Alternative splicing expands the prognostic impact of KRAS in microsatellite stable primary colorectal cancer

Abstract

KRAS mutation is a well-known marker for poor response to targeted treatment and patient prognosis in microsatellite stable (MSS) colorectal cancer (CRC). However, variation in clinical outcomes among patients wild-type for KRAS underlines that this is not a homogeneous population. Here, we evaluated the prognostic impact of KRAS alternative splicing in relation to mutation status in a single-hospital series of primary MSS CRCs (N = 258). Using splicing-sensitive microarrays and RNA sequencing, the relative expression of KRAS-4A versus KRAS-4B transcript variants was confirmed to be down-regulated in CRC compared to normal colonic mucosa (N = 41; p ≤ 0.001). This was independent of mutation status, however, gene set enrichment analysis revealed that the effect of splicing on KRAS signaling was specific to the KRAS wild-type subgroup, in which low relative KRAS-4A expression was associated with a higher level of KRAS signaling (p = 0.005). In concordance, the prognostic value of KRAS splicing was also dependent on mutation status, and for patients with Stage I-III KRAS wild-type MSS CRC, low relative KRAS-4A expression was associated with inferior overall survival (HR: 2.36, 95% CI: 1.07-5.18, p = 0.033), a result not found in mutant cases (p = 0.026). The prognostic association in the wild-type subgroup was independent of clinicopathological factors, including cancer stage in multivariable analysis (HR: 2.68, 95% CI: 1.18-6.09, p = 0.018). This suggests that KRAS has prognostic value beyond mutation status in MSS CRC, and highlights the importance of molecular heterogeneity in the clinically relevant KRAS wild-type subgroup.

Genome-Wide Profiling of Prognostic Alternative Splicing Signature in Colorectal Cancer

“…Present study found the epigenetic modifications of histones near the splicing sites affected the ratio of KRAS-4A vs. KRAS-4B by the differential AS patterns in colorectal cancer cell lines ( 27 ). In a very recent study, aberrant splicing regulation of the KRAS-4A vs. KRAS-4B transcript isoforms was associated with a higher level of KRAS signaling and poor prognosis, specifically in the microsatellite stable primary CRC ( 28 ). As we have known, CRC mutant for either K/N-RAS or BRAF intrinsically resist treatment with EGFR.…”

Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

“…Aberrant splicing events in CRC and/or other cancer types were identified using either microarray or RNAseq techniques in the past [14][15][16][17]. The roles of AS in CRC were reported for individual genes: ITGA6 [18], MAP4K4 [19], EPDR1, ZNF518B [20], FIR [21], BRAF [22], Rac1 [23], OCT4 [24], RON [25], CD44 [26,27], KRAS [28], ZNF148 [29], FAK [30]. Global AS analysis in CRC or Pan-Cancer has also been performed using large number of RNA-seq data (i.e.…”

The SRSF3-MBNL1-Acin1 circuit constitutes an emerging axis to lessen DNA fragmentation in colorectal cancer via an alternative splicing mechanism

“…Colorectal cancer (CRC) is a frequently diagnosed malignancy and the third leading cause of cancer-mediated lethality worldwide [7] . Variations in genetic backgrounds were demonstrated to be related to the development and prognosis of CRC [8 , 9] . Correlations between altered AS events and progression of CRC have been widely documented in recent studies [10 , 11] .…”