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Hyung D, Cho SY, Lee K, Yu N, Hong S, Park C. ASpedia-R: a package to retrieve junction-incorporating features and knowledge-based functions of human alternative splicing events. BIOINFORMATICS ADVANCES 2024; 4:vbae071. [PMID: 38827412 PMCID: PMC11142624 DOI: 10.1093/bioadv/vbae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/15/2024] [Accepted: 05/09/2024] [Indexed: 06/04/2024]
Abstract
Motivation Alternative splicing (AS) is a key regulatory mechanism that confers genetic diversity and phenotypic plasticity of human. The exons and their flanking regions include comprehensive junction-incorporating sequence features like splicing factor-binding sites and protein domains. These elements involve in exon usage and finally contribute to isoform-specific biological functions. Splicing-associated sequence features are involved in the multilayered regulation encompassing DNA and proteins. However, most analysis applications have investigated limited sequence features, like protein domains. It is insufficient to explain the comprehensive cause and effect of exon-specific biological processes. Results With the advent of RNA-seq technology, global AS event analysis has deduced more precise results. As accumulating analysis results, it could be a challenge to identify multi-omics sequence features for AS events. Therefore, application to investigate multi-omics sequence features is useful to scan critical evidence. ASpedia-R is an R package to interrogate junction-incorporating sequence features for human genes. Our database collected the heterogeneous profile encompassed from DNA to protein. Additionally, knowledge-based splicing genes were collected using text-mining to test the association with specific pathway terms. Our package retrieves AS events for high-throughput data analysis results via AS event ID converter. Finally, result profile could be visualized and saved to multiple formats: sequence feature result table, genome track figure, protein-protein interaction network, and gene set enrichment test result table. Our package is a convenient tool to understand global regulation mechanisms by splicing. Availability and implementation The package source code is freely available to non-commercial users at https://github.com/ncc-bioinfo/ASpedia-R.
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Affiliation(s)
- Daejin Hyung
- Research Institute, National Cancer Center, Goyang, Gyeonggi-do 10408, Republic of Korea
| | - Soo Young Cho
- Department of Molecular & Life Science, Hanyang University, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Kyubin Lee
- Department of Biochemistry and Molecular Genetic, University of Virginia, Charlottesville, VA 22908, USA
| | - Namhee Yu
- Research Institute, National Cancer Center, Goyang, Gyeonggi-do 10408, Republic of Korea
| | - Sehwa Hong
- Research Institute, National Cancer Center, Goyang, Gyeonggi-do 10408, Republic of Korea
| | - Charny Park
- Research Institute, National Cancer Center, Goyang, Gyeonggi-do 10408, Republic of Korea
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Song X, Tiek D, Miki S, Huang T, Lu M, Goenka A, Iglesia R, Yu X, Wu R, Walker M, Zeng C, Shah H, Weng SHS, Huff A, Zhang W, Koga T, Hubert C, Horbinski CM, Furnari FB, Hu B, Cheng SY. RNA splicing analysis deciphers developmental hierarchies and reveals therapeutic targets in adult glioma. J Clin Invest 2024; 134:e173789. [PMID: 38662454 PMCID: PMC11142752 DOI: 10.1172/jci173789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/16/2024] [Indexed: 06/02/2024] Open
Abstract
Widespread alterations in RNA alternative splicing (AS) have been identified in adult gliomas. However, their regulatory mechanism, biological significance, and therapeutic potential remain largely elusive. Here, using a computational approach with both bulk and single-cell RNA-Seq, we uncover a prognostic AS signature linked with neural developmental hierarchies. Using advanced iPSC glioma models driven by glioma driver mutations, we show that this AS signature could be enhanced by EGFRvIII and inhibited by in situ IDH1 mutation. Functional validations of 2 isoform switching events in CERS5 and MPZL1 show regulations of sphingolipid metabolism and SHP2 signaling, respectively. Analysis of upstream RNA binding proteins reveals PTBP1 as a key regulator of the AS signature where targeting of PTBP1 suppresses tumor growth and promotes the expression of a neuron marker TUJ1 in glioma stem-like cells. Overall, our data highlights the role of AS in affecting glioma malignancy and heterogeneity and its potential as a therapeutic vulnerability for treating adult gliomas.
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Affiliation(s)
- Xiao Song
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Deanna Tiek
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shunichiro Miki
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, UCSD, La Jolla, California, USA
| | - Tianzhi Huang
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Minghui Lu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Anshika Goenka
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rebeca Iglesia
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xiaozhou Yu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Runxin Wu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Maya Walker
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chang Zeng
- Department of Preventive Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, and
| | - Shao Huan Samuel Weng
- Proteomics Platform, Office of Shared Research Facilities, Biological Sciences Division, The University of Chicago, Chicago, Illinois, USA
| | - Allen Huff
- Proteomics Platform, Office of Shared Research Facilities, Biological Sciences Division, The University of Chicago, Chicago, Illinois, USA
| | - Wei Zhang
- Department of Preventive Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tomoyuki Koga
- Department of Neurosurgery, The University of Minnesota, Minneapolis, Minnesota, USA
| | - Christopher Hubert
- Department of Biochemistry, School of Medicine, Case Western Reserved University, Cleveland, Ohio, USA
| | - Craig M. Horbinski
- Departments of Pathology and Neurological Surgery, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Frank B. Furnari
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, UCSD, La Jolla, California, USA
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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3
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Polvèche H, Valat J, Fontrodona N, Lapendry A, Clerc V, Janczarski S, Mortreux F, Auboeuf D, Bourgeois CF. SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors. Database (Oxford) 2023; 2023:baad091. [PMID: 38128543 PMCID: PMC10735282 DOI: 10.1093/database/baad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/06/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
One challenge faced by scientists from the alternative RNA splicing field is to decode the cooperative or antagonistic effects of splicing factors (SFs) to understand and eventually predict splicing outcomes on a genome-wide scale. In this manuscript, we introduce SplicingLore, an open-access database and web resource that help to fill this gap in a straightforward manner. The database contains a collection of RNA-sequencing-derived lists of alternative exons regulated by a total of 75 different SFs. All datasets were processed in a standardized manner, ensuring valid comparisons and correlation analyses. The user can easily retrieve a factor-specific set of differentially included exons from the database or provide a list of exons and search which SF(s) control(s) their inclusion. Our simple workflow is fast and easy to run, and it ensures a reliable calculation of correlation scores between the tested datasets. As a proof of concept, we predicted and experimentally validated a novel functional cooperation between the RNA helicases DDX17 and DDX5 and the heterogeneous nuclear ribonucleoprotein C (HNRNPC) protein. SplicingLore is available at https://splicinglore.ens-lyon.fr/. Database URL: https://splicinglore.ens-lyon.fr/.
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Affiliation(s)
| | - Jessica Valat
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Valentine Clerc
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Stéphane Janczarski
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
- CECS/AFM, I-STEM, 28 rue Henri Desbrueres, Corbeil-Essonnes F-91100, France
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Park J, Park J, Chung YJ. Alternative splicing: a new breakthrough for understanding tumorigenesis and potential clinical applications. Genes Genomics 2023; 45:393-400. [PMID: 36656436 DOI: 10.1007/s13258-023-01365-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023]
Abstract
BACKGROUND Alternative splicing (AS) is a post-transcriptional process that produces transcript variants, thus leading to transcriptome complexity. Recently, the scope of AS studies has been greatly expanded toward clinical applications owing to the abundance of RNA sequencing data. OBJECTIVE This review consists of two parts. We first summarize bioinformatic resources that are useful for large-scale cancer-related AS studies. We then highlight the research efforts to utilize AS events for predicting clinical outcomes and planning therapeutic strategies. RESULTS Computational approaches to interrogate AS events have been reviewed under three categories: (1) databases to provide functional and clinical annotation of AS events, (2) analytical tools to identify cancer-associated AS event, and (3) methods to identify splicing-related DNA variants and splicing-derived neoantigens. We also present the recent progress in exploring the clinical utility of AS under four categories: (1) identification of AS events for cancer prognosis, (2) utilization of AS events in molecular classification of various cancers, (3) regulatory mechanisms of AS underlying drug resistance, and (4) potential use of AS in cancer therapy. CONCLUSION This review will be helpful for understanding the biological implications of AS in cancer and facilitate the development of AS markers for cancer prognosis and treatment. We anticipate that future studies will lead to the application of genome-wide AS profiles in cancer precision medicine.
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Affiliation(s)
- Jiyeon Park
- Precision Medicine Research Center, Seoul, Republic of Korea
- Integrated Research Center for Genome Polymorphism,, Seoul, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, Seoul, Republic of Korea
| | - Joonhyuck Park
- Department of Biomedicine & Health Sciences, Graduate School, Seoul, Republic of Korea.
- 4Department of Medical Life science, Seoul, Republic of Korea.
- Department of Medical Life science, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, 06591, Seoul, Republic of Korea.
| | - Yeun-Jun Chung
- Precision Medicine Research Center, Seoul, Republic of Korea.
- Integrated Research Center for Genome Polymorphism,, Seoul, Republic of Korea.
- Department of Biomedicine & Health Sciences, Graduate School, Seoul, Republic of Korea.
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, 06591, Seoul, Republic of Korea.
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5
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García-Ruiz S, Gustavsson EK, Zhang D, Reynolds RH, Chen Z, Fairbrother-Browne A, Gil-Martínez AL, Botia JA, Collado-Torres L, Ryten M. IntroVerse: a comprehensive database of introns across human tissues. Nucleic Acids Res 2023; 51:D167-D178. [PMID: 36399497 PMCID: PMC9825543 DOI: 10.1093/nar/gkac1056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Dysregulation of RNA splicing contributes to both rare and complex diseases. RNA-sequencing data from human tissues has shown that this process can be inaccurate, resulting in the presence of novel introns detected at low frequency across samples and within an individual. To enable the full spectrum of intron use to be explored, we have developed IntroVerse, which offers an extensive catalogue on the splicing of 332,571 annotated introns and a linked set of 4,679,474 novel junctions covering 32,669 different genes. This dataset has been generated through the analysis of 17,510 human control RNA samples from 54 tissues provided by the Genotype-Tissue Expression Consortium. IntroVerse has two unique features: (i) it provides a complete catalogue of novel junctions and (ii) each novel junction has been assigned to a specific annotated intron. This unique, hierarchical structure offers multiple uses, including the identification of novel transcripts from known genes and their tissue-specific usage, and the assessment of background splicing noise for introns thought to be mis-spliced in disease states. IntroVerse provides a user-friendly web interface and is freely available at https://rytenlab.com/browser/app/introverse.
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Affiliation(s)
- Sonia García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - David Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Regina H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Zhongbo Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Aine Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, WC2R 2LS, UK
| | - Ana Luisa Gil-Martínez
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- Department of Information and Communications Engineering Faculty of Informatics, Espinardo Campus, University of Murcia, Murcia, 30100, Spain
| | - Juan A Botia
- Department of Information and Communications Engineering Faculty of Informatics, Espinardo Campus, University of Murcia, Murcia, 30100, Spain
| | | | - Mina Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, WC1N 1EH, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, WC1N 1EH, UK
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Lee K, Hyung D, Cho SY, Yu N, Hong S, Kim J, Kim S, Han JY, Park C. Splicing signature database development to delineate cancer pathways using literature mining and transcriptome machine learning. Comput Struct Biotechnol J 2023; 21:1978-1988. [PMID: 36942103 PMCID: PMC10023904 DOI: 10.1016/j.csbj.2023.02.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Alternative splicing (AS) events modulate certain pathways and phenotypic plasticity in cancer. Although previous studies have computationally analyzed splicing events, it is still a challenge to uncover biological functions induced by reliable AS events from tremendous candidates. To provide essential splicing event signatures to assess pathway regulation, we developed a database by collecting two datasets: (i) reported literature and (ii) cancer transcriptome profile. The former includes knowledge-based splicing signatures collected from 63,229 PubMed abstracts using natural language processing, extracted for 202 pathways. The latter is the machine learning-based splicing signatures identified from pan-cancer transcriptome for 16 cancer types and 42 pathways. We established six different learning models to classify pathway activities from splicing profiles as a learning dataset. Top-ranked AS events by learning model feature importance became the signature for each pathway. To validate our learning results, we performed evaluations by (i) performance metrics, (ii) differential AS sets acquired from external datasets, and (iii) our knowledge-based signatures. The area under the receiver operating characteristic values of the learning models did not exhibit any drastic difference. However, random-forest distinctly presented the best performance to compare with the AS sets identified from external datasets and our knowledge-based signatures. Therefore, we used the signatures obtained from the random-forest model. Our database provided the clinical characteristics of the AS signatures, including survival test, molecular subtype, and tumor microenvironment. The regulation by splicing factors was additionally investigated. Our database for developed signatures supported retrieval and visualization system.
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Key Words
- AS, Alternative splicing
- AUCPR, the area under the precision-recall curve
- AUROC, the area under the receiver operating characteristic
- Alternative splicing
- DAS, differential alternative splicing
- Database
- EMT, epithelial mesenchymal transition
- Gene signature
- ML, machine learning
- Machine-learning
- NER, named entity recognition
- NLP, natural language process
- PCA, principal component analysis
- PSI, percent spliced in index
- RF, random-forest
- SF, splicing factor
- TCGA, The Cancer Genome Atlas
- Text-mining
- Tumor transcriptome
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Affiliation(s)
- Kyubin Lee
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Daejin Hyung
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Soo Young Cho
- Department of Molecular & Life Science, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Namhee Yu
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Sewha Hong
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Jihyun Kim
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
- Department of Precision Medicine, National Institute of Health, Korea Disease Control and Prevention Agency, Osong Health Technology Administration Complex, 187, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159, Republic of Korea
| | - Sunshin Kim
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Ji-Youn Han
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Charny Park
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
- Correspondence to: 323 Ilsan-ro, Ilsandonggu, Goyang-si, Gyeonggi-do 10408, Republic of Korea.
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7
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Li K, Luo T, Zhu Y, Huang Y, Wang A, Zhang D, Dong L, Wang Y, Wang R, Tang D, Yu Z, Shen Q, Lv M, Ling Z, Fang Z, Yuan J, Li B, Xia K, He X, Li J, Zhao G. Performance evaluation of differential splicing analysis methods and splicing analytics platform construction. Nucleic Acids Res 2022; 50:9115-9126. [PMID: 35993808 PMCID: PMC9458456 DOI: 10.1093/nar/gkac686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
A proportion of previously defined benign variants or variants of uncertain significance in humans, which are challenging to identify, may induce an abnormal splicing process. An increasing number of methods have been developed to predict splicing variants, but their performance has not been completely evaluated using independent benchmarks. Here, we manually sourced ∼50 000 positive/negative splicing variants from > 8000 studies and selected the independent splicing variants to evaluate the performance of prediction methods. These methods showed different performances in recognizing splicing variants in donor and acceptor regions, reminiscent of different weight coefficient applications to predict novel splicing variants. Of these methods, 66.67% exhibited higher specificities than sensitivities, suggesting that more moderate cut-off values are necessary to distinguish splicing variants. Moreover, the high correlation and consistent prediction ratio validated the feasibility of integration of the splicing prediction method in identifying splicing variants. We developed a splicing analytics platform called SPCards, which curates splicing variants from publications and predicts splicing scores of variants in genomes. SPCards also offers variant-level and gene-level annotation information, including allele frequency, non-synonymous prediction and comprehensive functional information. SPCards is suitable for high-throughput genetic identification of splicing variants, particularly those located in non-canonical splicing regions.
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Affiliation(s)
| | | | - Yan Zhu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuanfeng Huang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - An Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Di Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Lijie Dong
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yujian Wang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dongdong Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhen Yu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Qunshan Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Mingrong Lv
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhengbao Ling
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jing Yuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Bin Li
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaojin He
- Correspondence may also be addressed to Xiaojin He. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Jinchen Li
- To whom correspondence should be addressed. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Guihu Zhao
- Correspondence may also be addressed to Guihu Zhao. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
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8
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Tan S, Wang W, Jie W, Liu J. FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species. Comput Struct Biotechnol J 2022; 20:3676-3684. [PMID: 35891795 PMCID: PMC9293738 DOI: 10.1016/j.csbj.2022.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
Abstract
The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research and the food industry. Furthermore, there is a lack of online platform to analyze users’ new data individually and jointly with existing data for the comprehensive analysis of alternative splicing and gene expression. Here, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. It allows users to query the data in a variety of ways, including gene identifier/symbol, functional term, and BLAST alignment. Moreover, users can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, co-expression and cross-species analysis. In addition, functional enrichment is provided to confer biological significance. Notably, users are allowed to submit their own data and perform various analyses using the new data alone or alongside existing data in FishExp. Results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. All data in FishExp can be downloaded for more in-depth analysis. The manually curated sample information, uniform data processing and various tools make it efficient for users to gain new insights from these large data sets, facilitating scientific hypothesis generation. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp.
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Affiliation(s)
- Suxu Tan
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Wenwen Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wencai Jie
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinding Liu
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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9
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Lee K, Yu D, Hyung D, Cho SY, Park C. ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:466-482. [PMID: 35085775 PMCID: PMC9801047 DOI: 10.1016/j.gpb.2021.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 01/26/2023]
Abstract
Alternative splicing (AS) regulates biological processes governing phenotypes and diseases. Differential AS (DAS) gene test methods have been developed to investigate important exonic expression from high-throughput datasets. However, the DAS events extracted using statistical tests are insufficient to delineate relevant biological processes. In this study, we developed a novel application, Alternative Splicing Encyclopedia: Functional Interaction (ASpediaFI), to systemically identify DAS events and co-regulated genes and pathways. ASpediaFI establishes a heterogeneous interaction network of genes and their feature nodes (i.e., AS events and pathways) connected by co-expression or pathway gene set knowledge. Next, ASpediaFI explores the interaction network using the random walk with restart algorithm and interrogates the proximity from a query gene set. Finally, ASpediaFI extracts significant AS events, genes, and pathways. To evaluate the performance of our method, we simulated RNA sequencing (RNA-seq) datasets to consider various conditions of sequencing depth and sample size. The performance was compared with that of other methods. Additionally, we analyzed three public datasets of cancer patients or cell lines to evaluate how well ASpediaFI detects biologically relevant candidates. ASpediaFI exhibits strong performance in both simulated and public datasets. Our integrative approach reveals that DAS events that recognize a global co-expression network and relevant pathways determine the functional importance of spliced genes in the subnetwork. ASpediaFI is publicly available at https://bioconductor.org/packages/ASpediaFI.
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10
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Diez-Fuertes F, López-Huertas MR, García-Pérez J, Calonge E, Bermejo M, Mateos E, Martí P, Muelas N, Vílchez JJ, Coiras M, Alcamí J, Rodríguez-Mora S. Transcriptomic Evidence of the Immune Response Activation in Individuals With Limb Girdle Muscular Dystrophy Dominant 2 (LGMDD2) Contributes to Resistance to HIV-1 Infection. Front Cell Dev Biol 2022; 10:839813. [PMID: 35646913 PMCID: PMC9136291 DOI: 10.3389/fcell.2022.839813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
LGMDD2 is a rare form of muscular dystrophy characterized by one of the three heterozygous deletions described within the TNPO3 gene that result in the addition of a 15-amino acid tail in the C-terminus.TNPO3 is involved in the nuclear import of splicing factors and acts as a host cofactor for HIV-1 infection by mechanisms not yet deciphered. Further characterization of the crosstalk between HIV-1 infection and LGMDD2 disease may contribute to a better understanding of both the cellular alterations occurring in LGMDD2 patients and the role of TNPO3 in the HIV-1 cycle. To this regard, transcriptome profiling of PBMCs from LGMDD2 patients carrying the deletion c.2771delA in the TNPO3 gene was compared to healthy controls. A total of 545 differentially expressed genes were detected between LGMDD2 patients and healthy controls, with a high representation of G protein-coupled receptor binding chemokines and metallopeptidases among the most upregulated genes in LGMDD2 patients. Plasma levels of IFN-β and IFN-γ were 4.7- and 2.7-fold higher in LGMDD2 patients, respectively. An increase of 2.3-fold in the expression of the interferon-stimulated gene MxA was observed in activated PBMCs from LGMDD2 patients after ex vivo HIV-1 pseudovirus infection. Thus, the analysis suggests a pro-inflammatory state in LGMDD2 patients also described for other muscular dystrophies, that is characterized by the alteration of IL-17 signaling pathway and the consequent increase of metallopeptidases activity and TNF response. In summary, the increase in interferons and inflammatory mediators suggests an antiviral environment and resistance to HIV-1 infection but that could also impair muscular function in LGMDD2 patients, worsening disease evolution. Biomarkers of disease progression and therapeutic strategies based on these genes and mechanisms should be further investigated for this type of muscular dystrophy.
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Affiliation(s)
- Francisco Diez-Fuertes
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - María Rosa López-Huertas
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Javier García-Pérez
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Esther Calonge
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Mercedes Bermejo
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Elena Mateos
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Pilar Martí
- Neuromuscular Diseases Unit, Neurology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Nuria Muelas
- Neuromuscular Diseases Unit, Neurology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Juan Jesús Vílchez
- Neuromuscular Diseases Unit, Neurology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Mayte Coiras
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - José Alcamí
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Infectious Diseases Unit, IDIBAPS, Hospital Clinic, University of Barcelona, Barcelona, Spain
- *Correspondence: José Alcamí, ; Sara Rodríguez-Mora,
| | - Sara Rodríguez-Mora
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- *Correspondence: José Alcamí, ; Sara Rodríguez-Mora,
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11
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Park J, Kim D, Lee JO, Park HC, Ryu BY, Kim JH, Lee SH, Chung YJ. Dissection of molecular and histological subtypes of papillary thyroid cancer using alternative splicing profiles. Exp Mol Med 2022; 54:263-272. [PMID: 35277656 PMCID: PMC8980103 DOI: 10.1038/s12276-022-00740-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/10/2021] [Accepted: 12/27/2021] [Indexed: 12/01/2022] Open
Abstract
Despite growing evidence of the relevance of alternative splicing (AS) to cancer development and progression, the biological implications of AS for tumor behaviors, including papillary thyroid cancer (PTC), remain elusive. With the aim of further understanding the molecular and histological subtypes of PTC, we in this study explored whether AS events might act as new molecular determinants. For this purpose, AS profiles were analyzed in RNA-sequencing data from The Cancer Genome Atlas (TCGA) and from a Korean patient dataset. A total of 23 distinct exon-skipping (ES) events that correlated significantly with PTC oncogenic activity and differentiation scores were identified. The two top-ranked ES events, NUMA1_17515 in exon 18 of NUMA1 and TUBB3_38175 in exon 6 of TUBB3, showed high correlations with oncogenic activities and discriminated histological and molecular subtypes of PTC. Furthermore, two novel intron-retention (IR) events for TUBB3 were uncovered. All ES and IR events for the TUBB3 gene were predicted to induce nonsense-mediated mRNA decay. The relative abundances of intron reads in the PTC dataset from TCGA showed IR levels to differ significantly among PTC subtypes, possibly reflecting their different tumor behaviors. This study provides a landscape of AS changes among PTC subtypes and identified two significant AS events, NUMA1_17515 and TUBB3_38175, as potential AS biomarkers for PTC subclassification and characterization. The AS events identified in this study may be involved in the development of phenotypic differences underlying the functional characteristics and histological differentiation of PTCs. Two potential biomarkers uncovered by scientists in South Korea may help more accurately classify subtypes of papillary thyroid cancer, the most common form of thyroid cancer, and improve treatment regimens. Ascertaining the correct papillary thyroid cancer (PTC) subtype is important for patient prognoses and treatment plans. Growing evidence suggests that cancer progression may be influenced by ‘alternative splicing’ events, alterations to mRNA that change the structure of mRNA transcripts and affect the function of encoded proteins. Yeun-Jun Chung and Sug Hyung Lee at the Catholic University of Korea, Seoul, and co-workers explored alternative splicing events in PTC patient samples. They identified 25 distinct events associated with oncogenic activity and differentiation between PTC subtypes. Of these, two events associated with two separate genes are particularly significant and could prove useful as biomarkers for disease classification and characterisation.
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Affiliation(s)
- Jiyeon Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dongmoung Kim
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin-Ok Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyeon-Chun Park
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Brian Y Ryu
- Seoul National University Biomedical Informatics, Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics, Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sug Hyung Lee
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea. .,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea. .,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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12
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Vihinen M. Measuring and interpreting pervasive heterogeneity, poikilosis. FASEB Bioadv 2021; 3:611-625. [PMID: 34377957 PMCID: PMC8332472 DOI: 10.1096/fba.2021-00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 11/11/2022] Open
Abstract
Measurements are widely used in science, engineering, industry, and trade. They form the basis for experimental scientific research, approach, and progress; however, their foundations are seldom thought or questioned. Recently poikilosis, pervasive heterogeneity ranging from subatomic level to biosphere, was introduced. Poikilosis makes single point measurements and estimates obsolete and irrelevant as measurands display intervals of magnitudes. Consideration of poikilosis requires new lines of thinking in experimental design, conduction of studies, data analysis and interpretation. Measurements of poikilosis must consider lagom, normal, variation extent. Measurements, measures, and measurands as well as the measuring systems and uncertainties are discussed from the perspective of poikilosis. New systematics is introduced for description of uncertainty in measurements and for types of experimental designs. Poikilosis-aware experimenting, data analysis and interpretation are discussed. Instructions are provided for how to measure lagom and non-lagom effects of poikilosis. Consideration of poikilosis can solve scientific controversies and enigmas and can allow novel insight into systems, processes, mechanisms, and reactions and their interpretation, understanding, and manipulation. Furthermore, it will increase reproducibility of measurements and studies.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical ScienceLund UniversityLundSweden
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13
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Identification of prognostic alternative splicing events in sarcoma. Sci Rep 2021; 11:14949. [PMID: 34294833 PMCID: PMC8298452 DOI: 10.1038/s41598-021-94485-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/06/2021] [Indexed: 11/20/2022] Open
Abstract
Sarcoma is a rare malignancy with unfavorable prognoses. Accumulating evidence indicates that aberrant alternative splicing (AS) events are generally involved in cancer pathogenesis. The aim of this study was to identify the prognostic value of AS-related survival genes as potential biomarkers, and highlight the functional roles of AS events in sarcoma. RNA-sequencing and AS-event datasets were downloaded from The Cancer Genome Atlas (TCGA) sarcoma cohort and TCGA SpliceSeq, respectively. Survival-related AS events were further assessed using a univariate analysis. A multivariate Cox regression analysis was also performed to establish a survival-gene signature to predict patient survival, and the area-under-the-curve method was used to evaluate prognostic reliability. KOBAS 3.0 and Cytoscape were used to functionally annotate AS-related genes and to assess their network interactions. We detected 9674 AS events in 40,184 genes from 236 sarcoma samples, and the 15 most significant genes were then used to construct a survival regression model. We further validated the involvement of ten potential survival-related genes (TUBB3, TRIM69, ZNFX1, VAV1, KCNN2, VGLL3, AK7, ARMC4, LRRC1, and CRIP1) in the occurrence and development of sarcoma. Multivariate survival model analyses were also performed, and validated that a model using these ten genes provided good classifications for predicting patient outcomes. The present study has increased our understanding of AS events in sarcoma, and the gene-based model using AS-related events may serve as a potential predictor to determine the survival of sarcoma patients.
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14
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A machine learning-based framework for modeling transcription elongation. Proc Natl Acad Sci U S A 2021; 118:2007450118. [PMID: 33526657 DOI: 10.1073/pnas.2007450118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gene expression regulation. Characterizing the transcriptional elongation dynamics can thus help us understand many essential biological processes in eukaryotic cells. However, experimentally measuring Pol II elongation rates is generally time and resource consuming. We developed PEPMAN (polymerase II elongation pausing modeling through attention-based deep neural network), a deep learning-based model that accurately predicts Pol II pausing sites based on the native elongating transcript sequencing (NET-seq) data. Through fully taking advantage of the attention mechanism, PEPMAN is able to decipher important sequence features underlying Pol II pausing. More importantly, we demonstrated that the analyses of the PEPMAN-predicted results around various types of alternative splicing sites can provide useful clues into understanding the cotranscriptional splicing events. In addition, associating the PEPMAN prediction results with different epigenetic features can help reveal important factors related to the transcription elongation process. All these results demonstrated that PEPMAN can provide a useful and effective tool for modeling transcription elongation and understanding the related biological factors from available high-throughput sequencing data.
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15
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Abstract
Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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16
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Deng Y, Luo H, Yang Z, Liu L. LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers. Brief Bioinform 2020; 22:5895039. [PMID: 32820322 DOI: 10.1093/bib/bbaa179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023] Open
Abstract
Accumulating studies demonstrated that the roles of lncRNAs for tumorigenesis were isoform-dependent and their aberrant splicing patterns in cancers contributed to function specificity. However, there is no existing database focusing on cancer-related alternative splicing of lncRNAs. Here, we developed a comprehensive database called LncAS2Cancer, which collected 5335 bulk RNA sequencing and 1826 single-cell RNA sequencing samples, covering over 30 cancer types. By applying six state-of-the-art splicing algorithms, 50 859 alternative splicing events for 8 splicing types were identified and deposited in the database. In addition, the database contained the following information: (i) splicing patterns of lncRNAs under seven different conditions, such as gene interference, which facilitated to infer potential regulators; (ii) annotation information derived from eight sources and manual curation, to understand the functional impact of affected sequences; (iii) survival analysis to explore potential biomarkers; as well as (iv) a suite of tools to browse, search, visualize and download interesting information. LncAS2Cancer could not only confirm the known cancer-associated lncRNA isoforms but also indicate novel ones. Using the data deposited in LncAS2Cancer, we compared gene model and transcript overlap between lncRNAs and protein-coding genes and discusses how these factors, along with sequencing depth, affected the interpretation of splicing signals. Based on recurrent signals and potential confounders, we proposed a reliable score to prioritize splicing events for further elucidation. Together, with the broad collection of lncRNA splicing patterns and annotation, LncAS2Cancer will provide important new insights into the diverse functional roles of lncRNA isoforms in human cancers. LncAS2Cancer is freely available at https://lncrna2as.cd120.com/.
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Affiliation(s)
- Yulan Deng
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Hao Luo
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Zhenyu Yang
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University
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17
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Tian J, Wang Z, Mei S, Yang N, Yang Y, Ke J, Zhu Y, Gong Y, Zou D, Peng X, Wang X, Wan H, Zhong R, Chang J, Gong J, Han L, Miao X. CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. Nucleic Acids Res 2020; 47:D909-D916. [PMID: 30329095 PMCID: PMC6324030 DOI: 10.1093/nar/gky954] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing (AS) is a widespread process that increases structural transcript variation and proteome diversity. Aberrant splicing patterns are frequently observed in cancer initiation, progress, prognosis and therapy. Increasing evidence has demonstrated that AS events could undergo modulation by genetic variants. The identification of splicing quantitative trait loci (sQTLs), genetic variants that affect AS events, might represent an important step toward fully understanding the contribution of genetic variants in disease development. However, no database has yet been developed to systematically analyze sQTLs across multiple cancer types. Using genotype data from The Cancer Genome Atlas and corresponding AS values calculated by TCGASpliceSeq, we developed a computational pipeline to identify sQTLs from 9 026 tumor samples in 33 cancer types. We totally identified 4 599 598 sQTLs across all cancer types. We further performed survival analyses and identified 17 072 sQTLs associated with patient overall survival times. Furthermore, using genome-wide association study (GWAS) catalog data, we identified 1 180 132 sQTLs overlapping with known GWAS linkage disequilibrium regions. Finally, we constructed a user-friendly database, CancerSplicingQTL (http://www.cancersplicingqtl-hust.com/) for users to conveniently browse, search and download data of interest. This database provides an informative sQTL resource for further characterizing the potential functional roles of SNPs that control transcript isoforms in human cancer.
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Affiliation(s)
- Jianbo Tian
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Shufang Mei
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Nan Yang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Yang Yang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Juntao Ke
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Ying Zhu
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Yajie Gong
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Danyi Zou
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Xiating Peng
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Xiaoyang Wang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Hao Wan
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Rong Zhong
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Jiang Chang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Jing Gong
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.,HubeiKey Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Xiaoping Miao
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
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18
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Fochi S, Lorenzi P, Galasso M, Stefani C, Trabetti E, Zipeto D, Romanelli MG. The Emerging Role of the RBM20 and PTBP1 Ribonucleoproteins in Heart Development and Cardiovascular Diseases. Genes (Basel) 2020; 11:genes11040402. [PMID: 32276354 PMCID: PMC7230170 DOI: 10.3390/genes11040402] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a regulatory mechanism essential for cell differentiation and tissue organization. More than 90% of human genes are regulated by alternative splicing events, which participate in cell fate determination. The general mechanisms of splicing events are well known, whereas only recently have deep-sequencing, high throughput analyses and animal models provided novel information on the network of functionally coordinated, tissue-specific, alternatively spliced exons. Heart development and cardiac tissue differentiation require thoroughly regulated splicing events. The ribonucleoprotein RBM20 is a key regulator of the alternative splicing events required for functional and structural heart properties, such as the expression of TTN isoforms. Recently, the polypyrimidine tract-binding protein PTBP1 has been demonstrated to participate with RBM20 in regulating splicing events. In this review, we summarize the updated knowledge relative to RBM20 and PTBP1 structure and molecular function; their role in alternative splicing mechanisms involved in the heart development and function; RBM20 mutations associated with idiopathic dilated cardiovascular disease (DCM); and the consequences of RBM20-altered expression or dysfunction. Furthermore, we discuss the possible application of targeting RBM20 in new approaches in heart therapies.
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19
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Sun Y, Zhang Q, Liu B, Lin K, Zhang Z, Pang E. CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers. BMC PLANT BIOLOGY 2020; 20:119. [PMID: 32183712 PMCID: PMC7079458 DOI: 10.1186/s12870-020-2312-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation. DESCRIPTION To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene. CONCLUSION We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at http://cmb.bnu.edu.cn/alt_iso/index.php.
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Affiliation(s)
- Ying Sun
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Quanbao Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Bing Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
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20
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Liu J, Tan S, Huang S, Huang W. ASlive: a database for alternative splicing atlas in livestock animals. BMC Genomics 2020; 21:97. [PMID: 32000661 PMCID: PMC6993437 DOI: 10.1186/s12864-020-6472-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/09/2020] [Indexed: 11/17/2022] Open
Abstract
Background Alternative splicing is an important biological process whose precision must be tightly regulated during growth and development. Although there are species, disease (e.g. cancers), or study specific databases available in many organisms, no database exists in livestock animals specifically tailored for alternative splicing. Description We present in this study the development and implementation of a database for alternative splicing atlas in livestock animals (ASlive.org). Using publicly available RNASeq data sets across many tissues, cell types, and biological conditions totaling 28.6 T bases, we built a database of alternative splicing events in five major livestock and poultry animal species (cattle, sheep, pigs, horses, and chickens). The database contains many types of information on alternative splicing events, including basic information such as genomic locations, genes, and event types, quantitative measurements of alternative splicing in the form of percent spliced in (PSI), overlap with known DNA variants, as well as orthologous events across different lineage groups. Conclusions This database, the first of its kind in livestock animals, will provide a useful exploratory tool to assist functional annotation of animal genomes.
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Affiliation(s)
- Jinding Liu
- College of Information Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,Research Center for Correlation of Domain Knowledge, Nanjing Agricultural University, Nanjing, 210095, China.,Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Suxu Tan
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Shuiqing Huang
- College of Information Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,Research Center for Correlation of Domain Knowledge, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
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21
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Song X, Wan X, Huang T, Zeng C, Sastry N, Wu B, James CD, Horbinski C, Nakano I, Zhang W, Hu B, Cheng SY. SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes. Cancer Res 2019; 79:5288-5301. [PMID: 31462429 DOI: 10.1158/0008-5472.can-19-1504] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/16/2019] [Accepted: 08/19/2019] [Indexed: 01/29/2023]
Abstract
Misregulated alternative RNA splicing (AS) contributes to the tumorigenesis and progression of human cancers, including glioblastoma (GBM). Here, we showed that a major splicing factor, serine and arginine rich splicing factor 3 (SRSF3), was frequently upregulated in clinical glioma specimens and that elevated SRSF3 was associated with tumor progression and a poor prognosis for patients with glioma. In patient-derived glioma stem-like cells (GSC), SRSF3 expression promoted cell proliferation, self-renewal, and tumorigenesis. Transcriptomic profiling identified more than 1,000 SRSF3-affected AS events, with a preference for exon skipping in genes involved with cell mitosis. Motif analysis identified the sequence of CA(G/C/A)CC(C/A) as a potential exonic splicing enhancer for these SRSF3-regulated exons. To evaluate the biological impact of SRSF3-affected AS events, four candidates were selected whose AS correlated with SRSF3 expression in glioma tissues, and their splicing pattern was modified using a CRISPR/Cas9 approach. Two functionally validated AS candidates were further investigated for the mechanisms underlying their isoform-specific functions. Specifically, following knockout of SRSF3, transcription factor ETS variant 1 (ETV1) gene showed exon skipping at exon 7, while nudE neurodevelopment protein 1 (NDE1) gene showed replacement of terminal exon 9 with a mutually exclusive exon 9'. SRSF3-regulated AS of these two genes markedly increased their oncogenic activity in GSCs. Taken together, our data demonstrate that SRSF3 is a key regulator of AS in GBM and that understanding mechanisms of misregulated AS could provide critical insights for developing effective therapeutic strategies against GBMs. SIGNIFICANCE: SRSF3 is a significant regulator of glioma-associated alternative splicing, implicating SRSF3 as an oncogenic factor that contributes to the tumor biology of GBM.
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Affiliation(s)
- Xiao Song
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Xuechao Wan
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Tianzhi Huang
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Chang Zeng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Namratha Sastry
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Bingli Wu
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - C David James
- Department of Neurological Surgery, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Craig Horbinski
- Department of Neurological Surgery, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Pathology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ichiro Nakano
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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22
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Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes. Int J Mol Sci 2019; 20:ijms20153834. [PMID: 31390737 PMCID: PMC6695735 DOI: 10.3390/ijms20153834] [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: 07/16/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.
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23
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Alvelos MI, Juan-Mateu J, Colli ML, Turatsinze JV, Eizirik DL. When one becomes many-Alternative splicing in β-cell function and failure. Diabetes Obes Metab 2018; 20 Suppl 2:77-87. [PMID: 30230174 PMCID: PMC6148369 DOI: 10.1111/dom.13388] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/22/2018] [Accepted: 05/30/2018] [Indexed: 12/20/2022]
Abstract
Pancreatic β-cell dysfunction and death are determinant events in type 1 diabetes (T1D), but the molecular mechanisms behind β-cell fate remain poorly understood. Alternative splicing is a post-transcriptional mechanism by which a single gene generates different mRNA and protein isoforms, expanding the transcriptome complexity and enhancing protein diversity. Neuron-specific and certain serine/arginine-rich RNA binding proteins (RBP) are enriched in β-cells, playing crucial roles in the regulation of insulin secretion and β-cell survival. Moreover, alternative exon networks, regulated by inflammation or diabetes susceptibility genes, control key pathways and processes for the correct function and survival of β-cells. The challenge ahead of us is to understand the precise role of alternative splicing regulators and splice variants on β-cell function, dysfunction and death and develop tools to modulate it.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Jonàs Juan-Mateu
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Maikel Luis Colli
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Jean-Valéry Turatsinze
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
| | - Décio L. Eizirik
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Route de Lennik, 808 – CP618, B-1070 Brussels, Belgium
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24
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Bhuiyan SA, Ly S, Phan M, Huntington B, Hogan E, Liu CC, Liu J, Pavlidis P. Systematic evaluation of isoform function in literature reports of alternative splicing. BMC Genomics 2018; 19:637. [PMID: 30153812 PMCID: PMC6114036 DOI: 10.1186/s12864-018-5013-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/14/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Although most genes in mammalian genomes have multiple isoforms, an ongoing debate is whether these isoforms are all functional as well as the extent to which they increase the functional repertoire of the genome. To ground this debate in data, it would be helpful to have a corpus of experimentally-verified cases of genes which have functionally distinct splice isoforms (FDSIs). RESULTS We established a curation framework for evaluating experimental evidence of FDSIs, and analyzed over 700 human and mouse genes, strongly biased towards genes that are prominent in the alternative splicing literature. Despite this bias, we found experimental evidence meeting the classical definition for functionally distinct isoforms for ~ 5% of the curated genes. If we relax our criteria for inclusion to include weaker forms of evidence, the fraction of genes with evidence of FDSIs remains low (~ 13%). We provide evidence that this picture will not change substantially with further curation and conclude there is a large gap between the presumed impact of splicing on gene function and the experimental evidence. Furthermore, many functionally distinct isoforms were not traceable to a specific isoform in Ensembl, a database that forms the basis for much computational research. CONCLUSIONS We conclude that the claim that alternative splicing vastly increases the functional repertoire of the genome is an extrapolation from a limited number of empirically supported cases. We also conclude that more work is needed to integrate experimental evidence and genome annotation databases. Our work should help shape research around the role of splicing on gene function from presuming large general effects to acknowledging the need for stronger experimental evidence.
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Affiliation(s)
- Shamsuddin A. Bhuiyan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, Canada
| | - Sophia Ly
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Minh Phan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Brandon Huntington
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Ellie Hogan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Chao Chun Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - James Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
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