Tumor Antigenicity and a Pre-Existing Adaptive Immune Response in Advanced BRAF Mutant Colorectal Cancers

Simple Summary BRAF mutant metastatic CRCs (BRAF-mCRCs) are considered a unique clinical entity characterized by a dismal prognosis and that do not respond efficiently to both standard chemotherapy and to orally selective inhibitors of BRAF(V600E). In this study, the gene expression profiles of 89 immunotherapy-naive BRAF-CRCs were generated using the PanCancer IO 360 gene expression panel to improve the knowledge of the mechanisms involved in tumor-suppressive immune functions in BRAF-mCRCs. A significant fraction of BRAF-mCRCs shows a hot/inflamed profile and may be potential candidates for responding to immunotherapy. Only a partial overlap between these hot signatures and the presence of microsatellite instability (MSI) was observed, demonstrating that MSI tumors showed a not differential expression of MHC Class I antigen presentation pathway compared with microsatellite-stable tumors. The analysis of gene expression profiles is a promising strategy both for immune profiling of primary tumors before any treatment and for following the evolution of metastatic disease during therapy. The main hypothesis of this study is that gene expression profiles (GEPs) integrating both tumor antigenicity and a pre-existing adaptive immune response can be used to generate distinct immune-related signatures of BRAF mutant colorectal cancers (BRAF-CRCs) to identify actionable biomarkers predicting response to immunotherapy. GEPs of 89 immunotherapy-naive BRAF-CRCs were generated using the Pan-Cancer IO 360 gene expression panel and the NanoString nCounter platform and were correlated with microsatellite instability (MSI) status and with CD8+ tumor-infiltrating lymphocyte (TIL) content. Hot/inflamed profiles were found in 52% of all cases, and high scores of Tumor Inflammation Signature were observed in 42% of the metastatic BRAF-CRCs. A subset of MSI tumors showed a cold profile. Antigen Processing Machinery (APM) signature was not differentially expressed in MSI tumors compared with MSS cases. By contrast, the APM signature was significantly upregulated in CD8+ BRAF-CRCs versus CD8- tumors. Our study demonstrates that a significant fraction of BRAF-CRCs may be a candidate for immunotherapy and that the simultaneous analysis of MSI status and CD8+ TIL content increases accuracy in identifying patients who can potentially benefit from immune checkpoint inhibitors. GEPs may be very useful in expanding the spectrum of patients with BRAF-CRCs who can benefit from immune checkpoint blockade.