Extreme intratumor heterogeneity and driver evolution in mismatch repair deficient gastro-esophageal cancer

Mismatch repair deficient (dMMR) gastro-esophageal adenocarcinomas (GEAs) are a distinct subtype characterized by high immunotherapy sensitivity and better outcomes than MMR proficient counterparts. dMMR confers a hypermutator-phenotype that theoretically enables high evolvability but this has not been investigated by multi-region exome sequencing (MSeq). MSeq of four dMMR GEAs revealed extreme intratumor heterogeneity (ITH) (average: 1639 heterogeneous mutations/tumor), exceeding ITH in other solid tumor types >20-fold. Long phylogenetic trunks (average: 685 mutations/tumor) likely explain the exquisite sensitivity to checkpoint-inhibiting immunotherapies. Driver mutations in TP53, ACVR2A, ARID1A/B, dMMR- and WNT-pathway genes recurrently located to the phylogenetic trunk. The hypermutator-phenotype remained active during cancer progression. Subclonal and parallel driver evolution predominated in PIK3CA, epigenetic regulator and immune evasion genes. Chromosomal instability evolved late in carcinogenesis or during cancer progression. Extreme ITH and subclonal driver evolution support high evolvability of dMMR GEAs. Truncal ARID1A mutations may offer novel therapeutic opportunities.EGA study EGAS00001003434