The prevalence of HLA-I LOH in Chinese pan-cancer patients and genomic features of patients harboring HLA-I LOH

Loss of heterozygosity in HLA-I (HLA-I LOH) may facilitate immune evasion. However, the large population study of HLA-I LOH in Chinese pan-cancer patients remains to be explored. In this study, analysis was performed in 1504 advanced pan-cancer patients and 134 early-stage NSCLC patients using a 1021-gene panel. The consistency between the 1021-gene panel and whole-exome sequencing (WES) was evaluated in 45 samples, where concordant results were obtained in 95.6% (43/45) of the samples. Analytical results revealed that the prevalence of HLA-I LOH presents considerable differences across cancer types. HLA-I LOH was relevant to genomic instability, reflected in higher tumor mutation burden (TMB) level. The incidence of HLA-I LOH in MSS samples was significantly higher than that in MSI-H samples. The alteration frequencies of p53 pathway, RTK/RAS pathway, Notch pathway, Hippo pathway, and Nrf2 pathway in HLA-I LOH group were significantly higher than that in HLA-I stable group (p<0.0001, p<0.0001, p=0.032, p=0.013, p=0.003, respectively). In DNA damage response (DDR) pathways, alterations in CPF pathway and FA pathway are enriched in HLA-I LOH group (p<0.0001, p=0.023, respectively). Besides, HLA-I LOH was accompanied by higher mutation rates of several tumor suppressors, including TP53 and LRP1B. These results may shed light on follow-up research.