Cellular and transcriptional diversity over the course of human lactation

• Type of Material: Article
• Authors: Sarah K Nyquist, Broad Institute of MIT and Harvard; Patricia Gao, Massachusetts Institute of Technology; Tessa KJ Haining, Massachusetts Institute of Technology; Michael R Retchin, Massachusetts Institute of Technology; Yarden Golan, University of California, San Francisco; Riley S Drake, Broad Institute of MIT and Harvard, Cambridge; Kellie Kolb, Broad Institute of MIT and Harvard, Cambridge; Benjamin E Mead, Broad Institute of MIT and Harvard, Cambridge; Nadav Ahituv, University of California, San Francisco; Micaela Martinez, Emory University; Alex K Shalek, Broad Institute of MIT and Harvard, Cambridge; Bonnie Berger, Broad Institute of MIT and Harvard, Cambridge; Brittany A Goods, Thayer School of Engineering, Program in Quantitative Biomedical Sciences, Dartmouth College
• Language: English
• Date: 2022-04-12
• Publisher: National Academy of Science
• Publication Version: Final Published Version
• Copyright Statement: © 2022 the Author(s). Published by PNAS.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1073/pnas.2121720119
• Title of Journal or Parent Work: Proceedings of the National Academy of Sciences of the United States of America
• Volume: 119
• Issue: 15
• Start Page: e2121720119
• End Page: e2121720119
• Grant/Funding Information: M.E.M. was supported by Columbia University Office of the Provost grants for junior faculty who contribute to the diversity goals of the University.; Y.G. was supported by the Weizmann Institute of Science National Postdoctoral Award Program for Advancing Women in Science, the International Society for Research In Human Milk and Lactation Trainee Bridge Fund, and of the Human Frontier Science Program.; B.A.G. was supported by National Research Service Award postdoctoral Fellowship (F32-AI136459).; S.K.N. was supported by National Science Foundation Graduate Research Fellowship 1122374 and was partially funded by NIH R01HG010959 (to B.B.).; A.K.S. was supported, in part, by the Beckman Young Investigator Program, a Sloan Fellowship in Chemistry, and the Massachusetts Institute of Technology (Charles E. Reed Faculty Initiative).; B.E.M. was supported by a Massachusetts Institute of Technology-GlaxoSmithKline Gertrude B. Elion postdoctoral fellowship.
• Keywords: single-cell RNA-sequencing; macrophage; breast milk; Transcriptome; Gene Expression Profiling; Milk, Human; Female; Breast Feeding; Humans; mammary epithelial cell; maternal health; Lactation; RNA-Seq
• Research Categories: Computer Science; Biology, General

Abstract

Human breast milk (hBM) is a dynamic fluid that contains millions of cells, but their identities and phenotypic properties are poorly understood. We generated and analyzed single-cell RNA-sequencing (scRNA-seq) data to characterize the transcriptomes of cells from hBM across lactational time from 3 to 632 d postpartum in 15 donors. We found that the majority of cells in hBM are lactocytes, a specialized epithelial subset, and that cell-type frequencies shift over the course of lactation, yielding greater epithelial diversity at later points. Analysis of lactocytes reveals a continuum of cell states characterized by transcriptional changes in hormone-, growth factor-, and milk production-related pathways. Generalized additive models suggest that one subcluster, LC1 epithelial cells, increases as a function of time postpartum, daycare attendance, and the use of hormonal birth control. We identify several subclusters of macrophages in hBM that are enriched for tolerogenic functions, possibly playing a role in protecting the mammary gland during lactation. Our description of the cellular components of breast milk, their association with maternal–infant dyad metadata, and our quantification of alterations at the gene and pathway levels provide a detailed longitudinal picture of hBM cells across lactational time. This work paves the way for future investigations of how a potential division of cellular labor and differential hormone regulation might be leveraged therapeutically to support healthy lactation and potentially aid in milk production.