Y chromosome loss drives cellular plasticity through single-cell epigenetic and transcriptional heterogeneity in lung adenocarcinoma

Loss of the Y chromosome (LOY) is among the most frequent somatic alterations in the blood of aging men. In cancer, LOY is associated with poor survival across multiple solid entities, including non-small cell lung cancer. Yet, the molecular mechanisms linking LOY and adverse outcomes remain poorly understood. Beyond sex-determining loci, the Y chromosome encodes dosage-sensitive genes, including two epigenetic regulators, whose X-linked homologs escape X-inactivation in females. We hypothesized that LOY results in haploinsufficiency of these regulatory genes, promoting tumor cell plasticity and heterogeneity.We investigated the consequences of LOY in lung adenocarcinoma (LUAD), the most prevalent lung cancer subtype, showing higher incidence and mortality in men. We performed whole-genome and single-cell RNA sequencing of paired tumor and matched normal lung tissue from male LUAD patients, complemented by public datasets. LOY was enriched in malignant cells and less frequent in the tumor microenvironment. To define tumor-cell-intrinsic effects, we generated isogenic A549 single-cell clones with or without the Y chromosome. LOY clones and primary LOY LUAD samples exhibited strong activation of epithelial-to-mesenchymal transition (EMT) programs. Genes that were consistently upregulated in LOY compared to ROY included THY1, LOX, and CDH2, which we also found to be highly abundant on the protein level. These effects were accompanied by increased cell-state plasticity, enhanced adaptation to metabolic and genotoxic stress. At the epigenetic level, we found widespread differences in DNA methylation patterns, especially at gene promoters of EMT genes, indicating an epigenetic underpinning of the phenotype. At the single-cell level, LOY clones showed increased epigenetic and transcriptional heterogeneity. Functionally, LOY conferred a selective advantage in vivo, promoting tumor engraftment and metastatic outgrowth. Together, these findings identify LOY as a previously unrecognized driver of EMT activation and tumor plasticity through epigenetic and transcriptional reprogramming, providing a mechanistic explanation for its association with poor therapy response and adverse clinical outcome in male lung adenocarcinoma.