DNA methylation mediates the immunosuppressive tumour microenvironment in metastatic endometrial clear cell carcinoma.

BACKGROUND: Endometrial clear cell carcinoma (ECCC) is a rare and highly aggressive histological subtype of endometrial cancer with marked metastatic potential. The molecular characteristics and underlying mechanisms governing its metastatic behaviour remain poorly understood. This study aimed to delineate molecular distinctions between metastatic (Pm) and non-metastatic (Pn) primary ECCC tumours, elucidate DNA methylation-mediated regulatory mechanisms driving metastasis, and identify potential epigenetic biomarkers and therapeutic targets. METHODS: This multicentre study involved 51 individuals diagnosed with ECCC, leading to the establishment of two independent cohorts: a sequencing cohort (n = 35) for integrated whole-genome methylation and transcriptomic analysis, and a tissue microarray (TMA) cohort (n = 16) to validate key findings. FINDINGS: Tumours exhibiting metastasis were found to possess a profoundly immunosuppressive tumour microenvironment (TME), evidenced by reduced density of tumour-infiltrating lymphocytes (TILs), especially within subsets of anti-tumour immune cells. Further analysis highlighted differential hypermethylation events in Pm tumours that acted as crucial epigenetic switches regulating immune responses. Specifically, methylation at ETS1-binding sites influenced ETS1 regulon activity, thus broadly regulating immune response processes. Epigenetic silencing of key genes in the T cell receptor (TCR) signalling pathway, such as LCK, CD3E, and ZAP70, impaired T cell activation and inhibited the activity of interacting immune pathways. Additionally, we developed a Lasso-derived metastatic risk score model, incorporating TME features (TIL density) and epigenetic predictors (LCK methylation), which demonstrated strong predictive performance (area under the curve [AUC] = 0.859). INTERPRETATION: This study illuminated the "epigenetic-immune axis" as a central regulatory mechanism driving ECCC metastasis. DNA methylation systematically silenced immune response genes by targeting ETS1-binding sites and TCR signalling components, thus reconstructing the immunosuppressive TME to facilitate metastasis. The development of the metastatic risk score model and identification of LCK as a potential therapeutic target provide valuable strategies for precision treatment decisions and advancing targeted epigenetic-immune therapies in ECCC. FUNDING: This work was supported by the National Natural Science Foundation of China, Joint Foundation Programme, Qingdao Municipal Science and Technology Bureau Municipal Science, Shenzhen Science and Technology Programme, and the Affiliated Hospital of Qingdao University Young Investigator Fund.