carcinoma (HCC) to seek the novel therapeutic discoveries.

METHODS

Tumor Immune Dysfunction and Exclusion database was used to predict the response of LAIR1 expression to immune checkpoint blockade. CD8+ T cells were co-cultured with HCC cells, and the killing efficiency of leukocytes on HCC cells was detected by flow cytometry. Flow cytometry was also used to detect the expression of inhibitory receptors. In addition, Western blot, immunofluorescence, and nucleus/cytoplasm fractionation experiments were performed to explore the molecular mechanisms by which LAIR1 created a suppressive tumor microenvironment.

RESULTS

LAIR1 expression in HCC was associated with worse immune prognosis and T-cell dysfunction. HCC cells overexpressing LAIR1 co-cultured with CD8+ T cells induced exhaustion of latter. Mechanism studies indicated that LAIR1 in HCC cells up-regulated the phosphorylation of β-catenin by inducing the phosphorylation of GSK-3β, leading to the impairment of the expression and the nuclear localization signal of β-catenin. Low β-catenin expression and nuclear localization signal inhibited MYC-mediated PD-L1 expression. Therefore, PD-L1 up-regulated by LAIR1 caused the exhaustion of infiltrating CD8+ T cells in HCC, which aggravated the malignant progression of HCC.

CONCLUSION

LAIR1 increased PD-L1 expression through the GSK-3β/β-catenin/MYC/PD-L1 pathway and promoted immune evasion of HCC cells. Targeted inhibition of LAIR1 helped to enhance the immune killing effect of CD8+ T cells in HCC.