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Ha S, Gujrati H, Wang BD. Aberrant PI3Kδ splice isoform as a potential biomarker and novel therapeutic target for endocrine cancers. Front Endocrinol (Lausanne) 2023; 14:1190479. [PMID: 37670888 PMCID: PMC10475954 DOI: 10.3389/fendo.2023.1190479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/27/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction PI3K/AKT signaling pathway is upregulated in a broad spectrum of cancers. Among the class I PI3Ks (PI3Kδ/β/δ isoforms), PI3Kδ has been implicated in hematologic cancers and solid tumors. Alternative splicing is a post-transcriptional process for acquiring proteomic diversity in eukaryotic cells. Emerging evidence has highlighted the involvement of aberrant mRNA splicing in cancer development/progression. Methods Our previous studies revealed that PIK3CD-S is an oncogenic splice variant that promotes tumor aggressiveness and drug resistance in prostate cancer (PCa). To further evaluate the potential of utilizing PI3Kδ-S (encoded from PIK3CD-S) as a cancer biomarker and/or drug target, comprehensive analyses were performed in a series of patient samples and cell lines derived from endocrine/solid tumors. Specifically, IHC, immunofluorescence, western blot and RT-PCR assay results have demonstrated that PI3Kδ isoforms were highly expressed in endocrine/solid tumor patient specimens and cell lines. Results Differential PIK3CD-S/PIK3CD-L expression profiles were identified in a panel of endocrine/solid tumor cells. SiRNA knockdown of PIK3CD-L or PIK3CD-S differentially inhibits AKT/mTOR signaling in PCa, breast, colon and lung cancer cell lines. Moreover, siRNA knockdown of PTEN increased PI3Kδ levels and activated AKT/mTOR signaling, while overexpression of PTEN reduced PI3Kδ levels and inhibited AKT/mTOR signaling in cancer cells. Intriguingly, PI3Kδ-S levels remained unchanged upon either siRNA knockdown or overexpression of PTEN. Taken together, these results suggested that PTEN negatively regulates PI3Kδ-L and its downstream AKT/mTOR signaling, while PI3Kδ-S promotes AKT/mTOR signaling without regulation by PTEN. Lastly, PI3Kδ inhibitor Idelalisib and SRPK1/2 inhibitor SRPIN340 were employed to assess their efficacies on inhibiting the PI3Kδ-expressing endocrine/solid tumors. Our results have shown that Idelalisib effectively inhibited PI3Kδ-L (but not PI3Kδ-S) mediated AKT/mTOR signaling. In contrast, SRPIN340 reversed the aberrant mRNA splicing, thereby inhibiting AKT/mTOR signaling. In-vitro functional assays have further demonstrated that a combination of Idelalisib and SRPIN340 achieved a synergistic drug effect (with drastically reduced cell viabilities/growths of tumor spheroids) in inhibiting the advanced tumor cells. Conclusion In summary, our study has suggested a promising potential of utilizing PI3Kδ-S (an oncogenic isoform conferring drug resistance and exempt from PTEN regulation) as a prognostic biomarker and drug target in advanced endocrine cancers.
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Affiliation(s)
- Siyoung Ha
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD, United States
| | - Himali Gujrati
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD, United States
| | - Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD, United States
- Hormone Related Cancers Program, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD, United States
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Sun Y, Bae YE, Zhu J, Zhang Z, Zhong H, Cheng C, Deng Y, Wu C, Wu L. A Splicing Transcriptome-Wide Association Study Identifies Candidate Altered Splicing for Prostate Cancer Risk. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:372-380. [PMID: 37486714 DOI: 10.1089/omi.2023.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Prostate cancer (PCa) represents a huge public health burden among men. Many susceptibility genetic factors for PCa still remain unknown. In this study, we performed a large splicing transcriptome-wide association study (spTWAS) using three modeling strategies to develop alternative splicing genetic prediction models for identifying novel susceptibility loci and splicing introns for PCa risk by assessing 79,194 cases and 61,112 controls of European ancestry in the PRACTICAL, CRUK, CAPS, BPC3, and PEGASUS consortia. We identified 120 splicing introns of 97 genes showing an association with PCa risk at false discovery rate (FDR)-corrected threshold (FDR <0.05). Of them, 33 genes were enriched in PCa-related diseases and function categories. Fine-mapping analysis suggested that 21 splicing introns of 19 genes were likely causally associated with PCa risk. Thirty-five splicing introns of 34 novel genes were identified to be related to PCa susceptibility for the first time, and 11 of the genes were enriched in a cancer-related network. Our study identified novel loci and splicing introns associated with PCa risk, which can improve our understanding of the etiology of this common malignancy.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Longyan University, Longyan, P.R. China
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, P.R. China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, P.R. China
| | - Ye Eun Bae
- Department of Statistics, Florida State University, Tallahassee, Florida, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Zichen Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Chunmei Cheng
- College of Life Science, Longyan University, Longyan, P.R. China
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
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Cosi I, Moccia A, Pescucci C, Munagala U, Di Giorgio S, Sineo I, Conticello SG, Notaro R, De Angioletti M. Identification and characterization of novel ETV4 splice variants in prostate cancer. Sci Rep 2023; 13:5267. [PMID: 37002241 PMCID: PMC10066307 DOI: 10.1038/s41598-023-29484-1] [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: 09/26/2022] [Accepted: 02/06/2023] [Indexed: 04/03/2023] Open
Abstract
ETV4, one of ETS proteins overexpressed in prostate cancer, promotes migration, invasion, and proliferation in prostate cells. This study identifies a series of previously unknown ETV4 alternatively spliced transcripts in human prostate cell lines. Their expression has been validated using several unbiased techniques, including Nanopore sequencing. Most of these transcripts originate from an in-frame exon skipping and, thus, are expected to be translated into ETV4 protein isoforms. Functional analysis of the most abundant among these isoforms shows that they still bear an activity, namely a reduced ability to promote proliferation and a residual ability to regulate the transcription of ETV4 target genes. Alternatively spliced genes are common in cancer cells: an analysis of the TCGA dataset confirms the abundance of these novel ETV4 transcripts in prostate tumors, in contrast to peritumoral tissues. Since none of their translated isoforms have acquired a higher oncogenic potential, such abundance is likely to reflect the tumor deranged splicing machinery. However, it is also possible that their interaction with the canonical variants may contribute to the biology and the clinics of prostate cancer. Further investigations are needed to elucidate the biological role of these ETV4 transcripts and of their putative isoforms.
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Affiliation(s)
- Irene Cosi
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
- ICCOM - National Research Council, Sesto Fiorentino, Florence, Italy
| | - Annalisa Moccia
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Chiara Pescucci
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Uday Munagala
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Salvatore Di Giorgio
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Irene Sineo
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
| | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
- IFC - National Research Council, Pisa, Italy
| | - Rosario Notaro
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy
- IFC - National Research Council, Pisa, Italy
| | - Maria De Angioletti
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Viale Pieraccini 6, 50139, Florence, Italy.
- ICCOM - National Research Council, Sesto Fiorentino, Florence, Italy.
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Ha S, Wang BD. Molecular Insight into Drug Resistance Mechanism Conferred by Aberrant PIK3CD Splice Variant in African American Prostate Cancer. Cancers (Basel) 2023; 15:1337. [PMID: 36831678 PMCID: PMC9954641 DOI: 10.3390/cancers15041337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/22/2023] Open
Abstract
Targeting PI3Kδ has emerged as a promising therapy for hematologic and non-hematologic malignancies. Previously, we identified an oncogenic splice variant, PIK3CD-S, conferring Idelalisib resistance in African American (AA) prostate cancer (PCa). In the current study, we employed a comprehensive analysis combining molecular biology, biochemistry, histology, in silico simulation, and in vitro functional assays to investigate the PIK3CD-S expression profiles in PCa samples and to elucidate the drug resistance mechanism mediated by PI3Kδ-S (encoded by PIK3CD-S). The immunohistochemistry, RT-PCR, and Western blot assays first confirmed that PI3Kδ-S is highly expressed in AA PCa. Compared with PCa expressing the full-length PI3Kδ-L, PCa expressing PI3Kδ-S exhibits enhanced drug resistance properties, including a higher cell viability, more antiapoptotic and invasive capacities, and constitutively activated PI3K/AKT signaling, in the presence of PI3Kδ/PI3K inhibitors (Idelalisib, Seletalisib, Wortmannin, and Dactolisib). Molecular docking, ATP-competitive assays, and PI3 kinase assays have further indicated a drastically reduced affinity of PI3Kδ inhibitors with PI3Kδ-S vs. PI3Kδ-L, attributed to the lack of core binding residues in the PI3Kδ-S catalytic domain. Additionally, SRSF2 has been identified as a critical splicing factor mediating exon 20 skipping in PIK3CD pre-mRNA. The inhibition of the SRSF2 activity by SRPIN340 successfully sensitizes AA PCa cells to PI3Kδ inhibitors, suggesting a novel therapeutic option for Idelalisib-resistant tumors.
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Affiliation(s)
- Siyoung Ha
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy and Health Professions, Princess Anne, MD 21853, USA
| | - Bi-Dar Wang
- Department of Pharmaceutical Sciences, University of Maryland Eastern Shore School of Pharmacy and Health Professions, Princess Anne, MD 21853, USA
- Hormone Related Cancers Program, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
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Del Giudice M, Foster JG, Peirone S, Rissone A, Caizzi L, Gaudino F, Parlato C, Anselmi F, Arkell R, Guarrera S, Oliviero S, Basso G, Rajan P, Cereda M. FOXA1 regulates alternative splicing in prostate cancer. Cell Rep 2022; 40:111404. [PMID: 36170835 PMCID: PMC9532847 DOI: 10.1016/j.celrep.2022.111404] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/28/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an "exon definition" mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.
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Affiliation(s)
- Marco Del Giudice
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - John G Foster
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Serena Peirone
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alberto Rissone
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Livia Caizzi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Federica Gaudino
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Caterina Parlato
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Francesca Anselmi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
| | - Rebecca Arkell
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Salvatore Oliviero
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
| | - Giuseppe Basso
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy
| | - Prabhakar Rajan
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Division of Surgery and Interventional Science, University College London, Charles Bell House, 3 Road Floor, 43-45 Foley Street, London W1W 7TS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK; Department of Urology, Barts Health NHS Trust, the Royal London Hospital, Whitechapel Road, London E1 1BB, UK; Department of Uro-oncology, University College London NHS Foundation Trust, 47 Wimpole Street, London W1G 8SE, UK.
| | - Matteo Cereda
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov. le 142, km 3.95, 10060 Candiolo (TO), Italy; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
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Wang J, Zhang L, Zeng A, Xia D, Yu J, Yu G. DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2177-2187. [PMID: 33764878 DOI: 10.1109/tcbb.2021.3068875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Alternative splicing enables a gene translating into different isoforms and into the corresponding proteoforms, which actually accomplish various biological functions of a living body. Isoform-isoform interactions (IIIs) provide a higher resolution interactome to explore the cellular processes and disease mechanisms than the canonically studied protein-protein interactions (PPIs), which are often recorded at the coarse gene level. The knowledge of IIIs is critical to map pathways, understand protein complexity and functional diversity, but the known IIIs are very scanty. In this paper, we propose a deep learning based method called DeepIII to systematically predict genome-wide IIIs by integrating diverse data sources, including RNA-seq datasets of different human tissues, exon array data, domain-domain interactions (DDIs) of proteins, nucleotide sequences and amino acid sequences. Particularly, DeepIII fuses these data to learn the representation of isoform pairs with a four-layer deep neural networks, and then performs binary classification on the learnt representation to achieve the prediction of IIIs. Experimental results show that DeepIII achieves a superior prediction performance to the state-of-the-art solutions and the III network constructed by DeepIII gives more accurate isoform function prediction. Case studies further confirm that DeepIII can differentiate the individual interaction partners of different isoforms spliced from the same gene. The code and datasets of DeepIII are available at http://mlda.swu.edu.cn/codes.php?name=DeepIII.
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Irie K, Doi M, Usui N, Shimada S. Evolution of the Human Brain Can Help Determine Pathophysiology of Neurodevelopmental Disorders. Front Neurosci 2022; 16:871979. [PMID: 35431788 PMCID: PMC9010664 DOI: 10.3389/fnins.2022.871979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 02/03/2023] Open
Abstract
The evolution of humans brought about a co-occurring evolution of the human brain, which is far larger and more complex than that of many other organisms. The brain has evolved characteristically in humans in many respects, including macro-and micro-anatomical changes in the brain structure, changes in gene expression, and cell populations and ratios. These characteristics are essential for the execution of higher functions, such as sociality, language, and cognition, which express humanity, and are thought to have been acquired over evolutionary time. However, with the acquisition of higher functions also comes the risk of the disease in which they fail. This review focuses on human brain evolution and neurodevelopmental disorders (NDDs) and discusses brain development, molecular evolution, and human brain evolution. Discussing the potential for the development and pathophysiology of NDDs acquired by human brain evolution will provide insights into the acquisition and breakdown of higher functions from a new perspective.
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Affiliation(s)
- Koichiro Irie
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Center for Medical Research and Education, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Miyuki Doi
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Noriyoshi Usui
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
- *Correspondence: Noriyoshi Usui,
| | - Shoichi Shimada
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
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The aberrant upregulation of exon 10-inclusive SREK1 through SRSF10 acts as an oncogenic driver in human hepatocellular carcinoma. Nat Commun 2022; 13:1363. [PMID: 35296659 PMCID: PMC8927159 DOI: 10.1038/s41467-022-29016-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Deregulation of alternative splicing is implicated as a relevant source of molecular heterogeneity in cancer. However, the targets and intrinsic mechanisms of splicing in hepatocarcinogenesis are largely unknown. Here, we report a functional impact of a Splicing Regulatory Glutamine/Lysine-Rich Protein 1 (SREK1) variant and its regulator, Serine/arginine-rich splicing factor 10 (SRSF10). HCC patients with poor prognosis express higher levels of exon 10-inclusive SREK1 (SREK1L). SREK1L can sustain BLOC1S5-TXNDC5 (B-T) expression, a targeted gene of nonsense-mediated mRNA decay through inhibiting exon-exon junction complex binding with B-T to exert its oncogenic role. B-T plays its competing endogenous RNA role by inhibiting miR-30c-5p and miR-30e-5p, and further promoting the expression of downstream oncogenic targets SRSF10 and TXNDC5. Interestingly, SRSF10 can act as a splicing regulator for SREK1L to promote hepatocarcinogenesis via the formation of a SRSF10-associated complex. In summary, we demonstrate a SRSF10/SREK1L/B-T signalling loop to accelerate the hepatocarcinogenesis. Alternative splicing is dysregulated in hepatocellular carcinoma. Here, the authors investigate the role of the splice variant of Splicing Regulatory Glutamic Acid and Lysine Rich Protein 1 (SREK1) and its upstream regulator, Serine/arginine-rich splicing factor 10 (SRSF10) in sustaining the oncogenic signal.
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Vlassakis J, Yamauchi KA, Herr AE. Summit: Automated Analysis of Arrayed Single-Cell Gel Electrophoresis. SLAS Technol 2021; 26:637-649. [PMID: 34474610 DOI: 10.1177/24726303211036869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
New pipelines are required to automate the quantitation of emerging high-throughput electrophoretic (EP) assessment of DNA damage, or proteoform expression in single cells. EP cytometry consists of thousands of Western blots performed on a microscope slide-sized gel microwell array for single cells. Thus, EP cytometry images pose an analysis challenge that blends requirements for accurate and reproducible analysis encountered for both standard Western blots and protein microarrays. Here, we introduce the Summit algorithm to automate array segmentation, peak background subtraction, and Gaussian fitting for EP cytometry. The data structure storage of parameters allows users to perform quality control on identically processed data, yielding a ~6.5% difference in coefficient of quartile variation (CQV) of protein peak area under the curve (AUC) distributions measured by four users. Further, inspired by investigations of background subtraction methods to reduce technical variation in protein microarray measurements, we aimed to understand the trade-offs between EP cytometry analysis throughput and variation. We found an 11%-50% increase in protein peaks that passed quality control with a subtraction method similar to microarray "average on-boundary" versus an axial subtraction method. The background subtraction method only mildly influences AUC CQV, which varies between 1% and 4.5%. Finally, we determined that the narrow confidence interval for peak location and peak width parameters from Gaussian fitting yield minimal uncertainty in protein sizing. The AUC CQV differed by only ~1%-2% when summed over the peak width bounds versus the 95% peak width confidence interval. We expect Summit to be broadly applicable to other arrayed EP separations, or traditional Western blot analysis.
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Affiliation(s)
- Julea Vlassakis
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Kevin A Yamauchi
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.,The Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Amy E Herr
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
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10
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Androgen receptor and its splice variant, AR-V7, differentially induce mRNA splicing in prostate cancer cells. Sci Rep 2021; 11:1393. [PMID: 33446905 PMCID: PMC7809134 DOI: 10.1038/s41598-021-81164-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer (PCa) is dependent on the androgen receptor (AR). Advanced PCa is treated with an androgen deprivation therapy-based regimen; tumors develop resistance, although they typically remain AR-dependent. Expression of constitutively active AR variants lacking the ligand-binding domain including the variant AR-V7 contributes to this resistance. AR and AR-V7, as transcription factors, regulate many of the same genes, but also have unique activities. In this study, the capacity of the two AR isoforms to regulate splicing was examined. RNA-seq data from models that endogenously express AR and express AR-V7 in response to doxycycline were used. Both AR isoforms induced multiple changes in splicing and many changes were isoform-specific. Analyses of two endogenous genes, PGAP2 and TPD52, were performed to examine differential splicing. A novel exon that appears to be a novel transcription start site was preferentially induced by AR-V7 in PGAP2 although it is induced to a lesser extent by AR. The previously described AR induced promoter 2 usage that results in a novel protein derived from TPD52 (PrLZ) was not induced by AR-V7. AR, but not AR-V7, bound to a site proximal to promoter 2, and induction was found to depend on FOXA1.
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11
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Age-related injury responses of human oligodendrocytes to metabolic insults: link to BCL-2 and autophagy pathways. Commun Biol 2021; 4:20. [PMID: 33398046 PMCID: PMC7782481 DOI: 10.1038/s42003-020-01557-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/01/2020] [Indexed: 01/29/2023] Open
Abstract
Myelin destruction and oligodendrocyte (OL) death consequent to metabolic stress is a feature of CNS disorders across the age spectrum. Using cells derived from surgically resected tissue, we demonstrate that young (<age 5) pediatric-aged sample OLs are more resistant to in-vitro metabolic injury than fetal O4+ progenitor cells, but more susceptible to cell death and apoptosis than adult-derived OLs. Pediatric but not adult OLs show measurable levels of TUNEL+ cells, a feature of the fetal cell response. The ratio of anti- vs pro-apoptotic BCL-2 family genes are increased in adult vs pediatric (<age 5) mature OLs and in more mature OL lineage cells. Lysosomal gene expression was increased in adult and pediatric compared to fetal OL lineage cells. Cell death of OLs was increased by inhibiting pro-apoptotic BCL-2 gene and autophagy activity. These distinct age-related injury responses should be considered in designing therapies aimed at reducing myelin injury.
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12
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Minati R, Perreault C, Thibault P. A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens. Front Immunol 2020; 11:583287. [PMID: 33424836 PMCID: PMC7793940 DOI: 10.3389/fimmu.2020.583287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
The search for tumor-specific antigens (TSAs) has considerably accelerated during the past decade due to the improvement of proteogenomic detection methods. This provides new opportunities for the development of novel antitumoral immunotherapies to mount an efficient T cell response against one or multiple types of tumors. While the identification of mutated antigens originating from coding exons has provided relatively few TSA candidates, the possibility of enlarging the repertoire of targetable TSAs by looking at antigens arising from non-canonical open reading frames opens up interesting avenues for cancer immunotherapy. In this review, we outline the potential sources of TSAs and the mechanisms responsible for their expression strictly in cancer cells. In line with the heterogeneity of cancer, we propose that discrete families of TSAs may be enriched in specific cancer types.
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Affiliation(s)
- Robin Minati
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
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13
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Yang J, Xie K, Wang Z, Li C. Elevated KLF7 levels may serve as a prognostic signature and might contribute to progression of squamous carcinoma. FEBS Open Bio 2020; 10:1577-1586. [PMID: 32536035 PMCID: PMC7396437 DOI: 10.1002/2211-5463.12912] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 01/15/2023] Open
Abstract
Global efforts have been undertaken to define the genome-wide distribution of epigenetic markers in cancerous tissues, which provide an invaluable opportunity to understand cancer biology and identify predictive signatures. Several studies have focused on the gene expression patterns of squamous carcinoma to identify tumor subtypes and find prognostic and therapeutic targets because squamous carcinoma genomes showed high instability. However, the number of reliable reports referring prognostic significance of genes and their role in squamous carcinoma is still quite limited. Krüppel-like factor 7 (KLF7) is a transcription factor that is widely expressed in numerous human tissues at low levels. Members of the KLF family have established roles in tumor cell fate, stress response, cell survival and the tumor-initiating properties of cancer stem-like cells. Hence to investigate whether KFL7 expression from cancer tissue holds promise as a prognostic and/or therapeutic target, we analyzed gene expression profiles from squamous carcinoma and surgical margin tissues in The Cancer Genome Atlas. We identified significant up-regulation of KLF7 in squamous carcinoma, which was confirmed by immunohistochemical staining. Elevated KLF7 expression was associated with poor squamous carcinoma prognosis before and after correcting for confounding factors by multivariate Cox regression analysis. Several pathways, such as Neurotrophin and GnRH pathways, were activated in KLF7-up-regulated squamous carcinoma samples through Gene Set Enrichment Analysis. In conclusion, we consolidate the potential role(s) of KLF7 in squamous carcinoma carcinogenesis from The Cancer Genome Atlas surgical margin tissue, offering insights into expression signatures that are potentially useful for prognosis modalities.
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Affiliation(s)
- Jingrun Yang
- Department of DermatologyPLA General HospitalBeijingChina
| | - Kuixia Xie
- Dermatological DepartmentTianjin Fifth Centre HospitalTianjinChina
| | - Zihui Wang
- Department of PharmacyBeijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Chengxin Li
- Department of DermatologyPLA General HospitalBeijingChina
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14
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Elhasnaoui J, Miano V, Ferrero G, Doria E, Leon AE, Fabricio ASC, Annaratone L, Castellano I, Sapino A, De Bortoli M. DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage. Cancers (Basel) 2020; 12:cancers12061453. [PMID: 32503257 PMCID: PMC7352480 DOI: 10.3390/cancers12061453] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022] Open
Abstract
DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.
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Affiliation(s)
- Jamal Elhasnaoui
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Valentina Miano
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Giulio Ferrero
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Department of Computer Science, University of Turin, 10149 Turin, Italy
| | - Elena Doria
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
| | - Antonette E. Leon
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Aline S. C. Fabricio
- Regional Center for Biomarkers, Department of Clinical Pathology, Azienda ULSS 3 Serenissima, Campo SS Giovanni e Paolo 6777, 30122 Venice, Italy; (A.E.L.); (A.S.C.F.)
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Isabella Castellano
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (I.C.); (A.S.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Turin, Italy
| | - Michele De Bortoli
- Center for Molecular Systems Biology, University of Turin, Orbassano, 10043 Turin, Italy; (J.E.); (V.M.); (G.F.)
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy;
- Correspondence: ; Tel.: +39-0116-7050-58
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15
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Kim M, Lee S, Lim S, Kim S. SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq. PLoS One 2019; 14:e0223520. [PMID: 31644551 PMCID: PMC6808416 DOI: 10.1371/journal.pone.0223520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/23/2019] [Indexed: 01/19/2023] Open
Abstract
Motivation Intratumor heterogeneity (ITH) represents the diversity of cell populations that make up cancer tissue. The level of ITH in a tumor is usually measured by a genomic variation profile, such as copy number variation and somatic mutation. However, a recent study has identified ITH at the transcriptome level and suggested that ITH at gene expression levels is useful for predicting prognosis. Measuring ITH levels at the spliceome level is a natural extension. There are serious technical challenges in measuring spliceomic ITH (sITH) from bulk tumor RNA sequencing (RNA-seq) due to the complex splicing patterns. Results We propose an information-theoretic method to measure the sITH of bulk tumors to overcome the above challenges. This method has been extensively tested in experiments using synthetic data, xenograft tumor data, and TCGA pan-cancer data. As a result, we showed that sITH is closely related to cancer progression and clonal heterogeneity, along with clinically significant features such as cancer stage, survival outcome and PAM50 subtype. As far as we know, it is the first study to define ITH at the spliceome level. This method can greatly improve the understanding of cancer spliceome and has great potential as a diagnostic and prognostic tool.
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Affiliation(s)
- Minsu Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Sangseon Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Sangsoo Lim
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
- Bioinformatics Institute, Seoul National University, Seoul, 08826, Korea
- * E-mail:
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16
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Cao ZX, Xiao GA, Zhang W, Ji J, Ye C, Liu D, Tian QQ, Prof YHS. Comprehensive investigation of alternative splicing and development of a prognostic risk score for prostate cancer based on six-gene signatures. J Cancer 2019; 10:5585-5596. [PMID: 31632503 PMCID: PMC6775697 DOI: 10.7150/jca.31725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
Purpose: To systematically document alternative splicing profiles of prostate cancer in relatively large populations in order to construct a prognostic predictors model for prostate cancer. Methods: Splicing data and clinical information of 495 prostate cancer patients were obtained from The Cancer Genome Atlas (TCGA). The SpliceSeq database was used to extract information regarding splicing events. Multiple bioinformatic tools were used for functional and pathway enrichment analysis as well as for construction of gene interaction networks. Candidate gene expression profiles were verified with clinical samples using QRT-PCR. Results: We detected a total of 44070 alternative splicing events of 10381 genes in prostate cancer. 7 and 14 KEGG pathways were enriched and were associated with overall and recurrence-free survival, respectively. The expression of 396 genes among the 1526 overall survival genes associated alternative splicing events were associated with overall survival. The expression of 483 genes among the 1916 recurrence-free survival genes associated alternative splicing events were associated with recurrence-free survival. Lastly, we constructed the prognosis risk score system based on the expression profiles of six-gene signatures which in combination had an AUC of 0.941 for overall survival associated alternative splicing events, followed by overall survival associated gene expressions with an AUC of 0.794, a recurrence-free survival associated gene expression with an AUC of 0.752 and recurrence-free survival associated alternative splicing events with an AUC of 0.735, indicating its strong ability to predict patient outcome. The expression profile of the six genes was also confirmed in different prostate cell lines and clinic samples. Conclusion: Our comprehensive investigation of alternative splicing not only provided insight into the biological pathways of alternative splicing involved in the development of prostate cancer but also revealed new potential biomarkers for prognosticating as well as novel therapeutic targets for development of prostate cancer treatment.
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Affiliation(s)
- Zhe-Xu Cao
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Guang-An Xiao
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Wei Zhang
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Jin Ji
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Chen Ye
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Dan Liu
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Qin-Qin Tian
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Ying-Hao Sun Prof
- Department of Urology, Shanghai Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai 200433, China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University (Second Military Medical University), Shanghai 200433, China
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17
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Olender J, Wang BD, Ching T, Garmire LX, Garofano K, Ji Y, Knox T, Latham P, Nguyen K, Rhim J, Lee NH. A Novel FGFR3 Splice Variant Preferentially Expressed in African American Prostate Cancer Drives Aggressive Phenotypes and Docetaxel Resistance. Mol Cancer Res 2019; 17:2115-2125. [PMID: 31266816 DOI: 10.1158/1541-7786.mcr-19-0415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 01/08/2023]
Abstract
Alternative splicing (AS) has been shown to participate in prostate cancer development and progression; however, a link between AS and prostate cancer health disparities has been largely unexplored. Here we report on the cloning of a novel splice variant of FGFR3 that is preferentially expressed in African American (AA) prostate cancer. This novel variant (FGFR3-S) omits exon 14, comprising 123 nucleotides that encode the activation loop in the intracellular split kinase domain. Ectopic overexpression of FGFR3-S in European American (EA) prostate cancer cell lines (PC-3 and LNCaP) led to enhanced receptor autophosphorylation and increased activation of the downstream signaling effectors AKT, STAT3, and ribosomal S6 compared with FGFR3-L (retains exon 14). The increased oncogenic signaling imparted by FGFR3-S was associated with a substantial gain in proliferative and antiapoptotic activities, as well as a modest but significant gain in cell motility. Moreover, the FGFR3-S-conferred proliferative and motility gains were highly resistant to the pan-FGFR small-molecule inhibitor dovitinib and the antiapoptotic gain was insensitive to the cytotoxic drug docetaxel, which stands in marked contrast with dovitinib- and docetaxel-sensitive FGFR3-L. In an in vivo xenograft model, mice injected with PC-3 cells overexpressing FGFR3-S exhibited significantly increased tumor growth and resistance to dovitinib treatment compared with cells overexpressing FGFR3-L. In agreement with our in vitro and in vivo findings, a high FGFR3-S/FGFR3-L expression ratio in prostate cancer specimens was associated with poor patient prognosis. IMPLICATIONS: This work identifies a novel FGFR3 splice variant and supports the hypothesis that differential AS participates in prostate cancer health disparities.
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Affiliation(s)
- Jacqueline Olender
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, GW Cancer Center, Washington, D. C
| | - Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, Maryland
| | - Travers Ching
- Cancer Epidemiology Program, University of Hawaii, Honolulu, Hawaii
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kaitlin Garofano
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, GW Cancer Center, Washington, D. C
| | - Youngmi Ji
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland
| | - Tessa Knox
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, GW Cancer Center, Washington, D. C
| | - Patricia Latham
- Department of Pathology, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia
| | - Kenneth Nguyen
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, GW Cancer Center, Washington, D. C
| | - Johng Rhim
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of Health Sciences, Bethesda, Maryland
| | - Norman H Lee
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, GW Cancer Center, Washington, D. C.
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18
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Dysregulated Transcriptional Control in Prostate Cancer. Int J Mol Sci 2019; 20:ijms20122883. [PMID: 31200487 PMCID: PMC6627928 DOI: 10.3390/ijms20122883] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 12/24/2022] Open
Abstract
Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of the genome and lead to dysregulated gene expression. Single nucleotide variations and small mutations affecting the recruitment of transcription factor complexes to DNA regulatory elements are observed in an increasing number of cases. Genomic rearrangements may position coding regions under the novel control of regulatory elements, as exemplified by the TMPRSS2-ERG fusion and the amplified enhancer identified upstream of the androgen receptor (AR) gene. Super-enhancers are increasingly found to play important roles in aberrant oncogenic transcription. Several players involved in these processes are currently being evaluated as drug targets and may represent new vulnerabilities that can be exploited for prostate cancer treatment. They include factors involved in enhancer and super-enhancer function such as bromodomain proteins and cyclin-dependent kinases. In addition, non-coding RNAs with an important gene regulatory role are being explored. The rapid progress made in understanding the influence of the non-coding part of the genome and of transcription dysregulation in prostate cancer could pave the way for the identification of novel treatment paradigms for the benefit of patients.
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19
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Olender J, Lee NH. Role of Alternative Splicing in Prostate Cancer Aggressiveness and Drug Resistance in African Americans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1164:119-139. [PMID: 31576545 PMCID: PMC6777849 DOI: 10.1007/978-3-030-22254-3_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alternative splicing, the process of removing introns and joining exons of pre-mRNA, is critical for growth, development, tissue homeostasis, and species diversity. Dysregulation of alternative splicing can initiate and drive disease. Aberrant alternative splicing has been shown to promote the "hallmarks of cancer" in both hematological and solid cancers. Of interest, recent work has focused on the role of alternative splicing in prostate cancer and prostate cancer health disparities. We will provide a review of prostate cancer health disparities involving the African American population, alternative RNA splicing, and alternative splicing in prostate cancer. Lastly, we will summarize our work on differential alternative splicing in prostate cancer disparities and its implications for disparate health outcomes and therapeutic targets.
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Affiliation(s)
- Jacqueline Olender
- Department of Pharmacology and Physiology, GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Norman H Lee
- Department of Pharmacology and Physiology, GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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20
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Munkley J, Li L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL, Oltean S, Elliott DJ. Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer. eLife 2019; 8:47678. [PMID: 31478829 PMCID: PMC6788855 DOI: 10.7554/elife.47678] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/02/2019] [Indexed: 12/14/2022] Open
Abstract
Prostate is the most frequent cancer in men. Prostate cancer progression is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription by stimulating androgen receptor (AR) activity, yet also control pre-mRNA splicing through less clear mechanisms. Here we find androgens regulate splicing through AR-mediated transcriptional control of the epithelial-specific splicing regulator ESRP2. Both ESRP2 and its close paralog ESRP1 are highly expressed in primary prostate cancer. Androgen stimulation induces splicing switches in many endogenous ESRP2-controlled mRNA isoforms, including splicing switches correlating with disease progression. ESRP2 expression in clinical prostate cancer is repressed by ADT, which may thus inadvertently dampen epithelial splice programmes. Supporting this, treatment with the AR antagonist bicalutamide (Casodex) induced mesenchymal splicing patterns of genes including FLNB and CTNND1. Our data reveals a new mechanism of splicing control in prostate cancer with important implications for disease progression.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Ling Li
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - S R Gokul Krishnan
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Gerald Hysenaj
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Emma Scott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Caroline Dalgliesh
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Htoo Zarni Oo
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Teresa Mendes Maia
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal,VIB Center for Medical BiotechnologyVIBGhentBelgium,VIB Proteomics CoreVIBGhentBelgium,Department for Biomolecular MedicineGhent UniversityGhentBelgium
| | - Kathleen Cheung
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Ingrid Ehrmann
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Karen E Livermore
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Hanna Zielinska
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Oliver Thompson
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Bridget Knight
- NIHR Exeter Clinical Research FacilityRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Paul McCullagh
- Department of PathologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - John McGrath
- Exeter Surgical Health Services Research UnitRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Malcolm Crundwell
- Department of UrologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Mads Daugaard
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal
| | - Sebastian Oltean
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - David J Elliott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
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21
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Wang BD, Lee NH. Aberrant RNA Splicing in Cancer and Drug Resistance. Cancers (Basel) 2018; 10:E458. [PMID: 30463359 PMCID: PMC6266310 DOI: 10.3390/cancers10110458] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022] Open
Abstract
More than 95% of the 20,000 to 25,000 transcribed human genes undergo alternative RNA splicing, which increases the diversity of the proteome. Isoforms derived from the same gene can have distinct and, in some cases, opposing functions. Accumulating evidence suggests that aberrant RNA splicing is a common and driving event in cancer development and progression. Moreover, aberrant splicing events conferring drug/therapy resistance in cancer is far more common than previously envisioned. In this review, aberrant splicing events in cancer-associated genes, namely BCL2L1, FAS, HRAS, CD44, Cyclin D1, CASP2, TMPRSS2-ERG, FGFR2, VEGF, AR and KLF6, will be discussed. Also highlighted are the functional consequences of aberrant splice variants (BCR-Abl35INS, BIM-γ, IK6, p61 BRAF V600E, CD19-∆2, AR-V7 and PIK3CD-S) in promoting resistance to cancer targeted therapy or immunotherapy. To overcome drug resistance, we discuss opportunities for developing novel strategies to specifically target the aberrant splice variants or splicing machinery that generates the splice variants. Therapeutic approaches include the development of splice variant-specific siRNAs, splice switching antisense oligonucleotides, and small molecule inhibitors targeting splicing factors, splicing factor kinases or the aberrant oncogenic protein isoforms.
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Affiliation(s)
- Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.
| | - Norman H Lee
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, GW Cancer Center, Washington, DC 20037, USA.
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22
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Munkley J, Maia TM, Ibarluzea N, Livermore KE, Vodak D, Ehrmann I, James K, Rajan P, Barbosa-Morais NL, Elliott DJ. Androgen-dependent alternative mRNA isoform expression in prostate cancer cells. F1000Res 2018; 7:1189. [PMID: 30271587 PMCID: PMC6143958 DOI: 10.12688/f1000research.15604.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Background: Androgen steroid hormones are key drivers of prostate cancer. Previous work has shown that androgens can drive the expression of alternative mRNA isoforms as well as transcriptional changes in prostate cancer cells. Yet to what extent androgens control alternative mRNA isoforms and how these are expressed and differentially regulated in prostate tumours is unknown. Methods: Here we have used RNA-Seq data to globally identify alternative mRNA isoform expression under androgen control in prostate cancer cells, and profiled the expression of these mRNA isoforms in clinical tissue. Results: Our data indicate androgens primarily switch mRNA isoforms through alternative promoter selection. We detected 73 androgen regulated alternative transcription events, including utilisation of 56 androgen-dependent alternative promoters, 13 androgen-regulated alternative splicing events, and selection of 4 androgen-regulated alternative 3' mRNA ends. 64 of these events are novel to this study, and 26 involve previously unannotated isoforms. We validated androgen dependent regulation of 17 alternative isoforms by quantitative PCR in an independent sample set. Some of the identified mRNA isoforms are in genes already implicated in prostate cancer (including LIG4, FDFT1 and RELAXIN), or in genes important in other cancers (e.g. NUP93 and MAT2A). Importantly, analysis of transcriptome data from 497 tumour samples in the TGCA prostate adenocarcinoma (PRAD) cohort identified 13 mRNA isoforms (including TPD52, TACC2 and NDUFV3) that are differentially regulated in localised prostate cancer relative to normal tissue, and 3 ( OSBPL1A, CLK3 and TSC22D3) which change significantly with Gleason grade and tumour stage. Conclusions: Our findings dramatically increase the number of known androgen regulated isoforms in prostate cancer, and indicate a highly complex response to androgens in prostate cancer cells that could be clinically important.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Teresa M. Maia
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
- VIB Proteomics Core, Albert Baertsoenkaai 3, Ghent, 9000, Belgium
| | - Nekane Ibarluzea
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
- Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, 48903, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Valencia, 46010, Spain
| | - Karen E. Livermore
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Daniel Vodak
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Ehrmann
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Katherine James
- Interdisciplinary Computing and Complex BioSystems Research Group, Newcastle University, Newcastle upon Tyne, NE4 5TG, UK
- Life and Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Prabhakar Rajan
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, EC1M 6BQ, UK
| | - Nuno L. Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
| | - David J. Elliott
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
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23
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Adamopoulos PG, Raptis GD, Kontos CK, Scorilas A. Discovery and expression analysis of novel transcripts of the human SR-related CTD-associated factor 1 (SCAF1) gene in human cancer cells using Next-Generation Sequencing. Gene 2018; 670:155-165. [PMID: 29787824 DOI: 10.1016/j.gene.2018.05.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/13/2018] [Indexed: 02/07/2023]
Abstract
The human SR-related CTD associated factor 1 (SCAF1) gene is a new member of the human SR (Ser/Arg-rich) superfamily of pre-mRNA splicing factors, which has been discovered and cloned by members of our lab. SCAF1 interacts with the CTD domain of the RNA polymerase II polypeptide A and is firmly involved in pre-mRNA splicing. Although it was found to be expressed widely in multiple human tissues, its mRNA levels vary a lot. The significant relation of SCAF1 with cancer has been confirmed by many studies, since SCAF1 mRNA transcript was found to be overexpressed in breast and ovarian tumors, confirming its significant prognostic value as a cancer biomarker in both these human malignancies. In this study, we describe the discovery and cloning of fifteen novel transcripts of the human SCAF1 gene (SCAF1 v.2 - v.16), using nested PCR and NGS technology. In detail, extensive bioinformatic analysis revealed that these novel SCAF1 splice variants comprise a total of nine novel alternative splicing events between the annotated exons of the gene, thus producing seven novel SCAF1 transcripts with open-reading frames, which are predicted to encode novel SCAF1 isoforms and eight novel SCAF1 transcripts with premature termination codons that are likely long non-coding RNAs. Additionally, a novel 3' UTR was discovered and cloned using nested 3' RACE and was validated with Sanger sequencing. In order to validate the NGS findings as well as to investigate the expression profile of each novel transcript, RT-PCR experiments were carried out with the use of variant-specific primers. Since SCAF1 is implicated in many human malignancies, qualifying as a potential biomarker, the quantification of the presented novel transcripts in human samples may have clinical applications in different types of cancer.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios D Raptis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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24
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Magee RG, Telonis AG, Loher P, Londin E, Rigoutsos I. Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer. Sci Rep 2018; 8:5314. [PMID: 29593348 PMCID: PMC5871839 DOI: 10.1038/s41598-018-22488-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 02/19/2018] [Indexed: 12/31/2022] Open
Abstract
MicroRNA (miRNA) isoforms ("isomiRs") and tRNA-derived fragments ("tRFs") are powerful regulatory non-coding RNAs (ncRNAs). In human tissues, both types of molecules are abundant, with expression patterns that depend on a person's race, sex and population origin. Here, we present our analyses of the Prostate Cancer (PRAD) datasets of The Cancer Genome Atlas (TCGA) from the standpoint of isomiRs and tRFs. This study represents the first simultaneous examination of isomiRs and tRFs in a large cohort of PRAD patients. We find that isomiRs and tRFs have extensive correlations with messenger RNAs (mRNAs). These correlations are disrupted in PRAD, which suggests disruptions of the regulatory network in the disease state. Notably, we find that the profiles of isomiRs and tRFs differ in patients belonging to different races. We hope that the presented findings can lay the groundwork for future research efforts aimed at elucidating the functional roles of the numerous and distinct members of these two categories of ncRNAs that are present in PRAD.
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Affiliation(s)
- Rogan G Magee
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Eric Londin
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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25
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Li L, Feng J, Chen Y, Li S, Ou M, Sun W, Tang L. Estradiol shows anti-skin cancer activities through decreasing MDM2 expression. Oncotarget 2018; 8:8459-8474. [PMID: 28035066 PMCID: PMC5352414 DOI: 10.18632/oncotarget.14275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 11/30/2016] [Indexed: 12/19/2022] Open
Abstract
Estradiol plays important roles in many biological responses inducing tumor genesis and cancer treatment. However, the effects of estradiol on tumors were inconsistent among a lot of researches and the mechanism is not fully understood. Our previous study indicated that splicing factor hnRNPA1 could bind to the human homologue of mouse double minute (MDM2), an oncogene which has been observed to be over-expressed in numerous types of cancers. In this research, we investigated whether and how estradiol correlate to cancer cell behaviors through heterogeneous nuclear ribonucleoprotein (hnRNPA1) and MDM2. Results showed that 10×10-13Mestradiol elevated the expression of hnRNPA1 regardless ER expression in cells, and then down-regulated the expression of MDM2. At the same time, estradiol inhibited cell proliferation, migration and epithelial-mesenchymal transition progression of A375 and GLL19 cells. While, knocking down hnRNPA1 through the transfection of hnRNPA1 siRNA led to the increase of MDM2 at both protein level and gene level In vivo experiment, subcutaneous injection with estradiol every two days near the tumor at doses of 2.5mg/kg/d suppressed tumor growth and reduced MDM2 expression. In a word, via increasing hnRNPA1 level and then reducing the expression of MDM2, estradiol prevented carcinogenesis in melanomas. We confirmed therapeutic effect of estradiol, as well as a new way for estradiol to resist skin cancer.
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Affiliation(s)
- Li Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.,Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Ying Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shun Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Mengting Ou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Weichao Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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26
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Huang WT, Cen WL, He RQ, Xie Y, Zhang Y, Li P, Gan TQ, Chen G, Hu XH. Effect of miR‑146a‑5p on tumor growth in NSCLC using chick chorioallantoic membrane assay and bioinformatics investigation. Mol Med Rep 2017; 16:8781-8792. [PMID: 28990079 PMCID: PMC5779957 DOI: 10.3892/mmr.2017.7713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 09/22/2017] [Indexed: 12/12/2022] Open
Abstract
Our previous study demonstrated that the expression of miR-146a-5p was downregulated in non-small cell lung cancer (NSCLC) tissue, which affected the progression and prognosis of patients with NSCLC. Thus, the present study was conducted to investigate the functional mechanism of miR-146a-5p in tumorigenesis and angiogenesis in NSCLC. Following the construction of a H460 NSCLC cell line in which miR-146a-5p was overexpressed via lentivirus transduction, the NSCLC chick embryo chorioallantoic membrane (CAM) model was established by transplanting miR-146a-5p-overexpressing NSCLC cells into the CAM. Then, the size of the neoplasms within the CAM was measured, the vessel ratio was calculated, and the cellular morphology, metastasis and inflammation of tumor cell was observed using hematoxylin and eosin staining. The target genes of miR-146a-5p were predicted by 12 online software programs; these genes were then subjected to Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway annotations using the Database for Annotation, Visualization and Integrated Discovery 6.7 as well as constructed into a protein interaction network using protein-protein interaction from Search Tool for the Retrieval of Interacting Genes/Proteins. The xenograft tumor size and angiogenesis conditions of the miR-146a-5p-overexpressing group (volume 6.340±0.066 mm3, vessel ratio 9.326±0.083) was obviously restricted (P<0.001) when compared with the low expression group (volume 30.13±0.06 mm3, vessel ratio 16.94±0.11). In addition, marked necrosis along with inflammatory cell infiltration was observed with the HE-stained slices from the miR-146a-5p low expression group. Regarding the results of the target gene prediction, cancer and toll-like receptor signaling were the two most significant pathways represented among the target genes, while JUN, EGFR and RAC1 were the most relevant proteins among the selected potential targets of miR-146a-5p. In a CAM xenograft tumor model, overexpression of miR-146a-5p inhibited the tumorigenesis and angiogenesis of an NSCLC cell line. miR-146a-5p may act as a tumor suppressor gene in NSCLC and have moderate prognostic value in lung cancer.
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Affiliation(s)
- Wen-Ting Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Wei-Luan Cen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - You Xie
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ping Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ting-Qing Gan
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiao-Hua Hu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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27
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Munkley J, Livermore K, Rajan P, Elliott DJ. RNA splicing and splicing regulator changes in prostate cancer pathology. Hum Genet 2017; 136:1143-1154. [PMID: 28382513 PMCID: PMC5602090 DOI: 10.1007/s00439-017-1792-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/29/2017] [Indexed: 11/26/2022]
Abstract
Changes in mRNA splice patterns have been associated with key pathological mechanisms in prostate cancer progression. The androgen receptor (abbreviated AR) transcription factor is a major driver of prostate cancer pathology and activated by androgen steroid hormones. Selection of alternative promoters by the activated AR can critically alter gene function by switching mRNA isoform production, including creating a pro-oncogenic isoform of the normally tumour suppressor gene TSC2. A number of androgen-regulated genes generate alternatively spliced mRNA isoforms, including a prostate-specific splice isoform of ST6GALNAC1 mRNA. ST6GALNAC1 encodes a sialyltransferase that catalyses the synthesis of the cancer-associated sTn antigen important for cell mobility. Genetic rearrangements occurring early in prostate cancer development place ERG oncogene expression under the control of the androgen-regulated TMPRSS2 promoter to hijack cell behaviour. This TMPRSS2-ERG fusion gene shows different patterns of alternative splicing in invasive versus localised prostate cancer. Alternative AR mRNA isoforms play a key role in the generation of prostate cancer drug resistance, by providing a mechanism through which prostate cancer cells can grow in limited serum androgen concentrations. A number of splicing regulator proteins change expression patterns in prostate cancer and may help drive key stages of disease progression. Up-regulation of SRRM4 establishes neuronal splicing patterns in neuroendocrine prostate cancer. The splicing regulators Sam68 and Tra2β increase expression in prostate cancer. The SR protein kinase SRPK1 that modulates the activity of SR proteins is up-regulated in prostate cancer and has already given encouraging results as a potential therapeutic target in mouse models.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, England, UK
| | - Karen Livermore
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, England, UK
| | - Prabhakar Rajan
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, England, UK.
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28
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Abstract
STAR (signal transduction and activation of RNA) proteins regulate splicing of target genes that have roles in neural connectivity, survival and myelination in the vertebrate nervous system. These regulated splicing targets include mRNAs such as the Neurexins (Nrxn), SMN2 (survival of motor neuron) and MAG (myelin-associated glycoprotein). Recent work has made it possible to identify and validate STAR protein splicing targets in vivo by using genetically modified mouse models. In this review, we will discuss the importance of STAR protein splicing targets in the CNS (central nervous system).
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29
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Hormaechea-Agulla D, Jiménez-Vacas JM, Gómez-Gómez E, L-López F, Carrasco-Valiente J, Valero-Rosa J, Moreno MM, Sánchez-Sánchez R, Ortega-Salas R, Gracia-Navarro F, Culler MD, Ibáñez-Costa A, Gahete MD, Requena MJ, Castaño JP, Luque RM. The oncogenic role of the spliced somatostatin receptor sst5TMD4 variant in prostate cancer. FASEB J 2017; 31:4682-4696. [PMID: 28705809 DOI: 10.1096/fj.201601264rrr] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 06/27/2017] [Indexed: 12/17/2022]
Abstract
sst5TMD4, a splice variant of the sst5 gene, is overexpressed and associated with aggressiveness in various endocrine-related tumors, but its presence, functional role, and mechanisms of actions in prostate cancer (PCa)-the most common cancer type in males-is completely unexplored. In this study, formalin-fixed, paraffin-embedded prostate pieces from patients with localized PCa, which included tumoral and nontumoral adjacent regions (n = 45), fresh biopsies from patients with high-risk PCa (n = 52), and healthy fresh prostates from cystoprostatectomies (n = 14) were examined. In addition, PCa cell lines and xenograft models were used to determine the presence and functional role of sst5TMD4. Results demonstrated that sst5TMD4 is overexpressed (mRNA/protein) in PCa samples, and this is especially drastic in metastatic and/or high Gleason score tumor samples. Remarkably, sst5TMD4 expression was associated with an altered frequency of 2 single-nucleotide polymorphisms: rs197055 and rs12599155. In addition, PCa cell lines and xenograft models were used to demonstrate that sst5TMD4 overexpression increases cell proliferation and migration in PCa cells and induces larger tumors in nude mice, whereas its silencing decreased proliferation and migration. Remarkably, sst5TMD4 overexpression activated multiple intracellular pathways (ERK/JNK, MYC/MAX, WNT, retinoblastoma), altered oncogenes and tumor suppressor gene expression, and disrupted the normal response to somatostatin analogs in PCa cells. Altogether, we demonstrate that sst5TMD4 is overexpressed in PCa, especially in those patients with a worse prognosis, and plays an important pathophysiologic role in PCa, which suggesting its potential as a biomarker and/or therapeutic target.-Hormaechea-Agulla, D., Jiménez-Vacas, J. M., Gómez-Gómez, E., L.-López, F., Carrasco-Valiente, J., Valero-Rosa, J., Moreno, M. M., Sánchez-Sánchez, R., Ortega-Salas, R., Gracia-Navarro, F., Culler, M. D., Ibáñez-Costa, A., Gahete, M. D., Requena, M. J., Castaño, J. P., Luque, R. M. The oncogenic role of the spliced somatostatin receptor sst5TMD4 variant in prostate cancer.
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Affiliation(s)
- Daniel Hormaechea-Agulla
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
| | - Enrique Gómez-Gómez
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Urology Service, Hospital Universitario Reina Sofia (HURS)/Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain
| | - Fernando L-López
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
| | - Julia Carrasco-Valiente
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Urology Service, Hospital Universitario Reina Sofia (HURS)/Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain
| | - José Valero-Rosa
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Urology Service, Hospital Universitario Reina Sofia (HURS)/Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain
| | - María M Moreno
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Anatomical Pathology Service, Hospital Universitario Reina Sofia (HURS), Cordoba, Spain
| | - Rafael Sánchez-Sánchez
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Anatomical Pathology Service, Hospital Universitario Reina Sofia (HURS), Cordoba, Spain
| | - Rosa Ortega-Salas
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Anatomical Pathology Service, Hospital Universitario Reina Sofia (HURS), Cordoba, Spain
| | - Francisco Gracia-Navarro
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
| | | | - Alejandro Ibáñez-Costa
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
| | - Manuel D Gahete
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
| | - María J Requena
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Urology Service, Hospital Universitario Reina Sofia (HURS)/Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain
| | - Justo P Castaño
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; .,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
| | - Raúl M Luque
- Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Cordoba, Spain; .,Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.,Hospital Universitario Reina Sofia (HURS), Cordoba, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Cordoba, Spain.,Campus de Excelencia Internacional Agroalimentario (CEIA3), Cordoba, Spain
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30
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Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH. Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer. Nat Commun 2017; 8:15921. [PMID: 28665395 PMCID: PMC5497057 DOI: 10.1038/ncomms15921] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/15/2017] [Indexed: 12/12/2022] Open
Abstract
Clinical challenges exist in reducing prostate cancer (PCa) disparities. The RNA splicing landscape of PCa across racial populations has not been fully explored as a potential molecular mechanism contributing to race-related tumour aggressiveness. Here, we identify novel genome-wide, race-specific RNA splicing events as critical drivers of PCa aggressiveness and therapeutic resistance in African American (AA) men. AA-enriched splice variants of PIK3CD, FGFR3, TSC2 and RASGRP2 contribute to greater oncogenic potential compared with corresponding European American (EA)-expressing variants. Ectopic overexpression of the newly cloned AA-enriched variant, PIK3CD-S, in EA PCa cell lines enhances AKT/mTOR signalling and increases proliferative and invasive capacity in vitro and confers resistance to selective PI3Kδ inhibitor, CAL-101 (idelalisib), in mouse xenograft models. High PIK3CD-S expression in PCa specimens associates with poor survival. These results highlight the potential of RNA splice variants to serve as novel biomarkers and molecular targets for developmental therapeutics in aggressive PCa.
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Affiliation(s)
- Bi-Dar Wang
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, District Of Columbia 20037, USA
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, Maryland 21853, USA
| | - Kristin Ceniccola
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, District Of Columbia 20037, USA
| | - SuJin Hwang
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, District Of Columbia 20037, USA
| | - Ramez Andrawis
- Department of Urology, School of Medicine and Health Sciences, The George Washington University, Washington, District Of Columbia 20037, USA
| | - Anelia Horvath
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, District Of Columbia 20037, USA
| | - Jennifer A. Freedman
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jacqueline Olender
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, District Of Columbia 20037, USA
| | - Stefan Knapp
- Department of Clinical Pharmacology, University of Oxford, Oxford OX3 7BN, UK
- The Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford OX3 7BN, UK
| | - Travers Ching
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Lana Garmire
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Vyomesh Patel
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mariano A. Garcia-Blanco
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Steven R. Patierno
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Norman H. Lee
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, District Of Columbia 20037, USA
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31
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Vitting-Seerup K, Sandelin A. The Landscape of Isoform Switches in Human Cancers. Mol Cancer Res 2017; 15:1206-1220. [PMID: 28584021 DOI: 10.1158/1541-7786.mcr-16-0459] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/17/2017] [Accepted: 05/25/2017] [Indexed: 11/16/2022]
Abstract
Alternative usage of transcript isoforms from the same gene has been hypothesized as an important feature in cancers. However, differential usage of gene transcripts between conditions (isoform switching) has not been comprehensively characterized in and across cancer types. To this end, we developed methods for identification and visualization of isoform switches with predicted functional consequences. Using these methods, we characterized isoform switching in RNA-seq data from >5,500 cancer patients covering 12 solid cancer types. Isoform switches with potential functional consequences were common, affecting approximately 19% of multiple transcript genes. Among these, isoform switches leading to loss of DNA sequence encoding protein domains were more frequent than expected, particularly in pancancer switches. We identified several isoform switches as powerful biomarkers: 31 switches were highly predictive of patient survival independent of cancer types. Our data constitute an important resource for cancer researchers, available through interactive web tools. Moreover, our methods, available as an R package, enable systematic analysis of isoform switches from other RNA-seq datasets.Implications: This study indicates that isoform switches with predicted functional consequences are common and important in dysfunctional cells, which in turn means that gene expression should be analyzed at the isoform level. Visual Overview: http://mcr.aacrjournals.org/content/molcanres/15/9/1206/F1.large.jpg.Mol Cancer Res; 15(9); 1206-20. ©2017 AACR.
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Affiliation(s)
- Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
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32
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Li L, Wang X, Xiao G, Gazdar A. Integrative gene set enrichment analysis utilizing isoform-specific expression. Genet Epidemiol 2017; 41:498-510. [PMID: 28580727 DOI: 10.1002/gepi.22052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 02/12/2017] [Accepted: 03/14/2017] [Indexed: 01/01/2023]
Abstract
Gene set enrichment analysis (GSEA) aims at identifying essential pathways, or more generally, sets of biologically related genes that are involved in complex human diseases. In the past, many studies have shown that GSEA is a very useful bioinformatics tool that plays critical roles in the innovation of disease prevention and intervention strategies. Despite its tremendous success, it is striking that conclusions of GSEA drawn from isolated studies are often sparse, and different studies may lead to inconsistent and sometimes contradictory results. Further, in the wake of next generation sequencing technologies, it has been made possible to measure genome-wide isoform-specific expression levels, calling for innovations that can utilize the unprecedented resolution. Currently, enormous amounts of data have been created from various RNA-seq experiments. All these give rise to a pressing need for developing integrative methods that allow for explicit utilization of isoform-specific expression, to combine multiple enrichment studies, in order to enhance the power, reproducibility, and interpretability of the analysis. We develop and evaluate integrative GSEA methods, based on two-stage procedures, which, for the first time, allow statistically efficient use of isoform-specific expression from multiple RNA-seq experiments. Through simulation and real data analysis, we show that our methods can greatly improve the performance in identifying essential gene sets compared to existing methods that can only use gene-level expression.
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Affiliation(s)
- Lie Li
- Department of Statistical Science, Southern Methodist University, Dallas, Texas, United States of America
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, Texas, United States of America
| | - Guanghua Xiao
- Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Adi Gazdar
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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33
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Neuhaus J, Schiffer E, Mannello F, Horn LC, Ganzer R, Stolzenburg JU. Protease Expression Levels in Prostate Cancer Tissue Can Explain Prostate Cancer-Associated Seminal Biomarkers-An Explorative Concept Study. Int J Mol Sci 2017; 18:ijms18050976. [PMID: 28471417 PMCID: PMC5454889 DOI: 10.3390/ijms18050976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/20/2017] [Accepted: 04/29/2017] [Indexed: 01/05/2023] Open
Abstract
Previously, we described prostate cancer (PCa) detection (83% sensitivity; 67% specificity) in seminal plasma by CE-MS/MS. Moreover, advanced disease was distinguished from organ-confined tumors with 80% sensitivity and 82% specificity. The discovered biomarkers were naturally occurring fragments of larger seminal proteins, predominantly semenogelin 1 and 2, representing endpoints of the ejaculate liquefaction. Here we identified proteases putatively involved in PCa specific protein cleavage, and examined gene expression and tissue protein levels, jointly with cell localization in normal prostate (nP), benign prostate hyperplasia (BPH), seminal vesicles and PCa using qPCR, Western blotting and confocal laser scanning microscopy. We found differential gene expression of chymase (CMA1), matrix metalloproteinases (MMP3, MMP7), and upregulation of MMP14 and tissue inhibitors (TIMP1 and TIMP2) in BPH. In contrast tissue protein levels of MMP14 were downregulated in PCa. MMP3/TIMP1 and MMP7/TIMP1 ratios were decreased in BPH. In seminal vesicles, we found low-level expression of most proteases and, interestingly, we also detected TIMP1 and low levels of TIMP2. We conclude that MMP3 and MMP7 activity is different in PCa compared to BPH due to fine regulation by their inhibitor TIMP1. Our findings support the concept of seminal plasma biomarkers as non-invasive tool for PCa detection and risk stratification.
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Affiliation(s)
- Jochen Neuhaus
- Department of Urology, Research Laboratory, University of Leipzig, Liebigstraße 19, 04103 Leipzig, Germany.
| | - Eric Schiffer
- Numares AG, Regensburg, Am BioPark 9, 93053 Regensburg, Germany.
| | - Ferdinando Mannello
- Department of Biomolecular Sciences, University "Carlo Bo", Via O. Ubaldini 7, 61029 Urbino (PU), Italy.
| | - Lars-Christian Horn
- Institute of Pathology, University Hospital Leipzig, Liebigstraße 24, 04103 Leipzig, Germany.
| | - Roman Ganzer
- Department of Urology, University Hospital Leipzig, Liebigstraße 20, 04103 Leipzig, Germany.
| | - Jens-Uwe Stolzenburg
- Department of Urology, University Hospital Leipzig, Liebigstraße 20, 04103 Leipzig, Germany.
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34
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Bornholdt J, Saber AT, Lilje B, Boyd M, Jørgensen M, Chen Y, Vitezic M, Jacobsen NR, Poulsen SS, Berthing T, Bressendorff S, Vitting-Seerup K, Andersson R, Hougaard KS, Yauk CL, Halappanavar S, Wallin H, Vogel U, Sandelin A. Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo. ACS NANO 2017; 11:3597-3613. [PMID: 28345861 DOI: 10.1021/acsnano.6b07533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Increased use of nanomaterials in industry, medicine, and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well-characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24 h after intratracheal instillation of a single dose of the multiwalled carbon nanotube (MWCNT) Mitsui-7. Our results revealed a massive gene regulatory response, where expression of key inflammatory genes (e.g., Csf3, Il24, and Fgf23) was increased >100-fold 24 h after Mitsui-7 exposure. Many of the Mitsui-7-responsive transcription start sites were alternative transcription start sites for known genes, and the number of alternative transcription start sites used in a given gene was correlated with overall Mitsui-7 response. Strikingly, genes that were up-regulated after Mitsui-7 exposure only through their main annotated transcription start site were linked to inflammatory and defense responses, while genes up-regulated only through alternative transcription start sites were functionally heterogeneous and not inflammation-associated. Furthermore, we identified almost 12 000 active enhancers, many of which were Mitsui-7-responsive, and we identified similarly responding putative target genes. Overall, our study provides the location and activity of Mitsui-7-induced enhancers and transcription start sites, providing a useful resource for targeted experiments elucidating the biological effects of nanomaterials and the identification of biomarkers for early detection of MWCNT-induced inflammation.
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Affiliation(s)
- Jette Bornholdt
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Berit Lilje
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Boyd
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Jørgensen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Morana Vitezic
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Sarah Søs Poulsen
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Trine Berthing
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Simon Bressendorff
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Carole L Yauk
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Sabina Halappanavar
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Håkan Wallin
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Public Health, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Micro and Nanotechnology, Technical University of Denmark , 2800 Kongens Lyngby, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
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35
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Feng J, Li L, Tong L, Tang L, Wu S. The Involvement of Splicing Factor hnRNP A1 in UVB-induced Alternative Splicing of hdm2. Photochem Photobiol 2016; 92:318-324. [PMID: 26757361 DOI: 10.1111/php.12564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
Human homolog double minute 2 (hdm2), an oncoprotein, which binds to tumor suppressor p53 to facilitate its degradation, has been known to contribute to tumorigenesis. Its splicing variants are reported to be highly expressed in many cancers and can be induced by ultraviolet B light (UVB). However, the mechanisms of how UVB radiation induces hdm2 alternative splicing still remain unclear. In this study, we investigated the roles of two common splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and serine/arginine-rich splicing factor 1 (SRSF1), in regulating UVB-induced hdm2 splicing. Our study indicated that while the expression of both hnRNP A1 and SRSF1 are induced, only hnRNP A1 is involved in hdm2 alternative splicing upon UVB irradiation. Overexpression of hnRNP A1 resulted in decrease of full-length hdm2 (hdm2-FL) and increase of hdm2B, one of hdm2 alternate-splicing forms; while down-regulated hnRNP A1 expression led to the decrease of the hdm2-FL and hdm2B in HaCaT cells. Protein-mRNA binding assay confirmed that UVB irradiation could increase the binding of hnRNP A1 to hdm2 pre-mRNA. In conclusion, we elucidated that UVB induces alternative splicing of hdm2 by increasing the expression and the binding of hnRNP A1 to hdm2 full-length mRNA.
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Affiliation(s)
- Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.,Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Li Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Lingying Tong
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shiyong Wu
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
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36
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Stockley J, Markert E, Zhou Y, Robson CN, Elliott DJ, Lindberg J, Leung HY, Rajan P. The RNA-binding protein Sam68 regulates expression and transcription function of the androgen receptor splice variant AR-V7. Sci Rep 2015; 5:13426. [PMID: 26310125 PMCID: PMC4550848 DOI: 10.1038/srep13426] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/27/2015] [Indexed: 12/02/2022] Open
Abstract
Castration-resistant (CR) prostate cancer (PCa) partly arises due to persistence of androgen receptor (AR) transcriptional activity in the absence of cognate ligand. An emerging mechanism underlying the CRPCa phenotype and predicting response to therapy is the expression of the constitutively-active AR-V7 splice variant generated by AR cryptic exon 3b inclusion. Here, we explore the role of the RNA-binding protein (RBP) Sam68 (encoded by KHDRBS1), which is over-expressed in clinical PCa, on AR-V7 expression and transcription function. Using a minigene reporter, we show that Sam68 controls expression of exon 3b resulting in an increase in endogenous AR-V7 mRNA and protein expression in RNA-binding-dependent manner. We identify a novel protein-protein interaction between Sam68 and AR-V7 mediated by a common domain shared with full-length AR, and observe these proteins in the cell nucleoplasm. Using a luciferase reporter, we demonstrate that Sam68 co-activates ligand-independent AR-V7 transcriptional activity in an RNA-binding-independent manner, and controls expression of the endogenous AR-V7-specific gene target UBE2C. Our data suggest that Sam68 has separable effects on the regulation of AR-V7 expression and transcriptional activity, through its RNA-binding capacity. Sam68 and other RBPs may control expression of AR-V7 and other splice variants as well as their downstream functions in CRPCa.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Alternative Splicing/genetics
- Cell Line, Tumor
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Exons/genetics
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Male
- Models, Biological
- Prostatic Neoplasms/genetics
- Protein Binding
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Androgen/chemistry
- Receptors, Androgen/genetics
- Transcription, Genetic
- Ubiquitin-Conjugating Enzymes/genetics
- Ubiquitin-Conjugating Enzymes/metabolism
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Affiliation(s)
| | - Elke Markert
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Yan Zhou
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Craig N. Robson
- Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Johan Lindberg
- Department of Molecular Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hing Y. Leung
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Prabhakar Rajan
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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37
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Yu X, Zeng T, Wang X, Li G, Chen L. Unravelling personalized dysfunctional gene network of complex diseases based on differential network model. J Transl Med 2015; 13:189. [PMID: 26070628 PMCID: PMC4467679 DOI: 10.1186/s12967-015-0546-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/25/2015] [Indexed: 11/10/2022] Open
Abstract
In the conventional analysis of complex diseases, the control and case samples are assumed to be of great purity. However, due to the heterogeneity of disease samples, many disease genes are even not always consistently up-/down-regulated, leading to be under-estimated. This problem will seriously influence effective personalized diagnosis or treatment. The expression variance and expression covariance can address such a problem in a network manner. But, these analyses always require multiple samples rather than one sample, which is generally not available in clinical practice for each individual. To extract the common and specific network characteristics for individual patients in this paper, a novel differential network model, e.g. personalized dysfunctional gene network, is proposed to integrate those genes with different features, such as genes with the differential gene expression (DEG), genes with the differential expression variance (DEVG) and gene-pairs with the differential expression covariance (DECG) simultaneously, to construct personalized dysfunctional networks. This model uses a new statistic-like measurement on differential information, i.e., a differential score (DEVC), to reconstruct the differential expression network between groups of normal and diseased samples; and further quantitatively evaluate different feature genes in the patient-specific network for each individual. This DEVC-based differential expression network (DEVC-net) has been applied to the study of complex diseases for prostate cancer and diabetes. (1) Characterizing the global expression change between normal and diseased samples, the differential gene networks of those diseases were found to have a new bi-coloured topological structure, where their non hub-centred sub-networks are mainly composed of genes/proteins controlling various biological processes. (2) The differential expression variance/covariance rather than differential expression is new informative sources, and can be used to identify genes or gene-pairs with discriminative power, which are ignored by traditional methods. (3) More importantly, DEVC-net is effective to measure the expression state or activity of different feature genes and their network or modules in one sample for an individual. All of these results support that DEVC-net indeed has a clear advantage to effectively extract discriminatively interpretable features of gene/protein network of one sample (i.e. personalized dysfunctional network) even when disease samples are heterogeneous, and thus can provide new features like gene-pairs, in addition to the conventional individual genes, to the analysis of the personalized diagnosis and prognosis, and a better understanding on the underlying biological mechanisms.
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Affiliation(s)
- Xiangtian Yu
- School of Mathematics, Shandong University, Jinan, 250100, China. .,Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Tao Zeng
- Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Xiangdong Wang
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China. .,Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai, China.
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
| | - Luonan Chen
- Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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38
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Wang HC, Yang Y, Xu SY, Peng J, Jiang JH, Li CY. The CRISPR/Cas system inhibited the pro-oncogenic effects of alternatively spliced fibronectin extra domain A via editing the genome in salivary adenoid cystic carcinoma cells. Oral Dis 2015; 21:608-18. [PMID: 25684411 DOI: 10.1111/odi.12323] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/24/2015] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Affiliation(s)
- H-C Wang
- The Central Laboratory; Peking University School and Hospital of Stomatology; Haidian District Beijing China
| | - Y Yang
- The Central Laboratory; Peking University School and Hospital of Stomatology; Haidian District Beijing China
| | - S-Y Xu
- Department of Oral Implanting; Shandong University School of Stomatology; Lixia District Jinan China
| | - J Peng
- The Central Laboratory; Peking University School and Hospital of Stomatology; Haidian District Beijing China
| | - J-H Jiang
- The Department of Orthodontics; Peking University School and Hospital of Stomatology; Haidian District China
| | - C-Y Li
- The Central Laboratory; Peking University School and Hospital of Stomatology; Haidian District Beijing China
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39
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Tseng YT, Li W, Chen CH, Zhang S, Chen JJW, Zhou X, Liu CC. IIIDB: a database for isoform-isoform interactions and isoform network modules. BMC Genomics 2015; 16 Suppl 2:S10. [PMID: 25707505 PMCID: PMC4331710 DOI: 10.1186/1471-2164-16-s2-s10] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Protein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "proteins" of currently known PPIs generally refer to "genes." It is known that alternative splicing often impacts PPI by either directly affecting protein interacting domains, or by indirectly impacting other domains, which, in turn, impacts the PPI binding. Thus, proteins translated from different isoforms of the same gene can have different interaction partners. RESULTS Due to the limitations of current experimental capacities, little data is available for PPIs at the resolution of isoforms, although such high-resolution data is crucial to map pathways and to understand protein functions. In fact, alternative splicing can often change the internal structure of a pathway by rearranging specific PPIs. To fill the gap, we systematically predicted genome-wide isoform-isoform interactions (IIIs) using RNA-seq datasets, domain-domain interaction and PPIs. Furthermore, we constructed an III database (IIIDB) that is a resource for studying PPIs at isoform resolution. To discover functional modules in the III network, we performed III network clustering, and then obtained 1025 isoform modules. To evaluate the module functionality, we performed the GO/pathway enrichment analysis for each isoform module. CONCLUSIONS The IIIDB provides predictions of human protein-protein interactions at the high resolution of transcript isoforms that can facilitate detailed understanding of protein functions and biological pathways. The web interface allows users to search for IIIs or III network modules. The IIIDB is freely available at http://syslab.nchu.edu.tw/IIIDB.
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40
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Rajan P, Stockley J, Sudbery IM, Fleming JT, Hedley A, Kalna G, Sims D, Ponting CP, Heger A, Robson CN, McMenemin RM, Pedley ID, Leung HY. Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer. BMC Cancer 2014; 14:977. [PMID: 25519703 PMCID: PMC4301544 DOI: 10.1186/1471-2407-14-977] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although chemotherapy for prostate cancer (PCa) can improve patient survival, some tumours are chemo-resistant. Tumour molecular profiles may help identify the mechanisms of drug action and identify potential prognostic biomarkers. We performed in vivo transcriptome profiling of pre- and post-treatment prostatic biopsies from patients with advanced hormone-naive prostate cancer treated with docetaxel chemotherapy and androgen deprivation therapy (ADT) with an aim to identify the mechanisms of drug action and identify prognostic biomarkers. METHODS RNA sequencing (RNA-Seq) was performed on biopsies from four patients before and ~22 weeks after docetaxel and ADT initiation. Gene fusion products and differentially-regulated genes between treatment pairs were identified using TopHat and pathway enrichment analyses undertaken. Publically available datasets were interrogated to perform survival analyses on the gene signatures identified using cBioportal. RESULTS A number of genomic rearrangements were identified including the TMPRSS2/ERG fusion and 3 novel gene fusions involving the ETS family of transcription factors in patients, both pre and post chemotherapy. In total, gene expression analyses showed differential expression of at least 2 fold in 575 genes in post-chemotherapy biopsies. Of these, pathway analyses identified a panel of 7 genes (ADAM7, FAM72B, BUB1B, CCNB1, CCNB2, TTK, CDK1), including a cell cycle-related geneset, that were differentially-regulated following treatment with docetaxel and ADT. Using cBioportal to interrogate the MSKCC-Prostate Oncogenome Project dataset we observed a statistically-significant reduction in disease-free survival of patients with tumours exhibiting alterations in gene expression of the above panel of 7 genes (p = 0.015). CONCLUSIONS Here we report on the first "real-time" in vivo RNA-Seq-based transcriptome analysis of clinical PCa from pre- and post-treatment TRUSS-guided biopsies of patients treated with docetaxel chemotherapy plus ADT. We identify a chemotherapy-driven PCa transcriptome profile which includes the down-regulation of important positive regulators of cell cycle progression. A 7 gene signature biomarker panel has also been identified in high-risk prostate cancer patients to be of prognostic value. Future prospective study is warranted to evaluate the clinical value of this panel.
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Affiliation(s)
- Prabhakar Rajan
- />Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jacqueline Stockley
- />Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | | | | | - David Sims
- />MRC Functional Genomics Unit, Oxford, UK
| | | | | | | | - Rhona M McMenemin
- />Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Ian D Pedley
- />Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Hing Y Leung
- />Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, G61 1BD UK
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Sowalsky AG, Xia Z, Wang L, Zhao H, Chen S, Bubley GJ, Balk SP, Li W. Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer. Mol Cancer Res 2014; 13:98-106. [PMID: 25189356 DOI: 10.1158/1541-7786.mcr-14-0273] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
UNLABELLED Men with metastatic prostate cancer who are treated with androgen deprivation therapies (ADT) usually relapse within 2 to 3 years with disease that is termed castration-resistant prostate cancer (CRPC). To identify the mechanism that drives these advanced tumors, paired-end RNA-sequencing (RNA-seq) was performed on a panel of CRPC bone marrow biopsy specimens. From this genome-wide approach, mutations were found in a series of genes with prostate cancer relevance, including AR, NCOR1, KDM3A, KDM4A, CHD1, SETD5, SETD7, INPP4B, RASGRP3, RASA1, TP53BP1, and CDH1, and a novel SND1:BRAF gene fusion. Among the most highly expressed transcripts were 10 noncoding RNAs (ncRNAs), including MALAT1 and PABPC1, which are involved in RNA processing. Notably, a high percentage of sequence reads mapped to introns, which were determined to be the result of incomplete splicing at canonical splice junctions. Using quantitative PCR (qPCR), a series of genes (AR, KLK2, KLK3, STEAP2, CPSF6, and CDK19) were confirmed to have a greater proportion of unspliced RNA in CRPC specimens than in normal prostate epithelium, untreated primary prostate cancer, and cultured prostate cancer cells. This inefficient coupling of transcription and mRNA splicing suggests an overall increase in transcription or defect in splicing. IMPLICATIONS Inefficient splicing in advanced prostate cancer provides a selective advantage through effects on microRNA networks but may render tumors vulnerable to agents that suppress rate-limiting steps in splicing.
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Affiliation(s)
- Adam G Sowalsky
- Division of Hematology and Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Zheng Xia
- Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Liguo Wang
- Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Hao Zhao
- Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Shaoyong Chen
- Division of Hematology and Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Glenn J Bubley
- Division of Hematology and Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Steven P Balk
- Division of Hematology and Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts.
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.
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Rajan P, Sudbery IM, Villasevil MEM, Mui E, Fleming J, Davis M, Ahmad I, Edwards J, Sansom OJ, Sims D, Ponting CP, Heger A, McMenemin RM, Pedley ID, Leung HY. Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy. Eur Urol 2014; 66:32-9. [PMID: 24054872 PMCID: PMC4062940 DOI: 10.1016/j.eururo.2013.08.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/02/2013] [Indexed: 01/19/2023]
Abstract
BACKGROUND Androgen-deprivation therapy (ADT) is standard treatment for locally advanced or metastatic prostate cancer (PCa). Many patients develop castration resistance (castration-resistant PCa [CRPC]) after approximately 2-3 yr, with a poor prognosis. The molecular mechanisms underlying CRPC progression are unclear. OBJECTIVE To undertake quantitative tumour transcriptome profiling prior to and following ADT to identify functionally important androgen-regulated pathways or genes that may be reactivated in CRPC. DESIGN, SETTING, AND PARTICIPANTS RNA sequencing (RNA-seq) was performed on tumour-rich, targeted prostatic biopsies from seven patients with locally advanced or metastatic PCa before and approximately 22 wk after ADT initiation. Differentially regulated genes were identified in treatment pairs and further investigated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on cell lines and immunohistochemistry on a separate CRPC patient cohort. Functional assays were used to determine the effect of pathway modulation on cell phenotypes. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We searched for gene expression changes affecting key cell signalling pathways that may be targeted as proof of principle in a CRPC in vitro cell line model. RESULTS AND LIMITATIONS We identified ADT-regulated signalling pathways, including the Wnt/β-catenin signalling pathway, and observed overexpression of β-catenin in a subset of CRPC by immunohistochemistry. We validated 6 of 12 (50%) pathway members by qRT-PCR on LNCaP/LNCaP-AI cell RNAs, of which 4 (67%) demonstrated expression changes consistent with RNA-seq data. We show that the tankyrase inhibitor XAV939 (which promotes β-catenin degradation) reduced androgen-independent LNCaP-AI cell line growth compared with androgen-responsive LNCaP cells via an accumulation of cell proportions in the G0/G1 phase and reduction in the S and G2/M phases. Our biopsy protocol did not account for tumour heterogeneity, and pathway inhibition was limited to pharmacologic approaches. CONCLUSIONS RNA-seq of paired PCa samples revealed ADT-regulated signalling pathways. Proof-of-principle inhibition of the Wnt/β-catenin signalling pathway specifically delays androgen-independent PCa cell cycle progression and proliferation and warrants further investigation as a potential target for therapy for CRPC.
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Affiliation(s)
- Prabhakar Rajan
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Cancer Research UK Beatson Institute, Glasgow, UK; Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK.
| | - Ian M Sudbery
- Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - M Eugenia M Villasevil
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Cancer Research UK Beatson Institute, Glasgow, UK; Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK
| | - Ernest Mui
- Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK
| | - Janis Fleming
- Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK
| | - Mark Davis
- Department of Urology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, UK
| | - Imran Ahmad
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Cancer Research UK Beatson Institute, Glasgow, UK; Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK
| | - Joanne Edwards
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Cancer Research UK Beatson Institute, Glasgow, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK
| | - David Sims
- Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Chris P Ponting
- Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Andreas Heger
- Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Rhona M McMenemin
- Northern Centre for Cancer Care, Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, UK
| | - Ian D Pedley
- Northern Centre for Cancer Care, Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, UK
| | - Hing Y Leung
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Cancer Research UK Beatson Institute, Glasgow, UK; Cancer Research UK Beatson Institute, The Beatson Institute for Cancer Research, Glasgow, UK.
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Stockley J, Villasevil MEM, Nixon C, Ahmad I, Leung HY, Rajan P. The RNA-binding protein hnRNPA2 regulates β-catenin protein expression and is overexpressed in prostate cancer. RNA Biol 2014; 11:755-65. [PMID: 24823909 PMCID: PMC4156506 DOI: 10.4161/rna.28800] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/25/2014] [Accepted: 04/06/2014] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION The RNA-binding protein hnRNPA2 (HNRNPA2B1) is upregulated in cancer, where it controls alternative pre-mRNA splicing of cancer-relevant genes. Cytoplasmic hnRNPA2 is reported in aggressive cancers, but is functionally uncharacterized. We explored the role of hnRNPA2 in prostate cancer (PCa). METHODS hnRNPA2 function/localization/expression in PCa was determined using biochemical approaches (colony forming/proliferation/luciferase reporter assays/flow cytometry/immunohistocytochemistry). Binding of hnRNPA2 within cancer-relevant 3'-UTR mRNAs was identified by bioinformatics. RESULTS RNAi-mediated knockdown of hnRNPA2 reduced colony forming and proliferation, while hnRNPA2 overexpression increased proliferation of PCa cells. Nuclear hnRNPA2 is overexpressed in high-grade clinical PCa, and is also observed in the cytoplasm in some cases. Ectopic expression of a predominantly cytoplasmic variant hnRNPA2-ΔRGG also increased PCa cell proliferation, suggesting that cytoplasmic hnRNPA2 may also be functionally relevant in PCa. Consistent with its known cytoplasmic roles, hnRNPA2 was associated with 3'-UTR mRNAs of several cancer-relevant mRNAs including β-catenin (CTNNB1). Both wild-type hnRNPA2 and hnRNPA2-ΔRGG act on CTNNB1 3'-UTR mRNA, increasing endogenous CTNNB1 mRNA expression and β-catenin protein expression and nuclear localization. CONCLUSION Nuclear and cytoplasmic hnRNPA2 are present in PCa and appear to be functionally important. Cytoplasmic hnRNPA2 may affect the cancer cell phenotype through 3'-UTR mRNA-mediated regulation of β-catenin expression and other cancer-relevant genes.
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Affiliation(s)
- Jacqueline Stockley
- Institute of Cancer Sciences; College of Medical, Veterinary, and Life Sciences; University of Glasgow; Cancer Research UK Beatson Institute; Bearsden, UK
| | - M Eugenia M Villasevil
- Institute of Cancer Sciences; College of Medical, Veterinary, and Life Sciences; University of Glasgow; Cancer Research UK Beatson Institute; Bearsden, UK
| | - Colin Nixon
- Cancer Research UK Beatson Institute; The Beatson Institute for Cancer Research; Bearsden, UK
| | - Imran Ahmad
- Institute of Cancer Sciences; College of Medical, Veterinary, and Life Sciences; University of Glasgow; Cancer Research UK Beatson Institute; Bearsden, UK
| | - Hing Y Leung
- Institute of Cancer Sciences; College of Medical, Veterinary, and Life Sciences; University of Glasgow; Cancer Research UK Beatson Institute; Bearsden, UK
- Cancer Research UK Beatson Institute; The Beatson Institute for Cancer Research; Bearsden, UK
| | - Prabhakar Rajan
- Institute of Cancer Sciences; College of Medical, Veterinary, and Life Sciences; University of Glasgow; Cancer Research UK Beatson Institute; Bearsden, UK
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Munkley J, Rajan P, Laferty NP, Dalgliesh C, Jackson RM, Robson CN, Leung HY, Elliott DJ. A novel androgen-regulated isoform of the TSC2 tumour suppressor gene increases cell proliferation. Oncotarget 2014; 5:131-9. [PMID: 24318044 PMCID: PMC3960195 DOI: 10.18632/oncotarget.1405] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/19/2013] [Indexed: 01/07/2023] Open
Abstract
TSC2 (Tuberous sclerosis complex 2) is an important tumour suppressor gene, mutations within which are linked to the development of tuberous sclerosis and implicated in multiple tumour types. TSC2 protein complexes with TSC1 and blocks the ability of the Rheb (Ras homolog enriched in brain) GTPase to activate mTOR (mammalian target of rapamycin), a crucial signal transducer which regulates protein synthesis and cell growth. Here, we report the characterisation of a novel isoform of TSC2 which is under direct control of the ligand-activated androgen receptor. TSC2 isoform A (TSC2A) is derived from an internal androgen-regulated alternative promoter and encodes a 508-amino acid cytoplasmic protein corresponding to the C-terminal region of full-length TSC2, lacking the interaction domain for TSC1 and containing an incomplete interaction domain required for Rheb inactivation. Expression of TSC2A is induced in response to androgens and full-length TSC2 is co-ordinately down-regulated, indicating an androgen-driven switch in TSC2 protein isoforms. In contrast to the well-characterised suppressive effect on cell proliferation of full-length TSC2 protein, both LNCaP and HEK293 cells over-expressing TSC2 isoform A proliferate more rapidly (measured by MTT assays) and have increased levels of cells in S-phase (measured by both Edu staining and FACS analysis). Our work indicates, for the first time, a novel role for this well-known tumour suppressor gene, which encodes an activator of cell proliferation in response to androgen stimulation.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Prabhakar Rajan
- Beatson Institute for Cancer Research, Glasgow, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicholas P. Laferty
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Robert M. Jackson
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Craig N. Robson
- Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Hing Y. Leung
- Beatson Institute for Cancer Research, Glasgow, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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Zhou M, Wang H, Zhou K, Luo X, Pan X, Shi B, Jiang H, Zhang J, Li K, Wang HM, Gao H, Lu S, Yao M, Mao Y, Wang HY, Yang S, Gu J, Li C, Li Z. A novel EGFR isoform confers increased invasiveness to cancer cells. Cancer Res 2013; 73:7056-67. [PMID: 24240702 DOI: 10.1158/0008-5472.can-13-0194] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As a validated therapeutic target in several human cancers, the EGF receptor (EGFR) provides a focus to gain deeper insights into cancer pathophysiology. In this study, we report the identification of a naturally occurring and widely expressed EGFR isoform termed EGFRvA, which substitutes a Ser/Thr-rich peptide for part of the carboxyl-terminal regulatory domain of the receptor. Intriguingly, EGFRvA expression relates more closely to histopathologic grade and poor prognosis in patients with glioma. Ectopic expression of EGFRvA in cancer cells conferred a higher invasive capacity than EGFR in vitro and in vivo. Mechanistically, EGFRvA stimulated expression of STAT3, which upregulated heparin-binding EGF (HB-EGF). Reciprocally, HB-EGF stimulated phosphorylation of EGFRvA at Y845 along with STAT3, generating a positive feedback loop that may reinforce invasive function. The significance of EGFRvA expression was reinforced by findings that it is attenuated by miR-542-5p, a microRNA that is a known tumor suppressor. Taken together, our findings define this newfound EGFR isoform as a key theranostic molecule.
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Affiliation(s)
- Min Zhou
- Authors' Affiliations: State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine; Neurosurgery Department of Huashan Hospital, Fudan University; Shanghai Lung Tumor Clinical Medical Center, Chest Hospital Affiliated to Shanghai Jiao Tong University; Laboratory of Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, PR China; and Department of Dermatology, Duke University Medical Center, Durham, North Carolina
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Omenn GS. Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:866-73. [PMID: 24211518 DOI: 10.1016/j.bbapap.2013.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/17/2013] [Accepted: 10/31/2013] [Indexed: 12/24/2022]
Abstract
This article addresses three inter-related subjects: the development of the Human Plasma Proteome Peptide Atlas, the launch of the Human Proteome Project, and the emergence of alternative splice variant transcripts and proteins as important features of evolution and pathogenesis. The current Plasma Peptide Atlas provides evidence on which peptides have been detected for every protein confidently identified in plasma; there are links to their spectra and their estimated abundance, facilitating the planning of targeted proteomics for biomarker studies. The Human Proteome Project (HPP) combines a chromosome-centric C-HPP with a biology and disease-driven B/D-HPP, upon a foundation of mass spectrometry, antibody, and knowledgebase resource pillars. The HPP aims to identify the approximately 7000 "missing proteins" and to characterize all proteins and their many isoforms. Success will enable the larger research community to utilize newly-available peptides, spectra, informative MS transitions, and databases for targeted analyses of priority proteins for each organ and disease. Among the isoforms of proteins, splice variants have the special feature of greatly enlarging protein diversity without enlarging the genome; evidence is accumulating of striking differential expression of splice variants in cancers. In this era of RNA-sequencing and advanced mass spectrometry, it is no longer sufficient to speak simply of increased or decreased expression of genes or proteins without carefully examining the splice variants in the protein mixture produced from each multi-exon gene. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, MI, USA; Institute for Systems Biology, Seattle, WA, USA
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Expression of Tra2 β in Cancer Cells as a Potential Contributory Factor to Neoplasia and Metastasis. Int J Cell Biol 2013; 2013:843781. [PMID: 23935626 PMCID: PMC3723085 DOI: 10.1155/2013/843781] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/09/2013] [Indexed: 01/17/2023] Open
Abstract
The splicing regulator proteins SRSF1 (also known as ASF/SF2) and SRSF3 (also known as SRP20) belong to the SR family of proteins and can be upregulated in cancer. The SRSF1 gene itself is amplified in some cancer cells, and cancer-associated changes in the expression of MYC also increase SRSF1 gene expression. Increased concentrations of SRSF1 protein promote prooncogenic splicing patterns of a number of key regulators of cell growth. Here, we review the evidence that upregulation of the SR-related Tra2β protein might have a similar role in cancer cells. The TRA2B gene encoding Tra2β is amplified in particular tumours including those of the lung, ovary, cervix, stomach, head, and neck. Both TRA2B RNA and Tra2β protein levels are upregulated in breast, cervical, ovarian, and colon cancer, and Tra2β expression is associated with cancer cell survival. The TRA2B gene is a transcriptional target of the protooncogene ETS-1 which might cause higher levels of expression in some cancer cells which express this transcription factor. Known Tra2β splicing targets have important roles in cancer cells, where they affect metastasis, proliferation, and cell survival. Tra2β protein is also known to interact directly with the RBMY protein which is implicated in liver cancer.
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Vallet S, Podar K. New insights, recent advances, and current challenges in the biological treatment of multiple myeloma. Expert Opin Biol Ther 2013; 13 Suppl 1:S35-53. [PMID: 23768134 DOI: 10.1517/14712598.2013.807337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The availability of thalidomide, lenalidomide, and bortezomib has radically changed multiple myeloma (MM) treatment and significantly improved patients' outcome. Nevertheless, MM is still an incurable disease due to the development of resistance and relapse practically in all patients. Unraveling MM pathogenesis, identifying prognostically high-risk patient populations, and optimizing current treatment strategies are among the challenges we are facing to reach a cure for this disease. AREAS COVERED This article reviews recent advances of the genomic analysis of malignant plasma cells and summarizes new insights into the pathophysiologic role of the MM microenvironment and the clinical assessment of derived novel therapeutic strategies. Moreover, current efforts to improve risk stratification and drug development are discussed, and most recent results of Phase II and III clinical trials that aim to optimize existing treatment regimens and to assess the next-generation anti-MM strategies are discussed. A systematic search was conducted of the Pubmed Medline, Embase, and Cochrane Library databases for primary articles, as well as of conference abstracts (e.g., of the American Society of Hematology, the American Society of Clinical Oncology, the American Association of Cancer Research, the European Hematology Association, and the Multiple Myeloma Workshop 2013), practice guidelines, and registries of clinical trials. EXPERT OPINION Given continuing advances to overcome current treatment challenges in MM, we are confident that long-lasting responses can be expected in many of our patients within the next decade.
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Affiliation(s)
- Sonia Vallet
- University of Heidelberg, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Zhang Z, Pal S, Bi Y, Tchou J, Davuluri RV. Isoform level expression profiles provide better cancer signatures than gene level expression profiles. Genome Med 2013; 5:33. [PMID: 23594586 PMCID: PMC3706752 DOI: 10.1186/gm437] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/26/2013] [Accepted: 04/17/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The majority of mammalian genes generate multiple transcript variants and protein isoforms through alternative transcription and/or alternative splicing, and the dynamic changes at the transcript/isoform level between non-oncogenic and cancer cells remain largely unexplored. We hypothesized that isoform level expression profiles would be better than gene level expression profiles at discriminating between non-oncogenic and cancer cellsgene level. METHODS We analyzed 160 Affymetrix exon-array datasets, comprising cell lines of non-oncogenic or oncogenic tissue origins. We obtained the transcript-level and gene level expression estimates, and used unsupervised and supervised clustering algorithms to study the profile similarity between the samples at both gene and isoform levels. RESULTS Hierarchical clustering, based on isoform level expressions, effectively grouped the non-oncogenic and oncogenic cell lines with a virtually perfect homogeneity-grouping rate (97.5%), regardless of the tissue origin of the cell lines. However, gene levelthis rate was much lower, being 75% at best based on the gene level expressions. Statistical analyses of the difference between cancer and non-oncogenic samples identified the existence of numerous genes with differentially expressed isoforms, which otherwise were not significant at the gene level. We also found that canonical pathways of protein ubiquitination, purine metabolism, and breast-cancer regulation by stathmin1 were significantly enriched among genes thatshow differential expression at isoform level but not at gene level. CONCLUSIONS In summary, cancer cell lines, regardless of their tissue of origin, can be effectively discriminated from non-cancer cell lines at isoform level, but not at gene level. This study suggests the existence of an isoform signature, rather than a gene signature, which could be used to distinguish cancer cells from normal cells.
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Affiliation(s)
- ZhongFa Zhang
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Sharmistha Pal
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Yingtao Bi
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Julia Tchou
- Department of Surgery, Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Ramana V Davuluri
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
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Hart M, Wach S, Nolte E, Szczyrba J, Menon R, Taubert H, Hartmann A, Stoehr R, Wieland W, Grässer FA, Wullich B. The proto-oncogene ERG is a target of microRNA miR-145 in prostate cancer. FEBS J 2013; 280:2105-16. [PMID: 23480797 DOI: 10.1111/febs.12236] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 03/05/2013] [Accepted: 03/06/2013] [Indexed: 12/12/2022]
Abstract
Prostate cancer is a leading cause of cancer mortality in men. One of the distinct characteristics of prostate cancer is over-expression of the ERG proto-oncogene. The TMPRSS2-ERG gene fusion, the most common gene fusion, is found in approximately 50% of prostate cancer cases. We show that certain microRNAs are extensively deregulated in prostate cancer cell lines and primary clinical cancer samples. MicroRNAs are capable of modulating post-transcriptional gene expression via inhibition of protein synthesis. Independent target prediction methods have indicated that the 3' untranslated region of the ERG mRNA is a potential target of miR-145. miR-145 is consistently down-regulated in prostate cancer. Here we show that the ERG 3' untranslated region is a regulative target of miR-145 in vitro. Ectopic expression of miR-145 led to a reduction in expression of the ERG protein. We analyzed 26 prostate cancer samples and corresponding normal tissue. ERG protein expression was found to be elevated in the tumor samples, together with increased expression of several ERG isoforms. We identified ERG proteins of 35 and 24 kDa, which may represent unknown ERG splice variants. Analyses of miR-145 and ERG mRNA expression revealed a general down-regulation of miR-145 irrespective of the presence or absence of translocations involving ERG. This observation indicates that down-regulation of miR-145 may contribute to the increased expression of most ERG splice variants sharing the miR-145 target sequence in their 3' untranslated region.
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Affiliation(s)
- Martin Hart
- Department of Virology, Saarland University Medical School, Homburg/Saar, Germany
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