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

Abstract

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-naïve 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.

Opposing roles by KRAS and BRAF mutation on immune cell infiltration in colorectal cancer – possible implications for immunotherapy

“…In a study by Cen et al, where they compared the immune microenvironment in BRAF- mutated tumours to that of BRAF wild-type tumours, an increased immune cell infiltration was found along with an increased expression of immune checkpoints, e.g., PD1, PD-L1 and CTLA4 [ 19 ]. Bolzacchini et al further identified a gene expression based “hot/inflamed” immunoprofile in a high fraction (52%) of patients with advanced BRAF -mutant CRC, with only a partial overlap with MSI [ 41 ]. Additionally, 42% of the MSI tumours showed a “cold” immunoprofile.…”

Similarities and differences in gene expression profiles of BRCA1 methylated and mutated epithelial ovarian cancers

“…Gene expression analysis was conducted on the NanoString nCounter ® gene expression platform (NanoString Technologies, Seattle, WA, USA) using the NanoString PanCancer IO 360™ code set, as we previously described in Bolzacchini et al. ( 15 ). NanoString nCounter ® PanCancer IO360 code set included 20 reference genes and 750 target genes that were grouped in 13 categories as listed in Supplementary Table 2 , such as Release of Cancer Cell Antigens (74 genes involved in DNA damage response and repair), Tumor-Intrinsic Factors (155 genes), and Common Signalling Pathways (162 genes included in Wnt, Hedgehog, TGF-beta, NF-kB, Notch, PI3K-Akt, and RAS-MAPK pathways).…”

“…The obtained counts were then normalized to the geometric mean of 20 endogenous housekeeping genes followed by log2 transformation. Gene expression signatures were calculated as a weighted linear average of the constituent genes ( 15 ). The weighted scores used for the calculation of the signatures are NanoString ® intellectual property.…”