ArticleCell2023
Archival single-cell genomics reveals persistent subclones during DCIS progression.
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Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43citing papers in PubMed
11.5field-weighted citation impact, top 1% of its field
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Who cites it
43 citing papers in PubMed, 48 citations in OpenAlex.
- Integrated Multi-Omics Reveals Cellular States and Microenvironmental Remodeling in Coexisting DCIS and IDC.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A single-cell lens into the co-evolution of genotypes and phenotypes in cancer.Nature reviews. Cancer · 2026Review
- Diagnosis of Extensive DCIS with Progressive Microcalcifications over a Period of 11 Years.Diagnostics (Basel, Switzerland) · 2026Article
- scAmp enables focal gene amplification analysis from single-cell data.Nature communications · 2026Article
- A medium throughput approach for single cell copy number variation sequencing towards efficient application in clinics.Journal of advanced research · 2026Article
- Tumor evolution: signaling pathways, molecular mechanisms and therapeutic targets.Signal transduction and targeted therapy · 2026Review
- Single cell spatial transcriptomics track the evolutionary hierarchy and microenvironment remodeling during breast carcinoma invasion.Nature communications · 2026Article
- Transcriptome predictors of second breast events in ductal carcinoma in situ: a case‒control study including Black and White women.Breast cancer research : BCR · 2026Article
- Evolution of oncogene amplification across 86,000 cancer cell genomes.bioRxiv : the preprint server for biology · 2026Article
- Review
- Enforced ZFP281 expression delays breast cancer initiation and can provide lifelong protection against breast cancer metastasis.bioRxiv : the preprint server for biology · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations.Scientific reports · 2026Article
- scAmp analyzes focal gene amplifications at single-cell resolution.bioRxiv : the preprint server for biology · 2026Article
- Probing the Feasibility of Single-Cell Fixed RNA Sequencing from FFPE Tissue.International journal of molecular sciences · 2026Article
- Genomic evolution of pancreatic cancer at single-cell resolution.Nature genetics · 2026Article
- Review
- Targeting the PRMT1 axis in cancer: from epigenetic plasticity to contextual therapeutic interventions.Frontiers in oncology · 2026Review
- Spatially Discontinuous Mutation Topographies in Ductal Carcinoma In Situ Reveal Noncompetitive Growth Dynamics.Cancer research · 2025Article
- scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.Nature communications · 2025Article
Corrections and comments
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Authors and funding
33 authors at 6 institutions in 3 countries.
Kaile WangDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Tapsi KumarDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Junke WangDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
Darlan Conterno MinussiDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
Emi SeiDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Jianzhuo LiDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Tuan M TranDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Aatish ThennavanDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Min HuDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Anna K CasasentDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Zhenna XiaoDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Shanshan BaiDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Lei YangDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
Lorraine M KingDepartment of Surgery, Duke University School of Medicine, Durham, NC 27707, USA.
Vandna ShahSchool of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK.
Petra KristelDivision of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands.
Carolien L van der BordenDivision of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands.
Jeffrey R MarksDepartment of Surgery, Duke University School of Medicine, Durham, NC 27707, USA.
Yuehui ZhaoDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Amado J ZuritaDepartment of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
Ana AparicioDepartment of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
Brian ChapinDepartment of Urology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Jie YeDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Jianjun ZhangDepartment of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Don L GibbonsDepartment of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
Grand Challenge PRECISION ConsortiumGrand Challenge PRECISION Consortium, Cancer Research UK & KWF Dutch Cancer Foundation.
Ellinor SawyerSchool of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK.
Alastair M ThompsonDepartment of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Andrew FutrealDepartment of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
E Shelley HwangDepartment of Surgery, Duke University School of Medicine, Durham, NC 27707, USA.
Jelle WesselingDepartment of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands.
Esther H LipsDepartment of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands.
Nicholas E NavinDepartment of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Bioinformatics, UT MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: nnavin@mdanderson.org.
The University of Texas MD Anderson Cancer Center · USDuke University · USKing's College London · GBLeiden University Medical Center · NLThe Netherlands Cancer Institute · NLBaylor College of Medicine · US
Funding
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8MDELINEATING THE EVOLUTION AND ECOLOGY OF CHEMORESISTANCE IN BREAST CANCER WITH SINGLE CELL GENOMICSR01CA236864 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI NAVIN, NICHOLAS · 2020 to 2024
$2.3M(PQC3) Genomic Diversity and Microenvironment as Drivers of Metastasis in DCISR01CA185138 · NCI · DUKE UNIVERSITY · PI HWANG, E.SHELLEY, MALEY, CARLO · 2014 to 2017
$2.0MINVESTIGATING TUMOR INITIATION AND INVASION IN PREMALIGNANT BREAST CANCER WITH SPATIAL SINGLE CELL GENOMICSR01CA240526 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI NAVIN, NICHOLAS · 2019 to 2023
$1.8MCancer Research UK C38317/A24043NCI NIH HHS P30 CA016672NCI NIH HHS R01 CA185138NCI NIH HHS R01 CA236864NCI NIH HHS R01 CA240526
Abstract
Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.
Indexed as
Breast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, Intraductal, NoninfiltratingCell Line, TumorDisease ProgressionFemaleGenomicsHumansSingle-Cell Gene Expression Analysisarchival samplesArc-wellbreast cancerductal carcinoma in situ recurrenceFFPE materialpremalignanciessingle-cell DNA sequencingtumor evolution
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