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Guo J, Ma X, Liu D, Wang F, Xia J, Zhang B, Zhao P, Zhong F, Chen L, Long Q, Jiang L, Zhang S, Liao N, Wang J, Wu W, Sun J, Huang M, Cheng Z, Huang G, Zou C. A distinct subset of urothelial cells with enhanced EMT features promotes chemotherapy resistance and cancer recurrence by increasing COL4A1-ITGB1 mediated angiogenesis. Drug Resist Updat 2024; 76:101116. [PMID: 38968684 DOI: 10.1016/j.drup.2024.101116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
Drug resistance and tumor recurrence remain clinical challenges in the treatment of urothelial carcinoma (UC). However, the underlying mechanism is not fully understood. Here, we performed single-cell RNA sequencing and identified a subset of urothelial cells with epithelial-mesenchymal transition (EMT) features (EMT-UC), which is significantly correlated with chemotherapy resistance and cancer recurrence. To validate the clinical significance of EMT-UC, we constructed EMT-UC like cells by introducing overexpression of two markers, Zinc Finger E-Box Binding Homeobox 1 (ZEB1) and Desmin (DES), and examined their histological distribution characteristics and malignant phenotypes. EMT-UC like cells were mainly enriched in UC tissues from patients with adverse prognosis and exhibited significantly elevated EMT, migration and gemcitabine tolerance in vitro. However, EMT-UC was not specifically identified from tumorous tissues, certain proportion of them were also identified in adjacent normal tissues. Tumorous EMT-UC highly expressed genes involved in malignant behaviors and exhibited adverse prognosis. Additionally, tumorous EMT-UC was associated with remodeled tumor microenvironment (TME), which exhibited high angiogenic and immunosuppressive potentials compared with the normal counterparts. Furthermore, a specific interaction of COL4A1 and ITGB1 was identified to be highly enriched in tumorous EMT-UC, and in the endothelial component. Targeting the interaction of COL4A1 and ITGB1 with specific antibodies significantly suppressed tumorous angiogenesis and alleviated gemcitabine resistance of UC. Overall, our findings demonstrated that the driven force of chemotherapy resistance and recurrence of UC was EMT-UC mediated COL4A1-ITGB1 interaction, providing a potential target for future UC treatment.
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Affiliation(s)
- Jinan Guo
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Xiaoshi Ma
- The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Dongcheng Liu
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China; Shenzhen Aier Eye Hospital, Shenzhen, Guangdong, PR China
| | - Fei Wang
- Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, PR China
| | - Jinquan Xia
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Bin Zhang
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Pan Zhao
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Fuhua Zhong
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Lipeng Chen
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Qiaoyun Long
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Lu Jiang
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Siyu Zhang
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Naikai Liao
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Jigang Wang
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Weiqing Wu
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Jichao Sun
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China
| | - Mou Huang
- The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, PR China
| | - Zhiqiang Cheng
- The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, PR China.
| | - Guixiao Huang
- The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, PR China.
| | - Chang Zou
- The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, PR China.
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2
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Xu J, Tu M. Single-cell transcriptomics reveals tumor landscape in ovarian carcinosarcoma. J Zhejiang Univ Sci B 2024; 25:686-699. [PMID: 39155781 PMCID: PMC11337087 DOI: 10.1631/jzus.b2300407] [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: 06/12/2023] [Accepted: 09/21/2023] [Indexed: 08/20/2024]
Abstract
OBJECTIVES The present study used single-cell RNA sequencing (scRNA-seq) to characterize the cellular composition of ovarian carcinosarcoma (OCS) and identify its molecular characteristics. METHODS scRNA-seq was performed in resected primary OCS for an in-depth analysis of tumor cells and the tumor microenvironment. Immunohistochemistry staining was used for validation. The scRNA-seq data of OCS were compared with those of high-grade serous ovarian carcinoma (HGSOC) tumors and other OCS tumors. RESULTS Both malignant epithelial and malignant mesenchymal cells were observed in the OCS patient of this study. We identified four epithelial cell subclusters with different biological roles. Among them, epithelial subcluster 4 presented high levels of breast cancer type 1 susceptibility protein homolog (BRCA1) and DNA topoisomerase 2-α (TOP2A) expression and was related to drug resistance and cell cycle. We analyzed the interaction between epithelial and mesenchymal cells and found that fibroblast growth factor (FGF) and pleiotrophin (PTN) signalings were the main pathways contributing to communication between these cells. Moreover, we compared the malignant epithelial and mesenchymal cells of this OCS tumor with our previous published HGSOC scRNA-seq data and OCS data. All the epithelial subclusters in the OCS tumor could be found in the HGSOC samples. Notably, the mesenchymal subcluster C14 exhibited specific expression patterns in the OCS tumor, characterized by elevated expression of cytochrome P450 family 24 subfamily A member 1 (CYP24A1), collagen type XXIII α1 chain (COL23A1), cholecystokinin (CCK), bone morphogenetic protein 7 (BMP7), PTN, Wnt inhibitory factor 1 (WIF1), and insulin-like growth factor 2 (IGF2). Moreover, this subcluster showed distinct characteristics when compared with both another previously published OCS tumor and normal ovarian tissue. CONCLUSIONS This study provides the single-cell transcriptomics signature of human OCS, which constitutes a new resource for elucidating OCS diversity.
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Affiliation(s)
- Junfen Xu
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou 310006, China.
| | - Mengyan Tu
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
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3
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Liu D, Wang L, Guo Y. Advances in and prospects of immunotherapy for prostate cancer. Cancer Lett 2024; 601:217155. [PMID: 39127338 DOI: 10.1016/j.canlet.2024.217155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/07/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Immunotherapy has shown promising therapeutic effects in hematological malignancies and certain solid tumors and has emerged as a critical and highly potential treatment modality for cancer. However, prostate cancer falls under the category of immune-resistant cold tumors, for which immunotherapy exhibits limited efficacy in patients with solid tumors. Thus, it is important to gain a deeper understanding of the tumor microenvironment in prostate cancer to facilitate immune system activation and overcome immune suppression to advance immunotherapy for prostate cancer. In this review, we discuss the immunosuppressive microenvironment of prostate cancer, which is characterized by the presence of few tumor-infiltrating lymphocytes, abundant immunosuppressive cells, low immunogenicity, and a noninflammatory phenotype, which significantly influences the efficacy of immunotherapy for prostate cancer. Immunotherapy is mainly achieved by activating the host immune system and overcoming immunosuppression. In this regard, we summarize the therapeutic advances in immune checkpoint blockade, immunogenic cell death, reversal of the immunosuppressive tumor microenvironment, tumor vaccines, immune adjuvants, chimeric antigen receptor T-cell therapy, and overcoming penetration barriers in prostate cancer, with the aim of providing novel research insights and approaches to enhance the effectiveness of immunotherapy for prostate cancer.
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Affiliation(s)
- Deng Liu
- Department of Ultrasound, Southwest Hospital, Army Medical University, Chongqing, 400038, China; Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Luofu Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Yanli Guo
- Department of Ultrasound, Southwest Hospital, Army Medical University, Chongqing, 400038, China.
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4
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Kirk JS, Wang J, Long M, Rosario S, Tracz A, Ji Y, Kumar R, Liu X, Jamroze A, Singh PK, Puzanov I, Chatta G, Cheng Q, Huang J, Wrana JL, Lovell J, Yu H, Liu S, Shen MM, Liu T, Tang DG. Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells. Cell Stem Cell 2024; 31:1203-1221.e7. [PMID: 38878775 PMCID: PMC11297676 DOI: 10.1016/j.stem.2024.05.008] [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: 03/13/2023] [Revised: 02/26/2024] [Accepted: 05/20/2024] [Indexed: 06/22/2024]
Abstract
Understanding prostate response to castration and androgen receptor signaling inhibitors (ARSI) is critical to improving long-term prostate cancer (PCa) patient survival. Here, we use a multi-omics approach on 229,794 single cells to create a mouse single-cell reference atlas for interpreting mouse prostate biology and castration response. Our reference atlas refines single-cell annotations and provides a chromatin context, which, when coupled with mouse lineage tracing, demonstrates that castration-resistant luminal cells are distinct from the pre-existent urethra-proximal stem/progenitor cells. Molecular pathway analysis and therapeutic studies further implicate AP1 (JUN/FOS), WNT/β-catenin, FOXQ1, NF-κB, and JAK/STAT pathways as major drivers of castration-resistant luminal populations with relevance to human PCa. Our datasets, which can be explored through an interactive portal (https://visportal.roswellpark.org/data/tang/), can aid in developing combination treatments with ARSI for advanced PCa patients.
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Affiliation(s)
- Jason S Kirk
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Jie Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Mark Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Spencer Rosario
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Amanda Tracz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Yibing Ji
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Rahul Kumar
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Xiaozhuo Liu
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Anmbreen Jamroze
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Prashant K Singh
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Gurkamal Chatta
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Qing Cheng
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Jonathan Lovell
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Han Yu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Michael M Shen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Dean G Tang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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5
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Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu R, Zhang B, Kaochar S, Freedland S, Posadas E, Ellis L, Di Vizio D, Morrissey C, Nelson P, Brady L, Murali R, Campbell M, Yang W, Knudsen B, Mostaghel E, Ye H, Garraway I, You S, Freeman M. ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer. Nucleic Acids Res 2024; 52:7740-7760. [PMID: 38932701 PMCID: PMC11260453 DOI: 10.1093/nar/gkae547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024] Open
Abstract
Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.
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Affiliation(s)
- Chen Qian
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Qian Yang
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mirja Rotinen
- Department of Health Sciences, Public University of Navarre, Pamplona, Navarra, Spain
| | - Rongrong Huang
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Hyoyoung Kim
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Brad Gallent
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yiwu Yan
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Radu M Cadaneanu
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Baohui Zhang
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Salma Kaochar
- Department of Medicine Section Hematology/Oncology Baylor College of Medicine, Houston, 77030 TX, USA
| | - Stephen J Freedland
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Edwin M Posadas
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leigh Ellis
- Center for Prostate Disease Research, Mutha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and the Walter Reed National Military Medical Center; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20814, USA
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dolores Di Vizio
- Departments of Urology, Pathology and Laboratory Medicine, and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lauren Brady
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ramachandran Murali
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moray J Campbell
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Department of Pathology and Cancer Center, Stony Brook University, NY 11794, USA
| | - Beatrice S Knudsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah, Salt Lake City, UT 84108, USA
| | - Elahe A Mostaghel
- Geriatric Research, Education and Clinical Center (GRECC), U.S. Department of Veterans Affairs Puget Sound Health Care System, Seattle, WA 98133, USA
| | - Huihui Ye
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Isla P Garraway
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Sungyong You
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael R Freeman
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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6
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Lu B, Liu Y, Yao Y, Yang T, Zhang H, Yang X, Huang R, Zhou W, Pan X, Cui X. Advances in sequencing and omics studies in prostate cancer: unveiling molecular pathogenesis and clinical applications. Front Oncol 2024; 14:1355551. [PMID: 38800374 PMCID: PMC11116611 DOI: 10.3389/fonc.2024.1355551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Background Prostate cancer (PCa) is one of the most threatening health problems for the elderly males. However, our understanding of the disease has been limited by the research technology for a long time. Recently, the maturity of sequencing technology and omics studies has been accelerating the studies of PCa, establishing themselves as an essential impetus in this field. Methods We assessed Web of Science (WoS) database for publications of sequencing and omics studies in PCa on July 3rd, 2023. Bibliometrix was used to conduct ulterior bibliometric analysis of countries/affiliations, authors, sources, publications, and keywords. Subsequently, purposeful large amounts of literature reading were proceeded to analyze research hotspots in this field. Results 3325 publications were included in the study. Research associated with sequencing and omics studies in PCa had shown an obvious increase recently. The USA and China were the most productive countries, and harbored close collaboration. CHINNAIYAN AM was identified as the most influential author, and CANCER RESEARCH exhibited huge impact in this field. Highly cited publications and their co-citation relationships were used to filtrate literatures for subsequent literature reading. Based on keyword analysis and large amounts of literature reading, 'the molecular pathogenesis of PCa' and 'the clinical application of sequencing and omics studies in PCa' were summarized as two research hotspots in the field. Conclusion Sequencing technology had a deep impact on the studies of PCa. Sequencing and omics studies in PCa helped researchers reveal the molecular pathogenesis, and provided new possibilities for the clinical practice of PCa.
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Affiliation(s)
- Bingnan Lu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifan Liu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuntao Yao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyue Yang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoyu Zhang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyue Yang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Runzhi Huang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Wang Zhou
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuwu Pan
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Booijink R, Terstappen LWMM, Dathathri E, Isebia K, Kraan J, Martens J, Bansal R. Identification of functional and diverse circulating cancer-associated fibroblasts in metastatic castration-naïve prostate cancer patients. Mol Oncol 2024. [PMID: 38634185 DOI: 10.1002/1878-0261.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
In prostate cancer (PCa), cancer-associated fibroblasts (CAFs) promote tumor progression, drug resistance, and metastasis. Although circulating tumor cells are studied as prognostic and diagnostic markers, little is known about other circulating cells and their association with PCa metastasis. Here, we explored the presence of circulating CAFs (cCAFs) in metastatic castration-naïve prostate cancer (mCNPC) patients. cCAFs were stained with fibroblast activation protein (FAP), epithelial cell adhesion molecule (EpCAM), and receptor-type tyrosine-protein phosphatase C (CD45), then FAP+EpCAM- cCAFs were enumerated and sorted using fluorescence-activated cell sorting. FAP+EpCAM- cCAFs ranged from 60 to 776 (389 mean ± 229 SD) per 2 × 108 mononuclear cells, whereas, in healthy donors, FAP+ EpCAM- cCAFs ranged from 0 to 71 (28 mean ± 22 SD). The mCNPC-derived cCAFs showed positivity for vimentin and intracellular collagen-I. They were viable and functional after sorting, as confirmed by single-cell collagen-I secretion after 48 h of culturing. Two cCAF subpopulations, FAP+CD45- and FAP+CD45+, were identified, both expressing collagen-I and vimentin, but with distinctly different morphologies. Collectively, this study demonstrates the presence of functional and viable circulating CAFs in mCNPC patients, suggesting the role of these cells in prostate cancer.
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Affiliation(s)
- Richell Booijink
- Personalized Diagnostics and Therapeutics, Department of Bioengineering Technologies, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Leon W M M Terstappen
- Department of Medical Cell BioPhysics, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
- Department of General, Visceral and Pediatric Surgery, University Hospital Düsseldorf, Heinrich-Heine University, Germany
| | - Eshwari Dathathri
- Department of Medical Cell BioPhysics, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Khrystany Isebia
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Jaco Kraan
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - John Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Ruchi Bansal
- Personalized Diagnostics and Therapeutics, Department of Bioengineering Technologies, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
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8
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Feng DC, Zhu WZ, Wang J, Li DX, Shi X, Xiong Q, You J, Han P, Qiu S, Wei Q, Yang L. The implications of single-cell RNA-seq analysis in prostate cancer: unraveling tumor heterogeneity, therapeutic implications and pathways towards personalized therapy. Mil Med Res 2024; 11:21. [PMID: 38605399 PMCID: PMC11007901 DOI: 10.1186/s40779-024-00526-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
In recent years, advancements in single-cell and spatial transcriptomics, which are highly regarded developments in the current era, particularly the emerging integration of single-cell and spatiotemporal transcriptomics, have enabled a detailed molecular comprehension of the complex regulation of cell fate. The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine. Currently, single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors. Starting from the perspective of RNA sequencing technology, this review outlined the significance of single-cell RNA sequencing (scRNA-seq) in prostate cancer research, encompassing preclinical medicine and clinical applications. We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies, as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis, treatment, and drug resistance characteristics of prostate cancer. These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer. Furthermore, we explore the potential clinical applications stemming from other single-cell technologies in this review, paving the way for future research in precision medicine.
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Affiliation(s)
- De-Chao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Division of Surgery & Interventional Science, University College London, London, WC1E 6BT, UK.
| | - Wei-Zhen Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Deng-Xiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xu Shi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiao Xiong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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9
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Zou C, Li W, Zhang Y, Feng N, Chen S, Yan L, He Q, Wang K, Li W, Li Y, Wang Y, Xu B, Zhang D. Identification of an anaplastic subtype of prostate cancer amenable to therapies targeting SP1 or translation elongation. SCIENCE ADVANCES 2024; 10:eadm7098. [PMID: 38569039 PMCID: PMC10990282 DOI: 10.1126/sciadv.adm7098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Histopathological heterogeneity is a hallmark of prostate cancer (PCa). Using spatial and parallel single-nucleus transcriptomics, we report an androgen receptor (AR)-positive but neuroendocrine-null primary PCa subtype with morphologic and molecular characteristics of small cell carcinoma. Such small cell-like PCa (SCLPC) is clinically aggressive with low AR, but high stemness and proliferation, activity. Molecular characterization prioritizes protein translation, represented by up-regulation of many ribosomal protein genes, and SP1, a transcriptional factor that drives SCLPC phenotype and overexpresses in castration-resistant PCa (CRPC), as two potential therapeutic targets in AR-indifferent CRPC. An SP1-specific inhibitor, plicamycin, effectively suppresses CRPC growth in vivo. Homoharringtonine, a Food And Drug Administration-approved translation elongation inhibitor, impedes CRPC progression in preclinical models and patients with CRPC. We construct an SCLPC-specific signature capable of stratifying patients for drug selectivity. Our studies reveal the existence of SCLPC in admixed PCa pathology, which may mediate tumor relapse, and establish SP1 and translation elongation as actionable therapeutic targets for CRPC.
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Affiliation(s)
- Cheng Zou
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Wenchao Li
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Yuanzhen Zhang
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Ninghan Feng
- Department of Urology and Wuxi School of Medicine, Jiangnan University Medical Center, Wuxi 214002, Jiangsu Province, China
| | - Saisai Chen
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Lianlian Yan
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
| | - Qinju He
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
| | - Kai Wang
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Wenjun Li
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Yingying Li
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Yang Wang
- Department of Urology and Wuxi School of Medicine, Jiangnan University Medical Center, Wuxi 214002, Jiangsu Province, China
| | - Bin Xu
- Department of Urology, School of Medicine, Affiliated ZhongDa Hospital of Southeast University, Nanjing 210009, Jiangsu Province, China
- National Medicine-Engineering Interdisciplinary Industry-Education Integration Innovation Platform (Ministry of Education), Basic Medicine Research and Innovation Center, Southeast University, Nanjing 210009, Jiangsu Province, China
| | - Dingxiao Zhang
- The Affiliated XiangTan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, Hunan Province, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha 410082, Hunan Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
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10
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Gao W, Zhou J, Huang J, Zhang Z, Chen W, Zhang R, Kang T, Liao D, Zhong L. Up-regulation of RAN by MYBL2 maintains osteosarcoma cancer stem-like cells population during heterogeneous tumor generation. Cancer Lett 2024; 586:216708. [PMID: 38336287 DOI: 10.1016/j.canlet.2024.216708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Intratumor heterogeneity is one of the major features of cancers, leading to aggressive disease and treatment failure. Cancer stem-like cells (CSCs) are believed to give rise to the heterogeneous cell types within tumors. Hence, understanding the regulatory mechanism underlying the recurrence process of heterogeneous tumor by CSCs could facilitate the development of CSC-targeted therapies. Here, utilizing single-cell transcriptomics, we present the molecular profile of osteosarcoma CSCs-derived heterogeneous tumors consisting of CSC clusters, osteoprogenitor and differentiated cell types, such as pre-osteoblasts, osteoblasts and chondroblasts. Furthermore, by constructing the comprehensive map of modulated genes during CSCs self-renewal and differentiation, we identify RAN exhibiting specific peak expression in osteosarcoma CSCs clusters which is transcriptionally up-regulated by MYBL2. Functionality, MYBL2-RAN pathway promotes the CSCs self-renewal by enhancing the nuclear accumulation of MYC protein, which in turn boosts the overexpression of RAN as a positive feedback. Importantly, blockage of MYBL2-RAN pathway sensitizes CSCs to cisplatin treatment and synergistically enhanced the cisplatin-induced cytotoxicity. Both MYBL2 and RAN are highly expressed in clinical osteosarcoma tissues which indicate poor prognosis. Collectively, our study provides advanced insights into the regeneration process of heterogeneous tumor originating from CSCs and highlights the MYBL2-RAN pathway as a promising target for CSC-based therapy in osteosarcoma.
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Affiliation(s)
- Weijie Gao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, PR China
| | - Jing Zhou
- Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, School of Medicine, Hubei Polytechnic University, Huangshi, PR China
| | - Jintao Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Zhiguang Zhang
- Sun Yat-sen University School of Medicine, Shenzhen, PR China
| | - Wanqi Chen
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, PR China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Dan Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Li Zhong
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Center of Digestive Diseases, Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, PR China.
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11
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Li J, Gao P, Zhang S, Lin X, Chen J, Zhang S, Jiao Y, Yu W, Xia X, Yang L. The G protein-coupled estrogen receptor of the trigeminal ganglion regulates acute and chronic itch in mice. CNS Neurosci Ther 2024; 30:e14367. [PMID: 37452499 PMCID: PMC10848076 DOI: 10.1111/cns.14367] [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: 04/12/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
AIMS Itch is an unpleasant sensation that severely impacts the patient's quality of life. Recent studies revealed that the G protein-coupled estrogen receptor (GPER) may play a crucial role in the regulation of pain and itch perception. However, the contribution of the GPER in primary sensory neurons to the regulation of itch perception remains elusive. This study aimed to investigate whether and how the GPER participates in the regulation of itch perception in the trigeminal ganglion (TG). METHODS AND RESULTS Immunofluorescence staining results showed that GPER-positive (GPER+ ) neurons of the TG were activated in both acute and chronic itch. Behavioral data indicated that the chemogenetic activation of GPER+ neurons of the TG of Gper-Cre mice abrogated scratching behaviors evoked by acute and chronic itch. Conversely, the chemogenetic inhibition of GPER+ neurons resulted in increased itch responses. Furthermore, the GPER expression and function were both upregulated in the TG of the dry skin-induced chronic itch mouse model. Pharmacological inhibition of GPER (or Gper deficiency) markedly increased acute and chronic itch-related scratching behaviors in mouse. Calcium imaging assays further revealed that Gper deficiency in TG neurons led to a marked increase in the calcium responses evoked by agonists of the transient receptor potential ankyrin A1 (TRPA1) and transient receptor potential vanilloid V1 (TRPV1). CONCLUSION Our findings demonstrated that the GPER of TG neurons is involved in the regulation of acute and chronic itch perception, by modulating the function of TRPA1 and TRPV1. This study provides new insights into peripheral itch sensory signal processing mechanisms and offers new targets for future clinical antipruritic therapy.
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Affiliation(s)
- Jun Li
- Department of Anesthesiology, Chaohu Hospital Affiliated to Anhui Medical University, Hefei, Anhui, China
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Po Gao
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Siyu Zhang
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
- Department of Anesthesiology, The Second Affiliated Hospital of Jiaxing University, Zhejiang, China
| | - Xiaoqi Lin
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Junhui Chen
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Song Zhang
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Yingfu Jiao
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Weifeng Yu
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Xiaoqiong Xia
- Department of Anesthesiology, Chaohu Hospital Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Liqun Yang
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
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12
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Rade M, Kreuz M, Borkowetz A, Sommer U, Blumert C, Füssel S, Bertram C, Löffler D, Otto DJ, Wöller LA, Schimmelpfennig C, Köhl U, Gottschling AC, Hönscheid P, Baretton GB, Wirth M, Thomas C, Horn F, Reiche K. A reliable transcriptomic risk-score applicable to formalin-fixed paraffin-embedded biopsies improves outcome prediction in localized prostate cancer. Mol Med 2024; 30:19. [PMID: 38302875 PMCID: PMC10835874 DOI: 10.1186/s10020-024-00789-9] [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: 07/11/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Clinical manifestation of prostate cancer (PCa) is highly variable. Aggressive tumors require radical treatment while clinically non-significant ones may be suitable for active surveillance. We previously developed the prognostic ProstaTrend RNA signature based on transcriptome-wide microarray and RNA-sequencing (RNA-Seq) analyses, primarily of prostatectomy specimens. An RNA-Seq study of formalin-fixed paraffin-embedded (FFPE) tumor biopsies has now allowed us to use this test as a basis for the development of a novel test that is applicable to FFPE biopsies as a tool for early routine PCa diagnostics. METHODS All patients of the FFPE biopsy cohort were treated by radical prostatectomy and median follow-up for biochemical recurrence (BCR) was 9 years. Based on the transcriptome data of 176 FFPE biopsies, we filtered ProstaTrend for genes susceptible to FFPE-associated degradation via regression analysis. ProstaTrend was additionally restricted to genes with concordant prognostic effects in the RNA-Seq TCGA prostate adenocarcinoma (PRAD) cohort to ensure robust and broad applicability. The prognostic relevance of the refined Transcriptomic Risk Score (TRS) was analyzed by Kaplan-Meier curves and Cox-regression models in our FFPE-biopsy cohort and 9 other public datasets from PCa patients with BCR as primary endpoint. In addition, we developed a prostate single-cell atlas of 41 PCa patients from 5 publicly available studies to analyze gene expression of ProstaTrend genes in different cell compartments. RESULTS Validation of the TRS using the original ProstaTrend signature in the cohort of FFPE biopsies revealed a relevant impact of FFPE-associated degradation on gene expression and consequently no significant association with prognosis (Cox-regression, p-value > 0.05) in FFPE tissue. However, the TRS based on the new version of the ProstaTrend-ffpe signature, which included 204 genes (of originally 1396 genes), was significantly associated with BCR in the FFPE biopsy cohort (Cox-regression p-value < 0.001) and retained prognostic relevance when adjusted for Gleason Grade Groups. We confirmed a significant association with BCR in 9 independent cohorts including 1109 patients. Comparison of the prognostic performance of the TRS with 17 other prognostically relevant PCa panels revealed that ProstaTrend-ffpe was among the best-ranked panels. We generated a PCa cell atlas to associate ProstaTrend genes with cell lineages or cell types. Tumor-specific luminal cells have a significantly higher TRS than normal luminal cells in all analyzed datasets. In addition, TRS of epithelial and luminal cells was correlated with increased Gleason score in 3 studies. CONCLUSIONS We developed a prognostic gene-expression signature for PCa that can be applied to FFPE biopsies and may be suitable to support clinical decision-making.
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Affiliation(s)
- Michael Rade
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Markus Kreuz
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Angelika Borkowetz
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Ulrich Sommer
- Institute of Pathology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Susanne Füssel
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Catharina Bertram
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dennis Löffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dominik J Otto
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Basic Science Division, Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Livia A Wöller
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Carolin Schimmelpfennig
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Ulrike Köhl
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Ann-Cathrin Gottschling
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Pia Hönscheid
- Institute of Pathology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Gustavo B Baretton
- Institute of Pathology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Manfred Wirth
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Christian Thomas
- Department of Urology, Faculty of Medicine, University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Friedemann Horn
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.
- Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany.
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), University of Leipzig, 04105, Leipzig, Germany.
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13
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Wang Y, Song W, Li Y, Liu Z, Zhao K, Jia L, Wang X, Jiang R, Tian Y, He X. Integrated analysis of tumor microenvironment features to establish a diagnostic model for papillary thyroid cancer using bulk and single-cell RNA sequencing technology. J Cancer Res Clin Oncol 2023; 149:16837-16850. [PMID: 37733241 PMCID: PMC10645658 DOI: 10.1007/s00432-023-05420-8] [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: 07/08/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Characterizing tumor microenvironment using single-cell RNA sequencing has been a promising strategy for cancer diagnosis and treatment. However, a few studies have focused on diagnosing papillary thyroid cancer (PTC) through this technology. Therefore, our study explored tumor microenvironment (TME) features and identified potential biomarkers to establish a diagnostic model for papillary thyroid cancer. METHODS The cell types were identified using the markers from the CellMarker database and published research. The CellChat package was conducted to analyze the cell-cell interaction. The SCEVAN package was used to identify malignant thyroid cells. The SCP package was used to perform multiple single-cell downstream analyses, such as GSEA analysis, enrichment analysis, pseudotime trajectory analysis, and differential expression analysis. The diagnostic model of PTC was estimated using the calibration curves, receiver operating characteristic curves, and decision curve analysis. RT-qPCR was performed to validate the expression of candidate genes in human papillary thyroid samples. RESULTS Eight cell types were identified in the scRNA-seq dataset by published cell markers. Extensive cell-cell interactions like FN1/ITGB1 existed in PTC tissues. We identified 26 critical genes related to PTC progression. Further, eight subgroups of PTC tumor cells were identified and exhibited high heterogeneity. The MDK/LRP1, MDK/ALK, GAS6/MERTK, and GAS6/AXL were identified as potential ligand-receptor pairs involved in the interactions between fibroblasts/endothelial cells and tumor cells. Eventually, the diagnostic model constructed by TRPC5, TENM1, NELL2, DMD, SLC35F3, and AUTS2 showed a good efficiency for distinguishing the PTC and normal tissues. CONCLUSIONS Our study comprehensively characterized the tumor microenvironment in papillary thyroid cancer. Through combined analysis with bulk RNA-seq, six potential diagnostic biomarkers were identified and validated. The diagnostic model we constructed was a promising tool for PTC diagnosis. Our findings provide new insights into the heterogeneity of thyroid cancer and the theoretical basis for diagnosing thyroid cancer.
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Affiliation(s)
- Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Wenbin Song
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yingxi Li
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Zhaoyi Liu
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ke Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Lanning Jia
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Xiaoning Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ruoyu Jiang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yao Tian
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
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14
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Jain S, Malhotra KPK, Patiyal S, Raghava GPS. A Highly Accurate Model for Screening Prostate Cancer Using Propensity Index Panel of Ten Genes. J Comput Biol 2023; 30:1305-1314. [PMID: 37917795 DOI: 10.1089/cmb.2023.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Affiliation(s)
- Shipra Jain
- Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi, India
| | - Kawal Preet Kaur Malhotra
- Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi, India
| | - Gajendra Pal Singh Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi, India
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15
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Ma X, Chen L, Chen T, Chen K, Zhang H, Huang K, Zheng H, Jin H, Cheng Z, Xiao K, Guo J. Identification of a 24-gene panel and a novel marker of PODXL2 essential for the pathological diagnosis of early prostate cancer. Comput Struct Biotechnol J 2023; 21:5476-5490. [PMID: 38022698 PMCID: PMC10663703 DOI: 10.1016/j.csbj.2023.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/13/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Precise diagnosis of early prostate cancer (PCa) is critical for preventing tumor progression. However, the diagnostic outcomes of currently used markers are far from satisfactory due to the low sensitivity or specificity. Here, we identified a diagnostic subpopulation in PCa tissue with the integrating analysis of single-cell and bulk RNA-seq. The representative markers of this subpopulation were extracted to perform intersection analysis with early-PCa-related gene module generated from weighted correlation network analysis (WGCNA). A total of 24 overlapping genes were obtained, the diagnostic roles of which were validated by distinguishing normal and tumorous prostate samples from the public dataset. A least absolute shrinkage and selection operator (LASSO) model was constructed based on these genes and the obtained 24-gene panel showed high sensitivity and specificity for PCa diagnosis, with better identifying capability of PCa than the commercially used gene panel of Oncotype DX. The top two risk factors, TRPM4 and PODXL2, were verified to be highly expressed in early PCa tissues by multiplex immunostaining, and PODXL2 was more sensitive and specific compared to TRPM4 and the pathologically used marker AMACR for early PCa diagnosis, suggesting a novel and promising pathology marker.
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Affiliation(s)
- Xiaoshi Ma
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Lipeng Chen
- Clinical Medical Research Center, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Tao Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Kun Chen
- Department of Radiotherapy, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing 210000, Jiangsu, China
| | - Huirong Zhang
- Clinical Medical Research Center, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Kaipeng Huang
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Han Zheng
- Department of Urology, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu 241000, Anhui, China
| | - Hongtao Jin
- Department of Radiotherapy, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing 210000, Jiangsu, China
| | - Zhiqiang Cheng
- Department of Pathology, Third People’s Hospital of Shenzhen (The Second Affiliated Hospital of Southern University of Science and Technology), Shenzhen 518100, Guangdong, China
| | - Kefeng Xiao
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
| | - Jinan Guo
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
- Clinical Research Center for Geriatrtics, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China
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16
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Hong YC, Hu TY, Hsu CS, Yeh WW, Wong WZ, Shen TW, Chang CH, Hua K, Tung CY, Peng YC, Huang WJ, Chang PC, Lin TP. Single-cell analysis of castration-resistant prostate cancers to identify potential biomarkers for diagnosis and prognosis of neuroendocrine prostate cancer. Am J Cancer Res 2023; 13:4560-4578. [PMID: 37970364 PMCID: PMC10636664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/29/2023] [Indexed: 11/17/2023] Open
Abstract
The high heterogeneity and low percentage of neuroendocrine cells in prostate cancer limit the utility of traditional bulk RNA sequencing and even single-cell RNA sequencing to find better biomarkers for early diagnosis and stratification. Re-clustering of specific cell-type holds great promise for identification of intra-cell-type heterogeneity. However, this has not yet been used in studying neuroendocrine prostate cancer heterogeneity. Neuroendocrine cluster(s) were individually identified in each castration-resistant prostate cancer specimen and combined for trajectory analysis. Three neuroendocrine states were identified. Neuroendocrine state 2 with the highest AR score was considered the initial starting state of neuroendocrine transdifferentiation. State 1 and state 3 with distinct high neuroendocrine scores and marker genes enriched in N-Myc and REST target genes, respectively, were considered as two different types of neuroendocrine differentiated cancer cells. These two states contained distinct groups of prostate cancer biomarkers and a strong distinguishing ability of normal versus cancerous prostate across different pathological grading was found in the N-Myc-associated state. Our data highlight the central role of N-Myc and REST in mediating lineage plasticity and classifying neuroendocrine phenotypes.
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Affiliation(s)
- Yung-Chih Hong
- Faculty of Medicine, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Tze-Yun Hu
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Chih-Sin Hsu
- Cancer Progression Research Center, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Wayne W Yeh
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Wei-Ze Wong
- Faculty of Medicine, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Tsai-Wen Shen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Ching-Hsin Chang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Department of Urology, Taipei Medical University HospitalTaipei 11031, Taiwan
| | - Kate Hua
- Cancer Progression Research Center, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Chien-Yi Tung
- Cancer Progression Research Center, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Yu-Ching Peng
- Department of Pathology and Laboratory Medicine, Taipei Veterans General HospitalTaipei 11217, Taiwan
| | - William J Huang
- Faculty of Medicine, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Department of Urology, Taipei Veterans General HospitalTaipei 11217, Taiwan
| | - Pei-Ching Chang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Tzu-Ping Lin
- Faculty of Medicine, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Department of Urology, Taipei Veterans General HospitalTaipei 11217, Taiwan
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17
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Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu RM, Zhang B, Kaochar S, Freedland SJ, Posadas EM, Ellis L, Vizio DD, Morrissey C, Nelson PS, Brady L, Murali R, Campbell MJ, Yang W, Knudsen BS, Mostaghel EA, Ye H, Garraway IP, You S, Freeman MR. ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560025. [PMID: 37905039 PMCID: PMC10614109 DOI: 10.1101/2023.09.28.560025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that the HOX/CUT transcription factor ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 targets include the glucocorticoid receptor and the NE splicing factor SRRM4, among others. OC2 regulates gene expression by promoter binding, enhancement of chromatin accessibility, and formation of novel super-enhancers. OC2 also activates glucuronidation genes that irreversibly disable androgen, thereby evoking phenotypic heterogeneity indirectly by hormone depletion. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC. Our findings support enhanced efforts to therapeutically target this protein as a means of suppressing treatment-resistant disease.
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Affiliation(s)
- Chen Qian
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Qian Yang
- Department of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mirja Rotinen
- Department of Health Sciences, Public University of Navarre, Pamplona, Navarra, Spain
| | - Rongrong Huang
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Hyoyoung Kim
- Department of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Brad Gallent
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yiwu Yan
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Radu M. Cadaneanu
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Baohui Zhang
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Salma Kaochar
- Department of Medicine Section Hematology/Oncology Baylor College of Medicine, Houston, 77030, TX
| | - Stephen J. Freedland
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Edwin M. Posadas
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leigh Ellis
- Center for Prostate Disease Research, Mutha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and the Walter Reed National Military Medical Center; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20814, USA
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dolores Di Vizio
- Department of Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lauren Brady
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ramachandran Murali
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moray J. Campbell
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Department of Pathology and Cancer Center, Stony Brook University, NY 11794, USA
| | - Beatrice S. Knudsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84108, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah 84108, USA
| | - Elahe A. Mostaghel
- Geriatric Research, Education and Clinical Center (GRECC), U.S. Department of Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98133, USA
| | - Huihui Ye
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Isla P. Garraway
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Sungyong You
- Department of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael R. Freeman
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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18
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Liang L, Shang J, Zhang Y, Xu Y, Zhouteng Y, Wen J, Zhao Y, Feng N, Zhao R. Identification and validation of obesity related genes signature based on microenvironment phenotypes in prostate adenocarcinoma. Aging (Albany NY) 2023; 15:10168-10192. [PMID: 37788005 PMCID: PMC10599753 DOI: 10.18632/aging.205065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/20/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND The role of obesity related genes (ORGs) in the immune checkpoint inhibitors (ICIs) treatment of prostate adenocarcinoma (PRAD) has not yet been proved by research. METHODS We comprehensively evaluated the ORGs patterns in PRAD based on tumor microenvironment (TME) phenotypes and immunotherapy efficacies. Then we constructed a ORGs risk score for prognosis and a ORGs signature for accurate prediction of TME phenotype and immunotherapy efficacy in order to evaluate individual patients. RESULTS Two distinct ORGs patterns were generated. The two ORGs patterns were consistent with inflammatory and non-inflammatory TME phenotypes. ORGs patterns had an important role for predicting immunotherapy efficacies. Next, we constructed a ORGs risk score for predicting each patient's prognosis with high performance in TCGA-PRAD. The ORGs risk score could be well verified in the external cohorts including GSE70769 and GSE21034. Then, we developed a ORGs signature and found it was significantly positively correlated with tumor-infiltrating lymphocytes in TCGA-PRAD. We found that each patient in the high-risk ORGs signature group represented a non-inflamed TME phenotype on the single cell level. The patients with high ORGs signature had more sensitivity to immunotherapy. And those ORGs were verified. CONCLUSIONS ORGs pattern depicts different TME phenotypes in PRAD. The ORGs risk score and ORGs signature have an important role for predicting prognosis and immunotherapy efficacies.
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Affiliation(s)
- Linghui Liang
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University and Jiangnan University Medical Center, Wuxi, Jiangsu, China
| | - Jinwei Shang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuwei Zhang
- Nantong University Medical School, Nantong, Jiangsu, China
| | - Yuxin Xu
- Nanjing Medical University, Nanjing, Jiangsu, China
| | | | | | - Yuxin Zhao
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University and Jiangnan University Medical Center, Wuxi, Jiangsu, China
| | - Ruizhe Zhao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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19
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Ramírez-Mena A, Andrés-León E, Alvarez-Cubero MJ, Anguita-Ruiz A, Martinez-Gonzalez LJ, Alcala-Fdez J. Explainable artificial intelligence to predict and identify prostate cancer tissue by gene expression. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 240:107719. [PMID: 37453366 DOI: 10.1016/j.cmpb.2023.107719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/16/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND AND OBJECTIVE Prostate cancer is one of the most prevalent forms of cancer in men worldwide. Traditional screening strategies such as serum PSA levels, which are not necessarily cancer-specific, or digital rectal exams, which are often inconclusive, are still the screening methods used for the disease. Some studies have focused on identifying biomarkers of the disease but none have been reported for diagnosis in routine clinical practice and few studies have provided tools to assist the pathologist in the decision-making process when analyzing prostate tissue. Therefore, a classifier is proposed to predict the occurrence of PCa that provides physicians with accurate predictions and understandable explanations. METHODS A selection of 47 genes was made based on differential expression between PCa and normal tissue, GO gene ontology as well as the literature to be used as input predictors for different machine learning methods based on eXplainable Artificial Intelligence. These methods were trained using different class-balancing strategies to build accurate classifiers using gene expression data from 550 samples from 'The Cancer Genome Atlas'. Our model was validated in four external cohorts with different ancestries, totaling 463 samples. In addition, a set of SHapley Additive exPlanations was provided to help clinicians understand the underlying reasons for each decision. RESULTS An in-depth analysis showed that the Random Forest algorithm combined with majority class downsampling was the best performing approach with robust statistical significance. Our method achieved an average sensitivity and specificity of 0.90 and 0.8 with an AUC of 0.84 across all databases. The relevance of DLX1, MYL9 and FGFR genes for PCa screening was demonstrated in addition to the important role of novel genes such as CAV2 and MYLK. CONCLUSIONS This model has shown good performance in 4 independent external cohorts of different ancestries and the explanations provided are consistent with each other and with the literature, opening a horizon for its application in clinical practice. In the near future, these genes, in combination with our model, could be applied to liquid biopsy to improve PCa screening.
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Affiliation(s)
- Alberto Ramírez-Mena
- GENYO, Centre for Genomics and Oncological Research: Pfizer -University of Granada - Andalusian Regional Government, Granada, 18016, Spain.
| | - Eduardo Andrés-León
- Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), Spanish National Research Council (CSIC), Granada, 18016, Spain.
| | - Maria Jesus Alvarez-Cubero
- GENYO, Centre for Genomics and Oncological Research: Pfizer -University of Granada - Andalusian Regional Government, Granada, 18016, Spain; Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, 18071, Spain.
| | | | - Luis Javier Martinez-Gonzalez
- GENYO, Centre for Genomics and Oncological Research: Pfizer -University of Granada - Andalusian Regional Government, Granada, 18016, Spain.
| | - Jesus Alcala-Fdez
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, Granada, 18071, Spain.
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20
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Liu W, Wang M, Wang M, Liu M. Single-cell and bulk RNA sequencing reveal cancer-associated fibroblast heterogeneity and a prognostic signature in prostate cancer. Medicine (Baltimore) 2023; 102:e34611. [PMID: 37565899 PMCID: PMC10419654 DOI: 10.1097/md.0000000000034611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/14/2023] [Indexed: 08/12/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs), the central players in the tumor microenvironment (TME), can promote tumor progression and metastasis via various functions. However, the properties of CAFs in prostate cancer (PCa) have not been fully assessed. Therefore, we aimed to examine the CAF characteristics in PCa and construct a CAF-derived signature to predict PCa prognosis. CAFs were identified using single-cell RNA sequencing (scRNA-seq) data from 3 studies. We performed the FindAllMarkers function to extract CAF marker genes and constructed a signature to predict the biochemical relapse-free survival (bRFS) of PCa in the Cancer Genome Atlas (TCGA) cohort. Subsequently, different algorithms were applied to reveal the differences of the TME, immune infiltration, treatment responses in the high- and low-risk groups. Additionally, the CAF heterogeneity was assessed in PCa, which were confirmed by the functional enrichment analysis, gene set enrichment analysis (GSEA), and AUCell method. The scRNA-seq analysis identified a CAF cluster with 783 cells and determined 183 CAF marker genes. Cell-cell communication revealed extensive interactions between fibroblasts and immune cells. A CAF-related prognostic model, containing 7 genes (ASPN, AEBP1, ALDH1A1, BGN, COL1A1, PAGE4 and RASD1), was developed to predict bRFS and validated by 4 independent bulk RNA-seq cohorts. Moreover, the high-risk group of the signature score connected with an immunosuppressive TME, such as a higher level of M2 macrophages and lower levels of plasma cells and CD8+ T cells, and a reduced reaction rate for immunotherapy compared with low-risk group. After re-clustering CAFs via unsupervised clustering, we revealed 3 biologically distinct CAF subsets, namely myofibroblast-like CAFs (myCAFs), immune and inflammatory CAFs (iCAFs) and antigen-presenting CAFs (apCAFs). In conclusion, the CAF-derived signature, the first of its kind, can effectively predict PCa prognosis and serve as an indicator for immunotherapy. Furthermore, our study identified 3 CAF subpopulations with distinct functions in PCa.
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Affiliation(s)
- Wen Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Miaomiao Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Miao Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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21
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Chao S, Zhang F, Yan H, Wang L, Zhang L, Wang Z, Xue R, Wang L, Wu Z, Jiang B, Shi G, Xue Y, Du J, Bu P. Targeting intratumor heterogeneity suppresses colorectal cancer chemoresistance and metastasis. EMBO Rep 2023; 24:e56416. [PMID: 37338390 PMCID: PMC10398666 DOI: 10.15252/embr.202256416] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 06/21/2023] Open
Abstract
Intratumor heterogeneity (ITH) is a barrier to effective therapy. However, it is largely unknown how ITH is established at the onset of tumor progression, such as in colorectal cancer (CRC). Here, we integrate single-cell RNA-seq and functional validation to show that asymmetric division of CRC stem-like cells (CCSC) is critical for early ITH establishment. We find that CCSC-derived xenografts contain seven cell subtypes, including CCSCs, that dynamically change during CRC xenograft progression. Furthermore, three of the subtypes are generated by asymmetric division of CCSCs. They are functionally distinct and appear at the early stage of xenografts. In particular, we identify a chemoresistant and an invasive subtype, and investigate the regulators that control their generation. Finally, we show that targeting the regulators influences cell subtype composition and CRC progression. Our findings demonstrate that asymmetric division of CCSCs contributes to the early establishment of ITH. Targeting asymmetric division may alter ITH and benefit CRC therapy.
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Affiliation(s)
- Shanshan Chao
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Fei Zhang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Huiwen Yan
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of MedicineDuke UniversityDurhamNCUSA
| | - Liwen Zhang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Zhi Wang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Ruixin Xue
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Lei Wang
- Laboratory Animal Research Center, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Zhenzhen Wu
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Bing Jiang
- Nanozyme Medical Center, School of Basic Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Guizhi Shi
- Laboratory Animal Research Center, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- Aviation General Hospital of BeijingMedical University and Beijing Institute of Translational Medicine, University of Chinese Academy of SciencesBeijingChina
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Junfeng Du
- Department of General Surgery, The 7 Medical CenterChinese PLA General HospitalBeijingChina
- The 2 School of Clinical MedicineSouthern Medical UniversityGuangdongChina
- Medical Department of General Surgery, The 1 Medical CenterChinese PLA General HospitalBeijingChina
| | - Pengcheng Bu
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of BiophysicsChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
- Center for Excellence in BiomacromoleculesChinese Academy of SciencesBeijingChina
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22
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Chen W, Xu D, Liu Q, Wu Y, Wang Y, Yang J. Unraveling the heterogeneity of cholangiocarcinoma and identifying biomarkers and therapeutic strategies with single-cell sequencing technology. Biomed Pharmacother 2023; 162:114697. [PMID: 37060660 DOI: 10.1016/j.biopha.2023.114697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a common malignant tumor of the biliary tract that carries a high burden of morbidity and a poor prognosis. Due to the lack of precise diagnostic methods, many patients are often diagnosed at advanced stages of the disease. The current treatment options available are of varying efficacy, underscoring the urgency for the discovery of more effective biomarkers for early diagnosis and improved treatment. Recently, single-cell sequencing (SCS) technology has gained popularity in cancer research. This technology has the ability to analyze tumor tissues at the single-cell level, thus providing insights into the genomics and epigenetics of tumor cells. It also serves as a practical approach to study the mechanisms of cancer progression and to explore therapeutic strategies. In this review, we aim to assess the heterogeneity of CCA using single-cell sequencing technology, with the ultimate goal of identifying possible biomarkers and potential treatment targets.
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Affiliation(s)
- Wangyang Chen
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China
| | - Dongchao Xu
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China
| | - Qiang Liu
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China
| | - Yirong Wu
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China
| | - Yu Wang
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China.
| | - Jianfeng Yang
- Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Biliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Hangzhou Institute of Digestive Diseases, Hangzhou, Zhejiang Province 310003, China; Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, Zhejiang Province 310003, China; Zhejiang Provincial Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research, Hangzhou, Zhejiang Province 310003, China.
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23
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Zhang G, Xu X, Zhu L, Li S, Chen R, Lv N, Li Z, Wang J, Li Q, Zhou W, Yang P, Liu J. A Novel Molecular Classification Method for Glioblastoma Based on Tumor Cell Differentiation Trajectories. Stem Cells Int 2023; 2023:2826815. [PMID: 37964983 PMCID: PMC10643041 DOI: 10.1155/2023/2826815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2023] Open
Abstract
The latest 2021 WHO classification redefines glioblastoma (GBM) as the hierarchical reporting standard by eliminating glioblastoma, IDH-mutant and only retaining the tumor entity of "glioblastoma, IDH-wild type." Knowing that subclassification of tumors based on molecular features is supposed to facilitate the therapeutic choice and increase the response rate in cancer patients, it is necessary to carry out molecular classification of the newly defined GBM. Although differentiation trajectory inference based on single-cell sequencing (scRNA-seq) data holds great promise for identifying cell heterogeneity, it has not been used in the study of GBM molecular classification. Single-cell transcriptome sequencing data from 10 GBM samples were used to identify molecular classification based on differentiation trajectories. The expressions of identified features were validated by public bulk RNA-sequencing data. Clinical feasibility of the classification system was examined in tissue samples by immunohistochemical (IHC) staining and immunofluorescence, and their clinical significance was investigated in public cohorts and clinical samples with complete clinical follow-up information. By analyzing scRNA-seq data of 10 GBM samples, four differentiation trajectories from the glioblastoma stem cell-like (GSCL) cluster were identified, based on which malignant cells were classified into five characteristic subclusters. Each cluster exhibited different potential drug sensitivities, pathways, functions, and transcriptional modules. The classification model was further examined in TCGA and CGGA datasets. According to the different abundance of five characteristic cell clusters, the patients were classified into five groups which we named Ac-G, Class-G, Neo-G, Opc-G, and Undiff-G groups. It was found that the Undiff-G group exhibited the worst overall survival (OS) in both TCGA and CGGA cohorts. In addition, the classification model was verified by IHC staining in 137 GBM samples to further clarify the difference in OS between the five groups. Furthermore, the novel biomarkers of glioblastoma stem cells (GSCs) were also described. In summary, we identified five classifications of GBM and found that they exhibited distinct drug sensitivities and different prognoses, suggesting that the new grouping system may be able to provide important prognostic information and have certain guiding significance for the treatment of GBM, and identified the GSCL cluster in GBM tissues and described its characteristic program, which may help develop new potential therapeutic targets for GSCs in GBM.
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Affiliation(s)
- Guanghao Zhang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xiaolong Xu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Luojiang Zhu
- Neurosurgery Department, 922th Hospital of Joint Logistics Support Force, PLA, China
| | - Sisi Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Rundong Chen
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Nan Lv
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Zifu Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jing Wang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Qiang Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Wang Zhou
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Pengfei Yang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jianmin Liu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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24
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Zou Y, Ye F, Kong Y, Hu X, Deng X, Xie J, Song C, Ou X, Wu S, Wu L, Xie Y, Tian W, Tang Y, Wong C, Chen Z, Xie X, Tang H. The Single-Cell Landscape of Intratumoral Heterogeneity and The Immunosuppressive Microenvironment in Liver and Brain Metastases of Breast Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203699. [PMID: 36529697 PMCID: PMC9929130 DOI: 10.1002/advs.202203699] [Citation(s) in RCA: 94] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/11/2022] [Indexed: 05/07/2023]
Abstract
Distant metastasis remains the major cause of morbidity for breast cancer. Individuals with liver or brain metastasis have an extremely poor prognosis and low response rates to anti-PD-1/L1 immune checkpoint therapy compared to those with metastasis at other sites. Therefore, it is urgent to investigate the underlying mechanism of anti-PD-1/L1 resistance and develop more effective immunotherapy strategies for these patients. Using single-cell RNA sequencing, a high-resolution map of the entire tumor ecosystem based on 44 473 cells from breast cancer liver and brain metastases is depicted. Identified by canonical markers and confirmed by multiplex immunofluorescent staining, the metastatic ecosystem features remarkable reprogramming of immunosuppressive cells such as FOXP3+ regulatory T cells, LAMP3+ tolerogenic dendritic cells, CCL18+ M2-like macrophages, RGS5+ cancer-associated fibroblasts, and LGALS1+ microglial cells. In addition, PD-1 and PD-L1/2 are barely expressed in CD8+ T cells and cancer/immune/stromal cells, respectively. Interactions of the immune checkpoint molecules LAG3-LGALS3 and TIGIT-NECTIN2 between CD8+ T cells and cancer/immune/stromal cells are found to play dominant roles in the immune escape. In summary, this study dissects the intratumoral heterogeneity and immunosuppressive microenvironment in liver and brain metastases of breast cancer for the first time, providing insights into the most appropriate immunotherapy strategies for these patients.
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Affiliation(s)
- Yutian Zou
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Feng Ye
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Yanan Kong
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Xiaoqian Hu
- School of Biomedical SciencesFaculty of MedicineThe University of Hong Kong21 Sassoon RoadHong Kong999077China
| | - Xinpei Deng
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Jindong Xie
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Cailu Song
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Xueqi Ou
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Song Wu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Linyu Wu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Yi Xie
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Wenwen Tian
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Yuhui Tang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Chau‐Wei Wong
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Zhe‐Sheng Chen
- College of Pharmacy and Health SciencesSt. John's UniversityQueensNYUSA
| | - Xinhua Xie
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
| | - Hailin Tang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine651 East Dongfeng RoadGuangzhou510060China
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Pan J, Ma Z, Liu B, Qian H, Shao X, Liu J, Wang Q, Xue W. Identification of cancer-associated fibroblasts subtypes in prostate cancer. Front Immunol 2023; 14:1133160. [PMID: 37033924 PMCID: PMC10080037 DOI: 10.3389/fimmu.2023.1133160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/15/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Cancer-associated fibroblasts (CAFs) are one of the most abundant cell types in tumor microenvironment. However, the phenotypic and functional heterogeneities among CAFs have not been sufficiently investigated in prostate cancer. Methods We obtained and analyzed the single-cell RNA-sequencing data from 26 hormone-sensitive prostate cancer samples and 8 castration-resistant prostate cancer samples, along with the analysis of bulk-sequencing datasets. Furthermore, we performed multicolor immunofluorescence staining to verify the findings from the data analysis. Results We identified two major CAFs subtypes with distinct molecular characteristics and biological functions in prostate cancer microenvironment, namely αSMA+ CAV1+ CAFs-C0 and FN1+ FAP+ CAFs-C1. Another single-cell RNA-sequencing dataset containing 7 bone metastatic prostate cancer samples demonstrated that osteoblasts in the bone metastatic lesions comprised two subtypes with molecular characteristics and biological functions similar to CAFs-C0 and CAFs-C1 in the primary tumor sites. In addition, we discovered a transcriptional factor regulatory network depending on CAFs-C1. CAFs-C1, but not CAFs-C0, was associated with castration resistance and poor prognosis. We also found that CAFs-C1 signature was involved in treatment resistance to immune checkpoint inhibitors. Discussion In summary, our results identified the presence of heterogeneous CAFs subtypes in prostate cancer microenvironment and the potential of specific CAFs subtype as therapeutic target for castration-resistant prostate cancer.
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Affiliation(s)
- Jiahua Pan
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zehua Ma
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Liu
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyang Qian
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoguang Shao
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiazhou Liu
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Wang
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Qi Wang, ; Wei Xue,
| | - Wei Xue
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Qi Wang, ; Wei Xue,
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26
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Zhang M, Lu Y, Wang L, Mao Y, Hu X, Chen Z. Current Status of Research on Small Extracellular Vesicles for the Diagnosis and Treatment of Urological Tumors. Cancers (Basel) 2022; 15:cancers15010100. [PMID: 36612097 PMCID: PMC9817817 DOI: 10.3390/cancers15010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Extracellular vesicles (EVs) are important mediators of communication between tumor cells and normal cells. These vesicles are rich in a variety of contents such as RNA, DNA, and proteins, and can be involved in angiogenesis, epithelial-mesenchymal transition, the formation of pre-metastatic ecological niches, and the regulation of the tumor microenvironment. Small extracellular vesicles (sEVs) are a type of EVs. Currently, the main treatments for urological tumors are surgery, radiotherapy, and targeted therapy. However, urological tumors are difficult to diagnose and treat due to their high metastatic rate, tendency to develop drug resistance, and the low sensitivity of liquid biopsies. Numerous studies have shown that sEVs offer novel therapeutic options for tumor treatment, such as tumor vaccines and tumor drug carriers. sEVs have attracted a great deal of attention owing to their contribution to in intercellular communication, and as novel biomarkers, and role in the treatment of urological tumors. This article reviews the research and applications of sEVs in the diagnosis and treatment of urological tumors.
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Affiliation(s)
- Mengting Zhang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Yukang Lu
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Lanfeng Wang
- Department of Nephrology, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Yiping Mao
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xinyi Hu
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Zhiping Chen
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, China
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
- Correspondence: ; Tel.: +86-150-8373-7280
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Edwards N, Dillard C, Prashant NM, Hongyu L, Yang M, Ulianova E, Horvath A. SCExecute: custom cell barcode-stratified analyses of scRNA-seq data. Bioinformatics 2022; 39:6854977. [PMID: 36448703 PMCID: PMC9825775 DOI: 10.1093/bioinformatics/btac768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
MOTIVATION In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are not sufficiently supported by available tools designed for high-throughput sequencing data. RESULTS We introduce SCExecute, which executes a user-provided command on barcode-stratified, extracted on-the-fly, single-cell binary alignment map (scBAM) files. SCExecute extracts the alignments with each cell barcode from aligned, pooled single-cell sequencing data. Simple commands, monolithic programs, multi-command shell scripts or complex shell-based pipelines are then executed on each scBAM file. scBAM files can be restricted to specific barcodes and/or genomic regions of interest. We demonstrate SCExecute with two popular variant callers-GATK and Strelka2-executed in shell-scripts together with commands for BAM file manipulation and variant filtering, to detect single-cell-specific expressed single nucleotide variants from droplet scRNA-seq data (10X Genomics Chromium System).In conclusion, SCExecute facilitates custom cell-level analyses on barcoded scRNA-seq data using currently available tools and provides an effective solution for studying low (cellular) frequency transcriptome features. AVAILABILITY AND IMPLEMENTATION SCExecute is implemented in Python3 using the Pysam package and distributed for Linux, MacOS and Python environments from https://horvathlab.github.io/NGS/SCExecute. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Christian Dillard
- Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20037, USA
| | - N M Prashant
- Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20037, USA,Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Liu Hongyu
- Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20037, USA,Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Mia Yang
- Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20037, USA
| | - Evgenia Ulianova
- Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20037, USA
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Yuan LL, Chen Z, Qin J, Qin CJ, Bian J, Dong RF, Yuan TB, Xu YT, Kong LY, Xia YZ. Single-cell sequencing reveals the landscape of the tumor microenvironment in a skeletal undifferentiated pleomorphic sarcoma patient. Front Immunol 2022; 13:1019870. [DOI: 10.3389/fimmu.2022.1019870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Skeletal undifferentiated pleomorphic sarcoma (SUPS) is an invasive pleomorphic soft tissue sarcoma with a high degree of malignancy and poor prognosis. It is prone to recur and metastasize. The tumor microenvironment (TME) and the pathophysiology of SUPS are barely described. Single-cell RNA sequencing (scRNA-seq) provides an opportunity to dissect the landscape of human diseases at an unprecedented resolution, particularly in diseases lacking animal models, such as SUPS. We performed scRNA-seq to analyze tumor tissues and paracancer tissues from a SUPS patient. We identified the cell types and the corresponding marker genes in this SUPS case. We further showed that CD8+ exhausted T cells and Tregs highly expressed PDCD1, CTLA4 and TIGIT. Thus, PDCD1, CTLA4 and TIGIT were identified as potential targets in this case. We applied copy number karyotyping of aneuploid tumors (CopyKAT) to distinguish malignant cells from normal cells in fibroblasts. Our study identified eight malignant fibroblast subsets in SUPS with distinct gene expression profiles. C1-malignant Fibroblast and C6-malignant Fibroblast in the TME play crucial roles in tumor growth, angiogenesis, metastasis and immune response. Hence, targeting malignant fibroblasts could represent a potential strategy for this SUPS therapy. Intervention via tirelizumab enabled disease control, and immune checkpoint inhibitors (ICIs) of PD-1 may be considered as the first-line option in patients with SUPS. Taken together, scRNA-seq analyses provided a powerful basis for this SUPS treatment, improved our understanding of complex human diseases, and may afforded an alternative approach for personalized medicine in the future.
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Chen Y, Zhang P, Liao J, Cheng J, Zhang Q, Li T, Zhang H, Jiang Y, Zhang F, Zeng Y, Mo L, Yan H, Liu D, Zhang Q, Zou C, Wei GH, Mo Z. Single-cell transcriptomics reveals cell type diversity of human prostate. J Genet Genomics 2022; 49:1002-1015. [PMID: 35395421 DOI: 10.1016/j.jgg.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 12/29/2022]
Abstract
Extensive studies have been performed to describe the phenotypic changes occurring during malignant transformation of the prostate. However, the cell types and associated changes that contribute to the development of prostate diseases and cancer remain elusive, largely due to the heterogeneous composition of prostatic tissues. Here, we conduct a comprehensive evaluation of four human prostate tissues by single-cell RNA sequencing (scRNA-seq) to analyze their cellular compositions. We identify 18 clusters of cell types, each with distinct gene expression profiles and unique features; of these, one cluster of epithelial cells (Ep) is found to be associated with immune function. In addition, we characterize a special cluster of fibroblasts and aberrant signaling changes associated with prostate cancer (PCa). Moreover, we provide insights into the epithelial changes that occur during the cellular senescence and aging. These results expand our understanding of the unique functional associations between the diverse prostatic cell types and the contributions of specific cell clusters to the malignant transformation of prostate tissues and PCa development.
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Affiliation(s)
- Yang Chen
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China; Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Peng Zhang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 201114, China
| | - Jinling Liao
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Jiwen Cheng
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China; Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Tianyu Li
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China; Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Haiying Zhang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yonghua Jiang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Fangxing Zhang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China; Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yanyu Zeng
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Linjian Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China; Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Haibiao Yan
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Deyun Liu
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Qinyun Zhang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Chunlin Zou
- Key Laboratory of Longevity and Ageing-Related Disease of Chinese Ministry of Education, Center for Translational Medicine and School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Gong-Hong Wei
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 201114, China; Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China; Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China.
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Integrated Tissue and Blood miRNA Expression Profiles Identify Novel Biomarkers for Accurate Non-Invasive Diagnosis of Breast Cancer: Preliminary Results and Future Clinical Implications. Genes (Basel) 2022; 13:genes13111931. [DOI: 10.3390/genes13111931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify miRNAs that were closely related to breast cancer (BRCA). By integrating several methods including significance analysis of microarrays, fold change, Pearson’s correlation analysis, t test, and receiver operating characteristic analysis, we developed a decision-tree-based scoring algorithm, called Optimized Scoring Mechanism for Primary Synergy MicroRNAs (O-PSM). Five synergy miRNAs (hsa-miR-139-5p, hsa-miR-331-3p, hsa-miR-342-5p, hsa-miR-486-5p, and hsa-miR-654-3p) were identified using O-PSM, which were used to distinguish normal samples from pathological ones, and showed good results in blood data and in multiple sets of tissue data. These five miRNAs showed accurate categorization efficiency in BRCA typing and staging and had better categorization efficiency than experimentally verified miRNAs. In the Protein-Protein Interaction (PPI) network, the target genes of hsa-miR-342-5p have the most regulatory relationships, which regulate carcinogenesis proliferation and metastasis by regulating Glycosaminoglycan biosynthesis and the Rap1 signaling pathway. Moreover, hsa-miR-342-5p showed potential clinical application in survival analysis. We also used O-PSM to generate an R package uploaded on github (SuFei-lab/OPSM accessed on 22 October 2021). We believe that miRNAs included in O-PSM could have clinical implications for diagnosis, prognostic stratification and treatment of BRCA, proposing potential significant biomarkers that could be utilized to design personalized treatment plans in BRCA patients in the future.
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Yan Q, Wang M, Xia H, Dai C, Diao T, Wang Y, Hou H, Zhang H, Liu M, Long X. Single-cell RNA-sequencing technology demonstrates the heterogeneity between aged prostate peripheral and transitional zone. Clin Transl Med 2022; 12:e1084. [PMID: 36245324 PMCID: PMC9574492 DOI: 10.1002/ctm2.1084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/29/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Identifying cellular and functional heterogeneity within aged prostate is critical for understanding the spatial distribution of prostate diseases. METHODS Aged human prostate peripheral zone (PZ) and transitional zone (TZ) tissues were used for single-cell RNA-sequencing. Results were validated by immunofluorescence staining. RESULTS We found that club/hillock epithelial cells, compared with other epithelial cells, had significantly higher NOTCH signaling activity and expressed higher levels of neuro-stems but lower androgen-related genes. These cells were primarily found in the TZ and provided a stem-like niche around the proximal prostate ducts. Significant heterogeneity was observed in the aged luminal population. A novel TFF3+ luminal subtype with elevated MYC and E2F pathway activities was observed, primarily in the PZ. Further analysis revealed that epithelial cells in the TZ had higher levels of stem- and inflammation-related pathway activities but lower androgen/lineage-related pathway activities than those in the PZ. Notably, the activation of MYC, E2F and DNA repair pathways significantly increased in PZ luminal cells. In the immune landscape, we found that the immune microenvironment in the TZ is more complex and disordered with more infiltration of NK and Treg cells. CD8 T cell and macrophage in the TZ exhibit both inflammation activation and suppression phenotypes. In the stroma, the TZ had a higher fibroblast density, and fibroblasts in the TZ exhibited stronger transcriptome activity in immunity and proliferation. Ligand-receptor interaction analysis revealed that fibroblasts could contribute to a NOTCH signaling niche for club/hillock cells in the TZ and balance the prostate immune microenvironment. The activation of stem properties, inflammatory infiltration and loss of androgen/lineage activity are prominent features distinguishing the TZ from PZ. CONCLUSIONS Our study explains the heterogeneity between the TZ and PZ of aged prostate, which may help understand the spatial distribution of prostate diseases and establish a foundation for novel target discovery.
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Affiliation(s)
- Qiuxia Yan
- Peking University Fifth School of Clinical MedicineBeijingChina,Department of UrologyBeijing HospitalNational Center of GerontologyBeijingChina
| | - Miao Wang
- Department of UrologyBeijing HospitalNational Center of GerontologyBeijingChina
| | - Haoran Xia
- Department of UrologyBeijing HospitalNational Center of GerontologyBeijingChina
| | - Cao Dai
- Department of General SurgeryThe Third Affiliated Hospital Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tongxiang Diao
- Department of UrologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | | | - Huimin Hou
- Department of UrologyBeijing HospitalNational Center of GerontologyBeijingChina
| | - Hong Zhang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular SciencesPeking University Health Science CenterBeijingChina
| | - Ming Liu
- Department of UrologyBeijing HospitalNational Center of GerontologyBeijingChina
| | - Xingbo Long
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhouGuangdongChina,State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
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Derakhshan T, Boyce JA, Dwyer DF. Defining mast cell differentiation and heterogeneity through single-cell transcriptomics analysis. J Allergy Clin Immunol 2022; 150:739-747. [PMID: 36205448 PMCID: PMC9547083 DOI: 10.1016/j.jaci.2022.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022]
Abstract
Mast cells (MCs) are widely recognized as central effector cells during type 2 inflammatory reactions and thought to also play a role in innate immune responses, wound healing, and potentially cancer. Circulating progenitor cells mature to MCs in peripheral tissues, where they exhibit phenotypic and functional heterogeneity. This diversity likely originates from differences in MC development imprinted by microenvironmental signals. The advent of single-cell transcriptomics reveals MC diversity beyond differences in proteases that were classically used to identify MC phenotypes. Here, we provide an overview of the current knowledge on MC progenitor differentiation and characteristics, and MC heterogeneity seen in health versus disease, that are drastically advanced through single-cell profiling technologies. This powerful approach can provide detailed cellular maps of tissues to decipher the complex cellular functions and interactions that may lead to identifying candidate factors to target in therapies.
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Affiliation(s)
- Tahereh Derakhshan
- Jeff and Penny Vinik Center for Allergic Disease Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Harvard Medical School, Boston, Mass
| | - Joshua A Boyce
- Jeff and Penny Vinik Center for Allergic Disease Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Harvard Medical School, Boston, Mass
| | - Daniel F Dwyer
- Jeff and Penny Vinik Center for Allergic Disease Research, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass; Harvard Medical School, Boston, Mass.
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Quan Y, Zhang X, Wang M, Ping H. Histone lysine methylation patterns in prostate cancer microenvironment infiltration: Integrated bioinformatic analysis and histological validation. Front Oncol 2022; 12:981226. [PMID: 36237332 PMCID: PMC9552767 DOI: 10.3389/fonc.2022.981226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Background Epigenetic reprogramming through dysregulated histone lysine methylation (HLM) plays a crucial role in prostate cancer (PCa) progression. This study aimed to comprehensively evaluate HLM modification patterns in PCa microenvironment infiltration. Materials and methods Ninety-one HLM regulators in The Cancer Genome Atlas (TCGA) dataset were analyzed using bioinformatics. Differentially expressed genes (DEGs) and survival analyses were performed using TCGA-PRAD clinicopathologic and follow-up information. Consensus clustering analysis divided patients into subgroups. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DEGs. Tumor mutation burden (TMB) and tumor microenvironment (TME) cell infiltration were evaluated in different HLM clusters. Quantitative real-time PCR (qPCR) analysis assessed HLM regulators in clinical PCa tissues. Results The tumor vs. normal (TN), Gleason score (GS) > 7 vs. GS < 7, pathological T stage (pT) = 2 vs. pT = 3, and TP53 mutation vs. wild-type comparisons using TCGA-PRAD dataset revealed 3 intersecting HLM regulators (EZH2, NSD2, and KMT5C) that were consistently upregulated in advanced PCa (GS > 7, pT3, HR > 1, and TP53 mutation) (P < 0.05) and verified in clinical PCa tissues. Consensus clustering analysis revealed three distinct HLM modification patterns (HLMclusters). However, no significant differences in recurrence-free survival (RFS) rates were found among the groups (P > 0.05). We screened 189 HLM phenotype-related genes that overlapped in the pairwise comparisons of HLMclusters and P < 0.01 in the Cox regression analysis. Three distinct subgroups (geneClusters) were revealed based on the 189 genes, in which cluster A involved the most advanced PCa (PSA > 10, T3-4, GS8-10, and biochemical recurrence) and the poorest RFS. The HLM score (HLMscore) was calculated by principal component analysis (PCA) of HLM phenotype-related genes that have positive predictive value for RFS (P < 0.001) and immune therapy responses (in the CTLA4-positive and -negative responses accompanied by a PD1-negative response). Conclusion We comprehensively evaluated HLM regulators in the PCa microenvironment using TCGA-PRAD, revealing a nonnegligible role of HLM patterns in PCa complexity and heterogeneity. Elucidating the effects of HLM regulators in PCa may enhance prognostics, aggressiveness assessments, and immunotherapy strategies.
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Affiliation(s)
- Yongjun Quan
- Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiaodong Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Mingdong Wang
- Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Hao Ping
- Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing Tongren Hospital, Beijing, China
- *Correspondence: Hao Ping,
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Prostate Cancer Secretome and Membrane Proteome from Pten Conditional Knockout Mice Identify Potential Biomarkers for Disease Progression. Int J Mol Sci 2022; 23:ijms23169224. [PMID: 36012492 PMCID: PMC9409251 DOI: 10.3390/ijms23169224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is the second most common cause of mortality among men. Tumor secretome is a promising strategy for understanding the biology of tumor cells and providing markers for disease progression and patient outcomes. Here, transcriptomic-based secretome analysis was performed on the PCa tumor transcriptome of Genetically Engineered Mouse Model (GEMM) Pb-Cre4/Ptenf/f mice to identify potentially secreted and membrane proteins—PSPs and PMPs. We combined a selection of transcripts from the GSE 94574 dataset and a list of protein-coding genes of the secretome and membrane proteome datasets using the Human Protein Atlas Secretome. Notably, nine deregulated PMPs and PSPs were identified in PCa (DMPK, PLN, KCNQ5, KCNQ4, MYOC, WIF1, BMP7, F3, and MUC1). We verified the gene expression patterns of Differentially Expressed Genes (DEGs) in normal and tumoral human samples using the GEPIA tool. DMPK, KCNQ4, and WIF1 targets were downregulated in PCa samples and in the GSE dataset. A significant association between shorter survival and KCNQ4, PLN, WIF1, and F3 expression was detected in the MSKCC dataset. We further identified six validated miRNAs (mmu-miR-6962-3p, mmu-miR- 6989-3p, mmu-miR-6998-3p, mmu-miR-5627-5p, mmu-miR-15a-3p, and mmu-miR-6922-3p) interactions that target MYOC, KCNQ5, MUC1, and F3. We have characterized the PCa secretome and membrane proteome and have spotted new dysregulated target candidates in PCa.
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Cao YH, Ding J, Tang QH, Zhang J, Huang ZY, Tang XM, Liu JB, Ma YS, Fu D. Deciphering cell-cell interactions and communication in the tumor microenvironment and unraveling intratumoral genetic heterogeneity via single-cell genomic sequencing. Bioengineered 2022; 13:14974-14986. [PMID: 37105769 DOI: 10.1080/21655979.2023.2185434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
A tumor's heterogeneity has important implications in terms of its clonal origin, progression, stemness, and drug resistance. Therefore, because of its significance in treatment, it is important to understand the gene expression pattern of a single cell, track gene expression or mutation in heterogeneous cells, evaluate the clonal origin of cancer cells, and determine the selective evolution of different subpopulations of cancer cells. Researchers are able to trace a cell's mutation and identify different types of tumor cells by measuring the whole transcriptome with single-cell sequencing (scRNA-seq). This technology provides a better understanding of the molecular mechanisms driving tumor growth than that offered by traditional RNA sequencing methods. In addition, it has revealed changes in the mutations and functions of somatic cells as a tumor evolves; it has also clarified immune cell infiltration and activation. Research on scRNA-seq technology has recently advanced significantly, suggesting new strategies for the treatment of cancer. In short, cancer researchers have become increasingly dependent on scRNA-seq. This paper reviews the development, detection principles, and processes of scRNA-seq technology and their application in tumor research. It also considers potential clinical applications.
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Affiliation(s)
- Ya-Hong Cao
- Department of Respiratory, Nantong Traditional Chinese Medicine Hospital, Affiliated Nantong Traditional Chinese Medicine Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jie Ding
- Department of Clinical Laboratory, Jingjiang Traditional Chinese Medicine Hospital, Jingjiang, Jiangsu, China
| | - Qing-Hai Tang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region and College of Life Sciences and Environment, Hengyang Normal University, Hengyang, Hunan, China
| | - Jie Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Zhong-Yan Huang
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, Huangpu, China
| | - Xiao-Mei Tang
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, Huangpu, China
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yu-Shui Ma
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Da Fu
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, Huangpu, China
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Review: RNA-based diagnostic markers discovery and therapeutic targets development in cancer. Pharmacol Ther 2022; 234:108123. [PMID: 35121000 DOI: 10.1016/j.pharmthera.2022.108123] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
Abstract
The present review aimed to outline different types of RNAs in cancer diagnostics and treatment, and to provide novel insights into their clinical applications. RNAs, including mRNA, long non-coding (lnc)RNA, circular (circ)RNA and micro (mi)RNA, are now increasingly utilized in the diagnosis and treatment of various cancers. Each aforementioned type of RNA possess their own unique characteristics and could be aberrantly expressed as diagnostic markers or therapeutic targets in different cancers. In addition to mRNAs, which have become a promising alternative in cancer diagnostics and therapy, the uses of lncRNA, circRNA and miRNA in predictive tumor diagnostics and therapy has rapidly increased in recent years. In the present review, the mechanisms of mRNA, lncRNA, circRNA and miRNA in regulating and participating in the development of different cancers were determined, and their potential capacity in cancer diagnostics and therapy were investigated. In addition, the present review analyzed the assoaciations between different RNAs and their subsequent potential in cancer prediction and treatment.
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Mo L, Yu Z, Lv Y, Cheng J, Yan H, Lu W, Su C, Ling Q, Mo Z. Single-Cell RNA Sequencing of Metastatic Testicular Seminoma Reveals the Cellular and Molecular Characteristics of Metastatic Cell Lineage. Front Oncol 2022; 12:871489. [PMID: 35494058 PMCID: PMC9039315 DOI: 10.3389/fonc.2022.871489] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/11/2022] [Indexed: 12/03/2022] Open
Abstract
Background Testicular cancer is the most common solid malignancy in young men. Given the many histological classifications of testicular tumors, seminoma is one of the most treatable cancers. The survival rate in early-stage disease was more than 90%. Thus, seminoma at the cellular and molecular levels, especially at the single-cell level, is worth studying. Methods We performed a single-cell RNA sequencing (scRNA-seq) study on a patient who was diagnosed with testicular seminoma with lymph node metastasis. This study presented tumor tissue, PBMC, pelvic and renal hilus lymph node in a total of 18,206 high-quality single-cell transcriptome information. The characteristics of metastatic cell lineage were revealed by the comparison between different tumor cell subtypes at the scRNA level. Results A single-cell map of testicular seminoma with lymph node metastasis was constructed by scRNA-seq. We discovered the gene expression characteristics of the tumor cells in testicular seminoma, especially metastatic tumor cells. KRT8 and KRT18 were commonly expressed in the three tumor cell subtypes. However, TCF7L1, SCG3 and SV2C were the specifically expressed genes of tumor cell subtypes in primary tumor sites. Some molecular markers specifically expressed by the metastatic cell lineage, such as POU5F1, were identified. Conclusions We revealed the molecular characteristics of testicular seminoma at the single-cell level, especially the metastatic tumor cells. This study could provide new insights into the diagnosis and treatment of testicular seminoma.
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Affiliation(s)
- Linjian Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhenyuan Yu
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yufang Lv
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiwen Cheng
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Haibiao Yan
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenhao Lu
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Cheng Su
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiang Ling
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Transcriptome Analysis on Key Metabolic Pathways in Rhodotorula mucilaginosa Under Pb(II) Stress. Appl Environ Microbiol 2022; 88:e0221521. [PMID: 35311507 DOI: 10.1128/aem.02215-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodotorula mucilaginosa shows adaption to a broad range of Pb2+ stress. In this study, three key pathways, i.e., glycolysis (EMP), the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS), were investigated under 0-2,500 mg · L-1 Pb stress, primarily based on biochemical analysis and RNA sequencing. R. mucilaginosa cells showed similar metabolic response to low/medium (500/1000 mg · L-1) Pb2+ stress. High (2,500 mg · L-1) Pb2+ stress exerted severe cytotoxicity to R. mucilaginosa. The downregulation of HK under low-medium Pb2+ suggested a correlation with the low hexokinase enzymatic activity in vivo. However, IDH3, regulating a key step of circulation in TCA, was upregulated to promote ATP feedstock for downstream OXPHOS. Then, through activation of complex I & IV in the electron transport chain (ETC) and ATP synthase, ATP production was finally enhanced. This mechanism enabled fungal cells to compensate for ATP consumption under low-medium Pb2+ toxicity. Hence, R. mucilaginosa tolerance to such a broad range of Pb2+ concentrations can be attributed to energy adaption. In contrast, high Pb2+ stress caused ATP deficiency. Then, the subsequent degradation of intracellular defense systems further intensified Pb toxicity. This study correlated responses of EMP, TCA, and OXPHOS pathways in R. mucilaginosa under Pb stress, hence providing new insights into the fungal resistance to heavy metal stress. IMPORTANCE Glycolysis (EMP), the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS) are critical metabolism pathways for microorganisms to obtain energy during the resistance to heavy metal (HM) stress. However, these pathways at the genetic level have not been elucidated to evaluate their cytoprotective functions for Rhodotorula mucilaginosa under Pb stress. In this study, we investigated these three pathways based on biochemical analysis and RNA sequencing. Under low-medium (500-1,000 mg · L-1) Pb2+ stress, ATP production was stimulated mainly due to the upregulation of genes associated with the TCA cycle and the electron transport chain (ETC). Such an energy compensatory mechanism could allow R. mucilaginosa acclimation to a broad range of Pb2+ concentrations (up to 1000 mg · L-1). In contrast, high (2500 mg · L-1) Pb2+ stress exerted its excessive toxicity by provoking ATP deficiency and damage to intracellular resistance systems. This study provided new insights into R. mucilaginosa resistance to HM stress from the perspective of metabolism.
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Fang Y, Yang H, Hu G, Lu J, Zhou J, Gao N, Gu Y, Zhang C, Qiu J, Guo Y, Zhang Y, Wen Q, Qiao H. The POR rs10954732 polymorphism decreases susceptibility to hepatocellular carcinoma and hepsin as a prognostic biomarker correlated with immune infiltration based on proteomics. J Transl Med 2022; 20:88. [PMID: 35164791 PMCID: PMC8842912 DOI: 10.1186/s12967-022-03282-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/25/2022] [Indexed: 11/10/2022] Open
Abstract
The effect of the cytochrome P450 oxidoreductase (POR) rs10954732 (G > A) polymorphism on hepatocellular carcinoma (HCC) susceptibility is unknown. Here we found that A allele carriers showed a 69% decrease in susceptibility to HCC with overall survival (OS) prolonged to 199%, accompanied by lower activity for cytochrome P450 2E1. A total of 222 differentially expressed proteins were mainly enriched in neutrophil and T cell activation and involved in the immune and inflammatory responses, constituting the altered immune tumor microenvironment related with A allele by proteomics analysis. Hepsin (HPN) showed significant down-regulation in HCC and up-regulation in A allele carriers. A lower HPN level was associated with increased susceptibility to HCC and a worse prognosis. Moreover, HPN is a potential independent prognostic biomarker for HCC and is strongly associated with clinicopathological features, tumor-infiltrating status of immune cells both in our discovery cohort and database surveys. Our findings provide a new potential mechanism by which HPN may play an important role in the susceptibility of rs10954732 A allele carriers to HCC and their prognosis through tumor immune infiltration, thus offering potential insights for future studies on tumor immunotherapy.
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The Needle in the Haystack: The Presence of Castrate-resistant Prostate Cancer Cells in Hormone-naïve Prostate Cancer. Eur Urol 2022; 81:456-457. [DOI: 10.1016/j.eururo.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 11/23/2022]
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41
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Huang J, Zhu Z, Ji D, Sun R, Yang Y, Liu L, Shao Y, Chen Y, Li L, Sun B. Single-Cell Transcriptome Profiling Reveals Neutrophil Heterogeneity and Functional Multiplicity in the Early Stage of Severe Burn Patients. Front Immunol 2022; 12:792122. [PMID: 35116026 PMCID: PMC8803731 DOI: 10.3389/fimmu.2021.792122] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/23/2021] [Indexed: 01/07/2023] Open
Abstract
The pathophysiological mechanisms, especially the roles of immune cells, underlying early stages of severe burn injury have not yet been fully clarified. Here, we analyzed circulating neutrophils (PMNs) in healthy donors and early burned patients by single-cell RNA sequencing to provide a comprehensive transcriptional landscape of PMNs in heterogeneity and functional multiplicity. Circulating PMNs in the healthy donors and burned groups were divided into five subgroups (G3, G4, G5a, G5b, G5c) with different functions. The dominant subsets of PMNs in homeostasis and burn injury significantly differed between groups. In addition, cells in the same subpopulation had the same core identity markers but performed different functions in healthy and burned states. Under burned conditions, PMN activation was very evident and accompanied by clear degranulation and metabolic abnormalities. Interestingly, was found that PMN activation, degranulation, chemotaxis, phagocytosis and reactive oxygen species (ROS) production in burned patients significantly differed between day 1 and days 2 or 3, thus providing a theoretical basis for PMN interventions in early burn stages. Significantly, previously undescribed transcription factors were also identified, including ZNF-787, ZNF-467, ZNF-189, ZNF-770, ZNF-262. In conclusion, this study conducted for the first time a detailed analysis of the heterogeneity and functional multiplicity of PMNs in early stages of severe burn injuries. Our findings attempted to clarify the influence of PMN heterogeneity on the pathophysiology and related mechanisms of burn injuries, which can provide new ideas for further research in burn intervention.
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Affiliation(s)
- Jiamin Huang
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zhechen Zhu
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Dongdong Ji
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ran Sun
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yunxi Yang
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Lu Liu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yiming Shao
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yi Chen
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Linbin Li
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Binwei Sun
- Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- *Correspondence: Binwei Sun,
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Fu J, Li G, Luo R, Lu Z, Wang Y. Classification of pyroptosis patterns and construction of a novel prognostic model for prostate cancer based on bulk and single-cell RNA sequencing. Front Endocrinol (Lausanne) 2022; 13:1003594. [PMID: 36105400 PMCID: PMC9465051 DOI: 10.3389/fendo.2022.1003594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/09/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Emerging evidence suggests an important role for pyroptosis in tumorigenesis and recurrence, but it remains to be elucidated in prostate cancer (PCa). Considering the low accuracy of common clinical predictors of PCa recurrence, we aimed to develop a novel pyroptosis-related signature to predict the prognosis of PCa patients based on integrative analyses of bulk and single-cell RNA sequencing (RNA-seq) profiling. METHODS The RNA-seq data of PCa patients was downloaded from several online databases. PCa patients were stratified into two Classes by unsupervised clustering. A novel signature was constructed by Cox and the Least Absolute Shrinkage and Selection Operator (LASSO) regression. The Kaplan-Meier curve was employed to evaluate the prognostic value of this signature and the single sample Gene Set Enrichment Analysis (ssGSEA) algorithm was used to analysis tumor-infiltrating immune cells. At single-cell level, we also classified the malignant cells into two Classes and constructed cell developmental trajectories and cell-cell interaction networks. Furthermore, RT-qPCR and immunofluorescence were used to validate the expression of core pyroptosis-related genes. RESULTS Twelve prognostic pyroptosis-related genes were identified and used to classify PCa patients into two prognostic Classes. We constructed a signature that identified PCa patients with different risks of recurrence and the risk score was proven to be an independent predictor of the recurrence free survival (RFS). Patients in the high-risk group had a significantly lower RFS (P<0.001). The expression of various immune cells differed between the two Classes. At the single-cell level, we classified the malignant cells into two Classes and described the heterogeneity. In addition, we observed that malignant cells may shift from Class1 to Class2 and thus have a worse prognosis. CONCLUSION We have constructed a robust pyroptosis-related signature to predict the RFS of PCa patients and described the heterogeneity of prostate cancer cells in terms of pyroptosis.
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Cheng Q, Butler W, Zhou Y, Zhang H, Tang L, Perkinson K, Chen X, Jiang X“S, McCall SJ, Inman BA, Huang J. Pre-existing Castration-resistant Prostate Cancer–like Cells in Primary Prostate Cancer Promote Resistance to Hormonal Therapy. Eur Urol 2022; 81:446-455. [PMID: 35058087 PMCID: PMC9018600 DOI: 10.1016/j.eururo.2021.12.039] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/01/2021] [Accepted: 12/31/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hormonal therapy targeting the androgen receptor inhibits prostate cancer (PCa), but the tumor eventually recurs as castration-resistant prostate cancer (CRPC). OBJECTIVE To understand the mechanisms by which subclones within early PCa develop into CRPC. DESIGN, SETTING, AND PARTICIPANTS We isolated epithelial cells from fresh human PCa cases, including primary adenocarcinoma, locally recurrent CRPC, and metastatic CRPC, and utilized single-cell RNA sequencing to identify subpopulations destined to become either CRPC-adeno or small cell neuroendocrine carcinoma (SCNC). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We revealed dynamic transcriptional reprogramming that promotes disease progression among 23226 epithelial cells using single-cell RNA sequencing, and validated subset-specific progression using immunohistochemistry and large cohorts of publically available genomic data. RESULTS AND LIMITATIONS We identified a small fraction of highly plastic CRPC-like cells in hormone-naïve early PCa and demonstrated its correlation with biochemical recurrence and distant metastasis, independent of clinical characteristics. We show that progression toward castration resistance was initiated from subtype-specific lineage plasticity and clonal expansion of pre-existing neuroendocrine and CRPC-like cells in early PCa. CONCLUSIONS CRPC-like cells are present early in the development of PCa and are not exclusively the result of acquired evolutionary selection during androgen deprivation therapy. The lethal CRPC and SCNC phenotypes should be targeted earlier in the disease course of patients with PCa. PATIENT SUMMARY Here, we report the presence of pre-existing castration-resistant prostate cancer (CRPC)-like cells in primary prostate cancer, which represents a novel castration-resistant mechanism different from the adaptation mechanism after androgen deprivation therapy (ADT). Patients whose tumors harbor increased pre-existing neuroendocrine and CRPC-like cells may become rapidly resistant to ADT and may require aggressive early intervention.
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Tang DG. Understanding and targeting prostate cancer cell heterogeneity and plasticity. Semin Cancer Biol 2021; 82:68-93. [PMID: 34844845 PMCID: PMC9106849 DOI: 10.1016/j.semcancer.2021.11.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022]
Abstract
Prostate cancer (PCa) is a prevalent malignancy that occurs primarily in old males. Prostate tumors in different patients manifest significant inter-patient heterogeneity with respect to histo-morphological presentations and molecular architecture. An individual patient tumor also harbors genetically distinct clones in which PCa cells display intra-tumor heterogeneity in molecular features and phenotypic marker expression. This inherent PCa cell heterogeneity, e.g., in the expression of androgen receptor (AR), constitutes a barrier to the long-term therapeutic efficacy of AR-targeting therapies. Furthermore, tumor progression as well as therapeutic treatments induce PCa cell plasticity such that AR-positive PCa cells may turn into AR-negative cells and prostate tumors may switch lineage identity from adenocarcinomas to neuroendocrine-like tumors. This induced PCa cell plasticity similarly confers resistance to AR-targeting and other therapies. In this review, I first discuss PCa from the perspective of an abnormal organ development and deregulated cellular differentiation, and discuss the luminal progenitor cells as the likely cells of origin for PCa. I then focus on intrinsic PCa cell heterogeneity in treatment-naïve tumors with the presence of prostate cancer stem cells (PCSCs). I further elaborate on PCa cell plasticity induced by genetic alterations and therapeutic interventions, and present potential strategies to therapeutically tackle PCa cell heterogeneity and plasticity. My discussions will make it clear that, to achieve enduring clinical efficacy, both intrinsic PCa cell heterogeneity and induced PCa cell plasticity need to be targeted with novel combinatorial approaches.
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Affiliation(s)
- Dean G Tang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Experimental Therapeutics (ET) Graduate Program, The University at Buffalo & Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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Zhong A, Chen T, Xing Y, Pan X, Shi M. FUCA2 Is a Prognostic Biomarker and Correlated With an Immunosuppressive Microenvironment in Pan-Cancer. Front Immunol 2021; 12:758648. [PMID: 34745134 PMCID: PMC8565374 DOI: 10.3389/fimmu.2021.758648] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/07/2021] [Indexed: 11/23/2022] Open
Abstract
Background The expression of Fucosidase, alpha-L-2 (FUCA2) varies across tumors. However, its role in various tumor types and relationship with the tumor immune microenvironment (TIME) is poorly defined. Methods We analyzed profiles of FUCA2 expression using datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Next, gene alteration, clinical characteristics and prognostic values of FUCA2 were elucidated based on TCGA pan-cancer data. This was followed by gene set enrichment analysis by R software. Relationships between FUCA2 expression and immune infiltration and immune-related genes were also evaluated. Moreover, the association of immune cell infiltration with FUCA2 expression was evaluated across three different sources of immune cell infiltration data, namely the TIMER online, ImmuCellAI databases, as well as a published study. In addition, MTT assays was also conducted to validate the oncogene role of FUCA2 in lung cancer cells. Results FUCA2 was upregulated in most tumors, and this was significantly associated with poor survival rates. Gene set enrichment analysis uncovered that FUCA2 correlated with immune pathways in different tumor types. FUCA2 expression was positively related to tumor associated macrophages (TAMs), especially M2-like TAMs. Moreover, FUCA2 level showed a positive relationship with most immunosuppression genes, including programmed death-ligand 1 (PD-L1), transforming growth factor beta 1 (TGFB1), and interleukin-10 (IL10) in most cancer types. FUCA2 knockdown inhibited the cell viability in lung cancer cells. Conclusions Our study reveals that FUCA2 is a potential oncogene and is indicative biomarker of a worse prognosis in pan-cancer. High FUCA2 expression may contribute to increased infiltration of TAMs and associates with an immunosuppressive microenvironment, providing a potential target for tumor therapy.
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Affiliation(s)
- Anyuan Zhong
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ting Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yufei Xing
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xue Pan
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Minhua Shi
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Prashant NM, Alomran N, Chen Y, Liu H, Bousounis P, Movassagh M, Edwards N, Horvath A. SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data. BMC Genomics 2021; 22:689. [PMID: 34551708 PMCID: PMC8459565 DOI: 10.1186/s12864-021-07974-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In addition to cancer studies, SNVs from single cells have been useful in studies of transcriptional burst kinetics, allelic expression, chromosome X inactivation, ploidy estimations, and haplotype inference. RESULTS To aid these types of studies, we have developed a tool, SCReadCounts, for cell-level tabulation of the sequencing read counts bearing SNV reference and variant alleles from barcoded scRNA-seq alignments. Provided genomic loci and expected alleles, SCReadCounts generates cell-SNV matrices with the absolute variant- and reference-harboring read counts, as well as cell-SNV matrices of expressed Variant Allele Fraction (VAFRNA) suitable for a variety of downstream applications. We demonstrate three different SCReadCounts applications on 59,884 cells from seven neuroblastoma samples: (1) estimation of cell-level expression of known somatic mutations and RNA-editing sites, (2) estimation of cell- level allele expression of biallelic SNVs, and (3) a discovery mode assessment of the reference and each of the three alternative nucleotides at genomic positions of interest that does not require prior SNV information. For the later, we applied SCReadCounts on the coding regions of KRAS, where it identified known and novel somatic mutations in a low-to-moderate proportion of cells. The SCReadCounts read counts module is benchmarked against the analogous modules of GATK and Samtools. SCReadCounts is freely available ( https://github.com/HorvathLab/NGS ) as 64-bit self-contained binary distributions for Linux and MacOS, in addition to Python source. CONCLUSIONS SCReadCounts supplies a fast and efficient solution for estimation of cell-level SNV expression from scRNA-seq data. SCReadCounts enables distinguishing cells with monoallelic reference expression from those with no gene expression and is applicable to assess SNVs present in only a small proportion of the cells, such as somatic mutations in cancer.
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Affiliation(s)
- N M Prashant
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
- Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nawaf Alomran
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Yu Chen
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, 20057, USA
| | - Hongyu Liu
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Pavlos Bousounis
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Mercedeh Movassagh
- Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Nathan Edwards
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, 20057, USA
| | - Anelia Horvath
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
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Melo CM, Vidotto T, Chaves LP, Lautert-Dutra W, dos Reis RB, Squire JA. The Role of Somatic Mutations on the Immune Response of the Tumor Microenvironment in Prostate Cancer. Int J Mol Sci 2021; 22:9550. [PMID: 34502458 PMCID: PMC8431051 DOI: 10.3390/ijms22179550] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Immunotherapy has improved patient survival in many types of cancer, but for prostate cancer, initial results with immunotherapy have been disappointing. Prostate cancer is considered an immunologically excluded or cold tumor, unable to generate an effective T-cell response against cancer cells. However, a small but significant percentage of patients do respond to immunotherapy, suggesting that some specific molecular subtypes of this tumor may have a better response to checkpoint inhibitors. Recent findings suggest that, in addition to their function as cancer genes, somatic mutations of PTEN, TP53, RB1, CDK12, and DNA repair, or specific activation of regulatory pathways, such as ETS or MYC, may also facilitate immune evasion of the host response against cancer. This review presents an update of recent discoveries about the role that the common somatic mutations can play in changing the tumor microenvironment and immune response against prostate cancer. We describe how detailed molecular genetic analyses of the tumor microenvironment of prostate cancer using mouse models and human tumors are providing new insights into the cell types and pathways mediating immune responses. These analyses are helping researchers to design drug combinations that are more likely to target the molecular and immunological pathways that underlie treatment failure.
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Affiliation(s)
- Camila Morais Melo
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (C.M.M.); (T.V.); (L.P.C.); (W.L.-D.)
| | - Thiago Vidotto
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (C.M.M.); (T.V.); (L.P.C.); (W.L.-D.)
| | - Luiz Paulo Chaves
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (C.M.M.); (T.V.); (L.P.C.); (W.L.-D.)
| | - William Lautert-Dutra
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (C.M.M.); (T.V.); (L.P.C.); (W.L.-D.)
| | - Rodolfo Borges dos Reis
- Division of Urology, Department of Surgery and Anatomy, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil;
| | - Jeremy Andrew Squire
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (C.M.M.); (T.V.); (L.P.C.); (W.L.-D.)
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L3N6, Canada
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Sun G, Li Z, Rong D, Zhang H, Shi X, Yang W, Zheng W, Sun G, Wu F, Cao H, Tang W, Sun Y. Single-cell RNA sequencing in cancer: Applications, advances, and emerging challenges. Mol Ther Oncolytics 2021; 21:183-206. [PMID: 34027052 PMCID: PMC8131398 DOI: 10.1016/j.omto.2021.04.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cancer has become one of the greatest threats to human health, and new technologies are urgently needed to further clarify the mechanisms of cancer so that better detection and treatment strategies can be developed. At present, extensive genomic analysis and testing of clinical specimens shape the insights into carcinoma. Nevertheless, carcinoma of humans is a complex ecosystem of cells, including carcinoma cells and immunity-related and stroma-related subsets, with accurate characteristics obscured by extensive genome-related approaches. A growing body of research shows that sequencing of single-cell RNA (scRNA-seq) is emerging to be an effective way for dissecting human tumor tissue at single-cell resolution, presenting one prominent way for explaining carcinoma biology. This review summarizes the research progress of scRNA-seq in the field of tumors, focusing on the application of scRNA-seq in tumor circulating cells, tumor stem cells, tumor drug resistance, the tumor microenvironment, and so on, which provides a new perspective for tumor research.
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Affiliation(s)
- Guangshun Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhouxiao Li
- Department of Hand Surgery, Plastic Surgery and Aesthetic Surgery, Ludwig Maximilians University, Munich, Germany
| | - Dawei Rong
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Hao Zhang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xuesong Shi
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weijun Yang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wubin Zheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guoqiang Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Yangbai Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
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