Tobias MP Hartwich, Seungji Choi, Ayoung Hwang, Stefania Bellone, Luca Palmieri, Hae Seo, Taekeun Kim, Juhyeon Hong, Camilla Krakstad, Jone Trovik, Ingunn M. Stefansson, Hans Kristian Haugland, Michelle Greenman, Victoria Ettorre, Sarah Ottum, Cem Demirkiran, Yang Yang-Hartwich, Natalia Buza, Pei Hui, Salvatore Lopez, Gennaro Cormio, Mariantonietta Ramunno, Alfredo Zito, Emanuele Perrone, Anna Fagotti, Francesco Fanfani, Angela Santoro, Antonella Ravaggi, Eliana Bignotti, Franco Odicino, Laura Ardighieri, Elena Ratner, Roberto Angioli, Giuseppe Perrone, Daniela Luvero, Beatrice Conca, Jungmin Choi, Joseph Schlessinger, Alessandro D. Santin
Endometrial stromal sarcoma (ESS) is a rare uterine malignancy with limited treatment options. We performed integrated whole-genome, whole-exome, and transcriptome sequencing on 80 ESS tumors, comprising 32 low-grade (LG) and 48 high-grade (HG) tumors, to characterize their genetic landscape. The overall mutation burden was modest, with no significant difference between grades; however, we identified six hypermutated cases (7.5%) harboring POLE or mismatch repair mutations, genomic features predictive of immunotherapy response. We identified focal RAD54B amplifications in 15 tumors (18.8%), leading to elevated RAD54B expression and significantly shorter survival. This establishes RAD54B as an oncogenic driver in ESS. Known tumor suppressors (PTEN, TP53) were frequently mutated in HG-ESS but rare in LG-ESS, highlighting distinct grade-specific drivers of malignancy. HG-ESS exhibited widespread chromosomal gains, frequent loss of cell-cycle regulators (RB1, CDKN2A), and numerous private gene fusions arising from complex DNA rearrangements. In contrast, LG-ESS were defined by canonical fusions (e.g., JAZF1–SUZ12 ) and co-occurring deletions in metabolic regulator genes (TSC2, STK11). Finally, in an activating NRAS-mutant (p.Q61R) HG-ESS xenograft, the combination of MEK and FAK inhibition dramatically suppressed tumor growth and prolonged survival, highlighting a promising targeted treatment strategy. Overall, our comprehensive analysis defines the molecular basis of ESS and provides a strong preclinical rationale for precision therapies in this aggressive cancer.