Aging-associated alterations in the mammary gland revealed by single-cell RNA sequencing

Abstract

Aging of the mammary gland is closely associated with increased susceptibility to diseases such as cancer, but there have been limited systematic studies of aging-induced alterations within this organ. We performed high-throughput single-cell RNA-sequencing (scRNA-seq) profiling of mammary tissues from young and old nulliparous mice, including both epithelial and stromal cell types. Our analysis identified altered proportions and distinct gene expression patterns in numerous cell populations as a consequence of the aging process, independent of parity and lactation. In addition, we detected a subset of luminal cells that express both hormone-sensing and alveolar markers and decrease in relative abundance with age. These data provide a high-resolution landscape of aging mammary tissues, with potential implications for normal tissue functions and cancer predisposition.

Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland

“…S10D). Further analysis utilizing classic lineage markers confirmed the B-cell identity of hTM11, in addition to predicting identities of epithelial clusters hTM4, hTM6, hTM8 and hTM10 (EPCAM + , KRT8 + and KRT5 +) and non-epithelial clusters, based on the expression of immune markers (CD3E, Granzyme A (GZMA), Serpin Family E Member 1 (SER-PINE1), A Receptor Tyrosine Kinase (AXL) and HEXB, endothelial markers CLDN5 [13,27,77,[99][100][101][102][103][104], fibroblasts marker Myocilin (MYOC) [105], and adipocytes markers Gap Junction Protein Alpha 4 (GJA4), and Procollagen C-Endopeptidase Enhancer (PCOLCE) [106,107]. We also noted that some lineage specific markers of non-epithelial cells were expressed by epithelial lineages, such as HEXB and AXL (Supplementary Fig.…”

Mammary gland development from a single cell ‘omics view

“…Detailed discussion on this study, together with other early mammary scRNA-seq studies that classified new cell types based on expression of markers such as c-Kit ( Kit ), can be found in [92] . A more recent study in mice also found a hybrid luminal cell subpopulation, which expressed genes characteristic of both hormone sensing (HS) and alveolar progenitors (AV) termed HS-AV cells, which decreased with age [93] . Both the described “intermediate” [72] and “HS-AV” [93] luminal cells expressed higher levels of Prlr and Cited than luminal progenitor/alveolar cells, and higher levels of Csn3 and Trf than hormone responsive cells.…”

Mammary ductal epithelium controls cold-induced adipocyte thermogenesis

“…We integrated our data set with eight other publicly available single cell data sets, from both SVF and mammary gland tissues including Tabula Muris and Tabula Muris Senis (Fig. 1B and Table 1) 12–15 for i) cell type validation, ii) to increase confidence in projected cell type, iii) sex and age differences, and iv) mammary gland development (Fig. 1B).…”

“…Within each identified cell type, cold treated and room temperature single cells were compared for differential gene expression using Seurat’s FindMarkers function (Wilcoxon rank sum test) in a manner similar to Li et al 15 . Differentially expressed genes were identified using two criteria: (i) an expression difference of >= 1.5 fold and adjusted p-value < 0.05 in a grouped analysis between room temperature mice (n = 2) and cold treated mice (n = 2); (ii) an expression difference of >= 1.25 fold and consistent fold change direction in all 4 possible pairwise combinations of cold-treated vs room temperature mice.…”

“…Within each identified cell type, cold treated and room temperature single cells were compared for differential gene expression using Seurat's FindMarkers function (Wilcoxon rank sum test) in a manner similar to Li et al 15 . Differentially expressed genes were identified using two criteria: (i)…”