Single-cell and spatial RNA sequencing identify divergent microenvironments and progression signatures in early- versus late-onset prostate cancer
Data files
Feb 14, 2025 version files 1.70 GB
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PCSC002_SC_matrix.tar.gz
121.63 MB
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PCSC003_SC_matrix.tar.gz
69.47 MB
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PCSC005_SC_matrix.tar.gz
93 MB
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PCSC007_SC_matrix.tar.gz
81.98 MB
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PCSC008_SC_matrix.tar.gz
86.38 MB
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PCSC008_Spatial_matrix.tar.gz
16.95 MB
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PCSC009_SC_matrix.tar.gz
87.78 MB
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PCSC010_SC_matrix.tar.gz
77.53 MB
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PCSC010_Spatial_matrix.tar.gz
23.60 MB
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PCSC012_SC_matrix.tar.gz
46.92 MB
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PCSC013_SC_matrix.tar.gz
88.74 MB
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PCSC015_SC_matrix.tar.gz
64.81 MB
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README.md
5.67 KB
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Validate-PCSC001_SingleCell_matrix.tar.gz
109.08 MB
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Validate-PCSC002_SingleCell_matrix.tar.gz
82.35 MB
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Validate-PCSC003_SingleCell_matrix.tar.gz
82.18 MB
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Validate-PCSC003_Spatial_matrix.tar.gz
11.42 MB
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Validate-PCSC004_SingleCell_matrix.tar.gz
66.36 MB
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Validate-PCSC005_SingleCell_matrix.tar.gz
77.87 MB
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Validate-PCSC006_SingleCell_matrix.tar.gz
66.66 MB
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Validate-PCSC007_SingleCell_matrix.tar.gz
76.68 MB
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Validate-PCSC007_Spatial_matrix.tar.gz
18.69 MB
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Validate-PCSC008_SingleCell_matrix.tar.gz
83.28 MB
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Validate-PCSC009_SingleCell_matrix.tar.gz
84.35 MB
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Validate-PCSC010_SingleCell_matrix.tar.gz
79.74 MB
Abstract
The clinical and pathological outcomes differ between early- (EOPC; diagnosed in men ≤ 55 years of age) and late-onset prostate cancer (LOPC), potentially attributed to the changes in hormone levels and immune activities associated with ageing. Exploring the heterogeneity therein holds the potential for developing age-specific precision interventions. Here, through single-cell and spatial transcriptomic analyses of prostate cancer tissues, we identified that an androgen response-related transcriptional meta-program (AR-MP) might underlie the age-related heterogeneity of tumour cells and microenvironment. APOE+ tumour-associated macrophages infiltrated AR-MP-activated tumour cells in EOPC, potentially facilitating tumour progression and immunosuppression. By contrast, inflammatory cancer-associated fibroblasts in LOPC could downregulate the AR-MP of tumour cells, promote epithelial-to-mesenchymal transition and induce pre-existing castration resistance, which effects could also be caused by smoking. This study provides insight into precision treatments tailored to diverse age groups, emphasizing interventions that include targeting AR and tumour-associated macrophages in young patients but anchoring epithelial-to-mesenchymal transition and inflammatory cancer-associated fibroblasts in old counterparts.
https://doi.org/10.5061/dryad.4b8gthtqb
Description of the data and file structure
This dataset consists of matrices of single-cell RNA sequencing from 20 prostate cancer tissues, and of spatial transcriptomic sequencing from 4 prostate cancer tissues, emphasising the differences in tumour microenvironment associated with age-of-onset.
Files and variables
File: PCSC003_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC005_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC002_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC007_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC008_Spatial_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from SpaceRanger pipeline: filtered_feature_bc_matrix.h5.
File: PCSC008_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC009_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC010_Spatial_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from SpaceRanger pipeline: filtered_feature_bc_matrix.h5.
File: PCSC010_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC012_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC013_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: PCSC015_SC_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC003_Spatial_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from SpaceRanger pipeline: filtered_feature_bc_matrix.h5.
File: Validate-PCSC001_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC003_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC002_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC004_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC007_Spatial_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from SpaceRanger pipeline: filtered_feature_bc_matrix.h5.
File: Validate-PCSC005_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC006_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC008_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC007_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC009_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
File: Validate-PCSC010_SingleCell_matrix.tar.gz
Description: 10X Genomics-typed matrix files, which are generated from CellRanger pipeline: matrix.mtx.gz, features.tsv.gz and barcodes.tsv.gz.
Code/software
Seurat pipeline based on R software. The single-cell RNA sequencing matrix (each for three files including “barcodes.tsv.gz”, “features.tsv.gz”, “matrix.mtx.gz”) should be read with “Read10X()” and the spatial transcriptomic data (each for a “filtered_feature_bc_matrix.h5” file) should be read with “Read10X_h5()”.
The tumour samples used in this study for scRNA-seq and ST-seq were consecutively collected from treatment-naïve patients with aggressive PCa [ISUP grade group ≥ 4, or tumour stage T3/T4, or tumour in nodes (N1), or metastasis present (M1)] who underwent prostate biopsy or radical prostatectomy (RP), which consisted 9 EOPC and 11 LOPC patients in total.
Sequencing Protocol:
scRNA-seq (discovery cohort): The fresh tumour tissues were stored in the GEXSCOPE® Tissue Preservation Solution and transported on ice, which were then washed (Hanks Balanced Salt Solution), minced and digested (GEXSCOPE® Tissue Dissociation Solution), centrifuged and resuspended. GEXSCOPE® red blood cell lysis buffer was used to remove the red blood cells. Single-cell suspensions were converted to barcoded scRNA-seq libraries using the Chromium Single Cell Library, Gel Bead & Multiplex Kit (10x Genomics), following the manufacturer’s instructions. Eventually, libraries were prepared using 10x Genomics Library Kits and sequenced on Illumina Nova6000 with a pair-end 150 bp (PE150) reading strategy.
scRNA-seq (validation cohort): After washed, minced, digested, and removed for red blood cells, the single-cell suspensions were subjected to SeekOne® DD Single Cell 3’ library preparation kit (SeekGene) to prepare barcoded scRNA-seq libraries. Purified libraries were sequenced on Illumina Nova6000 with PE150 reading strategy.
ST-seq for frozen fresh sample: The fresh samples from EOPC-4, Rep-EOPC4, and Rep-LOPC1 were snap frozen in optimum cutting temperature (OCT) compound (SAKURA, Cat#: 4583) and stored at −80 °C, and then placed on the Visium Spatial Gene Expression slide (10x Genomics). Methoxylated sections were performed according to Visium Spatial Gene Expression for OCT (10x Genomics), incubated at −20°C for 30 min, then stained with hematoxylin and eosin (H&E), and finally stained for imaging. The Visium Spatial Gene Expression Slide & Reagent Kit (Cat:1000184,10x Genomics) was used to construct sequencing libraries according to the Visium Spatial Gene Expression User Guide (CG000408, 10x Genomics), which were sequenced using Illumina Nova6000 with PE150 under a sequencing depth of at least 50,000 reads per spot.
ST-seq for Formalin-fixed, paraffin-embedded (FFPE) sample: An additional tumour tissue from LOPC-3 was prepared as a FFPE sample and subjected to Visium CytAssist Spatial Gene Expression for FFPE (PN-1000520, 10× Genomics). Deparaffinization, hematoxylin, and eosin staining and decrosslinking were performed after overnight drying, followed by probe hybridization and probe connection. Then, RNA from the tissue section was digested to release the probes, which were captured by the capture sequences on the Visium CytAssist Spatial Gene Expression slide (10x Genomics) using the Visium CytAssist instrument. The probe extension and library construction steps were then conducted following the standard Visium for FFPE workflow outside of the instrument, which was finally sequenced on Illumina Nova6000 with a sequencing depth of at least 100,000 reads per spot with PE150.
Data processing to generate matrix:
Raw reads of scRNA-seq were processed to generate gene expression profiles using Cell Ranger (v.3.0.3, 10x Genomics). Reads from the 10x library were mapped to GRCh38 with ensemble version 92 gene annotation. ST-seq data were processed by Space Ranger (v.2.1.0, 10x Genomics) to generate RNA profiles and the result matrix files.