Luminal epithelial cells integrate variable responses to aging into stereotypical changes that underlie breast cancer susceptibility
- University of California, San Francisco, United States
- City Of Hope National Medical Center, United States
- Lawrence Berkeley National Laboratory, United States
Abstract
Effects from aging in single cells are heterogenous, whereas at the organ- and tissue-levels aging phenotypes tend to appear as stereotypical changes. The mammary epithelium is a bilayer of two major phenotypically and functionally distinct cell lineages: luminal epithelial and myoepithelial cells. Mammary luminal epithelia exhibit substantial stereotypical changes with age that merit attention because these cells are the putative cells-of-origin for breast cancers. We hypothesize that effects from aging that impinge upon maintenance of lineage fidelity increase susceptibility to cancer initiation. We generated and analyzed transcriptomes from primary luminal epithelial and myoepithelial cells from younger <30 (y)ears old and older >55y women. In addition to age-dependent directional changes in gene expression, we observed increased transcriptional variance with age that contributed to genome-wide loss of lineage fidelity. Age-dependent variant responses were common to both lineages, whereas directional changes were almost exclusively detected in luminal epithelia and involved altered regulation of chromatin and genome organizers such as SATB1. Epithelial expression of gap junction protein GJB6 increased with age, and modulation of GJB6 expression in heterochronous co-cultures revealed that it provided a communication conduit from myoepithelial cells that drove directional change in luminal cells. Age-dependent luminal transcriptomes comprised a prominent signal that could be detected in bulk tissue during aging and transition into cancers. A machine learning classifier based on luminal-specific aging distinguished normal from cancer tissue and was highly predictive of breast cancer subtype. We speculate that luminal epithelia are the ultimate site of integration of the variant responses to aging in their surrounding tissue, and that their emergent phenotype both endows cells with the ability to become cancer-cells-of-origin and represents a biosensor that presages cancer susceptibility.
Data availability
The datasets generated and analyzed during the current study include RNA-sequencing count data publicly available as part of GSE182338 (Miyano et al., 2021; Sayaman et al., 2021; Sayaman et al., 2022; Shalabi et al., 2021; Todhunter et al., 2021). The gene expression data that support the findings of this study are available from GSE102088 (Song et al., 2017); GSE81540 (Brueffer et al., 2020; Brueffer et al., 2018; Dahlgren et al., 2021); The Cancer Genome Atlas (TCGA) Research Network: https://www.cancer.gov/tcga; and The Genotype-Tissue Expression (GTEx) Project: https://gtexportal.org/. Single-cell RNAseq data sets used for validation are available from GSE161529 (Pal et al., 2021); GSE174588 (Nee et al., 2023); and GSE198732 (Murrow et al., 2022). Analysis was conducted using standard R/Bioconductor packages and statistical tests implemented in R. All package versions, model design, and parameters are described in detail in Supplementary Methods. Summary statistics at defined significance levels are provided in Supplementary Tables; full summary statistics are provided via FigShare (https://figshare.com/s/2a7ceffccfe3f35f3ce8).
Article and author information
Author details
Funding
National Cancer Institute (T32CA221709)
- Rosalyn W Sayaman
Yvonne Craig-Aldrich Fund for Cancer Research
- Mark LaBarge
City of Hope Center for Cancer and Aging
- Mark LaBarge
National Cancer Institute (K01CA279498)
- Rosalyn W Sayaman
National Cancer Institute (U01CA244109)
- Mark LaBarge
National Institute on Aging (R33AG059206)
- Mark LaBarge
National Institute of Biomedical Imaging and Bioengineering (R01EB024989)
- Mark LaBarge
National Cancer Institute (R01CA237602)
- Mark LaBarge
Department of Defense (BC141351)
- Mark LaBarge
Department of Defense (BC181737)
- Mark LaBarge
Conrad N. Hilton Foundation
- Mark LaBarge
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: The FACS-enriched luminal epithelial (LEP) and MEP myoepithelial (MEP) cells from finite lifespan, non-immortalized human mammary epithelial cells (HMECs) grown to 4th passage serve as our experimental model system. HMECs were cultured from breast tissue organoids collected from reduction mammoplasties (RM). Deidentified surgical discard tissue was obtained non-prospectively with consent for research and publication under a Lawrence Berkeley National Laboratory (Berkeley, CA) approved IRB 22997, or from City of Hope under IRB 17185 for sample distribution and collection.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Metrics
-
- 674
- views
-
- 110
- downloads
-
- 0
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Luminal epithelial cells integrate variable responses to aging into stereotypical changes that underlie breast cancer susceptibility
eLife 13:e95720.
https://doi.org/10.7554/eLife.95720
