The source of MHC class I presented peptides and its implications

The recent advancement of TCR-T cell therapies for cancer treatment

Adoptive cell therapies involve infusing engineered immune cells into cancer patients to recognize and eliminate tumor cells. Adoptive cell therapy, as a form of living drug, has undergone explosive growth over the past decade. The recognition of tumor antigens by the T-cell receptor (TCR) is one of the natural mechanisms that the immune system used to eliminate tumor cells. TCR-T cell therapy, which involves introducing exogenous TCRs into patients' T cells, is a novel cell therapy strategy. TCR-T cell therapy can target the entire proteome of cancer cells. Engineering T cells with exogenous TCRs to help patients combat cancer has achieved success in clinical trials, particularly in treating solid tumors. In this review, we examine the progress of TCR-T cell therapy over the past five years. This includes the discovery of new tumor antigens, protein engineering techniques for TCR, reprogramming strategies for TCR-T cell therapy, clinical studies on TCR-T cell therapy, and the advancement of TCR-T cell therapy in China. We also propose several potential directions for the future development of TCR-T cell therapy.

The biogenesis of the immunopeptidome

The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.

Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise

T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.

Antigen Processing, Presentation, and Tolerance: Role in Autoimmune Skin Diseases

Autoreactive T cells pose a constant risk for the emergence of autoimmune skin diseases in genetically predisposed individuals carrying certain HLA risk alleles. Immune tolerance mechanisms are opposed by broad HLA-presented self-immunopeptidomes, a predefined repertoire of polyspecific TCRs, the continuous generation of new antibody specificities by somatic recombination of Ig genes in B cells, and heightened proinflammatory reactivity. Increased autoantigen presentation by HLA molecules, cross-activation of pathogen-induced T cells against autologous structures, altered metabolism of self-proteins, and excessive production of proinflammatory signals may all contribute to the breakdown of immune tolerance and the development of autoimmune skin diseases.

CD4 T Cell-Dependent Rejection of Beta-2 Microglobulin Null Mismatch Repair-Deficient Tumors

Inactivation of beta-2 microglobulin (B2M) is considered a determinant of resistance to immune checkpoint inhibitors (ICPi) in melanoma and lung cancers. In contrast, B2M loss does not appear to affect response to ICPis in mismatch repair-deficient (MMRd) colorectal tumors where biallelic inactivation of B2M is frequently observed. We inactivated B2m in multiple murine MMRd cancer models. Although MMRd cells would not readily grow in immunocompetent mice, MMRd B2m null cells were tumorigenic and regressed when treated with anti-PD-1 and anti-CTLA4. The efficacy of ICPis against MMRd B2m null tumors did not require CD8⁺ T cells but relied on the presence of CD4⁺ T cells. Human tumors expressing low levels of B2M display increased intratumoral CD4⁺ T cells. We conclude that B2M inactivation does not blunt the efficacy of ICPi in MMRd tumors, and we identify a unique role for CD4⁺ T cells in tumor rejection. SIGNIFICANCE: B2M alterations, which impair antigen presentation, occur frequently in microsatellite-unstable colorectal cancers. Although in melanoma and lung cancers B2M loss is a mechanism of resistance to immune checkpoint blockade, we show that MMRd tumors respond to ICPis through CD4⁺ T-cell activation.This article is highlighted in the In This Issue feature, p. 1601.

Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface

Down regulation of the major histocompatibility class (MHC) I pathway plays an important role in tumour development, and can be achieved by suppression of HLA expression or mutations in the MHC peptide-binding pocket. The peptide-loading complex (PLC) loads peptides on the MHC-I molecule in a dynamic multi-step assembly process. The effects of cancer variants on ERp57 and tapasin components from the MHC-I pathway is less known, and they could have an impact on antigen presentation. Applying computational approaches, we analysed whether the ERp57-tapasin binding might be altered by missense mutations. The variants H408R(ERp57) and P96L, D100A, G183R(tapasin) at the protein–protein interface improved protein stability (ΔΔG) during the initial screen of 14 different variants. The H408R(ERp57) and P96L(tapasin) variants, located close to disulphide bonds, were further studied by molecular dynamics (MD). Identifying intramolecular a-a’ domain interactions, MD revealed open and closed conformations of ERp57 in the presence and absence of tapasin. In wild-type and mutant ERp57-tapasin complexes, residues Val97, Ser98, Tyr100, Trp405, Gly407(ERp57) and Asn94, Cys95, Arg97, Asp100(tapasin) formed common H-bond interactions. Moreover, comparing the H-bond networks for P96L and H408R with each other, suggests that P96L(tapasin) improved ERp57-tapasin binding more than the H408R(ERp57) mutant. During MD, the C-terminus domain (that binds MHC-I) in tapasin from the ERp57(H408R)-tapasin complex moved away from the PLC, whereas in the ERp57-tapasin(P96L) system was oppositely displaced. These findings can have implications for the function of PLC and, ultimately, for the presentation of MHC-I peptide complex on the tumour cell surface.

Peptide Channeling: The Key to MHC Class I Immunosurveillance?

MHC class I presentation of short peptides enables CD8⁺ T cell (T_CD8+) immunosurveillance of tumors and intracellular pathogens. A key feature of the class I pathway is that the immunopeptidome is highly skewed from the cellular degradome, indicating high selectivity of the access of protease-generated peptides to class I molecules. Similarly, in professional antigen-presenting cells, peptides from minute amounts of proteins introduced into the cytosol outcompete an overwhelming supply of constitutively generated peptides. Here, we propose that antigen processing is based on substrate channeling and review recent studies from the antigen processing and cell biology fields that provide a starting point for testing this hypothesis.

MHC-I presentation of peptides derived from intact protein products of the pioneer round of translation

Among the earliest protein products of most cellular genes are those synthesized during the pioneer round of translation (PRT), a key step in nonsense-mediated mRNA decay (NMD) that allows scanning of new transcripts for the presence of a premature termination codon (PTC). It has been demonstrated that at least some PRT degradation products can be targeted to major histocompatibility (MHC)-I presentation. To gain new insight into this putative PRT-to-MHC-I route, we have assembled 2 pairs of reporter genes so that the 2 genes in each pair encode an identical fusion protein between a model antigenic peptide and enhanced green fluorescent protein (EGFP), one of which harbors a PTC. We expressed these genes in different mouse and human cell lines and confirmed enhanced NMD activity for the PTC(+) gene in each pair by monitoring the effect of cycloheximide on the level of the respective mRNA. We then exploited several strategies for establishing the ratio between level of peptide presentation and total amount of protein product. We consistently observed significantly higher ratios for the PTC(+) mRNAs compared with the PTC(-) ones, pointing to correlation between the turnover of otherwise identical proteins and the fate of their template mRNA. Using confocal microscopy, we showed a clear link between NMD, the presence of misfolded EGFP polypeptides, and enhanced MHC-I peptide presentation. Altogether, these findings imply that identical full-length gene products differing only in 3' noncoding sequences can be differentially degraded and targeted to the MHC-I presentation pathway, suggesting a more general role for the PRT in establishing the MHC-I peptidome.-Weinstein-Marom, H., Hendel, L., Laron, E. A., Sharabi-Nov, A., Margalit, A., Gross, G. MHC-I presentation of peptides derived from intact protein products of the pioneer round of translation.

Nuclear processing of nascent transcripts determines synthesis of full-length proteins and antigenic peptides

Peptides presented on major histocompatibility (MHC) class I molecules form an essential part of the immune system's capacity to detect virus-infected or transformed cells. Earlier works have shown that pioneer translation peptides (PTPs) for the MHC class I pathway are as efficiently produced from introns as from exons, or from mRNAs targeted for the nonsense-mediated decay pathway. The production of PTPs is a target for viral immune evasion but the underlying molecular mechanisms that govern this non-canonical translation are unknown. Here, we have used different approaches to show how events taking place on the nascent transcript control the synthesis of PTPs and full-length proteins. By controlling the subcellular interaction between the G-quadruplex structure (G4) of a gly-ala encoding mRNA and nucleolin (NCL) and by interfering with mRNA maturation using multiple approaches, we demonstrate that antigenic peptides derive from a nuclear non-canonical translation event that is independently regulated from the synthesis of full-length proteins. Moreover, we show that G4 are exploited to control mRNA localization and translation by distinguishable mechanisms that are targets for viral immune evasion.

Soluble MHC class I complexes for targeted immunotherapy

Major histocompatibility complexes (MHC) have been used for more than two decades in clinical and pre-clinical approaches of tumor immunotherapy. They have been proven efficient for detecting anti-tumor-specific T cells when utilized as soluble multimers, immobilized on cells or artificial structures such as artificial antigen-presenting cells (aAPC) and have been shown to generate effective anti-tumor responses. In this review we summarize the use of soluble MHC class I complexes in tumor vaccination studies, highlighting the different strategies and their contradicting results. In summary, we believe that soluble MHC class I molecules represent an exciting tool with great potential to impact the understanding and development of immunotherapeutic approaches on many levels from monitoring to treatment.

Immunoribosomes: Where's there's fire, there's fire

The MHC class I antigen presentation pathway enables T cell immunosurveillance of cancer cells, viruses and other intracellular pathogens. Rapidly degraded newly synthesized proteins (DRiPs) are a major source of self-, and particularly, viral antigenic peptides. A number of findings support the idea that a substantial fraction of antigenic peptides are synthesized by "immunoribosomes", a subset of translating ribosomes that generate class I peptides with enhanced efficiency. Here, we review the evidence for the immunoribosome hypothesis.

Considerations in the Use of Codon Optimization for Recombinant Protein Expression

Codon optimization is a gene engineering approach that is commonly used for enhancing recombinant protein expression. This approach is possible because (1) degeneracy of the genetic code enables most amino acids to be encoded by multiple codons and (2) different mRNAs encoding the same protein can vary dramatically in the amount of protein expressed. However, because codon optimization potentially disrupts overlapping information encoded in mRNA coding regions, protein structure and function may be altered. This chapter discusses the use of codon optimization for various applications in mammalian cells as well as potential consequences, so that informed decisions can be made on the appropriateness of using this approach in each case.

Informatics for cancer immunotherapy

The rapid development of immunomodulatory cancer therapies has led to a concurrent increase in the application of informatics techniques to the analysis of tumors, the tumor microenvironment, and measures of systemic immunity. In this review, the use of tumors to gather genetic and expression data will first be explored. Next, techniques to assess tumor immunity are reviewed, including HLA status, predicted neoantigens, immune microenvironment deconvolution, and T-cell receptor sequencing. Attempts to integrate these data are in early stages of development and are discussed in this review. Finally, we review the application of these informatics strategies to therapy development, with a focus on vaccines, adoptive cell transfer, and checkpoint blockade therapies.

Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM. Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

Although mutations may represent attractive targets for immunotherapy, direct identification of mutated peptide ligands isolated from human leucocyte antigens (HLA) on the surface of native tumour tissue has so far not been successful. Using advanced mass spectrometry (MS) analysis, we survey the melanoma-associated immunopeptidome to a depth of 95,500 patient-presented peptides. We thereby discover a large spectrum of attractive target antigen candidates including cancer testis antigens and phosphopeptides. Most importantly, we identify peptide ligands presented on native tumour tissue samples harbouring somatic mutations. Four of eleven mutated ligands prove to be immunogenic by neoantigen-specific T-cell responses. Moreover, tumour-reactive T cells with specificity for selected neoantigens identified by MS are detected in the patient's tumour and peripheral blood. We conclude that direct identification of mutated peptide ligands from primary tumour material by MS is possible and yields true neoepitopes with high relevance for immunotherapeutic strategies in cancer.

Mechanism for cytoplasmic transduction peptide-HBcAg18-27-Tapasin to induce HBV specific CTL response in C57BL/6 mice

AIM: To observe whether the fusion protein cytoplasmic transduction peptide (CTP) -HBcAg_18-27-Tapasin can induce HBV-specific cytotoxic T lymphocyte (CTL) response in C57BL/6 mice via the JAK / STAT pathway.

METHODS: C57BL/6 mice were randomly divided into four groups: CTP-HBcAg_18-27-Tapasin alone group, CTP-HBcAg_18-27-Tapasin + AG490 group, AG490 alone group, and PBS group. Mice were immunized with the fusion protein through intramuscular injection, and AG490 was administered through intraperitoneal injection. The proliferation of T lymphocytes was observed using CCK-8 assay. The levels of the cytokines secreted by T lymphocytes were detected by ELISA, and the levels of intracellular cytokines of proliferative T lymphocytes were detected by flow cytometry. Expression levels of molecules of the JAK/STAT signal pathway were detected by real-time PCR.

RESULTS: The percentage of CD8⁺IFN-γ⁺ T cells, T lymphocytes proliferative activity and the levels of Th1 cytokines in the CTP-HBcAg_18-27-Tapasin alone group were significantly increased compared with the CTP-HBcAg_18-27-Tapasin + AG490 group (P < 0.01), although there was no statistical significance between the other groups. The expression levels of Jak2 and STAT4 were significantly higher in the CTP-HBcAg_18-27-Tapasin alone group than the rest groups (P < 0.05), and the expression levels of Tyk2 and STAT1 were also dramatically increased in the CTP-HBcAg_18-27-Tapasin alone group compared to other groups (P < 0.01).

CONCLUSION: CTP-HBcAg_18-27-Tapasin fusion protein increases HBV-specific CTL response via the JAK/STAT signal pathway in C57BL/6 mice.