Single-cell analysis of cellular state heterogeneity in human localized prostate cancer.

254 Background: Prostate cancer is the second most common malignancy in men worldwide. The development of cancer from prostate tissue involves complex interactions of tumor cells with surrounding epithelial and stromal cells and can occur multifocally, suggesting that prostate epithelial cells may undergo cellular state transitions towards carcinogenesis. Previous studies on localized prostate cancer molecular changes have focused on unsorted bulk tissue samples, leaving a gap in our understanding of the cellular heterogeneity in the tumor microenvironment. Single-cell analyses of tumor specimens have the potential to reveal, at unprecedented resolution, cellular composition, as well as instructive intercellular interactions. Methods: To characterize the localized prostate cancer tumor microenvironment, we performed single-cell RNA-sequencing (scRNA-seq) on prostate biopsies, radical prostatectomy specimens, and matched patient-derived organoids from localized prostate cancer patients. Results: Within prostate epithelial cells, we identified a population of club cells that may act as progenitor cells. Furthermore, we uncovered luminal-like epithelial cellular states augmented in androgen signaling across basal and club cell populations. By classifying tumor cells based on ERG expression status, we found that ERG- tumor cells, in contrast to ERG+ cells, share transcriptomic heterogeneity with surrounding luminal epithelial cells and are associated with common stromal and immune microenvironment responses. These results suggest that specific immune niches may arise based on TMPRSS2-ERG fusion status. Finally, we generated prostate epithelial organoids derived from matched localized prostate cancer patients and characterized their transcriptomic profiles by scRNA-seq. These patient-derived organoids recapitulated tumor-associated epithelial cell states but also harbored distinct cell types and states from their parent tissues. Conclusions: Our data from localized prostate cancer specimens and organoids provide diagnostically relevant insights and will help advance our understanding of the cancer cellular states associated with prostate carcinogenesis.

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Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

10.1101/2020.11.06.359802 ◽

2020 ◽

Author(s):

Hanbing Song ◽

Hannah N.W. Weinstein ◽

Paul Allegakoen ◽

Marc H. Wadsworth ◽

Jamie Xie ◽

...

Keyword(s):

Prostate Cancer ◽

Tumor Microenvironment ◽

Epithelial Cell ◽

Epithelial Cells ◽

Single Cell ◽

Single Cell Analysis ◽

Cell Types ◽

Prostate Biopsies ◽

Prostate Epithelial Cells ◽

Cancer Tumor

AbstractProstate cancer is the second most common malignancy in men worldwide and consists of a mixture of tumor and non-tumor cell types. To characterize the prostate cancer tumor microenvironment, we performed single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organoids from localized prostate cancer patients. We identify a population of tumor-associated club cells that may act as progenitor cells and uncover heterogeneous cellular states in prostate epithelial cells marked by high androgen signaling states that are enriched in prostate cancer. ERG- tumor cells, compared to ERG+ cells, demonstrate shared heterogeneity with surrounding luminal epithelial cells and appear to give rise to common tumor microenvironment responses. Finally, we show that prostate epithelial organoids recapitulate tumor-associated epithelial cell states and are enriched with distinct cell types and states from their parent tissues. Our results provide diagnostically relevant insights and advance our understanding of the cellular states associated with prostate carcinogenesis.

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Abstract 1: Loss of STAT1 predicts outcome in prostate cancer patients at diagnosis by regulating the proliferation of prostate epithelial cells.

10.1158/1538-7445.am2013-1 ◽

2013 ◽

Cited By ~ 4

Author(s):

Sophia Hatziieremia ◽

Pamela McCall ◽

Jennifer Willder ◽

Clare Orange ◽

Morag Seywright ◽

...

Keyword(s):

Prostate Cancer ◽

Epithelial Cells ◽

Cancer Patients ◽

Prostate Epithelial Cells

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Single-Cell Proteomics Defines the Cellular Heterogeneity of Localized Prostate Cancer

10.1101/2021.01.25.428046 ◽

2021 ◽

Author(s):

Laura De Vargas Roditi ◽

Andrea Jacobs ◽

Jan H. Rueschoff ◽

Pete Bankhead ◽

Stephane Chevrier ◽

...

Keyword(s):

Prostate Cancer ◽

Single Cell ◽

Immune Cell ◽

Cell Mass ◽

Prognostic Biomarkers ◽

Cellular Heterogeneity ◽

Localized Prostate Cancer ◽

Tissue Samples ◽

Molecular Alterations ◽

Cell To Cell Variability

ABSTRACTLocalized prostate cancer exhibits multiple genomic alterations and heterogeneity at the proteomic level. Single-cell technologies capture important cell-to-cell variability responsible for heterogeneity in biomarker expression that may be overlooked when molecular alterations are based on bulk tissue samples. The aim of this study was to identify novel prognostic biomarkers and describe the heterogeneity of prostate cancer and the associated immune cell infiltrates by simultaneously quantifying 36 proteins using single-cell mass cytometry analysis of over 1,6 million cells from 58 men with localized prostate cancer. To perform this task, we proposed a novel computational pipeline, Franken, which showed unprecedented combination of performance, sensitivity and scalability for high dimensional clustering compared to state of the art methods. We were able to describe subpopulations of immune, stromal, and prostate cells, including unique changes occurring in tumor tissues and high grade disease providing insights into the coordinated progression of prostate cancer. Our results further indicated that men with localized disease already harbor rare subpopulations that typically occur in castration-resistant and metastatic disease, which were confirmed through imaging. Our methodology could be used to discover novel prognostic biomarkers to personalize treatment and improve outcomes.

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MP38-15 DETECTION AND CHARACTERIZATION OF DISSEMINATED TUMOR CELLS FROM THE BONE MARROW IN LOCALIZED PROSTATE CANCER PATIENTS UNDERGOING RADICAL PROSTATECTOMY

The Journal of Urology ◽

10.1016/j.juro.2017.02.1168 ◽

2017 ◽

Vol 197 (4S) ◽

Author(s):

Stephanie Glavaris ◽

Emma van der Toom ◽

Michael Gorin ◽

James Verdone ◽

Changxue Lu ◽

...

Keyword(s):

Prostate Cancer ◽

Bone Marrow ◽

Radical Prostatectomy ◽

Cancer Patients ◽

Tumor Cells ◽

Disseminated Tumor Cells ◽

Localized Prostate Cancer

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Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

Nature Communications ◽

10.1038/s41467-021-27322-4 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

Hanbing Song ◽

Hannah N. W. Weinstein ◽

Paul Allegakoen ◽

Marc H. Wadsworth ◽

Jamie Xie ◽

...

Keyword(s):

Prostate Cancer ◽

Tumor Microenvironment ◽

Epithelial Cell ◽

Epithelial Cells ◽

Single Cell ◽

Single Cell Analysis ◽

Cell Types ◽

Prostate Biopsies ◽

Prostate Carcinogenesis ◽

Cancer Tumor

AbstractProstate cancer is the second most common malignancy in men worldwide and consists of a mixture of tumor and non-tumor cell types. To characterize the prostate cancer tumor microenvironment, we perform single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organoids from localized prostate cancer patients. We uncover heterogeneous cellular states in prostate epithelial cells marked by high androgen signaling states that are enriched in prostate cancer and identify a population of tumor-associated club cells that may be associated with prostate carcinogenesis. ERG-negative tumor cells, compared to ERG-positive cells, demonstrate shared heterogeneity with surrounding luminal epithelial cells and appear to give rise to common tumor microenvironment responses. Finally, we show that prostate epithelial organoids harbor tumor-associated epithelial cell states and are enriched with distinct cell types and states from their parent tissues. Our results provide diagnostically relevant insights and advance our understanding of the cellular states associated with prostate carcinogenesis.

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Prevalence and tissue concordance of BRCA2 copy number loss evaluated by single-cell, shallow whole genome sequencing of circulating tumor cells (CTCs) in castration-resistant prostate cancer (CRPC).

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.5531 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 5531-5531

Author(s):

Ethan Barnett ◽

Joseph Schonhoft ◽

Nikolaus D. Schultz ◽

Jerry Lee ◽

Samir Zaidi ◽

...

Keyword(s):

Prostate Cancer ◽

Whole Genome Sequencing ◽

Single Cell ◽

Tumor Cells ◽

Circulating Tumor Cells ◽

Genome Sequencing ◽

Copy Number ◽

Cellular Heterogeneity ◽

Cancer Tissue ◽

Whole Genome

5531 Background: Genomic studies have shown that up to 25% of prostate cancer tissue specimens harbor alterations in DNA Damage Repair (DDR) genes, which may sensitize the tumor to poly ADP-ribose polymerase inhibitors (PARPi). Trials evaluating PARPi in patients with DDR deficiencies have shown varied response rates and differences regarding which genomic alterations predict for sensitivity to these agents, with the majority of objective responses seen in BRCA2-altered tumors. These results highlight the need to develop biomarker assays which can predict benefit from PARPi therapy. Tissue and cell-free DNA (cfDNA) have been the most utilized sources of tumor material for analysis in this setting, but success rates of obtaining sufficient tumor for analysis from bone are low and detecting tumor-derived copy number variants (CNVs) in cfDNA is challenging. Circulating tumor cells (CTCs) represent an alternate source of genetic information, for which assays are available to isolate and sequence individual cells in a manner that eliminates background noise from stroma and healthy cells, while capturing inter-cellular heterogeneity. Methods: Blood samples, collected from 138 progressing metastatic CRPC patients within 30 days of a pre-treatment biopsy intended for sequencing using MSK-IMPACT, were sent to EPIC Sciences for CTC analysis. Detected CTCs underwent single cell, low pass whole genome sequencing. Prevalence and concordance of BRCA2 copy-loss, regardless of whether single copy or homozygous, was compared in matched tissue and CTC samples. Results: BRCA2 copy-loss was identified in 21% (23/108) and 50% (58/115) of successfully sequenced tissue and CTC samples, respectively. In the 58 patients with CTC-detected BRCA2 loss, BRCA2 loss was detected in 36% (220/565) of the sequenced CTCs, representing a median of 46% (range 4-100%) of CTCs found in each individual sample. When both sequencing assays were successful, BRCA2 loss was detected in CTCs in 84% (16/19) of the tissue-positive cases, whereas tissue sequencing detected BRCA2 loss in 35% (16/46) of CTC-positive cases. Conclusions: Data from this study supports the notion that single-cell CTC sequencing can detect BRCA2 copy-loss at a high frequency, including cases that were negative in tissue, while also characterizing inter-cellular heterogeneity. Further studies will investigate whether CTC BRCA2 copy-loss can predict the likelihood of response to PARPi.

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Circulating extracellular vesicles release oncogenic miR-424 in experimental models and patients with aggressive prostate cancer

Communications Biology ◽

10.1038/s42003-020-01642-5 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Domenico Albino ◽

Martina Falcione ◽

Valeria Uboldi ◽

Dada Oluwaseyi Temilola ◽

Giada Sandrini ◽

...

Keyword(s):

Prostate Cancer ◽

Epithelial Cells ◽

Cancer Patients ◽

Extracellular Vesicles ◽

Disease Recurrence ◽

Experimental Models ◽

Normal Prostate ◽

Primary Tumors ◽

Disease Evolution ◽

Prostate Epithelial Cells

AbstractExtracellular vesicles (EVs) are relevant means for transferring signals across cells and facilitate propagation of oncogenic stimuli promoting disease evolution and metastatic spread in cancer patients. Here, we investigated the release of miR-424 in circulating small EVs or exosomes from prostate cancer patients and assessed the functional implications in multiple experimental models. We found higher frequency of circulating miR-424 positive EVs in patients with metastatic prostate cancer compared to patients with primary tumors and BPH. Release of miR-424 in small EVs was enhanced in cell lines (LNCaPabl), transgenic mice (Pb-Cre4;Ptenflox/flox;Rosa26ERG/ERG) and patient-derived xenograft (PDX) models of aggressive disease. EVs containing miR-424 promoted stem-like traits and tumor-initiating properties in normal prostate epithelial cells while enhanced tumorigenesis in transformed prostate epithelial cells. Intravenous administration of miR-424 positive EVs to mice, mimicking blood circulation, promoted miR-424 transfer and tumor growth in xenograft models. Circulating miR-424 positive EVs from patients with aggressive primary and metastatic tumors induced stem-like features when supplemented to prostate epithelial cells. This study establishes that EVs-mediated transfer of miR-424 across heterogeneous cell populations is an important mechanism of tumor self-sustenance, disease recurrence and progression. These findings might indicate novel approaches for the management and therapy of prostate cancer.

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Prostate Epithelial Genes Define Docetaxel-Sensitive Prostate Cancer Molecular Subtype

10.1101/2020.08.26.269415 ◽

2020 ◽

Author(s):

Hyunho Han ◽

Kwibok Choi ◽

Young Jun Moon ◽

Ji Eun Heo ◽

Won Sik Ham ◽

...

Keyword(s):

Prostate Cancer ◽

Epithelial Cells ◽

Single Cell ◽

Molecular Subtype ◽

Prostate Gland ◽

Specific Antigen ◽

Prostate Adenocarcinoma ◽

The Cancer Genome Atlas ◽

Subtype B ◽

Prostate Epithelial Cells

ABSTRACTBACKGROUND & OBJECTIVESAnalysis of the transcriptomic landscape of prostate adenocarcinoma shows multidimensional gene expression variability. Understanding cancer transcriptome complexity can provide biological insight and therapeutic guidance. To avoid potential confounding factors, such as stromal contamination and stress-related material degradation, we utilized a set of genes expressed by prostate epithelial cells from single-cell transcriptome data of the human prostate gland.MATERIALS & METHODSAnalyzing publicly available bulk and single-cell RNA sequencing data, we defined 1,629 genes expressed by prostate epithelial cells. Consensus clustering and CIBERSORT deconvolution were used for class discovery and proportion estimate analysis. The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) dataset served as a training set. The resulting clusters were analyzed in association with clinical, pathologic, and genomic characteristics and impact on survival.RESULTSTCGA-PRAD tumors were separated into four subtypes: A (30.0%), B (26.0%), C (14.7%), D (4.2%), and mixed (25.0%). Subtype A was characterized by low frequency of ETS-family fusions and high expression of KLK3, which encodes prostate-specific antigen (PSA). Subtype B showed the highest expression of ACP3, encoding PAP (prostatic acid phosphatase). Subtypes C and D were commonly associated with advanced T/N stages, high Gleason grades, and p53 or PIK3CA mutations. In silico drug-sensitivity screening suggested that subtype B is likely sensitive to docetaxel and paclitaxel. Serum PSA/PAP ratio was predictive of a radiographic response to docetaxel in metastatic castration-resistant prostate cancer patients.CONCLUSIONWe propose four prostate adenocarcinoma subtypes with distinct transcriptomic, genomic, and pathologic characteristics. PSA/PAP ratio in advanced cancer may aid in determining which patients would benefit from maximized androgen receptor inhibition or early use of antimicrotubule agents. Molecular subtypes and biomarkers must be validated in a prospective cohort study.

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