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Flemington EK, Flemington SA, O’Grady TM, Baddoo M, Nguyen T, Dong Y, Ungerleider N. SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing. Nucleic Acids Res 2023; 51:e42. [PMID: 36864749 PMCID: PMC10123099 DOI: 10.1093/nar/gkad111] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes in physiologic, pathologic, and pharmacologic settings. High throughput RNA sequencing and specialized software to detect AS has greatly enhanced our ability to determine transcriptome-wide splicing changes. Despite the richness of this data, deriving meaning from sometimes thousands of AS events is a substantial bottleneck for most investigators. We present SpliceTools, a suite of data processing modules that arms investigators with the ability to quickly produce summary statistics, mechanistic insights, and functional significance of AS changes through command line or through an online user interface. Utilizing RNA-seq datasets for 186 RNA binding protein knockdowns, nonsense mediated RNA decay inhibition, and pharmacologic splicing inhibition, we illustrate the utility of SpliceTools to distinguish splicing disruption from regulated transcript isoform changes, we show the broad transcriptome footprint of the pharmacologic splicing inhibitor, indisulam, we illustrate the utility in uncovering mechanistic underpinnings of splicing inhibition, we identify predicted neo-epitopes in pharmacologic splicing inhibition, and we show the impact of splicing alterations induced by indisulam on cell cycle progression. Together, SpliceTools puts rapid and easy downstream analysis at the fingertips of any investigator studying AS.
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Affiliation(s)
| | | | - Tina M O’Grady
- Department of Pathology, Tulane University, New Orleans, LA, USA
| | - Melody Baddoo
- Department of Pathology, Tulane University, New Orleans, LA, USA
| | - Trang Nguyen
- Department of Pathology, Tulane University, New Orleans, LA, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University, New Orleans, LA, USA
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2
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O’Grady TM, Baddoo M, Flemington SA, Ishaq EY, Ungerleider NA, Flemington EK. Reversal of splicing infidelity is a pre-activation step in B cell differentiation. Front Immunol 2022; 13:1060114. [PMID: 36601126 PMCID: PMC9806119 DOI: 10.3389/fimmu.2022.1060114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells. Methods We analyzed exon usage and intron retention in RNA-Seq data from subsets of human B cells at various stages of differentiation, and in an in vitro laboratory model of B cell activation and differentiation (Epstein Barr virus infection). Results Blood naïve B cells were found to have an unusual splicing profile, with unannotated splicing events in over 30% of expressed genes. Splicing changed substantially upon naïve B cell entry into secondary lymphoid tissue and before activation, involving significant increases in exon commitment and reductions in intron retention. These changes preferentially involved short introns with weak splice sites and were likely mediated by an overall increase in splicing efficiency induced by the lymphoid environment. The majority of transcripts affected by splicing changes showed restoration of encoded conserved protein domains and/or reduced targeting to the nonsense-mediated decay pathway. Affected genes were enriched in functionally important immune cell activation pathways such as antigen-mediated signaling, cell cycle control and mRNA processing and splicing. Discussion Functional observations from donor B cell subsets in progressive states of differentiation and from timecourse experiments using the in vitro model suggest that these widespread changes in mRNA splicing play a role in preparing naïve B cells for the decisive step of antigen-mediated activation and differentiation.
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Affiliation(s)
- Tina M. O’Grady
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Melody Baddoo
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Samuel A. Flemington
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Eman Y. Ishaq
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Nathan A. Ungerleider
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Erik K. Flemington
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
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Postel MD, Culver JO, Ricker C, Craig DW. Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum. Hum Mutat 2022; 43:1590-1608. [PMID: 35510381 PMCID: PMC9560997 DOI: 10.1002/humu.24394] [Citation(s) in RCA: 6] [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: 12/22/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.
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Affiliation(s)
- Mackenzie D. Postel
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Julie O. Culver
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Charité Ricker
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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4
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Chen S, Zheng J, Zhang B, Tang X, Cun Y, Wu T, Xu Y, Ma T, Cheng J, Yu Z, Wang H. Identification and characterization of virus-encoded circular RNAs in host cells. Microb Genom 2022; 8. [PMID: 35731570 PMCID: PMC9455708 DOI: 10.1099/mgen.0.000848] [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] [Indexed: 11/25/2022] Open
Abstract
Emerging evidence has identified viral circular RNAs (circRNAs) in human cells infected by viruses, interfering with the immune system and inducing diseases including human cancer. However, the biogenesis and regulatory mechanisms of virus-encoded circRNAs in host cells remain unknown. In this study, we used the circRNA detection tool CIRI2 to systematically determine the virus-encoded circRNAs in virus-infected cancer cell lines and cancer patients, by analysing RNA-Seq datasets derived from RNase R-treated samples. Based on the thousands of viral circRNAs we identified, the biological characteristics and potential roles of viral circRNAs in regulating host cell function were determined. In addition, we developed a Viral-circRNA Database (http://www.hywanglab.cn/vcRNAdb/), which is open to all users to search, browse and download information on circRNAs encoded by viruses upon infection.
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Affiliation(s)
- Shuting Chen
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Jie Zheng
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Bingyue Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Xinyue Tang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Yewei Cun
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Tao Wu
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Yue Xu
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Ting Ma
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Jingxin Cheng
- Department of Obstetrics and Gynecology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, PR China
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, PR China
| | - Haiyun Wang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
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5
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Xiao Q, Dai J, Luo J. A survey of circular RNAs in complex diseases: databases, tools and computational methods. Brief Bioinform 2021; 23:6407737. [PMID: 34676391 DOI: 10.1093/bib/bbab444] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) are a category of novelty discovered competing endogenous non-coding RNAs that have been proved to implicate many human complex diseases. A large number of circRNAs have been confirmed to be involved in cancer progression and are expected to become promising biomarkers for tumor diagnosis and targeted therapy. Deciphering the underlying relationships between circRNAs and diseases may provide new insights for us to understand the pathogenesis of complex diseases and further characterize the biological functions of circRNAs. As traditional experimental methods are usually time-consuming and laborious, computational models have made significant progress in systematically exploring potential circRNA-disease associations, which not only creates new opportunities for investigating pathogenic mechanisms at the level of circRNAs, but also helps to significantly improve the efficiency of clinical trials. In this review, we first summarize the functions and characteristics of circRNAs and introduce some representative circRNAs related to tumorigenesis. Then, we mainly investigate the available databases and tools dedicated to circRNA and disease studies. Next, we present a comprehensive review of computational methods for predicting circRNA-disease associations and classify them into five categories, including network propagating-based, path-based, matrix factorization-based, deep learning-based and other machine learning methods. Finally, we further discuss the challenges and future researches in this field.
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Affiliation(s)
- Qiu Xiao
- Hunan Normal University and Hunan Xiangjiang Artificial Intelligence Academy, Changsha, China
| | - Jianhua Dai
- Hunan Normal University and Hunan Xiangjiang Artificial Intelligence Academy, Changsha, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
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6
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 PMCID: PMC8130916 DOI: 10.1371/journal.ppat.1009217] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt’s Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response. Burkitt’s Lymphoma and gastric cancer are both associated with EBV, a prolific DNA tumor virus that latently resides in nearly all human beings. Despite mostly restricting viral gene expression to noncoding RNAs, EBV has important influences on the fitness of infected tumor cells. Here, we show that the miRNA class of viral noncoding RNAs are a major viral contributor to remodeling the tumor cell regulatory machinery in patient tumor samples. First, an assessment of miRNA expression in clinical tumor samples showed that EBV miRNAs are expressed at unexpectedly high levels relative to cell miRNAs. Using a highly specific miRNA target identification approach, CLASH, we comprehensively identified both viral and cellular miRNA targets and the relative abundance of each miRNA-mRNA interaction. We also show that viral miRNAs bind to and alter the expression of their mRNA targets more effectively than their cellular miRNA counterparts. Pathway analysis of the most effectively targeted mRNAs revealed enrichment of immune signaling pathways and we show a corresponding inverse correlation between EBV miRNA expression and infiltrating immune cells in EBV positive primary tumors. Altogether, this study shows that EBV miRNAs are key regulators of the tumor cell phenotype and the immune cell microenvironment.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (ST); (EKF)
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
- * E-mail: (ST); (EKF)
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7
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 DOI: 10.1101/2020.12.21.423766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 05/21/2023] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt's Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi's sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
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8
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Chen L, Wang C, Sun H, Wang J, Liang Y, Wang Y, Wong G. The bioinformatics toolbox for circRNA discovery and analysis. Brief Bioinform 2021; 22:1706-1728. [PMID: 32103237 PMCID: PMC7986655 DOI: 10.1093/bib/bbaa001] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.
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Affiliation(s)
- Liang Chen
- Department of Computer Science, Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University
| | | | - Huiyan Sun
- School of Artificial Intelligence, Jilin University
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science and Bond Life Science Center, University of Missouri
| | - Yanchun Liang
- College of Computer Science and Technology, Jilin University
| | - Yan Wang
- College of Computer Science and Technology, Jilin University
| | - Garry Wong
- Faculty of Health Sciences, University of Macau
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Li Q, Lai H, Li Y, Chen B, Chen S, Li Y, Huang Z, Meng Z, Wang P, Hu Z, Huang S. RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Res 2021; 49:D201-D211. [PMID: 33179749 PMCID: PMC7779070 DOI: 10.1093/nar/gkaa1056] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/17/2020] [Accepted: 10/21/2020] [Indexed: 01/22/2023] Open
Abstract
Splicing is an essential step of RNA processing for multi-exon genes, in which introns are removed from a precursor RNA, thereby producing mature RNAs containing splice junctions. Here, we develope the RJunBase (www.RJunBase.org), a web-accessible database of three types of RNA splice junctions (linear, back-splice, and fusion junctions) that are derived from RNA-seq data of non-cancerous and cancerous tissues. The RJunBase aims to integrate and characterize all RNA splice junctions of both healthy or pathological human cells and tissues. This new database facilitates the visualization of the gene-level splicing pattern and the junction-level expression profile, as well as the demonstration of unannotated and tumor-specific junctions. The first release of RJunBase contains 682 017 linear junctions, 225 949 back-splice junctions and 34 733 fusion junctions across 18 084 non-cancerous and 11 540 cancerous samples. RJunBase can aid researchers in discovering new splicing-associated targets and provide insights into the identification and assessment of potential neoepitopes for cancer treatment.
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Affiliation(s)
- Qin Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyan Lai
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuchen Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bing Chen
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Siyuan Chen
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng Wang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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10
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Circular RNAs add diversity to androgen receptor isoform repertoire in castration-resistant prostate cancer. Oncogene 2019; 38:7060-7072. [PMID: 31409897 PMCID: PMC6842090 DOI: 10.1038/s41388-019-0947-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 06/03/2019] [Indexed: 12/13/2022]
Abstract
Deregulated expression of circular RNAs (circRNAs) is associated with various human diseases, including many types of cancer. Despite their growing links to cancer, there has been limited characterization of circRNAs in metastatic castration-resistant prostate cancer, the major cause of prostate cancer mortality. Here, through the analysis of an exome-capture RNA-seq dataset from 47 metastatic castration-resistant prostate cancer samples and ribodepletion and RNase R RNA-sequencing of patient-derived xenografts (PDXs) and cell models, we identified 13 circRNAs generated from the key prostate cancer driver gene-androgen receptor (AR). We validated and characterized the top four most abundant, clinically relevant AR circRNAs. Expression of these AR circRNAs was upregulated during castration-resistant progression of PDXs. The upregulation was not due to global increase of circRNA formation in these tumors. Instead, the levels of AR circRNAs correlated strongly with that of the linear AR transcripts (both AR and AR-variants) in clinical samples and PDXs, indicating a transcriptional mechanism of regulation. In cultured cells, androgen suppressed the expression of these AR circRNAs and the linear AR transcripts, and the suppression was attenuated by an antiandrogen. Using nuclear/cytoplasmic fractionation and RNA in-situ hybridization assays, we demonstrated predominant cytoplasmic localization of these AR circRNAs, indicating likely cytoplasmic functions. Overall, this is the first comprehensive characterization of circRNAs arising from the AR gene. With greater resistance to exoribonuclease compared to the linear AR transcripts and detectability of AR circRNAs in patient plasma, these AR circRNAs may serve as surrogate circulating markers for AR/AR-variant expression and castration-resistant prostate cancer progression.
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