Abstract LB309: Y chromosome loss drives cellular plasticity through single-cell epigenetic and transcriptional heterogeneity in lung adenocarcinoma

Abstract 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. Citation Format: Kathleen Schlüter, Mei-Ju May Chen, Gizem Altun, Sergio Manzano Sanchez, Dung-Chi Wu, Nan Zhang, Ofir Griess, Luc Husemann, Fabian Bradic, Joseph Cornick, Oliver Mücke, Riccardo Moro, Katherine Kelly, Sara Chocarro, Etienne Sollier, Maria Jose Alonso-De Gennaro, Siavash Mansouri, Madeleine Dorsch, Patricia Munteanu, Balazs Hegedüs, Hauke Winter, Laura V. Klotz, Mark Kriegsmann, Felix JF Herth, Marc A. Schneider, Daniel Kazdal, Albrecht Stenzinger, Alexander Schramm, Felix J. Hartmann, Pavlo Lutsik, Ursula Klingmüller, Rajkumar Savai, Rocio Sotillo, Barbara M. Grüner, Guy Ron, Efrat Shema, Michael Scherer, Christoph Plass, Maria Llamazares-Prada. Y chromosome loss drives cellular plasticity through single-cell epigenetic and transcriptional heterogeneity in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(8_Suppl):Abstract nr LB309.