Highlights•Multi-omics definition of four robust molecular TET subtypes associated with survival•Thymomas have the lowest mutational burden among adult cancers•Enrichment of HRAS, NRAS, TP53, and recurrent GTF2I mutations are observed•Expression of autoimmune targets and aneuploidy links thymoma to myasthenia gravisSummaryThymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.Graphical abstract

The Integrated Genomic Landscape of Thymic Epithelial Tumors