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Cheng S, Li L, Yeh Y, Shi Y, Franco O, Corey E, Yu X. Unveiling novel double-negative prostate cancer subtypes through single-cell RNA sequencing analysis. NPJ Precis Oncol 2024; 8:171. [PMID: 39095562 DOI: 10.1038/s41698-024-00667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into cancer heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising publicly available cohorts and data generated by our research team, and established the Human Prostate Single cell Atlas (HuPSA) and Mouse Prostate Single cell Atlas (MoPSA) datasets. Through comprehensive analysis, we identified two novel double-negative PCa populations: KRT7 cells characterized by elevated KRT7 expression and progenitor-like cells marked by SOX2 and FOXA2 expression, distinct from NEPCa, and displaying stem/progenitor features. Furthermore, HuPSA-based deconvolution re-classified human PCa specimens, validating the presence of these novel subtypes. We then developed a user-friendly web application, "HuPSA-MoPSA" ( https://pcatools.shinyapps.io/HuPSA-MoPSA/ ), for visualizing gene expression across all newly established datasets. Our study provides comprehensive tools for PCa research and uncovers novel cancer subtypes that can inform clinical diagnosis and treatment strategies.
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Affiliation(s)
- Siyuan Cheng
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA, USA.
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA, USA.
| | - Lin Li
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA, USA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA, USA
| | - Yunshin Yeh
- Pathology & Laboratory Medicine Service, Overton Brooks VA Medical Center, Shreveport, LA, USA
| | - Yingli Shi
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA, USA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA, USA
| | - Omar Franco
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA, USA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Xiuping Yu
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA, USA.
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA, USA.
- Department of Urology, LSU Health Shreveport, Shreveport, LA, USA.
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2
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Cheng S, Li L, Yeh Y, Shi Y, Franco O, Corey E, Yu X. Unveiling Novel Double-Negative Prostate Cancer Subtypes Through Single-Cell RNA Sequencing Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.11.553009. [PMID: 38746150 PMCID: PMC11092429 DOI: 10.1101/2023.08.11.553009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into disease heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising both publicly available cohorts and data generated by our research team, and established the HuPSA (Human Prostate Single cell Atlas) and the MoPSA (Mouse Prostate Single cell Atlas) datasets. Through comprehensive analysis, we identified two novel double-negative PCa populations: KRT7 cells characterized by elevated KRT7 expression, and progenitor-like cells marked by SOX2 and FOXA2 expression, distinct from NEPCa, and displaying stem/progenitor features. Furthermore, HuPSA-based deconvolution allowed for the re-classification of human PCa specimens, validating the presence of these novel subtypes. Leveraging these findings, we developed a user-friendly web application, "HuPSA-MoPSA" (https://pcatools.shinyapps.io/HuPSA-MoPSA/), for visualizing gene expression across all newly-established datasets. Our study provides comprehensive tools for PCa research and uncovers novel cancer subtypes that can inform clinical diagnosis and treatment strategies.
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Affiliation(s)
- Siyuan Cheng
- Department of Biochemistry and Molecular biology, LSU Health Shreveport, Shreveport, LA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA
| | - Lin Li
- Department of Biochemistry and Molecular biology, LSU Health Shreveport, Shreveport, LA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA
| | - Yunshin Yeh
- Pathology & Laboratory Medicine Service, Overton Brooks VA Medical Center, Shreveport, LA
| | - Yingli Shi
- Department of Biochemistry and Molecular biology, LSU Health Shreveport, Shreveport, LA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA
| | - Omar Franco
- Department of Biochemistry and Molecular biology, LSU Health Shreveport, Shreveport, LA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA
| | - Xiuping Yu
- Department of Biochemistry and Molecular biology, LSU Health Shreveport, Shreveport, LA
- Feist-Weiller Cancer Center, LSU Health Shreveport, Shreveport, LA
- Department of Urology, LSU Health Shreveport, Shreveport, LA
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Kim WK, Buckley AJ, Lee DH, Hiroto A, Nenninger CH, Olson AW, Wang J, Li Z, Vikram R, Adzavon YM, Yau TY, Bao Y, Kahn M, Geradts J, Xiao GQ, Sun Z. Androgen deprivation induces double-null prostate cancer via aberrant nuclear export and ribosomal biogenesis through HGF and Wnt activation. Nat Commun 2024; 15:1231. [PMID: 38336745 PMCID: PMC10858246 DOI: 10.1038/s41467-024-45489-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Androgen deprivation therapy (ADT) targeting androgen/androgen receptor (AR)- signaling pathways is the main therapy for advanced prostate cancer (PCa). However, ADT eventually fails in most patients who consequently develop castration-resistant prostate cancer (CRPC). While more potent AR antagonists and blockers for androgen synthesis were developed to improve clinical outcomes, they also show to induce more diverse CRPC phenotypes. Specifically, the AR- and neuroendocrine-null PCa, DNPC, occurs in abiraterone and enzalutamide-treated patients. Here, we uncover that current ADT induces aberrant HGF/MET signaling activation that further elevates Wnt/β-catenin signaling in human DNPC samples. Co-activation of HGF/MET and Wnt/β-catenin axes in mouse prostates induces DNPC-like lesions. Single-cell RNA sequencing analyses identify increased expression and activity of XPO1 and ribosomal proteins in mouse DNPC-like cells. Elevated expression of XPO1 and ribosomal proteins is also identified in clinical DNPC specimens. Inhibition of XPO1 and ribosomal pathways represses DNPC growth in both in vivo and ex vivo conditions, evidencing future therapeutic targets.
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Affiliation(s)
- Won Kyung Kim
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Alyssa J Buckley
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Dong-Hoon Lee
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Alex Hiroto
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Christian H Nenninger
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Adam W Olson
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jinhui Wang
- Integrative Genomics Core, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Zhuo Li
- Electronic Microscopy Core, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Rajeev Vikram
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yao Mawulikplimi Adzavon
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Tak-Yu Yau
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yigang Bao
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Michael Kahn
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Joseph Geradts
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, Greenville, USA
| | - Guang-Qian Xiao
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zijie Sun
- Department of Cancer Biology and Molecular Medicine, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA.
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4
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Hiroto A, Kim WK, Pineda A, He Y, Lee DH, Le V, Olson AW, Aldahl J, Nenninger CH, Buckley AJ, Xiao GQ, Geradts J, Sun Z. Stromal androgen signaling acts as tumor niches to drive prostatic basal epithelial progenitor-initiated oncogenesis. Nat Commun 2022; 13:6552. [PMID: 36323713 PMCID: PMC9630272 DOI: 10.1038/s41467-022-34282-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
The androgen receptor (AR)-signaling pathways are essential for prostate tumorigenesis. Although significant effort has been devoted to directly targeting AR-expressing tumor cells, these therapies failed in most prostate cancer patients. Here, we demonstrate that loss of AR in stromal sonic-hedgehog Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development using in vivo assays and mouse models. Single-cell RNA sequencing and other analyses identified a robust increase of insulin-like growth factor (IGF) binding protein 3 expression in AR-deficient stroma through attenuation of AR suppression on Sp1-regulated transcription, which further inhibits IGF1-induced Wnt/β-catenin activation in adjacent basal epithelial cells and represses their oncogenic growth and tumor development. Epithelial organoids from stromal AR-deficient mice can regain IGF1-induced oncogenic growth. Loss of human prostate tumor basal cell signatures reveals in basal cells of stromal AR-deficient mice. These data demonstrate a distinct mechanism for prostate tumorigenesis and implicate co-targeting stromal and epithelial AR-signaling for prostate cancer.
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Affiliation(s)
- Alex Hiroto
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Won Kyung Kim
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Ariana Pineda
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yongfeng He
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Dong-Hoon Lee
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Vien Le
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Adam W Olson
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Joseph Aldahl
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Christian H Nenninger
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Alyssa J Buckley
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Guang-Qian Xiao
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joseph Geradts
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Zijie Sun
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA.
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5
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Kim WK, Olson AW, Mi J, Wang J, Lee DH, Le V, Hiroto A, Aldahl J, Nenninger CH, Buckley AJ, Cardiff R, You S, Sun Z. Aberrant androgen action in prostatic progenitor cells induces oncogenesis and tumor development through IGF1 and Wnt axes. Nat Commun 2022; 13:4364. [PMID: 35902588 PMCID: PMC9334353 DOI: 10.1038/s41467-022-32119-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 07/18/2022] [Indexed: 12/26/2022] Open
Abstract
Androgen/androgen receptor (AR) signaling pathways are essential for prostate tumorigenesis. However, the fundamental mechanisms underlying the AR functioning as a tumor promoter in inducing prostatic oncogenesis still remain elusive. Here, we demonstrate that a subpopulation of prostatic Osr1 (odd skipped-related 1)-lineage cells functions as tumor progenitors in prostate tumorigenesis. Single cell transcriptomic analyses reveal that aberrant AR activation in these cells elevates insulin-like growth factor 1 (IGF1) signaling pathways and initiates oncogenic transformation. Elevating IGF1 signaling further cumulates Wnt/β-catenin pathways in transformed cells to promote prostate tumor development. Correlations between altered androgen, IGF1, and Wnt/β-catenin signaling are also identified in human prostate cancer samples, uncovering a dynamic regulatory loop initiated by the AR through prostate cancer development. Co-inhibition of androgen and Wnt-signaling pathways significantly represses the growth of AR-positive tumor cells in both ex-vivo and in-vivo, implicating co-targeting therapeutic strategies for these pathways to treat advanced prostate cancer.
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Affiliation(s)
- Won Kyung Kim
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Adam W Olson
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jiaqi Mi
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jinhui Wang
- Integrative Genomics Core, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Dong-Hoon Lee
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Vien Le
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Alex Hiroto
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Joseph Aldahl
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Christian H Nenninger
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Alyssa J Buckley
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Robert Cardiff
- Center for Comparative Medicine, University of California at Davis, Davis, CA, USA
| | - Sungyong You
- Division of Cancer Biology and Therapeutics, Departments of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zijie Sun
- Department of Cancer Biology, Cancer Center and Beckman Research Institute, City of Hope, Duarte, CA, USA.
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