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RNA-sequencing of milk cells extracted from pre-partum secretions and longitudinally from mature human milk across the first year of lactation

ABSTRACT: Changes in mammary cell behavior mediating normal breast development during pregnancy and lactation are poorly understood due to limited availability of breast biopsies during this time. Human milk contains a hierarchy of cells including stem cells, mature milk producing cells (lactocytes) and myoepithelial cells. Here we non-invasively sampled the total epithelial cell population of the lactating mammary gland from mature HM collected from healthy mother/infant dyads during the first year postpartum, and explored temporal changes in the mammary cell transcriptome using RNA sequencing. Comparisons were done with mammary secretions from late pregnancy from the same women and with purchased resting mammary tissue. Distinct gene signatures were found for the different mammary developmental stages examined. Cell adhesion pathways were differentially regulated between the resting gland and pregnancy, whereas immune cell signaling and morphogenesis/cancer pathways differed between lactation and pregnancy or the resting gland, respectively. The transcriptome of lactation remained consistent in the first year postpartum in these successfully lactating women. The gene signatures characteristic of HM cells confirmed lactation genes previously reported in animal models and the HM fat globule. This study identifies key genes and molecular pathways undergoing controlled regulation as the mammary gland transitions from a quiescent into a functional organ, providing experimental targets for the molecular investigation of mammary gland pathologies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85494 | GEO | 2018/12/26

REPOSITORIES: GEO

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Project description:Studies of normal human mammary gland development and function have mostly relied on cell culture, limited surgical specimens, and rodent models. Although RNA extracted from human milk has been used to assay the mammary transcriptome non-invasively, the transcriptome derived from the milk fat layer has not been compared with the mammary-derived transcriptome nor have sources of RNA been quantified in milk. In this study the effects of milk collection and processing on RNA quality and origin were assessed in humans and rhesus macaques. Total RNA in milk was quantitated in acridine orange-stained milk using an automated whole slide scanner and custom-built Globulator software. Total RNA extracted from milk fat, cells in milk, and mammary biopsies of lactating rhesus macaques were compared using RNA sequencing and analysis. Compared with human milk, milk from macaques contained similar amounts of RNA-containing cytoplasmic crescents, but more cells. Total RNA extracted from milk fractions was also evaluated for factors that affect RNA quality. Degradation of RNA extracted from human milk fat was positively correlated with geographic distance from collection site, storage time, and sample type. There were no differences in RNA degradation in macaque milk collected after 10 min or 4 hr accumulation, suggesting that degradation of RNA extracted from milk fat may not occur in the mammary gland. Using RNA-Seq, RNA extracted from macaque milk fat and cells in milk more accurately represented RNA from mammary epithelial cells (cells that produce milk) than did RNA from mammary tissue. Mammary epithelium-specific transcripts were more abundant in macaque milk fat whereas adipose or stroma-specific transcripts were more abundant in mammary tissue. Functional analyses confirmed the validity of milk as a source of RNA from mammary epithelial cells. Analysis of highly abundant putative microRNAs in macaque milk fat revealed a potentially novel non-coding RNA species that is conserved in humans. RNA extracted from the milk fat during lactation accurately portrayed the RNA profile of milk-producing mammary epithelial cells. However, this sample type clearly requires protocols that minimize RNA degradation. Transcript profiles from milk cells, milk fat, and mammary tissue from 6 lactating rhesus macaques at 30 and 90 days lactation; 34 samples run in triplicate

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RNA-sequencing of milk cells extracted from pre-partum secretions and longitudinally from mature human milk across the first year of lactation

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