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To systematically chart cancer-intrinsic regulatory programs, we constructed a pan-cancer single-cell transcriptomic and epigenomic atlas encompassing 60 human cell lines representing 16 tissue origins and 20 cancer types, comprising 240,957 single-nucleus RNA-seq and 223,347 single-nucleus ATAC-seq profiles. Integrative analyses revealed extensive pan-cancer cell-state heterogeneity, core gene-regulatory networks, and a conserved epithelial-mesenchymal transition (EMT) axis that transcends tissue of origin. Copy-number variation analysis identified transcription factor amplification and downstream hyperactivation as key drivers of cancer cell-state reprogramming. To further examine how regulatory programs diverge within a cancer lineage and contribute to clinically divergent outcomes, we performed a focused comparison of cutaneous melanoma with acral melanoma, a rare, UV-independent subtype underrepresented in existing pan-cancer atlases. The comparison uncovered a universal inflammation-suppressive program in acral melanoma and an inflamed regulatory landscape in cutaneous melanoma, with the JAK-STAT pathway and downstream transcriptional responses as central discriminators. Integration of single-cell and bulk datasets across models and patient cohorts further linked in vitro tumor-intrinsic gene regulations with in vivo microenvironmental composition and immunotherapy responses. Together, by extending single-cell multi-omic profiling to rare alongside common cancer subtypes, this atlas offers a resource for mapping pan-cancer and subtype-specific gene-regulatory programs that shape cancer cell-state plasticity.<\/jats:p>","DOI":"10.64898\/2026.05.31.729161","type":"posted-content","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T23:05:13Z","timestamp":1780527913000},"source":"Crossref","is-referenced-by-count":0,"title":["Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9317-9279","authenticated-orcid":false,"given":"Zihan","family":"Xu","sequence":"first","affiliation":[{"name":"Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA"},{"name":"The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9450-3092","authenticated-orcid":false,"given":"Aileen","family":"Ugurbil","sequence":"additional","affiliation":[{"name":"Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA"},{"name":"The Tri-Institutional M.D.-Ph. 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