​​Whole-genome sequencing reveals distinct mutational mechanisms across endometrial cancer subtypes

Uterine corpus endometrial carcinoma (UCEC) is among the most prevalent gynecologic malignancies worldwide and represents a growing public health burden, particularly in high-income countries. Despite advances in clinical management, UCEC mortality continues to rise, with marked racial and socioeconomic disparities. The Cancer Genome Atlas (TCGA) previously established a molecular framework classifying UCEC into four major subtypes: POLE-ultramutated, microsatellite instability-high (MSI), copy-number low (CN-Low), and copy-number high (CN-High). However, the lack of whole-genome sequencing (WGS) has limited comprehensive characterization of UCEC genomic architecture. Here, we analyzed WGS data from 440 TCGA UCEC tumors, together with matched multi-omics data, to systematically characterize subtype-specific mutational processes, structural variation, and their clinical associations. Among driver genes, POLE-ultramutated tumors exhibited extensive multiple mutations, depleted frameshift indels, and increased subclonal heterogeneity. Across UCEC, LINE-1 retrotransposition events predominantly originated from a germline source at chr22q12.1, with endometrioid-like CN-High tumors displaying the highest level of transposable element activity. CN-High tumors also showed high frequent extrachromosomal DNA (ecDNA) amplification, dominated by co-amplification of the MYC - PVT1 and ERBB2 - MIEN1 loci, whereas ecDNA events were rare in other subtypes. Within CN-High tumors, LINE-1 insertion burden was strongly correlated with ecDNA formation, suggesting a mechanistic link between retrotransposition-associated genomic instability and oncogene amplification via ecDNA. In contrast, serous-like CN-Low tumors were characterized by higher patient body mass index (BMI), lower replication stress and increased X-chromosome inactivation. Mutational signature analysis revealed striking subtype specificity. APOBEC signatures were largely restricted to CN-High tumors. SBS39, a previously uncharacterized signature, was highly prevalent in CN-High tumors and significantly associated with BMI. MSI tumors exhibited a novel DBS signature enriched for A/T-containing reversed doublet substitutions (XY→YX), while indel mutagenesis was nearly ubiquitous and restricted to ID1 and ID2 signatures. Notably, the ID2-to-ID1 ratio in MSI tumors was approximately ten-fold higher than in non-MSI tumors, indicating a strong bias toward template-strand replication slippage associated with mismatch repair deficiency. Together, these findings uncover previously unrecognized, subtype-specific genomic features in UCEC and define distinct mutational mechanisms with potential implications for refined risk stratification and therapeutic strategies.