DOI: 10.5281/zenodo.15532702
title: Single-cell analysis uncovers preserved prostate cancer lineages and universally altered pathways in Matrigel-free patient-derived organoids

description: Patient-derived organoids (PDOs) offer new opportunities to model various cancers. However, their application in prostate cancer (PCa) has been hampered by poor take-rates and overgrowth of benign cell types. Initial experiments with 136 samples highlighted the limitations of existing culture conditions, while 30 additional samples were subsequently used to explore the effects of niche factors, carbon source, and extracellular matrix (ECM) composition on organoid outcome. Single-cell RNA sequencing (scRNA-seq) reveals that Matrigel-free PDOs exhibit cellular heterogeneity and preserve patient-specific PCa cell populations with active AR signaling, while enriching in intermediate club cell populations. In contrast, Matrigel fails to maintain primary PCa cells and produces in vitro basal-like benign transcriptomic profiles that are divergent from patient samples. Furthermore, we redefine cell type-signatures, identifying RNA- and protein-based biomarkers discriminating tumor versus all other cell types ex vivo, and show that expression of laminin-binding integrins is a hallmark of Matrigel-derived organoids. Finally, integrating previously-published datasets with our new data, we generate the first Prostate PDO single-cell atlas (PPScA). The PPScA captures a spectrum of cellular identities and malignancies, while revealing pathways universally altered in PDOs as compared to primary PCa tissues. Altogether, our study represents a significant advancement in the field, providing methodological improvements and novel cellular biology insights.
description: File Name



Description





scRNAseq_metadata.csv



Contains sequencing statistics and sample-specific annotations for all 17 samples (PDOs and Tissue) generated in the original paper (Dolgos et al., 2025).





SR_sample_matrix.mtx



Sparse matrix file for each sample generated in the original paper (Dolgos et al., 2025), containing gene expression data (genes x cells) after genome alignment and cell demultiplexing. No quality control has been applied yet.





SR_sample_features.tsv



Tab-separated file containing gene identifiers (e.g., gene symbols or Ensembl IDs) for each sample generated in the original paper (Dolgos et al., 2025).





SR_sample_barcodes.tsv



Tab-separated file containing unique cell barcodes for each sample generated in the original paper (Dolgos et al., 2025).





Dolgos_early_passage_PDOs_matrix.mtx



Sparse matrix file for the combined early passage PDO samples of the original paper (Dolgos et al., 2025). This data has undergone quality control to exclude low-quality cells.





Dolgos_early_passage_PDOs_features.tsv



Tab-separated file containing gene identifiers for the combined early passage PDO samples of the original paper (Dolgos et al., 2025).





Dolgos_early_passage_PDOs_barcodes.tsv



Tab-separated file containing unique cell barcodes for the combined early passage PDO samples of the original paper (Dolgos et al., 2025).





Dolgos_early_passage_PDOs_metadata.csv



Contains per-cell metadata for the combined early passage PDO samples of the original paper. Includes UMAP coordinates, size factors used for log normalization, clustering annotations, cell cycle phase annotations, culture conditions, and various signature scores.





Dolgos_early_passage_PDOs_loupe.cloupe



Loupe file enabling direct, script-free exploration for the combined early passage PDO samples of the original paper in Loupe Browser, with full interactive visualization of metadata and gene-expression overlays on the original UMAP embeddings.





Atlas_PCa_PDOs_matrix.mtx



Sparse matrix file for the combined PCa PDOs datasets (Dolgos_PDOs, Huang_PDOs, Song_PDOs, McCray_PDOs). This data has undergone quality control to exclude low-quality cells.





Atlas_PCa_PDOs_features.tsv



Tab-separated file containing gene identifiers for the combined PCa PDOs datasets (Dolgos_PDOs, Huang_PDOs, Song_PDOs, McCray_PDOs) .





Atlas_PCa_PDOs_barcodes.tsv



Tab-separated file containing unique cell barcodes for the combined PCa PDOs datasets (Dolgos_PDOs, Huang_PDOs, Song_PDOs, McCray_PDOs) .





Atlas_PCa_PDOs_metadata.csv



Contains per-cell metadata for the combined PCa PDOs datasets (Dolgos_PDOs, Huang_PDOs, Song_PDOs, McCray_PDOs). Includes UMAP coordinates, size factors used for log normalization, culture conditions and cell annotations.





Atlas_PCa_PDOs_loupe.cloupe



Loupe file enabling direct, script-free exploration of the combined PCa PDO datasets (Dolgos_PDOs, Huang_PDOs, Song_PDOs, McCray_PDOs) in Loupe Browser, with full interactive visualization of metadata and gene-expression overlays on the original UMAP embeddings.



Dolgos_Matched_Tissue_PDOs_matrix.mtx
Sparse matrix file for the combined PCa tissues and PDOs datasets from the original paper (Dolgos et al., 2025). This data has undergone quality control to exclude low-quality cells.


Dolgos_Matched_Tissue_PDOs_features.tsv
Tab-separated file containing gene identifiers for the combined PCa tissues and PDOs datasets from the original paper (Dolgos et al., 2025).


Dolgos_Matched_Tissue_PDOs_barcodes.tsv
Tab-separated file containing unique cell barcodes for the combined PCa tissues and PDOs datasets from the original paper (Dolgos et al., 2025).


Dolgos_Matched_Tissue_PDOs_metadata.csv
combined PCa tissues and PDOs datasets from the original paper (Dolgos et al., 2025). Includes UMAP coordinates, size factors used for log normalization, infer cnv score and cell annotations.




Dolgos_Matched_Tissue_PDOs_loupe.cloupe



Loupe file enabling direct, script-free exploration of the combined PCa PDO datasets (Dolgos_PDOs, Huang_PDOs, Song_PDOs, McCray_PDOs) in Loupe Browser, with full interactive visualization of metadata and gene-expression overlays on the original UMAP embeddings.





Dataset_Material_matrix.mtx



Sparse matrix of single-cell gene expression data for a given dataset (Dataset = Song, Huang, McCray, Henry, or Tabula_Sapiens) and material (Material = PDOs or Tissue). Data are provided either as released by the authors (after quality control) or after reproducing the QC described in the original publications (see Materials and Methods).





Dataset_Material_features.tsv



Tab-separated file listing gene identifiers for the PCa datasets (Dataset = Song, Huang, McCray, Hirz, Chen, Henry, or Tabula_Sapiens) and material (Material = PDOs or Tissue), either as provided by the authors (after quality control) or after reproducing the QC described in the original publications (see Materials and Methods).





Dataset_Material_barcodes.tsv



Tab-separated file listing cell barcodes for the PCa datasets (Dataset = Song, Huang, McCray, Hirz, Chen, Henry, or Tabula_Sapiens) and material (Material = PDOs or Tissue), either as provided by the authors (after quality control) or after reproducing the QC described in the original publications (see Materials and Methods).





Dataset_Material_metadata.csv



Contains per-cell metadata for the combined for the PCa datasets (Dataset = Song, Huang, McCray, Hirz, Chen, Henry, or Tabula_Sapiens) and material (Material = PDOs or Tissue). Includes UMAP coordinates, size factors used for log normalization, cell annotations and original metadata (i.e cell type) when made accessible by the author.





Dataset_Material_loupe.cloupe



Loupe file enabling direct, script-free exploration of PCa datasets (Dataset = Song, Huang, McCray, Hirz, Chen, Henry, or Tabula_Sapiens) and material (Material = PDOs or Tissue) in Loupe Browser, with full interactive visualization of metadata and gene-expression overlays on the original UMAP embeddings.