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Deng W, Murugan S, Lindberg J, Chellappa V, Shen X, Pawitan Y, Vu TN. Fusion Gene Detection Using Whole-Exome Sequencing Data in Cancer Patients. Front Genet 2022; 13:820493. [PMID: 35251131 PMCID: PMC8888970 DOI: 10.3389/fgene.2022.820493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 12/13/2022] Open
Abstract
Several fusion genes are directly involved in the initiation and progression of cancers. Numerous bioinformatics tools have been developed to detect fusion events, but they are mainly based on RNA-seq data. The whole-exome sequencing (WES) represents a powerful technology that is widely used for disease-related DNA variant detection. In this study, we build a novel analysis pipeline called Fuseq-WES to detect fusion genes at DNA level based on the WES data. The same method applies also for targeted panel sequencing data. We assess the method to real datasets of acute myeloid leukemia (AML) and prostate cancer patients. The result shows that two of the main AML fusion genes discovered in RNA-seq data, PML-RARA and CBFB-MYH11, are detected in the WES data in 36 and 63% of the available samples, respectively. For the targeted deep-sequencing of prostate cancer patients, detection of the TMPRSS2-ERG fusion, which is the most frequent chimeric alteration in prostate cancer, is 91% concordant with a manually curated procedure based on four other methods. In summary, the overall results indicate that it is challenging to detect fusion genes in WES data with a standard coverage of ∼ 15–30x, where fusion candidates discovered in the RNA-seq data are often not detected in the WES data and vice versa. A subsampling study of the prostate data suggests that a coverage of at least 75x is necessary to achieve high accuracy.
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Affiliation(s)
- Wenjiang Deng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sarath Murugan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xia Shen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine, Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Yudi Pawitan, ; Trung Nghia Vu,
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Yudi Pawitan, ; Trung Nghia Vu,
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Grinev VV, Barneh F, Ilyushonak IM, Nakjang S, Smink J, van Oort A, Clough R, Seyani M, McNeill H, Reza M, Martinez-Soria N, Assi SA, Ramanouskaya TV, Bonifer C, Heidenreich O. RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. Nat Commun 2021; 12:520. [PMID: 33483506 PMCID: PMC7822815 DOI: 10.1038/s41467-020-20848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia. Here we show that the RUNX1/RUNX1T1 oncogene is a regulator of alternative RNA splicing in leukemic cells. The comprehensive analysis of RUNX1/RUNX1T1-associated splicing events identifies two principal mechanisms that underlie the differential production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start site selection, and (ii) direct or indirect control of the expression of genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5'-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals alternative splicing as an important component of transcriptome re-organization in leukemia by an aberrant transcriptional regulator.
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Affiliation(s)
- Vasily V. Grinev
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Farnaz Barneh
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Ilya M. Ilyushonak
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Sirintra Nakjang
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Job Smink
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Anita van Oort
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Richard Clough
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Michael Seyani
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Hesta McNeill
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Mojgan Reza
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Natalia Martinez-Soria
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Salam A. Assi
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Tatsiana V. Ramanouskaya
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Constanze Bonifer
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Olaf Heidenreich
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands ,grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK ,grid.1006.70000 0001 0462 7212Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
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Neckles C, Sundara Rajan S, Caplen NJ. Fusion transcripts: Unexploited vulnerabilities in cancer? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1562. [PMID: 31407506 PMCID: PMC6916338 DOI: 10.1002/wrna.1562] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Gene fusions are an important class of mutations in several cancer types and include genomic rearrangements that fuse regulatory or coding elements from two different genes. Analysis of the genetics of cancers harboring fusion oncogenes and the proteins they encode have enhanced cancer diagnosis and in some cases patient treatment. However, the effect of the complex structure of fusion genes on the biogenesis of the resulting chimeric transcripts they express is not well studied. There are two potential RNA‐related vulnerabilities inherent to fusion‐driven cancers: (a) the processing of the fusion precursor messenger RNA (pre‐mRNA) to the mature mRNA and (b) the mature mRNA. In this study, we discuss the effects that the genetic organization of fusion oncogenes has on the generation of translatable mature RNAs and the diversity of fusion transcripts expressed in different cancer subtypes, which can fundamentally influence both tumorigenesis and treatment. We also discuss functional genomic approaches that can be utilized to identify proteins that mediate the processing of fusion pre‐mRNAs. Furthermore, we assert that an enhanced understanding of fusion transcript biogenesis and the diversity of the chimeric RNAs present in fusion‐driven cancers will increase the likelihood of successful application of RNA‐based therapies in this class of tumors. This article is categorized under:RNA Processing > RNA Editing and Modification RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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