Comparative molecular analyses between BRAFV600E colorectal cancers and BRAFV600E melanomas
Mohamed E. Salem, Joanne Xiu, Alberto Puccini, Axel Grothey, Richard M. Goldberg, Jimmy Hwang, Zoran Gatalica, Rebecca A. Feldman, Michelle Saul, W. Michael Korn, Michael Hall, WafikS. El-Deiry, Anthony F. Shields, John L. Marshall, Heinz-Josef Lenz, Ari VanderWalde
Studies have failed to replicate the efficacy of BRAF inhibitors used as monotherapy previously seen in BRAFV600E melanoma (Mel) in BRAFV600E colorectal cancers (CRC), likely due to the existence of additional resistance mechanisms as well as molecular and biological differences between the two tumor types.
Feedback reactivation of the MAPK pathway via the RTK EGF receptor mediated by high expression of EGFR in CRC compared to Mel led to promising combinatorial treatment strategy in targeting BRAF mutation in CRC.
Discovery of additional mechanism accounting for the innate resistance of BRAF-mutated CRC to BRAF inhibition will inform additional combinatorial strategies to further improve the efficacy of BRAF inhibition in CRC.
Tumor samples submitted to Caris Life Sciences for NGS DNA sequencing and RNA sequencing between the years 2015 and 2019 were retrospectively studied. Only microsatellite stable (MSS) tumors with either BRAFV600E mutation or wild type (WT) BRAF status were included in this initial analysis. Chi-square tests determined differences.
NGS was performed on genomic DNA isolated from FFPE tumor samples using the NextSeq (592-genes) (Illumina, Inc., San Diego, CA). All variants were detected with > 99% confidence based on allele frequency and amplicon coverage, with an average sequencing depth of coverage > 500 and an analytic sensitivity of 5%.
The copy number alteration (CNA) was determined by NGS; ≥6 copies was considered amplified and gene log ratio of selected genes of <=-1.2 was considered deleted.
Microsatellite instability (MSI)/MMR proficiency status was evaluated by a combination of fragment analysis, IHC and NGS.
Gene fusion was tested by RNA sequencing (ArcherDx fusion assay on MiSeq platform or Agilent SureSelectXT assay on NovaSeq)