Comprehensive analysis reveals the molecular heterogeneity and the differences in prognosis and immunotherapy sensitivity in hypermutated colorectal cancer

This study aimed to investigate the molecular heterogeneity, accurately evaluate the prognosis, and identify those patients who would benefit most from immunotherapy in the hypermutated colorectal cancer (CRC) cohort. The unsupervised clustering analysis of CRC somatic mutation data from the Cancer Genome Atlas database was performed by combining tumor mutational burden (TMB) and indel burden to identify the subtypes within the hypermutated CRC cohort. Then, the somatic mutations, transcriptome, and gene mutations in the DNA damage repair signaling pathway of these subtypes were compared to obtain the corresponding molecular features. The proportion of 22 immune cells infiltrated in the samples was calculated using the CIBERSORT algorithm, and immunotherapeutic sensitivity was predicted for the patients using immunophenoscores (IPS). Five distinct clusters were identified from the hypermutated CRC sample, each exhibiting different characteristics regarding somatic mutations, gene expression, immune infiltration, and prognosis. The proportion of M2 macrophage infiltrated in Cluster 6 was significantly higher than in Cluster 1 (P = .018) and Cluster 3 (P = .003). The proportion of infiltrating M1 macrophages was significantly higher in Cluster 3 than in Cluster 1 (P = .026) and Cluster 6 (P = .016). Cluster 1 had a longer OS time compared to Cluster 3 (P = .015) and Cluster 6 (P = .005). In all 4 IPS types, Cluster 3 demonstrated higher IPS than Cluster 6 (P < .05), Cluster 2 demonstrated lower IPS than Cluster 5 (P < .05). In the IPS-CTLA4 type, the IPS of Cluster 1 was significantly higher than that of Cluster 6 (P = .038). In the non-POLE mutant cohort, the patients with the lowest TMB and indel burden had longer overall survival. The patients with higher levels of M1 macrophage infiltration showed higher sensitivity to anti-PD-1/PD-L1 immunotherapy or combined anti-PD-1/PD-L1 and anti-CTLA4 immunotherapy. In the POLE mutant cohort, the patients from the low TMB cohort may be better candidates for immunotherapy than those from the higher TMB cohort.