Density of immunogenic antigens does not explain the presence or absence of the T-cell–inflamed tumor microenvironment in melanoma

Abstract

Melanoma metastases can be categorized by gene expression for the presence of a T-cell–inflamed tumor microenvironment, which correlates with clinical efficacy of immunotherapies. T cells frequently recognize mutational antigens corresponding to nonsynonymous somatic mutations (NSSMs), and in some cases shared differentiation or cancer–testis antigens. Therapies are being pursued to trigger immune infiltration into non–T-cell–inflamed tumors in the hope of rendering them immunotherapy responsive. However, whether those tumors express antigens capable of T-cell recognition has not been explored. To address this question, 266 melanomas from The Cancer Genome Atlas (TCGA) were categorized by the presence or absence of a T-cell–inflamed gene signature. These two subsets were interrogated for cancer–testis, differentiation, and somatic mutational antigens. No statistically significant differences were observed, including density of NSSMs. Focusing on hypothetical HLA-A2+binding scores, 707 peptides were synthesized, corresponding to all identified candidate neoepitopes. No differences were observed in measured HLA-A2 binding between inflamed and noninflamed cohorts. Twenty peptides were randomly selected from each cohort to evaluate priming and recognition by human CD8+T cells in vitro with 25% of peptides confirmed to be immunogenic in both. A similar gene expression profile applied to all solid tumors of TCGA revealed no association between T-cell signature and NSSMs. Our results indicate that lack of spontaneous immune infiltration in solid tumors is unlikely due to lack of antigens. Strategies that improve T-cell infiltration into tumors may therefore be able to facilitate clinical response to immunotherapy once antigens become recognized.

Assessing Tumor-infiltrating Lymphocytes in Solid Tumors: A Practical Review for Pathologists and Proposal for a Standardized Method From the International Immunooncology Biomarkers Working Group: Part 1: Assessing the Host Immune Response, TILs in Invasive Breast Carcinoma and Ductal Carcinoma In Situ, Metastatic Tumor Deposits and Areas for Further Research

“…It has been hypothesized that a higher mutational burden will correspond to a greater potential for neoantigen formation and a higher immune infiltrate [119]. The tumor types with high average mutation load such as melanoma and non-small cell lung carcinoma, as well as the most highly mutated individual tumors within these types, appear to respond better to immunotherapy [120,121], however the mutational load does not necessarily correlate with the expression of immune-related genes in the tumor or the effector T cell infiltrate [122–124]. Specific mutational signatures such as homologous recombination pathway defects [125], POLE mutations, or microsatellite instability may prove to be important.…”

Immunotherapy for Breast Cancer: What Are We Missing?

“…One hypothesis to explain cold tumors is that a network of immunosuppression develops in the tumor microenvironment as a reaction to a nascent anti-tumor T cell response and actively excludes further T cell infiltration. A recent study of TCGA data indicates that the lack of spontaneous immune infiltration in non-inflamed human melanoma tumors is unlikely due to lack of antigens per se (58). In patients with pancreas cancer, we have reported that the cytolytic index, defined by expression of granzyme A and perforin 1, is inversely proportional to the number of predicted neo-epitopes (59).…”

Mechanistic and pharmacologic insights on immune checkpoint inhibitors

“…Broadly speaking, resistance mechanisms can be categorized as tumor-intrinsic, environmental, or genetic. Tumor-intrinsic molecular alterations that that may lead to resistance have been identified in human samples, such as β-catenin, FGFR3, PTEN, and JAK 1/2 [55, 57–59]. Exploration into the mechanisms at play and/or their use as predictive biomarkers is ongoing.…”

“…Ongoing research is aimed at understanding the mechanisms behind development of the non-T cell-inflamed, or immune resistant, phenotype. Additionally, mutational burden has been linked with improved response to immune checkpoint blockade and this characteristic appears to be independent of the T cell inflamed phenotype [55]. Yet neoantigen burden is not consistent as a predictive biomarker on its own, since there are observed responses in some patients with relatively low tumor mutational burden and vice versa.…”