Landscape of somatic mutations in a large cohort of Chinese patients with immune dysregulations

This study aims to characterize pathogenic somatic mutations in patients with autoinflammatory or autoimmune diseases lacking disease-causing germline mutations, explore their contribution to disease pathogenesis and progression, and evaluate their implications for diagnosis and targeted therapy. We performed a systematic analysis of somatic mutations in a selected panel of 185 immune-related genes in 2912 patients with autoinflammatory or autoimmune diseases, recruited from 41 medical centers across China, who were previously negative for germline mutations based on whole exome sequencing (WES). We identified both previously reported and novel somatic mutations in genes such as UBA1, KRAS and NLRP3. Pathogenic somatic mutations in TNFAIP3 were discovered firstly in the patients with autoinflammatory diseases. The pathogenic somatic mutations detection rate was 1.35% in adults and 0.97% in children, emphasizing the importance of genetic diagnosis and novel gene discovery for somatic mutations. In addition, somatic mutations in Ras-related genes were identified in seven patients and 39 clonal hematopoiesis-associated mutations were identified in 36 adult patients. Moreover, myeloid cells harboring somatic mutations expanded during disease flare and reduced during remission. Disregarding the dynamic elevation of the variant allele fraction during disease progression led to therapeutic failure. This study delineated the genetic landscape of pathogenic somatic mutations underlying autoinflammatory and autoimmune diseases, offering valuable insights for genetic diagnosis and targeted therapies.