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

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, Tuan Tran, Ken Chen, Benedikt Nilges, Nachiket Kashikar, Oliver Braubach, Bassem Cheikh, Nadya Nikulina, Hui Chen, Mediget Teshome, Brian Menegaz, Huma Javaid, Chandandeep Nagi, Jessica Montalvan, Tatyana Lev, Sharmila Mallya, Delia F. Tifrea, Robert Edwards, Erin Lin, Ritesh Parajuli, Summer Hanson, Sebastian Winocour, Alastair Thompson, Bora Lim, Devon A. Lawson (), Kai Kessenbrock () and Nicholas Navin ()
Additional contact information
Tapsi Kumar: UT MD Anderson Cancer Center
Kevin Nee: University of California, Irvine
Runmin Wei: UT MD Anderson Cancer Center
Siyuan He: UT MD Anderson Cancer Center
Quy H. Nguyen: University of California, Irvine
Shanshan Bai: UT MD Anderson Cancer Center
Kerrigan Blake: University of California, Irvine
Maren Pein: University of California, Irvine
Yanwen Gong: 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
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

Nature, 2023, vol. 620, issue 7972, 181-191

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41586-023-06252-9

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