{"doi":"10.1101/2023.07.23.550157","title":"Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery","abstract":"Although three-dimensional (3D) genome structures are altered in cancer cells, little is known about how these changes evolve and diversify during cancer progression. Leveraging genome-wide chromatin tracing to visualize 3D genome folding directly in tissues, we generated 3D genome cancer atlases of murine lung and pancreatic adenocarcinoma. Our data reveal stereotypical, non-monotonic, and stage-specific alterations in 3D genome folding heterogeneity, compaction, and compartmentalization as cancers progress from normal to preinvasive and ultimately to invasive tumors, discovering a potential structural bottleneck in early tumor progression. Remarkably, 3D genome architectures distinguish histologic cancer states in single cells, despite considerable cell-to-cell heterogeneity. Gene-level analyses of evolutionary changes in 3D genome compartmentalization not only showed compartment-associated genes are more homogeneously regulated, but also elucidated prognostic and dependency genes in lung adenocarcinoma and a previously unappreciated role for polycomb-group protein Rnf2 in 3D genome regulation. Our results demonstrate the utility of mapping the single-cell cancer 3D genome in tissues and illuminate its potential to identify new diagnostic, prognostic, and therapeutic biomarkers in cancer.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":396912,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.6289,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":666342,"name":"Shengyan Jin","orcid":"0000-0002-8667-7586","position":1,"is_corresponding":false},{"id":1172958,"name":"Sherry S. Agabiti","orcid":null,"position":2,"is_corresponding":false},{"id":706157,"name":"Tyler B Jensen","orcid":"0000-0003-0220-4026","position":3,"is_corresponding":false},{"id":1161530,"name":"Tianqi Yang","orcid":"0009-0005-1864-8280","position":4,"is_corresponding":false},{"id":270681,"name":"Jonathan S. D. Radda","orcid":"0000-0002-2242-9604","position":5,"is_corresponding":false},{"id":722956,"name":"Christian Ruiz","orcid":"0000-0003-1470-8061","position":6,"is_corresponding":false},{"id":1043746,"name":"Gabriel Baldissera","orcid":null,"position":7,"is_corresponding":false},{"id":804343,"name":"Moein Rajaei","orcid":"0009-0006-7079-2033","position":8,"is_corresponding":false},{"id":447165,"name":"Jeffrey P. Townsend","orcid":"0000-0002-9890-3907","position":9,"is_corresponding":false},{"id":254927,"name":"Mandar D. Muzumdar","orcid":"0000-0001-7424-7223","position":10,"is_corresponding":false},{"id":270684,"name":"Siyuan Wang","orcid":"0000-0001-6550-4064","position":11,"is_corresponding":false},{"id":494428,"name":"Miao Liu","orcid":"0000-0002-7975-6702","position":0,"is_corresponding":true}],"reference_count":119,"raw_metadata":null,"created_at":"2026-07-19T01:19:35.497854Z","pmid":"37546882","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}