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We profiled plasma-derived cell-free DNA methylation and extracellular vesicle-associated microRNAs from 79 patients with metastatic NSCLC treated with immune checkpoint inhibitors (ICIs). High-dimensional omics data were integrated using Multi-Omics Factor Analysis (MOFA2) to uncover latent molecular subtypes, which we termed MOFA-Derived Clusters (MDCs), independently established at baseline (MDC-T1) and post-second cycle (MDC-T2). Differential expression and methylation analyses, pathway enrichment, and immune phenotyping via flow cytometry were used to characterize the molecular and immunological landscape of each MDC. External validation was performed using independent NSCLC cohorts for miRNAs (Genova\n                      <jats:italic>et al<\/jats:italic>\n                      , 2024, n=54) and methylation (SMC Cohort, GSE119144, n=57).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>MDCs captured divergent survival outcomes and reflected biologically coherent processes including angiogenesis, cytoskeletal remodeling, and immune signaling. Projection of MDCs onto later time points (T3, T4) supported the temporal relevance of early molecular signatures. MDCs also displayed immunological correlates via circulating immune cell subsets. Importantly, MDC classifiers demonstrated consistent survival stratification in external cohorts, particularly MDC-T2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>This study defines a multiomic, liquid biopsy-based framework for molecular subtyping in NSCLC to manage ICI treatment. Our MDC signatures reveal clinically meaningful, treatment-informative biology and offer a path toward minimally invasive patient stratification in immuno-oncology.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1136\/jitc-2025-013592","type":"journal-article","created":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T19:15:30Z","timestamp":1768590930000},"page":"e013592","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":6,"title":["Integrative multiomic profiling of cfDNA methylation and EV-miRNAs identifies immunotherapy-outcome molecular subtypes in NSCLC"],"prefix":"10.1136","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8976-8099","authenticated-orcid":false,"given":"Juan Luis","family":"Onieva","sequence":"first","affiliation":[{"name":"Group of Translational Research in Cancer Immunotherapy and Epigenetics (B-05), Medical Oncology Unit of Virgen de la Victoria Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"},{"name":"Facultad de Medicina, Campus de Teatinos s\/n, Universidad de M\u00e1laga, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"P\u00e9rez-Ruiz","sequence":"additional","affiliation":[{"name":"Medical Oncology Unit of Regional University Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"},{"name":"Group of Translational Research in Cancer Immunotherapy and Epigenetics (B-05), IBIMA Plataforma Bionand, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura Cristina","family":"Figueroa-Ortiz","sequence":"additional","affiliation":[{"name":"Group of Translational Research in Cancer Immunotherapy and Epigenetics (B-05), Medical Oncology Unit of Virgen de la Victoria Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"},{"name":"Facultad de Medicina, Campus de Teatinos s\/n, Universidad de M\u00e1laga, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Miguel","family":"Jurado","sequence":"additional","affiliation":[{"name":"Medical Oncology Unit of Regional University Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5664-5535","authenticated-orcid":false,"given":"Beatriz","family":"Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Group of Translational Research in Cancer Immunotherapy and Epigenetics (B-05), Medical Oncology Unit of Virgen de la Victoria Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Carlos Ben\u00edtez","sequence":"additional","affiliation":[{"name":"Group of Translational Research in Cancer Immunotherapy and Epigenetics (B-05), Medical Oncology Unit of Virgen de la Victoria Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Rueda-Dom\u00ednguez","sequence":"additional","affiliation":[{"name":"Group of Translational Research in Cancer Immunotherapy and Epigenetics (B-05), Medical Oncology Unit of Virgen de la Victoria Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"},{"name":"Facultad de Medicina, Campus de Teatinos s\/n, Universidad de M\u00e1laga, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8586-6502","authenticated-orcid":false,"given":"Isabel","family":"Barrag\u00e1n","sequence":"additional","affiliation":[{"name":"Group of Translational Research in Cancer Immunotherapy and Epigenetics (B-05), Medical Oncology Unit of Virgen de la Victoria Hospital, IBIMA Plataforma Bionand, M\u00e1laga, Spain"},{"name":"Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden"},{"name":"Precision Cancer Medicine in Lung Cancer - Preclinical, Translational & Clinical Research \u2013 Simon Ekman's research group. 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