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A spatially resolved single-cell genomic atlas of the adult human breast

Author

Listed:
  • Tapsi Kumar

    (UT MD Anderson Cancer Center
    University of Texas MD Anderson Cancer Center)

  • Kevin Nee

    (University of California, Irvine)

  • Runmin Wei

    (UT MD Anderson Cancer Center)

  • Siyuan He

    (UT MD Anderson Cancer Center
    University of Texas MD Anderson Cancer Center)

  • Quy H. Nguyen

    (University of California, Irvine)

  • Shanshan Bai

    (UT MD Anderson Cancer Center)

  • Kerrigan Blake

    (University of California, Irvine
    University of California, Irvine)

  • Maren Pein

    (University of California, Irvine
    University of California, Irvine)

  • Yanwen Gong

    (University of California, Irvine
    University of California, Irvine)

  • Emi Sei

    (UT MD Anderson Cancer Center)

  • Min Hu

    (UT MD Anderson Cancer Center)

  • Anna K. Casasent

    (UT MD Anderson Cancer Center)

  • Aatish Thennavan

    (UT MD Anderson Cancer Center)

  • Jianzhuo Li

    (UT MD Anderson Cancer Center)

  • Tuan Tran

    (UT MD Anderson Cancer Center)

  • Ken Chen

    (UT MD Anderson Cancer Center)

  • Benedikt Nilges

    (Resolve Biosciences)

  • Nachiket Kashikar

    (Resolve Biosciences)

  • Oliver Braubach

    (Akoya Biosciences)

  • Bassem Cheikh

    (Akoya Biosciences)

  • Nadya Nikulina

    (Akoya Biosciences)

  • Hui Chen

    (UT MD Anderson Cancer Center)

  • Mediget Teshome

    (UT MD Anderson Cancer Center)

  • Brian Menegaz

    (Baylor Medical College)

  • Huma Javaid

    (Baylor Medical College)

  • Chandandeep Nagi

    (Baylor Medical College)

  • Jessica Montalvan

    (Baylor Medical College)

  • Tatyana Lev

    (University of California, Irvine
    University of California, Irvine)

  • Sharmila Mallya

    (University of California, Irvine)

  • Delia F. Tifrea

    (University of California, Irvine)

  • Robert Edwards

    (University of California, Irvine)

  • Erin Lin

    (University of California, Irvine)

  • Ritesh Parajuli

    (University of California, Irvine)

  • Summer Hanson

    (University of Chicago Medicine)

  • Sebastian Winocour

    (Baylor College of Medicine)

  • Alastair Thompson

    (Baylor College of Medicine)

  • Bora Lim

    (Baylor College of Medicine)

  • Devon A. Lawson

    (University of California, Irvine)

  • Kai Kessenbrock

    (University of California, Irvine)

  • Nicholas Navin

    (UT MD Anderson Cancer Center
    University of Texas MD Anderson Cancer Center
    UT MD Anderson Cancer Center)

Abstract

The adult human breast is comprised of an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue1–3. Although most previous studies have focused on the breast epithelial system4–6, many of the non-epithelial cell types remain understudied. Here we constructed the comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics study profiled 714,331 cells from 126 women, and 117,346 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states. These data reveal abundant perivascular, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide a reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.

Suggested Citation

  • Tapsi Kumar & Kevin Nee & Runmin Wei & Siyuan He & Quy H. Nguyen & Shanshan Bai & Kerrigan Blake & Maren Pein & Yanwen Gong & Emi Sei & Min Hu & Anna K. Casasent & Aatish Thennavan & Jianzhuo Li & Tua, 2023. "A spatially resolved single-cell genomic atlas of the adult human breast," Nature, Nature, vol. 620(7972), pages 181-191, August.
    • Handle: RePEc:nat:nature:v:620:y:2023:i:7972:d:10.1038_s41586-023-06252-9
    DOI: 10.1038/s41586-023-06252-9
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    Cited by:

    1. Chunman Zuo & Junjie Xia & Luonan Chen, 2024. "Dissecting tumor microenvironment from spatially resolved transcriptomics data by heterogeneous graph learning," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Quentin Blampey & Kevin Mulder & Margaux Gardet & Stergios Christodoulidis & Charles-Antoine Dutertre & Fabrice André & Florent Ginhoux & Paul-Henry Cournède, 2024. "Sopa: a technology-invariant pipeline for analyses of image-based spatial omics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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