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

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 (pinteraction = 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. What's new? Patients with microsatellite stable (MSS) colorectal cancer (CRC) that lacks KRAS mutation benefit from targeted therapy. Nonetheless, variations in clinical outcome suggest that KRAS wild‐type CRC is a heterogeneous disease. Here, two KRAS transcript variants, KRAS‐4A and KRAS‐4B, generated through alternative splicing, were investigated in relation to KRAS mutation status and MSS CRC prognosis. Aberrant splicing resulting in low expression of the KRAS‐4A transcript variant, relative to the KRAS‐4B transcript, was associated with increased KRAS signaling and poor patient prognosis specifically in KRAS wild‐type MSS CRC. The findings suggest that KRAS splicing is of prognostic relevance in KRAS wild‐type CRC.