ArticleNature cancer2024
Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages.
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Article in Nature cancer, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16citing papers in PubMed
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Who cites it
16 citing papers in PubMed.
- Review
- Single-cell transcriptomics profiling elucidates RBP-driven metastatic signaling pathways in ERiScience · 2026Article
- Geospatial genetic evolution and phenotypic plasticity in triple-negative breast cancer.Genome medicine · 2026Article
- Beyond the chaos: How architecture structures tumour biology.The FEBS journal · 2026Review
- Multimodal spatial alignment and morphology mapping with MOSAICField.bioRxiv : the preprint server for biology · 2026Article
- The puppet master in the breast cancer "microecological community": spatial and metabolic regulation of macrophage heterogeneity.Molecular cancer · 2026Review
- Predictive value of peripheral blood cell-free DNA breast cancer gene mutation profiling for postoperative pathological malignancy in BI-RADS 4 breast nodules.Frontiers in genetics · 2026Article
- Circular RNAs in Plasma and Beyond: Potential Biomarkers for Breast Cancer.Oncology research · 2026Review
- Cellular reprogramming during anti-PD-1 and chemotherapy treatment in early-stage primary hormone receptor-positive breast cancer.Nature communications · 2025Article
- Antibody-oligonucleotide conjugates for spatial proteomics: principles, applications, and challenges.Acta biochimica et biophysica Sinica · 2025Article
- Characterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancer.Genome medicine · 2025Article
- KLF5 facilitates lung adenocarcinoma metastasis by regulating the epithelial-mesenchymal transition pathway through RHPN2.Journal of translational medicine · 2025Article
- The Role of Non-Coding Regions in Breast Cancer: From Gene Regulation to Therapeutic Implications.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Single cell sequencing and spatial multiomics of diabetic kidney segmentation insights zonation-specific therapeutic metabolic pathways.Cell insight · 2025Article
- Advancements in the Application of scRNA-Seq in Breast Research: A Review.International journal of molecular sciences · 2024Review
- Phase separation rewires chromatin in breast cancer.Nature cancer · 2024Article
Corrections and comments
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Authors and funding
60 authors.
Michael D Iglesia *Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-0841-2144
Reyka G Jayasinghe *Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-2368-4890
Siqi Chen *Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Nadezhda V Terekhanova *Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
John M Herndon *Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-8378-9654
Erik StorrsDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Alla KarpovaDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-0467-0215
Daniel Cui ZhouDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-7834-2778
Nataly Naser Al DeenDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Andrew T ShinkleDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Rita Jui-Hsien LuDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Wagma CaravanDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-4082-6723
Andrew HoustonDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Yanyan ZhaoDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Kazuhito SatoDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-0589-7454
Preet LalDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Cherease StreetDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA.
Fernanda Martins RodriguesDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-2140-0690
Austin N Southard-SmithDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-0022-6897
André Luiz N Targino da CostaDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Houxiang ZhuDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Chia-Kuei MoDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Lisa CrowsonDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Robert S FultonMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
Matthew A WyczalkowskiDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-4197-551X
Catrina C FronickMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
Lucinda A FultonMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
Hua SunDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-2169-0808
Sherri R DaviesDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-7141-8354
Elizabeth L AppelbaumMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
Sara E ChasnoffDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA.
Madelyn CarmodyDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA.
Candace BrooksDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA.
Ruiyang LiuDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Michael C WendlDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Clara OhDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Diane BenderBursky Center for Human Immunology & Immunotherapy, Washington University in St. Louis, St. Louis, MO, USA.
Carlos CruchagaDepartment of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-0276-2899
Oscar HarariDepartment of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-2635-6975
Andrea BredemeyerDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-2970-5998
Kory LavineDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-1948-9945
Ron BoseDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0003-1977-8894
Julie MargenthalerDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Jason M HeldDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0001-8024-2736
Samuel AchilefuDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
Foluso AdemuyiwaDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-6766-2258
Rebecca AftDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA.
Cynthia MaDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-8156-7492
Graham A ColditzDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-7307-0291
Tao JuDepartment of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA.
Stephen T OhDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-8564-5400
James FitzpatrickWashington University Center for Cellular Imaging, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-7907-3602
E Shelley HwangDepartment of Surgery, Duke University Medical Center, Durham, NC, England.ORCID 0000-0002-8571-1148
Kooresh I ShoghiSiteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
Milan G ChhedaDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0001-8282-9098
Deborah J VeisDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0001-7101-5582
Feng ChenDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0002-2307-7954
Ryan C FieldsDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA.ORCID 0000-0001-6176-8943
William E GillandersDepartment of Surgery, Washington University in St. Louis, St. Louis, MO, USA. gillandersw@wustl.edu.ORCID 0000-0002-0465-3071
Li DingDepartment of Medicine, Washington University in St. Louis, St. Louis, MO, USA. lding@wustl.edu.ORCID 0000-0003-1517-2975
Funding
Washington University Center for Cellular ImagingP30CA091842 · NCI · WASHINGTON UNIVERSITY · PI TIMOTHY J. EBERLEIN · 2001 to 2026
$128.0MMVP Data Integration into the ADSP Phenotype Harmonization ConsortiumU24AG074855 · NIA · VANDERBILT UNIVERSITY MEDICAL CENTER · PI CUCCARO, MICHAEL L, HOHMAN, TIMOTHY J · 2021 to 2025
$37.5MWASHINGTON UNIVERSITY HUMAN TUMOR ATLAS RESEARCH CENTERU2CCA233303 · NCI · WASHINGTON UNIVERSITY · PI DING, LI · 2018 to 2023
$9.7MInvestigating the Functional Impact of AD Risk Genes on Neuro-Vascular InteractionsU01AG072464 · NIA · REGENERATIVE RESEARCH FOUNDATION · PI HARARI, OSCAR, KAMPMANN, MARTIN · 2021 to 2025
$8.7MWASHINGTON UNIVERSITY CO-CLINICAL IMAGING RESEARCH RESOURCEU24CA209837 · NCI · WASHINGTON UNIVERSITY · PI Li Ding, Shunqiang Li · 2017 to 2026
$6.3MSpecification and Function of Tissue Resident and Recruited Macrophages in Cardiac Remodeling and Heart FailureR35HL161185 · NHLBI · WASHINGTON UNIVERSITY · PI Kory J. Lavine · 2022 to 2026
$4.3MMENDELIAN RANDOMIZATION FOR UNBIAS BIOMARKER DISCOVERY FOR AD AND OTHER COMPLEX TRAITSR01AG057777 · NIA · WASHINGTON UNIVERSITY · PI HARARI, OSCAR · 2018 to 2022
$4.1MNANOPHOTOSENSITIZERS FOR REGENERATIVE PHOTOTHERAPYR01CA260855 · NCI · WASHINGTON UNIVERSITY · PI ACHILEFU, SAMUEL · 2021 to 2025
$3.5MFFNP-PET as a predictive biomarker of response to endocrine therapy approaches in advanced breast cancerR01CA273194 · NCI · WASHINGTON UNIVERSITY · PI DEHDASHTI, FARROKH, MA, CYNTHIA X · 2022 to 2025
$3.1MPathogenic Variant Discovery Across a Broad Spectrum of Human DiseasesR01HG009711 · NHGRI · WASHINGTON UNIVERSITY · PI CHEN, FENG, DING, LI · 2017 to 2020
$2.2MHuman iPSC model of Cerebro-Vascular Interactions in ADRDR61NS138655 · NINDS · REGENERATIVE RESEARCH FOUNDATION · PI TEMPLE, SALLY · 2024 to 2024
$1.9MDeep Discovery and Clinical Interpretation of Germline and Somatic Cancer DriversU24CA211006 · NCI · WASHINGTON UNIVERSITY · PI DING, LI, GOVINDAN, RAMASWAMY · 2016 to 2020
$1.8MNCI NIH HHS P30 CA091842NCI NIH HHS R01 CA260855NCI NIH HHS R01 CA273194NCI NIH HHS U24 CA209837NCI NIH HHS U24 CA211006NCI NIH HHS U2C CA233303NHGRI NIH HHS R01 HG009711NHLBI NIH HHS R35 HL161185NIA NIH HHS R01 AG057777NIA NIH HHS R56 AG067764NIA NIH HHS U01 AG072464NIA NIH HHS U24 AG074855NINDS NIH HHS R61 NS138655
Abstract
Breast cancer (BC) is defined by distinct molecular subtypes with different cells of origin. The transcriptional networks that characterize the subtype-specific tumor-normal lineages are not established. In this work, we applied bulk, single-cell and single-nucleus multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 patients with BC to show characteristic links in gene expression and chromatin accessibility between BC subtypes and their putative cells of origin. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal BC and luminal mature cells and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like (SOX6 and KCNQ3) and luminal A/B (FAM155A and LRP1B) lineages. Exhausted CTLA4-expressing CD8
Indexed as
Breast NeoplasmsChromatinGene Expression Regulation, NeoplasticCD8-Positive T-LymphocytesCell LineageFemaleGene Regulatory NetworksHumansSingle-Cell AnalysisChromatin
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