ArticleNature medicine2024
Single-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry.
Article in Nature medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution.Nature metabolism · 2025Guideline
- ELISA (Embedding-Linked Interactive Single-cell Agent): an interpretable hybrid generative Artificial Intelligence agent for expression-grounded discovery in single-cell genomics.Briefings in bioinformatics · 2026Article
- Single-nucleus RNA sequencing reveals cell type-specific responses to heat stress in bovine mammary gland.Journal of animal science and biotechnology · 2026Article
- Adipocyte-rich microenvironment promotes TNBC progression through SIRT6-associated ACSL5 dysregulation and lipid storage-associated phenotypes.Journal of experimental & clinical cancer research : CR · 2026Article
- Shortcomings of silhouette in single-cell integration benchmarking.Nature biotechnology · 2026Article
- SOX9 and SEMA7A regulate cell plasticity in the postpartum mammary gland with implications for breast cancer.bioRxiv : the preprint server for biology · 2026Article
- Defining breast epithelial cell types in the single-cell era.Developmental cell · 2025Review
- Spatial Transcriptomics Decodes Breast Cancer Microenvironment Heterogeneity: From Multidimensional Dynamic Profiling to Precision Therapy Blueprint Construction.Biomolecules · 2025Review
- Genetic Ancestry, Intrinsic Tumor Subtypes, and Breast Cancer Survival in Latin American Women.Cancer research communications · 2025Article
- scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration.Genome biology · 2025Article
- MammOnc-DB, an integrative breast cancer data analysis platform for target discovery.NPJ breast cancer · 2025Article
- Myeloid-driven immunosuppression in head and neck cancer: single-cell ATAC/RNA and spatial transcriptomic perspectives.Frontiers in oncology · 2025Review
- Advancements in the Application of scRNA-Seq in Breast Research: A Review.International journal of molecular sciences · 2024Review
- A triple hormone receptor ER, AR, and VDR signature is a robust prognosis predictor in breast cancer.Breast cancer research : BCR · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
15 authors.
Funding
Abstract
Single-nucleus analysis allows robust cell-type classification and helps to establish relationships between chromatin accessibility and cell-type-specific gene expression. Here, using samples from 92 women of several genetic ancestries, we developed a comprehensive chromatin accessibility and gene expression atlas of the breast tissue. Integrated analysis revealed ten distinct cell types, including three major epithelial subtypes (luminal hormone sensing, luminal adaptive secretory precursor (LASP) and basal-myoepithelial), two endothelial and adipocyte subtypes, fibroblasts, T cells, and macrophages. In addition to the known cell identity genes FOXA1 (luminal hormone sensing), EHF and ELF5 (LASP), TP63 and KRT14 (basal-myoepithelial), epithelial subtypes displayed several uncharacterized markers and inferred gene regulatory networks. By integrating breast epithelial cell gene expression signatures with spatial transcriptomics, we identified gene expression and signaling differences between lobular and ductal epithelial cells and age-associated changes in signaling networks. LASP cells and fibroblasts showed genetic ancestry-dependent variability. An estrogen receptor-positive subpopulation of LASP cells with alveolar progenitor cell state was enriched in women of Indigenous American ancestry. Fibroblasts from breast tissues of women of African and European ancestry clustered differently, with accompanying gene expression differences. Collectively, these data provide a vital resource for further exploring genetic ancestry-dependent variability in healthy breast biology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.