Defining cellular population dynamics at single-cell resolution during prostate cancer progression
- Division of Human Biology, Fred Hutchinson Cancer Center, United States
- University of Washington Molecular and Cellular Biology Program, United States
- Division of Vaccine and infectious Diseases, Fred Hutchinson Cancer Center, United States
- Division of Public Health Sciences, Translational Research Program, Fred Hutchinson Cancer Center, United States
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, United States
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, United States
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, United States
- Center for Data Visualization, Fred Hutchinson Cancer Center, United States
- University of Washington Departments of Medicine and Genome Sciences, United States
- Translational Data Science Integrated Research Center, Fred Hutchinson Cancer Center, United States
- Division of Basic Sciences, Fred Hutchinson Cancer Center, United States
Figures
Figure 1 with 2 supplements
Proliferative split in basal cancer cells enables expansion of intermediate cells.
(A) Simplified schematic of single-cell RNA sequencing of WT and Ptenfl/fl ventral prostates. (B) UMAP of WT and Ptenfl/fl epithelial cells. Left, both conditions superposed; middle, WT only; right, …
Figure 1—figure supplement 1
Epithelial cells contain published subtypes and urethral cells.
(A) UMAP visualization of all cells in WT and Ptenfl/fl ventral prostates, colored and labeled by cell ID. (B) Violin plots of rtTA-eGFP transgene expression. Left, transgene expression in WT and Pte…
Figure 1—figure supplement 2
Basal proliferation is subset-specific and intermediate cells express luminal markers.
(A) Bar plot of cell cycle phase assignments in WT basal cells and Ptenfl/fl hyper- and hypo-proliferative basal cells. (B) Bar plot of CCP signature composite score in WT (n=3) basal cells and Ptenf…
Figure 2 with 1 supplement
Immune recruitment in Ptenfl/fl prostates is mediated by both epithelial and immune cell signaling.
(A) Top immune-related GSEA results enriched in Ptenfl/fl compared to WT mice for each epithelial subtype. All pathways are enriched with FDR <0.05. (B) UMAP visualization of immune cells labeled by …
Figure 2—figure supplement 1
Immune cells contain pro-tumorigenic subtypes and macrophages are recruited by fibroblast signaling.
(A) UMAP of immune cells in WT and Ptenfl/fl prostates, labeled by cell types. (B) Relative abundance of immune cell types in WT (n=3) and Ptenfl/fl (n=2) mice (***p<0.001, n.s.=not significant, …
Figure 3 with 1 supplement
Intermediate cells are primed for survival and diversification in the context of castration.
(A) Simplified schematic of setup for single-cell sequencing of Ptenfl/fl intact and Ptenfl/fl castrated (cx) ventral prostates. (B) Split UMAP visualizations of Ptenfl/fl and Ptenfl/fl cx …
Figure 3—figure supplement 1
Castration-resistant intermediate cells are phenotypically diverse.
(A) Composite score of CCP signature in WT, Ptenfl/fl intact, and Ptenfl/fl cx epithelial cells (Data presented as +/-SD, *p<0.05, permutation test) (B) Heatmap of top differentially expressed genes …
Figure 4 with 1 supplement
Intermediate cells are enriched for a signature of treatment resistance that correlates with advanced human disease.
(A) Diagram of clinical trial used to establish gene signature of androgen deprivation treatment resistance (NCT02430480). (B) Enrichment plot of ADT resistance gene signature relative to …
Figure 4—figure supplement 1
5 Genes expressed in intermediate cells correlate with poor disease outcomes in human patients.
(A) Heatmap of top 5 resistance genes in intermediate clusters, labeled by AR status and condition (intact or castrate). (B) Heatmap of the top 5 genes enriched in castrated intermediate cells (Figur…
Figure 5 with 1 supplement
Castration remodels immune environment via fibroblast signaling and increases TNF pathway activity.
(A) Combined UMAP visualization of immune cells in Ptenfl/fl and Ptenfl/fl cx ventral prostates. (B) Relative abundance of immune cells in Ptenfl/fl intact (n=2) and cx (n=3) mice. Y-axis shows the …
Figure 5—figure supplement 1
Epithelial-mediated macrophage recruitment is not interrupted by castration.
(A) Plot of signaling interactions between macrophage subtypes and epithelial cells in Ptenfl/fl intact and Ptenfl/fl cx prostates. (B) Dot plot of epithelial ligand and macrophage receptor gene …
Figure 6 with 1 supplement
4EBP1M expression is lethal in epithelial cells and decreases EGFR and TNF ligands in epithelial cells and fibroblasts.
(A) Simplified schematic of the eIF4F translation initiation complex and how the 4EBP1M protein functions in the Ptenfl/fl;4ebp1M mouse model when treated with doxycycline. (B) UMAP visualization of …
Figure 6—figure supplement 1
Interactive Portal, Enabling Gene- and Cell- Specific Comparisons Across the Spectrum of Prostate Cancer Initiation and Progression in vivo.
Interactive website can be found at https://atlas.fredhutch.org/hsieh-prostate/.
Tables
Table 1
Transgene abundance in PTEN mouse epithelia.
| Cell Type | Ptenfl/fl | Ptenfl/fl cx | Ptenfl/fl;4ebp1M | |
|---|---|---|---|---|
| Basal | All | 1795 | 2718 | 1565 |
| rtTA-eGFP+ | 255 (14.2%) | 422 (15.5%) | 41 (2.6%) | |
| Intermediate | All | 2391 | 8230 | 4760 |
| rtTA-eGFP+ | 438 (18.3%) | 1073 (13.0%) | 43 (0.90%) | |
Table 2
Basal proliferative subset proportions in rtTA-eGFP+ cells.
| Basal Subset | Hypo-proliferative | Hyper-proliferative |
|---|---|---|
| Ptenfl/fl | 188 (73.7%) | 60 (23.5%) |
| Ptenfl/fl cx | 313 (74.1%) | 98 (23.2%) |
| Ptenfl/fl;4ebp1M | 38 (97.4%) | 1 (2.6%) |
Additional files
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Supplementary file 1
Quality control metrics and Figure 1 supplementary information.
(A) Quality control measures for each mouse replicate. (B) Breakdown of cell ID numbers and relative abundance (%) per mouse condition. (C) Breakdown of cell ID numbers and relative abundance (%) per mouse replicate. (D) Genes upregulated in Ptenfl/fl compared to WT mice for each epithelial subtype. Thresholds set at avg_log2FC >0.25 and FDR <0.05. (E) Breakdown of cell cycle phase assignment for every cell ID in WT and Ptenfl/fl mice. (F) Differentially expressed genes between hyper-proliferative and hypo-proliferative basal cells in Ptenfl/fl mice. Thresholds set at avg_log2FC >0.25 and FDR <0.05. Positive avg_log2FC values indicate upregulation in hypo-proliferative basal cells.
- https://cdn.elifesciences.org/articles/79076/elife-79076-supp1-v2.xlsx
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Supplementary file 2
CellphoneDB cell-cell interaction data in Ptenfl/fl mice (see Figure 2).
The first gene in the “pair” column is expressed in the first cell ID in the “clusters” column and the second gene is expressed in the second cell ID.
- https://cdn.elifesciences.org/articles/79076/elife-79076-supp2-v2.xlsx
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Supplementary file 3
Differentially expressed genes in Ptenfl/fl and Ptenfl/fl cx intermediate cells.
6-way comparison between clusters 0–5 (see Figure 3E). Each sheet shows significantly up- or down-regulated genes for one cluster relative to all others. Thresholds set at avg_log2FC >0.25 and FDR <0.05.
- https://cdn.elifesciences.org/articles/79076/elife-79076-supp3-v2.xlsx
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Supplementary file 4
CellphoneDB cell-cell interaction data in Ptenfl/fl cx mice (see Figure 5).
The first gene in the “pair” column is expressed in the first cell ID in the “clusters” column and the second gene is expressed in the second cell ID.
- https://cdn.elifesciences.org/articles/79076/elife-79076-supp4-v2.xlsx
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Supplementary file 5
Differentially expressed genes and CellphoneDB cell-cell interaction data in Ptenfl/fl;4ebp1M cx mice (see Figure 6).
(A) Genes upregulated in Ptenfl/fl;4ebp1M cx compared to Ptenfl/fl cx mice for each epithelial subtype. Thresholds set at avg_log2FC >0.25 and FDR <0.05. (B) Genes upregulated in Ptenfl/fl;4ebp1M cx compared to Ptenfl/fl cx mice for each epithelial subtype, filtered for cells expressing the rtTA-eGFP transgene. Thresholds set at avg_log2FC >0.25 and FDR <0.05. (C) CellphoneDB cell-cell interaction data in Ptenfl/fl;4ebp1M cx mice (see Figure 6E–H). The first gene in the “pair” column is expressed in the first cell ID in the “clusters” column and the second gene is expressed in the second cell ID.
- https://cdn.elifesciences.org/articles/79076/elife-79076-supp5-v2.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/79076/elife-79076-mdarchecklist1-v2.pdf
