Genome‐wide analysis of somatic noncoding mutation patterns and mitochondrial heteroplasmic shift in type <scp>B1</scp> and <scp>B2</scp> thymomas

Type B1 and B2 thymomas are lymphocyte-rich malignant tumours with few somatic mutations in protein-coding regions of the nuclear genome; nonetheless, noncoding regions remain uncharacterized. Here, we developed a method to isolate pure thymoma cells from lymphocyte-rich tissues, and then performed genome-wide deep sequencing. The total number of somatic mutations was ~80 times higher in noncoding regions than in coding regions in type B12 thymomas (1,671.3 versus 21.1 per case). Coding mutations were identified in epigenetic regulators, DNA repair genes, and some other genes. Nevertheless, 40% of the cases exhibited fewer than four nonsynonymous mutations in coding regions. A systematic noncoding analysis identified 405.0 mutations per case in cis-regulatory elements and detected six recurrent mutations: one interferon regulatory factor (IRF8), two E3 ubiquitin ligases (UBR2 and RNF213), and three intergenic regions. Tumour-specific/enriched mitochondrial heteroplasmic shift was observed in 90% of cases, with a significant proportion of mutations located in the D-loop region. When tracing the evolutionary lineage of mtDNA mutation, the majority of cases can be explained by a linear evolutionary model. This suggests that positive selection may be operating on the mitochondrial genome during thymoma development. In summary, numerous noncoding mutations and mitochondrial heteroplasmic shift were detected in type B1 and B2 thymomas, some of which may be functional. Given the paucity of coding mutations observed in this disease entity, other factors such as disruption of the noncoding landscape and tumour-specific/enriched mitochondrial heteroplasmic shift, may contribute to the development of thymoma. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.