Abstract
Effects from aging in single cells are unpredictable, whereas aging phenotypes at the organ- and tissue-levels tend to appear as stereotypical changes. The mammary epithelium is a bilayer of two major phenotypically and functionally distinct cell lineages, the luminal epithelial and myoepithelial cells. Mammary epithelia exhibit substantial stereotypical changes with age that merits attention because they are putative breast cancer-cells-of-origin. We hypothesize that effects from aging that impinge upon maintenance of lineage fidelity increases susceptibility to cancer initiation. We identified two models of age-dependent changes in gene expression, directional changes and increased variance, which 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 implicated downregulation 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 detectable 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 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 aging phenotype both endows cells with the ability to become cancer-cells-of-origin and embodies a biosensor that presages cancer susceptibility.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
↵9 Lead contact
Supplementary Methods added; Materials Design Analysis section added to Methods; Number of genes (k), technical replicates (l), and sample (m) and subject (n) biological replicates annotated in figures and legends for each analysis or experiment; Minor errors in transcribing total number of genes and number of subjects in parts of manuscript and figures corrected (no effect on results).
List of abbreviations
- 18αGA
- 18 alpha-glycyrrhetinic acid
- adj. p
- Adjusted p-value (test statistic)
- AGM
- Axon guidance molecule
- AUC
- Area under the receiving operator characteristic curve
- BH
- Benjamini-Hochberg
- CAM
- Cell adhesion molecule
- ChIP
- Chromatin immunoprecipitation
- Cor
- correlation
- DE
- Differential expression or differentially expressed (in context)
- DV
- Differential variability or differentially variable (in context)
- EMT
- Epithelial-to-mesenchymal transition
- FDR
- False discovery rate
- GEO
- Gene Expression Omnibus
- GSEA
- Gene set enrichment analysis
- GTEx
- The Genotype-Tissue Expression Project
- HMEC
- Human mammary epithelial cells
- KS
- Kolmogorov-Smirnov test
- KW
- Kruskal-Wallis test
- LEP
- Luminal epithelial cells
- Lfc
- log2 fold change (test statistic)
- LRP
- Ligand-receptor pair
- MEP
- Myoepithelial cells
- ML
- Machine learning
- MSigDB
- Molecular Signatures Database
- PAM50
- Basal PAM50 Basal-like intrinsic subtype
- PAM50
- PAM50 Her2-enriched intrinsic subtype
- PAM50
- LumA PAM50 Luminal A intrinsic subtype
- PAM50
- LumB PAM50 Luminal B intrinsic subtype
- PAM50
- Normal PAM50 Normal-like intrinsic subtype
- PcG
- Polycomb group
- PPI
- Protein-protein interaction
- PRC
- Polycomb repressor complex
- Rlog
- Regularized log
- SEC
- Super elongation complex
- SPP
- Signaling Pathways Project
- STRING
- Search Tool for the Retrieval of Interacting Genes/Proteins
- TCGA
- The Cancer Genome Atlas
- TF
- Transcription factor
- TSS
- Transcription start site