Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Single-Cell Isolation and Single-Cell RNA Sequencing (scRNAseq) of Normal Breast Cells
2.2. Single-Cell Transcriptomic Landscape of the Breast Shows 10 Distinct Cell Clusters
2.3. EpCAM and ITGA6 Expression in Breast Single-Cell Clusters
2.4. Cytokeratin Gene Expression in the Three Breast Epithelial Cell Types
2.5. Five Cell Cluster Signatures Representing 86% of Breast Tumors in TCGA Dataset
2.6. Single-Cell Cluster Signatures Correlating with the Breast Cancer Subtypes
2.7. Poor Patient Survival in Cluster 9 TNBC Tumors
3. Discussions
3.1. Inclusive Single-Cell Landscape of the Normal Breast
3.2. Three Epithelial Cell Types (Clusterd 2, 7, and 9)
3.3. Nonepithelial Cells in the Breast That Do Not Contribute to Breast Cancer
3.4. Fibroblasts (Cluster 3 and 6) and Cancer-Associated Fibroblasts (CAFs)
3.5. Breast Cancer Subtypes Related to the Normal Cell Types in the Breast
4. Methods and Materials
4.1. Breast Tissue Sample and Tissue Processing
4.2. Single-Cell Isolation and Sequencing
4.3. Single-Cell RNA Sequencing Data Analysis
4.4. The Cancer Genome Atlas (TCGA) Data Analysis
4.5. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Cell Cluster | Number of Cells | % Total Cells | Genes | Proposed Cell Type |
---|---|---|---|---|
0 | 769 | 24.1 | ACTA2, MYH11, MYL9, MYLK, TAGLN | Smooth muscle |
1 | 749 | 23.5 | EMCN, ENG, PLVAP, SELE, SELP | Endothelial |
2 | 453 | 14.2 | * KRT18, KRT19, KRT7, KRT8 | Luminal epithelial |
3 | 336 | 10.5 | COL1A1/A2, COL3A1, COL6A1/A2/A3, ALDH1A1 | Stroma fibroblasts |
4 | 305 | 9.6 | EDN1, EFNB2, ELTD1, ESAM | Endothelial subset |
5 | 188 | 5.9 | Adipocyte markers: APOE, CFD, STEAP4 Macrophage markers: CCL2, CEBPD Fibroblast markers: COL4A1, COL6A3 EMT markers: SNAI2, TGFB1 | Mesenchymal progenitor |
6 | 161 | 5.0 | COL14A1, COL1A1/A2, COL6A2, ALDH1A1 | Stroma fibroblast subset |
7 | 153 | 4.8 | * KRT5, KRT14, KRT17, ACTA2, TAGLN | Basal/myoepithelial |
8 | 48 | 1.5 | C2, CD3D, CD7, CD8A, CD69, IL1B, TNF, GZMK | Immune CTL |
9 | 31 | 1.0 | EPCAM, * KRT6B, KRT15, KRT16, KRT81, KRT23 | Other epithelial |
All | 3193 | 100.0% |
Cluster | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
---|---|---|---|---|---|---|---|---|---|---|
EPCAM | 0.01 ± 0.09 | 0 | 0.42 ± 0.59 | 0.01 ± 0.07 | 0.01 ± 0.12 | 0 ± 0.05 | 0 | 0.12 ± 0.38 | 0 | 1.15 ± 0.68 |
ITGA6 | 0.01 ± 0.08 | 0.59 ± 0.72 | 0.01 ± 0.11 | 0.02 ± 0.17 | 0.35 ± 0.62 | 0.02 ± 0.17 | 0 | 0.22 ± 0.51 | 0.02 ± 0.12 | 0.15 ± 0.38 |
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Peng, S.; Hebert, L.L.; Eschbacher, J.M.; Kim, S. Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer. Cancers 2020, 12, 3639. https://doi.org/10.3390/cancers12123639
Peng S, Hebert LL, Eschbacher JM, Kim S. Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer. Cancers. 2020; 12(12):3639. https://doi.org/10.3390/cancers12123639
Chicago/Turabian StylePeng, Sen, Lora L. Hebert, Jennifer M. Eschbacher, and Suwon Kim. 2020. "Single-Cell RNA Sequencing of a Postmenopausal Normal Breast Tissue Identifies Multiple Cell Types That Contribute to Breast Cancer" Cancers 12, no. 12: 3639. https://doi.org/10.3390/cancers12123639