Distinct KRAS mutation codons differentially associate with microsatellite instability in colorectal carcinoma

Background: MSI/MMR and KRAS are key biomarkers in colorectal carcinomas (CRC) for PD1 inhibitors, EGFR mAbs, and KRAS G12C inhibitors. MSI High is reported to be less common in KRAS mutant CRC. However, because KRAS mutation location influences protein function and CRC pathophysiology, we hypothesized that MSI also differs by KRAS mutation site. Methods: MSI High prevalence was assessed by KRAS mutation location in CRCs using logistic regression in 2 databases: MSK-CHORD, and Caris CODEai. BRAF V600E CRCs were excluded. Results: In MSK-CHORD's 4,805 CRCs (non BRAF V600E, NRAS wt, and no prior EGFRmab), 8.7% were MSI-H. However, MSI-H prevalence differed markedly by KRAS mutation site: 8.8% of KRAS wt and 13.5-15.9% of codon 13/61/146 CRCs; but only 5.1% of codon 12 mutant CRCs were MSI-H (all p≤0.001). Notably, MSI-H also varied within KRAS codons: only 2.0% of G12C and 2.8% of G12V (both C>A) were MSI-H, vs 7.8% of G12D, 4.8% of G12A, and 3.8% of G12S. For confirmation of institutional findings, we analyzed data from a large reference laboratory. In Caris CODEai's 83,532 non BRAF V600E CRCs, 5.4% were MSI-H. Again, MSI-H prevalence varied by KRAS mutation site: 6.4% of KRAS wt, 5.6-6.9% of codon 13/61/117/146, and 19.2-26.9% of codon 14/59 mutant CRCs were MSI-H; compared to only 1.9% of codon 12 mut CRCs (all p<0.001). We then tested this finding in other cancer types in Caris CODEai. A similar result was observed in pancreatic cancer: among 40,497 only 0.7% were MSI-H, from 0.7% of KRAS wt to 0.4-0.5% of codon 12/61, but 7.8% of codon 13 (p<0.001). Conclusions: MSI-H prevalence varied by KRAS mutation location in CRC, with codon 12 muts-especially C>A-associated with low MSI-H rates, whereas codon 13/59/61/146 muts were enriched among MSI-H CRCs. Our data suggest that MSI/MMR mutational processes are associated with distinct codon-resolved KRAS biology and may give rise to specific KRAS muts, which warrants further investigation and could refine predictive biomarker interpretation.$$table_{639CE3DC-D7C9-4D54-BCC3-73A53B9D4E63}$$ MSI-High prevalence by KRAS status in MSK-CHORD CRC KRAS_ status Total_ n MSI-H_ n MSI-H_ % wt 2510 222 8.8 codon_12 1517 78 5.1 codon_13 436 49 13.5 codon_59 10 5 50.0 codon_61 94 13 13.8 codon_117 26 8 30.8 codon_146 164 26 15.9 in_codon_12 G12A_(C>G) 104 5 4.8 G12C_(C>A) 153 3 2.0 G12D_(C>T) 658 51 7.8 G12R_(C>G) 24 2 8.3 G12S_(C>T) 105 4 3.8 G12V_(C>A) 469 13 2.8 in_codon_13 G13C_(C>A) 19 2 10.5 G13D_(C>T) 412 55 13.4 in_codon_61 Q61H_(T>G,T>A) 50 5 10.0 Q61K_ (GA>TT, G>T, GA>TG) 21 8 38.1 Q61L_(T>A) 7 0 0 Q61R_(T>C, TT>GC) 15 0 0 in_codon_146 A146P_(C>G) 9 2 22.2 A146T_(C>T) 128 23 18.0 A146V_(G>A) 26 1 3.9 in_codon_59 A59T_(C>T) 10 5 50.0 in_codon_117 K117N_(T>A,T>G) 24 8 33.3