ProstatePlasticity-Workbench

Publication

This repository supports the analyses and visualizations for the manuscript:

Jiang C., Song Y., et al. (2025). Innate immunity and the NF-κB pathway control prostate stem cell plasticity, reprogramming and tumor initiation. Nature Cancer, 2025 Sep;6(9):1537-1558.

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Contents

• 02_Marker_Genes – Scripts for identifying marker genes in scRNA-seq data.
• 04_Slingshot_scripts – Pseudotime trajectory analyses using Slingshot.
• 06_SCENIC – Gene regulatory network inference with pySCENIC.
• 07_Human_public_Data – Processing pipelines for public human single-cell datasets.
• 08_bulKRNA-seq – Bulk RNA-seq alignment and analysis pipelines.
• 09_bulkATAC-seq – Bulk ATAC-seq processing: alignment, peak calling, and motif prediction.
• R scripts in root: Related to scRNA-seq data analysis:
  • 01_UMAP.R – UMAP embedding and visualization.
  • 02_ScatterPlot.R – Generation of scatter plots.
  • 03_marker_genes.R – Visualization of marker gene expression.
  • 04-01_Slingshot_analysis_HY_BC_Prox.R – Slingshot analysis for HY_BC_Prox lineage.
  • 04-02_Slingshot_analysis_HY_Nkx3-1.R – Slingshot analysis for HY_Nkx3-1 lineage.
  • 05_DEG_analysis.R – Differential expression analysis.

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Getting Started

Clone the repository:

git clone https://github.com/yurasong/PTEN_codes.git
cd PTEN_codes

Each code file contains its own instructions for running the specific analyses.

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Data Availability

All raw sequencing datasets that support the findings of this study have been deposited in the NCBI Gene Expression Omnibus (GEO) under the following accession numbers:

• GSE270187: scRNA-seq (WT, PTEN 6W, PTEN 10M)
• GSE270189: bulk RNA-seq, Rapamycin treated
• GSE270190: bulk RNA-seq, cell fate upon PTEN deletion in BC
• GSE286018: bulk RNA-seq of P65/Pten knock BCs
• GSE286019: bulk RNA-seq of basal-derived and luminal-derived tumors
• GSE270191: ATAC-seq of pooled BC/LC of WT and PTEN-deleted cells
• GSE288787: ATAC-seq of BCs from different lobes upon PTEN deletion

Previously published human prostate cancer datasets re‐analyzed in this study were available via:

• Song, H., et al. Nat Commun (2022): GitHub repository of the author (scRNA-seq-Analysis-of-Prostate-Cancer-Samples)
• Tuong ZK., et al. Cell Rep (2021): the Prostate Cell Atlas (prostatecellatlas.org)
• Hirz T., et al. Nat Commun (2023): GSE181294
• Wong, H.Y., et al. Nat Commun 13 (2022): GSE185344

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License

All rights are reserved by the authors.