Comprehensive molecular analysis of microsatellite-stable (MSS) tumors with high mutational burden in gastrointestinal (GI) cancers.

Abstract

3631 Background: Mutational signatures contributing to high tumor mutation burden (TMB-H) independent from microsatellite instability-high (MSI-H) status are not well-studied. We aimed to characterize specific molecular features of a large cohort of GI tumors with TMB-H & MSS. Methods: We sequenced23392 GI tumors, including 2707 gastroesophageal (GE), 11616 colorectal (CRC), and 9069 others. Samples were analyzed using Next-generation sequencing (NGS) and immunohistochemistry (IHC) (Caris Life Sciences, Phoenix, AZ). MMR/MSI status was evaluated by a combination of IHC, Fragment Analysis and NGS. Tumors with TMB ≥ 17 mutations/Mb were defined as TMB-H. PD-L1 was tested by IHC [22C3 (CPS score, positivity: CPS ≥ 1%) in GE tumors and SP142 (Positivity: TPS ≥ 5%) in other cancers]. Findings were compared in four groups (TMB-H/L & MSI-H/MSS) using Fisher-Exact or Chi-square and adjusted for multiple comparison by Benjamini-Hochberg. Significance was determined by adjusted (adj) p < .05. Results: Overall, TMB-H & MSS was observed in 1% of patients (pts) (n = 237, including 45 GE, 124 CRC, 68 others), while TMB-H & MSI-H, TMB-L & MSS, TMB-L & MSI-H were observed in 4% (n = 936), 94.4% (n = 22089) and 0.6% (n = 130) respectively. Compared to other groups, TMB-H & MSS showed the most prevalent amplifications (AMPs), including CCND1 (5.6%), FGF3/4/19 (4.9%, 4.3%, 4.4%) , MYC (4.3%) (Top 5, adj p < .05), and the highest mutation rates in POLE (21.6%), RB1 (13.1%), CDC73 (10.3%), RUNX1 (6.5%), and genes involved in PI3K & MAPK ( PIK3R1 17%, mTOR 3.4%, MAP2K1 3.8% , MAP2K4 5.6%) and Wnt ( APC 48.5% , SMAD2 6.5% , TCF7L2 3.8%) pathways (adj p < .05). The rates of HER2 AMP and high-expression (IHC) were the highest in TMB-H & MSS, followed by TMB-L & MSS, TMB-H & MSI-H, TMB-L & MSI-H (adj p< .0001); PD-L1 positive rate was similar between TMB-H & MSS and TMB-L & MSI-H, while the highest and lowest in TMB-H & MSI-H and TMB-L & MSS respectively in GE and other GI cancers (adj p < .01) (Table). Conclusions: This is the largest study to investigate the special molecular landscape of pts with TMB-H & MSS in GI cancers. Our data may provide novel insights for pt selection and more effective targeted combination immunotherapies (e.g. HER2, PI3K inhibitors) in GI cancers. [Table: see text]