Mutational Analysis of Gene Fusions Predicts Novel MHC Class I–Restricted T-Cell Epitopes and Immune Signatures in a Subset of Prostate Cancer

Abstract

Purpose Gene fusions are frequently found in prostate cancer and may result in the formation of unique chimeric amino acid sequences (CASQs) that span the breakpoint of two fused gene products. This study evaluated the potential for fusion-derived CASQs to be a source of tumor neoepitopes, and determined their relationship to patterns of immune signatures in prostate cancer patients. Experimental Design A computational strategy was used to identify CASQs and their corresponding predicted MHC class I epitopes using RNA-Seq data from The Cancer Genome Atlas of prostate tumors. In vitro peptide-specific T cell expansion was performed to identify CASQ-reactive T cells. A multivariate analysis was used to relate patterns of in silico-predicted tumor-infiltrating immune cells with prostate tumors harboring these mutational events. Results Eighty-seven percent of tumors contained gene fusions with a mean of 12 per tumor. In total, 41% of fusion-positive tumors were found to encode CASQs. Within these tumors, 87% gave rise to predicted MHC class I-binding epitopes. This observation was more prominent when patients were stratified into low- and intermediate/high-risk categories. One of the identified CASQ from the recurrent TMPRSS2:ERG type VI fusion contained several high-affinity HLA-restricted epitopes. These peptides bound HLA-A*02:01 in vitro and were recognized by CD8+ T cells. Finally, the presence of fusions and CASQs were associated with expression of immune cell infiltration. Conclusions Mutanome analysis of gene fusion-derived CASQs can give rise to patient-specific predicted neoepitopes. Moreover, these fusions predicted patterns of immune-cell infiltration within a sub-group of prostate cancer patients.

Detailed Molecular and Immune Marker Profiling of Archival Prostate Cancer Samples Reveals an Inverse Association between TMPRSS2:ERG Fusion Status and Immune Cell Infiltration

“…4 At fusion level, it has been postulated that TMPRSS2:ERG fusions generate chimeric amino acid sequences that are targetable by T cells. 10 Prediction algorithms have been used to identify potentially antigenic epitopes from TMPRSS2:ERG fusions. 11 Herein, we studied the relationship between immune cell infiltration and mutations in prostate cancer by using an integrative approach combining image analysis and DNA and RNA sequencing.…”

Association of tumor-infiltrating T-cell density with molecular subtype, racial ancestry and clinical outcomes in prostate cancer

“…Finally, gene fusions in prostate cancer can result in the formation of unique chimeric amino acid sequences that span the breakpoint of the two fused gene products and potentially generating fusion proteins with neoepitopes. In a recent computational study, type VI TMPRSS2-ERG gene fusions contained high-affinity HLA-restricted epitopes and were recognized by CD8+ T-cells in vitro ( 54 ). Though these mechanistic possibilities are intriguing, it is also possible that the association of higher lymphocyte densities with ERG rearrangement is due to a confounding additional molecular alteration, which is itself associated with ERG fusion.…”

The Role of Somatic Mutations on the Immune Response of the Tumor Microenvironment in Prostate Cancer

“…This finding suggests that the Tmprss2-Erg fusion promotes recruitment of regulatory T cells to the tumor site [50]. Recent studies have shown an association between low levels of TILs comparing TMPRSS2-ERG fusions producing chimeric transcripts in the coding in the fusion-positive cases results in suppression of immune response by alteration of cytokine production [51,52].…”