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 Ben 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; Nicholas Navin

doi:10.1038/s41586-023-06252-9

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 Ben CheikhNadya 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, Nicholas Navin

Research output: Contribution to journal › Article › peer-review

18 Scopus citations

Abstract

The adult human breast is comprised of an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue^1–3. Although most previous studies have focused on the breast epithelial system^4–6, 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.

Original language	English (US)
Pages (from-to)	181-191
Number of pages	11
Journal	Nature
Volume	620
Issue number	7972
DOIs	https://doi.org/10.1038/s41586-023-06252-9
State	Published - Aug 3 2023

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Kumar, T., Nee, K., Wei, R., He, S., Nguyen, Q. H., Bai, S., Blake, K., Pein, M., Gong, Y., Sei, E., Hu, M., Casasent, A. K., Thennavan, A., Li, J., Tran, T., Chen, K., Nilges, B., Kashikar, N., Braubach, O., ... Navin, N. (2023). A spatially resolved single-cell genomic atlas of the adult human breast. Nature, 620(7972), 181-191. https://doi.org/10.1038/s41586-023-06252-9

Kumar, T, Nee, K, Wei, R, He, S, Nguyen, QH, Bai, S, Blake, K, Pein, M, Gong, Y, Sei, E, Hu, M, Casasent, AK, Thennavan, A, Li, J, Tran, T, Chen, K, Nilges, B, Kashikar, N, Braubach, O, Ben Cheikh, B, Nikulina, N, Chen, H, Teshome, M, Menegaz, B, Javaid, H, Nagi, C, Montalvan, J, Lev, T, Mallya, S, Tifrea, DF, Edwards, R, Lin, E, Parajuli, R, Hanson, S, Winocour, S, Thompson, A, Lim, B, Lawson, DA, Kessenbrock, K & Navin, N 2023, 'A spatially resolved single-cell genomic atlas of the adult human breast', Nature, vol. 620, no. 7972, pp. 181-191. https://doi.org/10.1038/s41586-023-06252-9

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title = "A spatially resolved single-cell genomic atlas of the adult human breast",

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.",

author = "Tapsi Kumar and Kevin Nee and Runmin Wei and Siyuan He and Nguyen, {Quy H.} and Shanshan Bai and Kerrigan Blake and Maren Pein and Yanwen Gong and Emi Sei and Min Hu and Casasent, {Anna K.} and Aatish Thennavan and Jianzhuo Li and Tuan Tran and Ken Chen and Benedikt Nilges and Nachiket Kashikar and Oliver Braubach and {Ben Cheikh}, Bassem and Nadya Nikulina and Hui Chen and Mediget Teshome and Brian Menegaz and Huma Javaid and Chandandeep Nagi and Jessica Montalvan and Tatyana Lev and Sharmila Mallya and Tifrea, {Delia F.} and Robert Edwards and Erin Lin and Ritesh Parajuli and Summer Hanson and Sebastian Winocour and Alastair Thompson and Bora Lim and Lawson, {Devon A.} and Kai Kessenbrock and Nicholas Navin",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive licence to Springer Nature Limited.",

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month = aug,

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doi = "10.1038/s41586-023-06252-9",

language = "English (US)",

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AU - Kumar, Tapsi

AU - Nee, Kevin

AU - Wei, Runmin

AU - He, Siyuan

AU - Nguyen, Quy H.

AU - Bai, Shanshan

AU - Blake, Kerrigan

AU - Pein, Maren

AU - Gong, Yanwen

AU - Sei, Emi

AU - Hu, Min

AU - Casasent, Anna K.

AU - Thennavan, Aatish

AU - Li, Jianzhuo

AU - Tran, Tuan

AU - Chen, Ken

AU - Nilges, Benedikt

AU - Kashikar, Nachiket

AU - Braubach, Oliver

AU - Ben Cheikh, Bassem

AU - Nikulina, Nadya

AU - Chen, Hui

AU - Teshome, Mediget

AU - Menegaz, Brian

AU - Javaid, Huma

AU - Nagi, Chandandeep

AU - Montalvan, Jessica

AU - Lev, Tatyana

AU - Mallya, Sharmila

AU - Tifrea, Delia F.

AU - Edwards, Robert

AU - Lin, Erin

AU - Parajuli, Ritesh

AU - Hanson, Summer

AU - Winocour, Sebastian

AU - Thompson, Alastair

AU - Lim, Bora

AU - Lawson, Devon A.

AU - Kessenbrock, Kai

AU - Navin, Nicholas

PY - 2023/8/3

Y1 - 2023/8/3

N2 - 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.

AB - 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.

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

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