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Elfman J, Goins L, Heller T, Singh S, Wang YH, Li H. Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction. Nucleic Acids Res 2024; 52:4409-4421. [PMID: 38587197 PMCID: PMC11077074 DOI: 10.1093/nar/gkae258] [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: 12/17/2022] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
Gene fusions and their chimeric products are commonly linked with cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. Large-scale efforts to annotate structural variations have identified gene fusions capable of generating chimeric transcripts even in normal tissues. In this study, we present a bottom-up approach targeting population-specific chimeric RNAs, identifying 58 such instances in the GTEx cohort, including notable cases such as SUZ12P1-CRLF3, TFG-ADGRG7 and TRPM4-PPFIA3, which possess distinct patterns across different ancestry groups. We provide direct evidence for an additional 29 polymorphic chimeric RNAs with associated structural variants, revealing 13 novel rare structural variants. Additionally, we utilize the All of Us dataset and a large cohort of clinical samples to characterize the association of the SUZ12P1-CRLF3-causing variant with patient phenotypes. Our study showcases SUZ12P1-CRLF3 as a representative example, illustrating the identification of elusive structural variants by focusing on those producing population-specific fusion transcripts.
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Affiliation(s)
- Justin Elfman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lynette Goins
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - Tessa Heller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Sandeep Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA
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2
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Demin DE, Murashko MM, Uvarova AN, Stasevich EM, Shyrokova EY, Gorlachev GE, Zaretsky AR, Korneev KV, Ustiugova AS, Tkachenko EA, Kostenko VV, Tatosyan KA, Sheetikov SA, Spirin PV, Kuprash DV, Schwartz AM. Adversary of DNA integrity: A long non-coding RNA stimulates driver oncogenic chromosomal rearrangement in human thyroid cells. Int J Cancer 2023; 152:1452-1462. [PMID: 36510744 DOI: 10.1002/ijc.34396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/01/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
The flurry of publications devoted to the functions of long non-coding RNAs (lncRNAs) published in the last decade leaves no doubt about the exceptional importance of lncRNAs in various areas including tumor biology. However, contribution of lncRNAs to the early stages of oncogenesis remains poorly understood. In this study we explored a new role for lncRNAs: stimulation of specific chromosomal rearrangements upon DNA damage. We demonstrated that lncRNA CASTL1 (ENSG00000269945) stimulates the formation of the CCDC6-RET inversion (RET/PTC1) in human thyroid cells subjected to radiation or chemical DNA damage. Facilitation of chromosomal rearrangement requires lncRNA to contain regions complementary to the introns of both CCDC6 and RET genes as deletion of these regions deprives CASTL1 of the ability to stimulate the gene fusion. We found that CASTL1 expression is elevated in tumors with CCDC6-RET fusion which is the most frequent rearrangement in papillary thyroid carcinoma. Our results open a new venue for the studies of early oncogenesis in various tumor types, especially those associated with physical or chemical DNA damage.
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Affiliation(s)
- Denis Eriksonovich Demin
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Matvey Mikhailovich Murashko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Aksinya Nicolaevna Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Mikhailovna Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Yurievna Shyrokova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrew Rostislavovich Zaretsky
- Department of Molecular Technologies, Research Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation
| | - Kirill Viktorovich Korneev
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,National Research Center for Hematology, Moscow, Russia
| | - Alina Sergeevna Ustiugova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena Andreevna Tkachenko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Valentina Vitalevna Kostenko
- Laboratory for the Transmission of Intracellular Signals in Normal and Pathological Conditions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Karina Aleksandrovna Tatosyan
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Saveliy Andreevich Sheetikov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,National Research Center for Hematology, Moscow, Russia
| | - Pavel Vladimirovich Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Vladimirovich Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anton Markovich Schwartz
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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3
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Elfman J, Goins L, Heller T, Singh S, Wang YH, Li H. Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526864. [PMID: 36778239 PMCID: PMC9915695 DOI: 10.1101/2023.02.02.526864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have found examples of gene fusions with potential to produce chimeric transcripts in normal tissues. In this report, we provide a means for targeting population-specific chimeric RNAs to enrich for those generated by gene fusion events. We identify 57 such chimeric RNAs from the GTEx cohort, including SUZ12P1-CRLF3 and TFG-ADGRG7 , whose distribution we assessed across the populations of the 1000 Genomes Project. We reveal that SUZ12P1-CRLF3 results from a common complex structural variant in populations with African heritage, and identify its likely mechanism for formation. Additionally, we utilize a large cohort of clinical samples to characterize the SUZ12P1-CRLF3 chimeric RNA, and find an association between the variant and indications of Neurofibramatosis Type I. We present this gene fusion as a case study for identifying hard-to-find and potentially functional structural variants by selecting for those which produce population-specific fusion transcripts. KEY POINTS - Discovery of 57 polymorphic chimeric RNAs- Characterization of SUZ12P1-CRLF3 polymorphic chimeric RNA and corresponding rearrangement- Novel bottom-up approach to identify structural variants which produce transcribed gene fusions.
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Dorney R, Dhungel BP, Rasko JEJ, Hebbard L, Schmitz U. Recent advances in cancer fusion transcript detection. Brief Bioinform 2022; 24:6918739. [PMID: 36527429 PMCID: PMC9851307 DOI: 10.1093/bib/bbac519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Extensive investigation of gene fusions in cancer has led to the discovery of novel biomarkers and therapeutic targets. To date, most studies have neglected chromosomal rearrangement-independent fusion transcripts and complex fusion structures such as double or triple-hop fusions, and fusion-circRNAs. In this review, we untangle fusion-related terminology and propose a classification system involving both gene and transcript fusions. We highlight the importance of RNA-level fusions and how long-read sequencing approaches can improve detection and characterization. Moreover, we discuss novel bioinformatic tools to identify fusions in long-read sequencing data and strategies to experimentally validate and functionally characterize fusion transcripts.
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Affiliation(s)
- Ryley Dorney
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - Bijay P Dhungel
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lionel Hebbard
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
| | - Ulf Schmitz
- Corresponding author. Ulf Schmitz, Department of Molecular and Cell Biology, College of Public Health, Medical and Vet Sciences, James Cook University, Douglas, QLD 4811, Australia. E-mail:
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Li SH, Yang YP, He RQ, He J, Feng X, Yu XX, Yao YX, Zhang GL, Li J, Cheng JW, Chen G, Huang ZG. Comprehensive expression analysis reveals upregulated LUZP2 in prostate cancer tissues. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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6
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Chimeric RNA Design Principles for RNA-Mediated Gene Fusion. Cells 2022; 11:cells11061002. [PMID: 35326453 PMCID: PMC8947500 DOI: 10.3390/cells11061002] [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: 02/15/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 12/02/2022] Open
Abstract
One common genetic alteration in cancer is gene fusion resulting from chromosomal translocations. The mechanisms that create such oncogenic fusion genes are not well understood. Previously, we provided the direct evidence that expression of a designed chimeric RNA can drive the formation of TMPRSS2-ERG gene fusion. Central to this RNA-mediated gene fusion mechanism is a proposed three-way junction formed by RNA/DNA hybrid and the intergenic DNA stem formed by target genes. In this study, we determined the important parameters for chimeric RNA-mediated gene fusion using TMPRSS2-ERG fusion gene as the model. Our results indicate that both the chimeric RNA lengths and the sizes of unpaired bulges play important roles in inducing TMPRSS2-ERG gene fusion. The optimal length of unpaired bulges was about 35 nt, while the optimal chimeric RNA length was about 50 nt for targeting. These observations were consistent regardless of the target locations within TMPRSS2 and ERG genes. These empirically determined parameters provide important insight for searching cellular RNAs that may initiate oncogenic fusion genes. The knowledge could also facilitate the development of useful genomic technology for manipulating mammalian genomes.
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