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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-read sequencing resolves a complex structural variant in PRKN Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.14.23293948. [PMID: 37790330 PMCID: PMC10543050 DOI: 10.1101/2023.08.14.23293948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background PRKN mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. Objectives To identify complex structural variants in PRKN using long-read sequencing. Methods We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of AMP-PD and UK-Biobank datasets. Results Multiple ligation probe amplification identified a heterozygous exon 3 deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4,941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN isoforms. Conclusions This is the first report describing a large 7Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read whole genome sequencing for structural variant analysis in unresolved young-onset PD cases.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Risa Nonaka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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52
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Wang J, Han GZ. Genome mining shows that retroviruses are pervasively invading vertebrate genomes. Nat Commun 2023; 14:4968. [PMID: 37591904 PMCID: PMC10435555 DOI: 10.1038/s41467-023-40732-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Endogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
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Affiliation(s)
- Jianhua Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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53
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Holloway K, Neherin K, Dam KU, Zhang H. Cellular senescence and neurodegeneration. Hum Genet 2023; 142:1247-1262. [PMID: 37115318 DOI: 10.1007/s00439-023-02565-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
Advancing age is a major risk factor of Alzheimer's disease (AD). The worldwide prevalence of AD is approximately 50 million people, and this number is projected to increase substantially. The molecular mechanisms underlying the aging-associated susceptibility to cognitive impairment in AD are largely unknown. As a hallmark of aging, cellular senescence is a significant contributor to aging and age-related diseases including AD. Senescent neurons and glial cells have been detected to accumulate in the brains of AD patients and mouse models. Importantly, selective elimination of senescent cells ameliorates amyloid beta and tau pathologies and improves cognition in AD mouse models, indicating a critical role of cellular senescence in AD pathogenesis. Nonetheless, the mechanisms underlying when and how cellular senescence contributes to AD pathogenesis remain unclear. This review provides an overview of cellular senescence and discusses recent advances in the understanding of the impact of cellular senescence on AD pathogenesis, with brief discussions of the possible role of cellular senescence in other neurodegenerative diseases including Down syndrome, Parkinson's disease, multiple sclerosis, and amyotrophic lateral sclerosis.
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Affiliation(s)
- Kristopher Holloway
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Kashfia Neherin
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Kha Uyen Dam
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Hong Zhang
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
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54
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Bilgrav Saether K, Nilsson D, Thonberg H, Tham E, Ameur A, Eisfeldt J, Lindstrand A. Transposable element insertions in 1000 Swedish individuals. PLoS One 2023; 18:e0289346. [PMID: 37506127 PMCID: PMC10381067 DOI: 10.1371/journal.pone.0289346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
The majority of rare diseases are genetic, and regardless of advanced high-throughput genomics-based investigations, 60% of patients remain undiagnosed. A major factor limiting our ability to identify disease-causing alterations is a poor understanding of the morbid and normal human genome. A major genomic contributor of which function and distribution remain largely unstudied are the transposable elements (TE), which constitute 50% of our genome. Here we aim to resolve this knowledge gap and increase the diagnostic yield of rare disease patients investigated with clinical genome sequencing. To this end we characterized TE insertions in 1000 Swedish individuals from the SweGen dataset and 2504 individuals from the 1000 Genomes Project (1KGP), creating seven population-specific TE insertion databases. Of note, 66% of TE insertions in SweGen were present at >1% in the 1KGP databases, proving that most insertions are common across populations. Focusing on the rare TE insertions, we show that even though ~0.7% of those insertions affect protein coding genes, they rarely affect known disease casing genes (<0.1%). Finally, we applied a TE insertion identification workflow on two clinical cases where disease causing TE insertions were suspected and could verify the presence of pathogenic TE insertions in both. Altogether we demonstrate the importance of TE insertion detection and highlight possible clinical implications in rare disease diagnostics.
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Affiliation(s)
- Kristine Bilgrav Saether
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Håkan Thonberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Lannes L, Furman CM, Hickman AB, Dyda F. Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding. Nat Commun 2023; 14:4470. [PMID: 37491363 PMCID: PMC10368747 DOI: 10.1038/s41467-023-40210-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
The Hermes DNA transposon is a member of the eukaryotic hAT superfamily, and its transposase forms a ring-shaped tetramer of dimers. Our investigation, combining biochemical, crystallography and cryo-electron microscopy, and in-cell assays, shows that the full-length Hermes octamer extensively interacts with its transposon left-end through multiple BED domains of three Hermes protomers contributed by three dimers explaining the role of the unusual higher-order assembly. By contrast, the right-end is bound to no BED domains at all. Thus, this work supports a model in which Hermes multimerizes to gather enough BED domains to find its left-end among the abundant genomic DNA, facilitating the subsequent interaction with the right-end.
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Affiliation(s)
- Laurie Lannes
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christopher M Furman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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56
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Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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57
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Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci 2023; 24:11591. [PMID: 37511347 PMCID: PMC10380595 DOI: 10.3390/ijms241411591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements.
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Affiliation(s)
| | - Federica Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (E.C.); (M.B.); (A.C.); (M.A.B.)
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58
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Park EG, Lee DH, Kim WR, Lee YJ, Bae WH, Kim JM, Shin HJ, Ha H, Yi JM, Cho SG, Choi YH, Leem SH, Cha HJ, Kim SW, Kim HS. Human Endogenous Retrovirus-H-Derived miR-4454 Inhibits the Expression of DNAJB4 and SASH1 in Non-Muscle-Invasive Bladder Cancer. Genes (Basel) 2023; 14:1410. [PMID: 37510314 PMCID: PMC10379226 DOI: 10.3390/genes14071410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Although most human endogenous retroviruses (HERVs) have been silenced and lost their ability to translocate because of accumulated mutations during evolution, they still play important roles in human biology. Several studies have demonstrated that HERVs play pathological roles in numerous human diseases, especially cancer. A few studies have revealed that long non-coding RNAs that are transcribed from HERV sequences affect cancer progression. However, there is no study on microRNAs derived from HERVs related to cancer. In this study, we identified 29 microRNAs (miRNAs) derived from HERV sequences in the human genome. In particular, we discovered that miR-4454, which is HERV-H-derived miRNA, was upregulated in non-muscle-invasive bladder cancer (NMIBC) cells. To figure out the effects of upregulated miR-4454 in NMIBC, genes whose expression was downregulated in NMIBC, as well as tumor suppressor genes, were selected as putative target genes of miR-4454. The dual-luciferase assay was used to determine the negative relationship between miR-4454 and its target genes, DNAJB4 and SASH1, and they were confirmed to be promising target genes of miR-4454. Taken together, this study suggests that the upregulation of miR-4454 derived from HERV-H in NMIBC reduces the expression of the tumor suppressor genes, DNAJB4 and SASH1, to promote NMIBC progression.
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Affiliation(s)
- Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Jung-min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Hongseok Ha
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea;
| | - Joo Mi Yi
- Department of Microbiology and Immunology, Inje University College of Medicine, Busan 47392, Republic of Korea;
| | - Ssang Goo Cho
- Department of Stem Cell & Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Korean Medicine, Dong-Eui University, Busan 47227, Republic of Korea;
| | - Sun Hee Leem
- Department of Biological Science, Dong-A University, Busan 49315, Republic of Korea;
| | - Hee Jae Cha
- Department of Parasitology and Genetics, College of Medicine, Kosin University, Busan 49104, Republic of Korea;
| | - Sang Woo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea;
| | - Heui Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea;
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Tan K, Wilkinson MF. Developmental regulators moonlighting as transposons defense factors. Andrology 2023; 11:891-903. [PMID: 36895139 PMCID: PMC11162177 DOI: 10.1111/andr.13427] [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: 01/11/2023] [Revised: 02/17/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND The germline perpetuates genetic information across generations. To maintain the integrity of the germline, transposable elements in the genome must be silenced, as these mobile elements would otherwise engender widespread mutations passed on to subsequent generations. There are several well-established mechanisms that are dedicated to providing defense against transposable elements, including DNA methylation, RNA interference, and the PIWI-interacting RNA pathway. OBJECTIVES Recently, several studies have provided evidence that transposon defense is not only provided by factors dedicated to this purpose but also factors with other roles, including in germline development. Many of these are transcription factors. Our objective is to summarize what is known about these "bi-functional" transcriptional regulators. MATERIALS AND METHODS Literature search. RESULTS AND CONCLUSION We summarize the evidence that six transcriptional regulators-GLIS3, MYBL1, RB1, RHOX10, SETDB1, and ZBTB16-are both developmental regulators and transposable element-defense factors. These factors act at different stages of germ cell development, including in pro-spermatogonia, spermatogonial stem cells, and spermatocytes. Collectively, the data suggest a model in which specific key transcriptional regulators have acquired multiple functions over evolutionary time to influence developmental decisions and safeguard transgenerational genetic information. It remains to be determined whether their developmental roles were primordial and their transposon defense roles were co-opted, or vice versa.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
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Zhang M, Sun W, You X, Xu D, Wang L, Yang J, Li E, He S. LINE-1 repression in Epstein-Barr virus-associated gastric cancer through viral-host genome interaction. Nucleic Acids Res 2023; 51:4867-4880. [PMID: 36942479 PMCID: PMC10250212 DOI: 10.1093/nar/gkad203] [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: 12/14/2022] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/23/2023] Open
Abstract
Long INterspersed Element 1 (LINE-1 or L1) acts as a major remodeling force in genome regulation and evolution. Accumulating evidence shows that virus infection impacts L1 expression, potentially impacting host antiviral response and diseases. The underlying regulation mechanism is unclear. Epstein-Barr virus (EBV), a double-stranded DNA virus linked to B-cell and epithelial malignancies, is known to have viral-host genome interaction, resulting in transcriptional rewiring in EBV-associated gastric cancer (EBVaGC). By analyzing publicly available datasets from the Gene Expression Omnibus (GEO), we found that EBVaGC has L1 transcriptional repression compared with EBV-negative gastric cancer (EBVnGC). More specifically, retrotransposition-associated young and full-length L1s (FL-L1s) were among the most repressed L1s. Epigenetic alterations, especially increased H3K9me3, were observed on FL-L1s. H3K9me3 deposition was potentially attributed to increased TASOR expression, a key component of the human silencing hub (HUSH) complex for H3K9 trimethylation. The 4C- and HiC-seq data indicated that the viral DNA interacted in the proximity of the TASOR enhancer, strengthening the loop formation between the TASOR enhancer and its promoter. These results indicated that EBV infection is associated with increased H3K9me3 deposition, leading to L1 repression. This study uncovers a regulation mechanism of L1 expression by chromatin topology remodeling associated with viral-host genome interaction in EBVaGC.
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Affiliation(s)
- Mengyu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Yancheng Medical Research Center, Medical School, Nanjing University, Yancheng 224000, China
| | - Weikang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaoxin You
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Dongge Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Lingling Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Jingping Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Erguang Li
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Institute of Medical Virology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing 210093, China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
| | - Susu He
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Yancheng Medical Research Center, Medical School, Nanjing University, Yancheng 224000, China
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61
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Singh B, Dopkins N, Fei T, Marston JL, Michael S, Reyes-Gopar H, Curty G, Heymann JJ, Chadburn A, Martin P, Leal FE, Cesarman E, Nixon DF, Bendall ML. Locus specific human endogenous retroviruses reveal new lymphoma subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544208. [PMID: 37333202 PMCID: PMC10274920 DOI: 10.1101/2023.06.08.544208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The heterogeneity of cancers are driven by diverse mechanisms underlying oncogenesis such as differential 'cell-of-origin' (COO) progenitors, mutagenesis, and viral infections. Classification of B-cell lymphomas have been defined by considering these characteristics. However, the expression and contribution of transposable elements (TEs) to B cell lymphoma oncogenesis or classification have been overlooked. We hypothesized that incorporating TE signatures would increase the resolution of B-cell identity during healthy and malignant conditions. Here, we present the first comprehensive, locus-specific characterization of TE expression in benign germinal center (GC) B-cells, diffuse large B-cell lymphoma (DLBCL), Epstein-Barr virus (EBV)-positive and EBV-negative Burkitt lymphoma (BL), and follicular lymphoma (FL). Our findings demonstrate unique human endogenous retrovirus (HERV) signatures in the GC and lymphoma subtypes whose activity can be used in combination with gene expression to define B-cell lineage in lymphoid malignancies, highlighting the potential of retrotranscriptomic analyses as a tool in lymphoma classification, diagnosis, and the identification of novel treatment groups.
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Affiliation(s)
- Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jez L. Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Helena Reyes-Gopar
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Gislaine Curty
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Jonas J. Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Peter Martin
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Fabio E. Leal
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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62
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Kojima S, Koyama S, Ka M, Saito Y, Parrish EH, Endo M, Takata S, Mizukoshi M, Hikino K, Takeda A, Gelinas AF, Heaton SM, Koide R, Kamada AJ, Noguchi M, Hamada M, Kamatani Y, Murakawa Y, Ishigaki K, Nakamura Y, Ito K, Terao C, Momozawa Y, Parrish NF. Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk. Nat Genet 2023:10.1038/s41588-023-01390-2. [PMID: 37169872 DOI: 10.1038/s41588-023-01390-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
Mobile genetic elements (MEs) are heritable mutagens that recursively generate structural variants (SVs). ME variants (MEVs) are difficult to genotype and integrate in statistical genetics, obscuring their impact on genome diversification and traits. We developed a tool that accurately genotypes MEVs using short-read whole-genome sequencing (WGS) and applied it to global human populations. We find unexpected population-specific MEV differences, including an Alu insertion distribution distinguishing Japanese from other populations. Integrating MEVs with expression quantitative trait loci (eQTL) maps shows that MEV classes regulate tissue-specific gene expression by shared mechanisms, including creating or attenuating enhancers and recruiting post-transcriptional regulators, supporting class-wide interpretability. MEVs more often associate with gene expression changes than SNVs, thus plausibly impacting traits. Performing genome-wide association study (GWAS) with MEVs pinpoints potential causes of disease risk, including a LINE-1 insertion associated with keloid and fasciitis. This work implicates MEVs as drivers of human divergence and disease risk.
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Affiliation(s)
- Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan.
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Mirei Ka
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
- Next-Generation Precision Medicine Development, Integrative Genomics Laboratory, Graduate School of Medicine, Department of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuka Saito
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Erica H Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Mikiko Endo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sadaaki Takata
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Misaki Mizukoshi
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Takeda
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Asami F Gelinas
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Steven M Heaton
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Rie Koide
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Anselmo J Kamada
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
- Paleovirology Lab, Department of Biology, University of Oxford, Oxford, UK
| | - Michiya Noguchi
- Cell Engineering Division, BioResource Research Center, RIKEN, Tsukuba, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukio Nakamura
- Cell Engineering Division, BioResource Research Center, RIKEN, Tsukuba, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nicholas F Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan.
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63
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Zhou J, Hu J, Wang Y, Gao S. Induction and application of human naive pluripotency. Cell Rep 2023; 42:112379. [PMID: 37043354 DOI: 10.1016/j.celrep.2023.112379] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/18/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
Over the past few decades, many attempts have been made to capture different states of pluripotency in vitro. Naive and primed pluripotent stem cells, corresponding to the pluripotency states of pre- and post-implantation epiblasts, respectively, have been well characterized in mice and can be interconverted in vitro. Here, we summarize the recently reported strategies to generate human naive pluripotent stem cells in vitro. We discuss their applications in studies of regulatory mechanisms involved in early developmental processes, including identification of molecular features, X chromosome inactivation modeling, transposable elements regulation, metabolic characteristics, and cell fate regulation, as well as potential for extraembryonic differentiation and blastoid construction for embryogenesis modeling. We further discuss the naive pluripotency-related research, including 8C-like cell establishment and disease modeling. We also highlight limitations of current naive pluripotency studies, such as imperfect culture conditions and inadequate responsiveness to differentiation signals.
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Affiliation(s)
- Jianfeng Zhou
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jindian Hu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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64
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Shah NM, Jang HJ, Liang Y, Maeng JH, Tzeng SC, Wu A, Basri NL, Qu X, Fan C, Li A, Katz B, Li D, Xing X, Evans BS, Wang T. Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements. Nat Genet 2023; 55:631-639. [PMID: 36973455 DOI: 10.1038/s41588-023-01349-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/23/2023] [Indexed: 03/29/2023]
Abstract
Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in tumors to create new TE-chimeric transcripts, which can produce immunogenic antigens. We performed a comprehensive screen for these TE exaptation events in 33 TCGA tumor types, 30 GTEx adult tissues and 675 cancer cell lines, and identified 1,068 TE-exapted candidates with the potential to generate shared tumor-specific TE-chimeric antigens (TS-TEAs). Whole-lysate and HLA-pulldown mass spectrometry data confirmed that TS-TEAs are presented on the surface of cancer cells. In addition, we highlight tumor-specific membrane proteins transcribed from TE promoters that constitute aberrant epitopes on the extracellular surface of cancer cells. Altogether, we showcase the high pan-cancer prevalence of TS-TEAs and atypical membrane proteins that could potentially be therapeutically exploited and targeted.
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Affiliation(s)
- Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - H Josh Jang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Yonghao Liang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ju Heon Maeng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Angela Wu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Noah L Basri
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xuan Qu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy Li
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin Katz
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
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65
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Bowles H, Kabiljo R, Al Khleifat A, Jones A, Quinn JP, Dobson RJB, Swanson CM, Al-Chalabi A, Iacoangeli A. An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data. FRONTIERS IN BIOINFORMATICS 2023; 2:1062328. [PMID: 36845320 PMCID: PMC9945273 DOI: 10.3389/fbinf.2022.1062328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/12/2022] [Indexed: 02/10/2023] Open
Abstract
There is a growing interest in the study of human endogenous retroviruses (HERVs) given the substantial body of evidence that implicates them in many human diseases. Although their genomic characterization presents numerous technical challenges, next-generation sequencing (NGS) has shown potential to detect HERV insertions and their polymorphisms in humans. Currently, a number of computational tools to detect them in short-read NGS data exist. In order to design optimal analysis pipelines, an independent evaluation of the available tools is required. We evaluated the performance of a set of such tools using a variety of experimental designs and datasets. These included 50 human short-read whole-genome sequencing samples, matching long and short-read sequencing data, and simulated short-read NGS data. Our results highlight a great performance variability of the tools across the datasets and suggest that different tools might be suitable for different study designs. However, specialized tools designed to detect exclusively human endogenous retroviruses consistently outperformed generalist tools that detect a wider range of transposable elements. We suggest that, if sufficient computing resources are available, using multiple HERV detection tools to obtain a consensus set of insertion loci may be ideal. Furthermore, given that the false positive discovery rate of the tools varied between 8% and 55% across tools and datasets, we recommend the wet lab validation of predicted insertions if DNA samples are available.
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Affiliation(s)
- Harry Bowles
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Renata Kabiljo
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ashley Jones
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
- NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Neurology, King’s College Hospital, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
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66
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Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
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Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
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67
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Vezain M, Thauvin-Robinet C, Vial Y, Coutant S, Drunat S, Urtizberea JA, Rolland A, Jacquin-Piques A, Fehrenbach S, Nicolas G, Lecoquierre F, Saugier-Veber P. Retrotransposon insertion as a novel mutational cause of spinal muscular atrophy. Hum Genet 2023; 142:125-138. [PMID: 36138164 DOI: 10.1007/s00439-022-02473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting from biallelic alterations of the SMN1 gene: deletion, gene conversion or, in rare cases, intragenic variants. The disease severity is mainly influenced by the copy number of SMN2, a nearly identical gene, which produces only low amounts of full-length (FL) mRNA. Here we describe the first example of retrotransposon insertion as a pathogenic SMN1 mutational event. The 50-year-old patient is clinically affected by SMA type III with a diagnostic odyssey spanning nearly 30 years. Despite a mild disease course, he carries a single SMN2 copy. Using Exome Sequencing and Sanger sequencing, we characterized a SINE-VNTR-Alu (SVA) type F retrotransposon inserted in SMN1 intron 7. Using RT-PCR and RNASeq experiments on lymphoblastoid cell lines, we documented the dramatic decrease of FL transcript production in the patient compared to subjects with the same SMN1 and SMN2 copy number, thus validating the pathogenicity of this SVA insertion. We described the mutant FL-SMN1-SVA transcript characterized by exon extension and showed that it is subject to degradation by nonsense-mediated mRNA decay. The stability of the SMN-SVA protein may explain the mild course of the disease. This observation exemplifies the role of retrotransposons in human genetic disorders.
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Affiliation(s)
- Myriam Vezain
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD-Génétique des Anomalies du Développement, Bourgogne Franche-Comté University, F-21000 , Dijon, France.,Genetics Center, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Yoann Vial
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, 48 boulevard Sérurier, 75019 , Paris, France
| | - Sophie Coutant
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Séverine Drunat
- INSERM UMR 1141, PROTECT, Paris University, F-75019, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, F-75019, Paris, France
| | - Jon Andoni Urtizberea
- Myology Institute, AP-HP Pitié-Salpêtrière University Hospital, F-75013, Paris, France
| | - Anne Rolland
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Pediatrics Department, Valence Hospital, 179 boulevard du Maréchal Juin, 26000, Valence, France
| | - Agnès Jacquin-Piques
- Department of Neurology, Clinical Neurophysiology, Competence Center of Neuromuscular Diseases, Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Séverine Fehrenbach
- Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Gaël Nicolas
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - François Lecoquierre
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France. .,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France. .,Laboratoire de Génétique Moléculaire, UFR-Santé, 22 boulevard Gambetta, 76183, Rouen, France.
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Chen X, Bourque G, Goubert C. Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments. Methods Mol Biol 2023; 2607:63-83. [PMID: 36449158 DOI: 10.1007/978-1-0716-2883-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Transposable element (TE) insertions are a major source of structural variation in the human genome. Due to the repetitive nature and biological importance of TEs, many bioinformatic tools have been developed to identify and genotype TE insertion polymorphisms using high-throughput short-reads. In this chapter, we outline recently developed methods to characterize TE insertion polymorphisms in human populations. We also provide detailed protocols to tackle this question primarily using three software: MELT2, ERVcaller, and TypeREF.
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Affiliation(s)
- Xun Chen
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
- Human Genetics, McGill University, Montreal, QC, Canada
| | - Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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De Novo Somatic Mosaicism of CYBB Caused by Intronic LINE-1 Element Insertion Resulting in Chronic Granulomatous Disease. J Clin Immunol 2023; 43:88-100. [PMID: 35997928 DOI: 10.1007/s10875-022-01347-w] [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: 05/27/2022] [Accepted: 08/10/2022] [Indexed: 01/21/2023]
Abstract
Chronic granulomatosis disease (CGD) is a rare inborn error of immunity, characterized by phagocytic respiratory outbreak dysfunction. Mutations causing CGD occur in CYBB on the X chromosome and in the autosomal genes CYBA, NCF1, NCF2, NCF4, RAC2, and CYBC1. Nevertheless, some patients are clinically diagnosed with CGD, due to abnormal respiratory outbursts, while the pathogenic gene mutation is unidentified. Here, we report a patient with CGD who first presented with Bacillus Calmette-Guérin disease and had recurrent pneumonia. He was diagnosed with CGD by nitro blue tetrazolium and respiratory burst tests. Detailed assessment of neutrophil activity revealed that patient neutrophils were almost entirely nonfunctional. Sanger sequencing detected a 6-kb insertion of a LINE-1 transposable element in the third intron of CYBB, leading to abnormal splicing and pseudoexon insertion, as well as introduction of a premature termination codon, resulting in predicted protein truncation. Clonal analysis demonstrated that the patient had somatic mosaicism, and the phagocytes were almost all variant CYBB, while the mosaicism rate of PBMC was about 65%. Finally, deep RNA sequencing and gp91phox expression analysis confirmed the pathogenicity of the mutation. In conclusion, we demonstrate that insertion of a LINE-1 transposon in a CYBB intron was responsible for CGD in our patient. Intron LINE-1 transposon element insertion should be examined in CGD patients without any known disease-causing gene mutation, in addition to identification of new genes.
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Dericquebourg A, Fretigny M, Chatron N, Tardy B, Zawadzki C, Chambost H, Vinciguerra C, Jourdy Y. Whole F9 gene sequencing identified deep intronic variations in genetically unresolved hemophilia B patients. J Thromb Haemost 2022; 21:828-837. [PMID: 36696202 DOI: 10.1016/j.jtha.2022.12.005] [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: 05/25/2022] [Revised: 09/20/2022] [Accepted: 12/02/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND The disease-causative variant remains unidentified in approximately 0.5% to 2% of hemophilia B patients using conventional genetic investigations, and F9 deep intronic variations could be responsible for these phenotypes. OBJECTIVES This study aimed to characterize deep intronic variants in hemophilia B patients for whom genetic investigations failed. METHODS We performed whole F9 sequencing in 17 genetically unsolved hemophilia B patients. The pathogenic impact of the candidate variants identified was studied using both in silico analysis (MaxEntScan and spliceAI) and minigene assay. RESULTS In total, 9 candidate variants were identified in 15 patients; 7 were deep intronic substitutions and 2 corresponded to insertions of mobile elements. The most frequent variants found were c.278-1806A>C and the association of c.278-1244A>G and c.392-864T>G, identified in 4 and 6 unrelated individuals, respectively. In silico analysis predicted splicing impact for 4 substitutions (c.278-1806A>C, c.392-864T>G, c.724-2385G>T, c.723+4297T>A). Minigene assay showed a deleterious splicing impact for these 4 substitutions and also for the c.278-1786_278-1785insLINE. In the end, 5 variants were classified as likely pathogenic using the American College of Medical Genetics and Genomics guidelines, and 4 as of unknown significance. Thus, the hemophilia B-causing variant was identified in 13/17 (76%) families. CONCLUSION We elucidated the causing defect in three-quarters of the families included in this study, and we reported new F9 deep intronic variants that can cause hemophilia B.
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Affiliation(s)
- Amy Dericquebourg
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
| | - Mathilde Fretigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
| | - Nicolas Chatron
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France; Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, Lyon, France
| | - Brigitte Tardy
- Hémostase clinique-CRC hémophilie, Saint Etienne, France
| | - Christophe Zawadzki
- Pôle de Biologie Pathologie Génétique, Institut d'Hématologie -Transfusion, CHU Lille, Lille, France
| | - Hervé Chambost
- Department of Pediatric Hematology, Immunology, and Oncology, APHM, La Timone Children's Hospital, Marseille, France; INSERM, INRAe, C2VN, Aix Marseille Univ, Marseille, France
| | - Christine Vinciguerra
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France
| | - Yohann Jourdy
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France; Université Claude Bernard Lyon 1, UR4609 Hémostase et thrombose, Lyon, France.
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71
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Brochu H, Wang R, Tollison T, Pyo CW, Thomas A, Tseng E, Law L, Picker LJ, Gale M, Geraghty DE, Peng X. Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines. Commun Biol 2022; 5:1387. [PMID: 36536032 PMCID: PMC9762870 DOI: 10.1038/s42003-022-04344-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Rhesus cytomegalovirus (RhCMV)-based vaccination against Simian Immunodeficiency virus (SIV) elicits MHC-E-restricted CD8+ T cells that stringently control SIV infection in ~55% of vaccinated rhesus macaques (RM). However, it is unclear how accurately the RM model reflects HLA-E immunobiology in humans. Using long-read sequencing, we identified 16 Mamu-E isoforms and all Mamu-E splicing junctions were detected among HLA-E isoforms in humans. We also obtained the complete Mamu-E genomic sequences covering the full coding regions of 59 RM from a RhCMV/SIV vaccine study. The Mamu-E gene was duplicated in 32 (54%) of 59 RM. Among four groups of Mamu-E alleles: three ~5% divergent full-length allele groups (G1, G2, G2_LTR) and a fourth monomorphic group (G3) with a deletion encompassing the canonical Mamu-E exon 6, the presence of G2_LTR alleles was significantly (p = 0.02) associated with the lack of RhCMV/SIV vaccine protection. These genomic resources will facilitate additional MHC-E targeted translational research.
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Affiliation(s)
- Hayden Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ruihan Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Tammy Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Alexander Thomas
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | | | - Lynn Law
- Department of Immunology, University of Washington, Seattle, WA, USA
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA, USA
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, 27607, USA.
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.
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72
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Bernardt TM, Treviso EM, Cancian M, Silva MDM, da Rocha JBT, Loreto ELS. Chemotherapy Drugs Act Differently in the Expression and Somatic Mobilization of the mariner Transposable Element in Drosophila simulans. Genes (Basel) 2022; 13:genes13122374. [PMID: 36553641 PMCID: PMC9777735 DOI: 10.3390/genes13122374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Transposable elements (TEs) are abundant in genomes. Their mobilization can lead to genetic variability that is useful for evolution, but can also have deleterious biological effects. Somatic mobilization (SM) has been linked to degenerative diseases, such as Alzheimer's disease and cancer. We used a Drosophila simulans strain, in which SM can be measured by counting red spots in the eyes, to investigate how chemotherapeutic agents affect expression and SM of the mariner TE. Flies were treated with Cisplatin, Dacarbazine, and Daunorubicin. After acute exposure, relative expression of mariner was quantified by RT-qPCR and oxidative stress was measured by biochemical assays. Exposure to 50 and 100 µg/mL Cisplatin increased mariner expression and ROS levels; catalase activity increased at 100 µg/mL. With chronic exposure, the number of spots also increased, indicating higher mariner SM. Dacarbazine (50 and 100 µg/mL) did not significantly alter mariner expression or mobilization or ROS levels, but decreased catalase activity (100 µg/mL). Daunorubicin (25 and 50 µM) increased mariner expression, but decreased mariner SM. ROS and catalase activity were also reduced. Our data suggest that stress factors may differentially affect the expression and SM of TEs. The increase in mariner transposase gene expression is necessary, but not sufficient for mariner SM.
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Affiliation(s)
- Taís Maus Bernardt
- Biological Sciences, Federal University of Santa Maria (UFSM), Santa Maria 97105-000, RS, Brazil
| | - Estéfani Maria Treviso
- Biological Sciences, Federal University of Santa Maria (UFSM), Santa Maria 97105-000, RS, Brazil
| | - Mariana Cancian
- Genetic and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, RS, Brazil
| | - Monica de Medeiros Silva
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
| | - João Batista Teixeira da Rocha
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
| | - Elgion Lucio Silva Loreto
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
- Correspondence:
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73
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Senaratne TN, Saitta SC. Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU. Neoreviews 2022; 23:e829-e840. [PMID: 36450644 DOI: 10.1542/neo.23-12-e829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.
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Affiliation(s)
- T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sulagna C Saitta
- Division of Clinical Genetics, Department of Pediatrics, Division of Reproductive Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
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74
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Lavia P, Sciamanna I, Spadafora C. An Epigenetic LINE-1-Based Mechanism in Cancer. Int J Mol Sci 2022; 23:14610. [PMID: 36498938 PMCID: PMC9738484 DOI: 10.3390/ijms232314610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
In the last fifty years, large efforts have been deployed in basic research, clinical oncology, and clinical trials, yielding an enormous amount of information regarding the molecular mechanisms of cancer and the design of effective therapies. The knowledge that has accumulated underpins the complexity, multifactoriality, and heterogeneity of cancer, disclosing novel landscapes in cancer biology with a key role of genome plasticity. Here, we propose that cancer onset and progression are determined by a stress-responsive epigenetic mechanism, resulting from the convergence of upregulation of LINE-1 (long interspersed nuclear element 1), the largest family of human retrotransposons, genome damage, nuclear lamina fragmentation, chromatin remodeling, genome reprogramming, and autophagy activation. The upregulated expression of LINE-1 retrotransposons and their protein products plays a key role in these processes, yielding an increased plasticity of the nuclear architecture with the ensuing reprogramming of global gene expression, including the reactivation of embryonic transcription profiles. Cancer phenotypes would thus emerge as a consequence of the unscheduled reactivation of embryonic gene expression patterns in an inappropriate context, triggering de-differentiation and aberrant proliferation in differentiated cells. Depending on the intensity of the stressing stimuli and the level of LINE-1 response, diverse degrees of malignity would be generated.
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Affiliation(s)
- Patrizia Lavia
- Institute of Molecular Biology and Pathology (IBPM), CNR Consiglio Nazionale delle Ricerche, c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Ilaria Sciamanna
- Center for Animal Research and Welfare (BENA), ISS Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Corrado Spadafora
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133 Rome, Italy
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75
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Angileri KM, Bagia NA, Feschotte C. Transposon control as a checkpoint for tissue regeneration. Development 2022; 149:dev191957. [PMID: 36440631 PMCID: PMC10655923 DOI: 10.1242/dev.191957] [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: 03/11/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022]
Abstract
Tissue regeneration requires precise temporal control of cellular processes such as inflammatory signaling, chromatin remodeling and proliferation. The combination of these processes forms a unique microenvironment permissive to the expression, and potential mobilization of, transposable elements (TEs). Here, we develop the hypothesis that TE activation creates a barrier to tissue repair that must be overcome to achieve successful regeneration. We discuss how uncontrolled TE activity may impede tissue restoration and review mechanisms by which TE activity may be controlled during regeneration. We posit that the diversification and co-evolution of TEs and host control mechanisms may contribute to the wide variation in regenerative competency across tissues and species.
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Affiliation(s)
- Krista M. Angileri
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Nornubari A. Bagia
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
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76
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Savage AL, Iacoangeli A, Schumann GG, Rubio-Roldan A, Garcia-Perez JL, Al Khleifat A, Koks S, Bubb VJ, Al-Chalabi A, Quinn JP. Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis. Gene 2022; 843:146799. [PMID: 35963498 DOI: 10.1016/j.gene.2022.146799] [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: 03/24/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals' whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.
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Affiliation(s)
- Abigail L Savage
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Alejandro Rubio-Roldan
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain
| | - Jose L Garcia-Perez
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain; MRC-HGU Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, Western Australia 6009, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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Paloviita P, Vuoristo S. The non-coding genome in early human development - Recent advancements. Semin Cell Dev Biol 2022; 131:4-13. [PMID: 35177347 DOI: 10.1016/j.semcdb.2022.02.010] [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: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Not that long ago, the human genome was discovered to be mainly non-coding, that is comprised of DNA sequences that do not code for proteins. The initial paradigm that non-coding is also non-functional was soon overturned and today the work to uncover the functions of non-coding DNA and RNA in human early embryogenesis has commenced. Early human development is characterized by large-scale changes in genomic activity and the transcriptome that are partly driven by the coordinated activation and repression of repetitive DNA elements scattered across the genome. Here we provide examples of recent novel discoveries of non-coding DNA and RNA interactions and mechanisms that ensure accurate non-coding activity during human maternal-to-zygotic transition and lineage segregation. These include studies on small and long non-coding RNAs, transposable element regulation, and RNA tailing in human oocytes and early embryos. High-throughput approaches to dissect the non-coding regulatory networks governing early human development are a foundation for functional studies of specific genomic elements and molecules that has only begun and will provide a wider understanding of early human embryogenesis and causes of infertility.
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Affiliation(s)
- Pauliina Paloviita
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland
| | - Sanna Vuoristo
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland.
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Jourdy Y, Chatron N, Fretigny M, Dericquebourg A, Sanlaville D, Vinciguerra C. Comprehensive analysis of F8 large deletions: Characterization of full breakpoint junctions and description of a possible DNA breakage hotspot in intron 6. J Thromb Haemost 2022; 20:2293-2305. [PMID: 35894111 DOI: 10.1111/jth.15835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Large F8 deletions represent 3-5% of the variations found in severe hemophilia A patients, but only a few deletion breakpoints have been characterized precisely. OBJECTIVES Resolving at the nucleotide level 24 F8 large deletions to provide new data on the mechanisms involved in these rearrangements. METHODS Breakpoint junctions of 24 F8 large deletions were characterized using a combination of long-range polymerase chain reaction, whole F8 NGS sequencing, and Sanger sequencing. Repeat elements, non-B DNA, and secondary structures were analyzed around the breakpoints. RESULTS Deletions ranged from 1.667 kb to 0.5 Mb in size. Nine involved F8 neighboring genes. Simple blunt ends and 2-4 bp microhomologies were identified at the breakpoint junctions of 10 (42%) and 8 (33%) deletions, respectively. Five (21%) deletions resulted from homeologous recombination between two Alu elements. The remaining case corresponded to a more complex rearrangement with an insertion of a 19 bp-inverted sequence at the junction. Four different breakpoints were located in a 562-bp region in F8 intron 6. This finding suggested that this region, composed of two Alu elements, is a DNA breakage hotspot. Non-B DNA and secondary structures were identified in the junction regions and may contribute to DNA breakage. CONCLUSION Molecular characterization of deletion breakpoints revealed that non-homologous non-replicative DNA repair mechanisms and replication-based mechanisms seemed to be the main causative mechanisms of F8 large deletions. Moreover, we identified a possible F8 DNA breakage hotspot involved in non-recurrent rearrangements.
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Affiliation(s)
- Yohann Jourdy
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
- Université Claude Bernard Lyon 1, UR 4609, Hémostase et thrombose, Lyon, France
| | - Nicolas Chatron
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, Lyon, France
| | - Mathilde Fretigny
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
| | - Amy Dericquebourg
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
- Université Claude Bernard Lyon 1, UR 4609, Hémostase et thrombose, Lyon, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, Lyon, France
| | - Christine Vinciguerra
- Hospices Civils de Lyon, Groupe Hospitalier Est, Service d'hématologie biologique, Bron, France
- Université Claude Bernard Lyon 1, UR 4609, Hémostase et thrombose, Lyon, France
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79
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Abstract
The enormous diversity of antibodies is a key element to combat infections. Antibodies containing pathogen receptors were a surprising discovery that contrasted antibody diversification through classic recombination events. However, such insert-containing antibodies were thus far exclusively detected in African individuals exposed to malaria parasites and were identified as screening byproducts or through hypothesis-driven search. The prevalence and complexity of insertion events remained elusive. In this study, we devise an unbiased, systematic approach to identify inserts in the human antibody repertoire. We show that inserts from distant genomic regions occur in the majority of donors and are independent of Plasmodium falciparum preexposure. Our findings suggest that four distinct classes of insertion events contribute diversity to the human antibody repertoire. Recombination of antibody genes in B cells can involve distant genomic loci and contribute a foreign antigen-binding element to form hybrid antibodies with broad reactivity for Plasmodium falciparum. So far, antibodies containing the extracellular domain of the LAIR1 and LILRB1 receptors represent unique examples of cross-chromosomal antibody diversification. Here, we devise a technique to profile non-VDJ elements from distant genes in antibody transcripts. Independent of the preexposure of donors to malaria parasites, non-VDJ inserts were detected in 80% of individuals at frequencies of 1 in 104 to 105 B cells. We detected insertions in heavy, but not in light chain or T cell receptor transcripts. We classify the insertions into four types depending on the insert origin and destination: 1) mitochondrial and 2) nuclear DNA inserts integrated at VDJ junctions; 3) inserts originating from telomere proximal genes; and 4) fragile sites incorporated between J-to-constant junctions. The latter class of inserts was exclusively found in memory and in in vitro activated B cells, while all other classes were already detected in naïve B cells. More than 10% of inserts preserved the reading frame, including transcripts with signs of antigen-driven affinity maturation. Collectively, our study unravels a mechanism of antibody diversification that is layered on the classical V(D)J and switch recombination.
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80
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Patel AJ, Warda S, Maag JL, Misra R, Miranda-Román MA, Pachai MR, Lee CJ, Li D, Wang N, Bayshtok G, Fishinevich E, Meng Y, Wong EW, Yan J, Giff E, Pappalardi MB, McCabe MT, Fletcher JA, Rudin CM, Chandarlapaty S, Scandura JM, Koche RP, Glass JL, Antonescu CR, Zheng D, Chen Y, Chi P. PRC2-Inactivating Mutations in Cancer Enhance Cytotoxic Response to DNMT1-Targeted Therapy via Enhanced Viral Mimicry. Cancer Discov 2022; 12:2120-2139. [PMID: 35789380 PMCID: PMC9437570 DOI: 10.1158/2159-8290.cd-21-1671] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/19/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023]
Abstract
Polycomb repressive complex 2 (PRC2) has oncogenic and tumor-suppressive roles in cancer. There is clinical success of targeting this complex in PRC2-dependent cancers, but an unmet therapeutic need exists in PRC2-loss cancer. PRC2-inactivating mutations are a hallmark feature of high-grade malignant peripheral nerve sheath tumor (MPNST), an aggressive sarcoma with poor prognosis and no effective targeted therapy. Through RNAi screening in MPNST, we found that PRC2 inactivation increases sensitivity to genetic or small-molecule inhibition of DNA methyltransferase 1 (DNMT1), which results in enhanced cytotoxicity and antitumor response. Mechanistically, PRC2 inactivation amplifies DNMT inhibitor-mediated expression of retrotransposons, subsequent viral mimicry response, and robust cell death in part through a protein kinase R (PKR)-dependent double-stranded RNA sensor. Collectively, our observations posit DNA methylation as a safeguard against antitumorigenic cell-fate decisions in PRC2-loss cancer to promote cancer pathogenesis, which can be therapeutically exploited by DNMT1-targeted therapy. SIGNIFICANCE PRC2 inactivation drives oncogenesis in various cancers, but therapeutically targeting PRC2 loss has remained challenging. Here we show that PRC2-inactivating mutations set up a tumor context-specific liability for therapeutic intervention via DNMT1 inhibitors, which leads to innate immune signaling mediated by sensing of derepressed retrotransposons and accompanied by enhanced cytotoxicity. See related commentary by Guil and Esteller, p. 2020. This article is highlighted in the In This Issue feature, p. 2007.
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Affiliation(s)
- Amish J. Patel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah Warda
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesper L.V. Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rohan Misra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Miguel A. Miranda-Román
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mohini R. Pachai
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cindy J. Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dan Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Naitao Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gabriella Bayshtok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eve Fishinevich
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yinuo Meng
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Elissa W.P. Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juan Yan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Giff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa B. Pappalardi
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Michael T. McCabe
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Jonathan A. Fletcher
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charles M. Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Joseph M. Scandura
- Laboratory of Molecular Hematopoiesis, Hematology and Oncology, Weill Cornell Medicine, New York, New York
- Richard T. Silver MD Myeloproliferative Neoplasm Center, Weill Cornell Medicine, New York, New York
- Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob L. Glass
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Deyou Zheng
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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81
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Kim WR, Park EG, Lee HE, Park SJ, Huh JW, Kim JN, Kim HS. Hsa-miR-422a Originated from Short Interspersed Nuclear Element Increases ARID5B Expression by Collaborating with NF-E2. Mol Cells 2022; 45:465-478. [PMID: 35444070 PMCID: PMC9260135 DOI: 10.14348/molcells.2022.2158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 12/03/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate the expression of target messenger RNA (mRNA) complementary to the 3' untranslated region (UTR) at the post-transcriptional level. Hsa-miR-422a, which is commonly known as miRNA derived from transposable element (MDTE), was derived from short interspersed nuclear element (SINE). Through expression analysis, hsa-miR-422a was found to be highly expressed in both the small intestine and liver of crab-eating monkey. AT-Rich Interaction Domain 5 B (ARID5B) was selected as the target gene of hsa-miR-422a, which has two binding sites in both the exon and 3'UTR of ARID5B. To identify the interaction between hsa-miR-422a and ARID5B, a dual luciferase assay was conducted in HepG2 cell line. The luciferase activity of cells treated with the hsa-miR-422a mimic was upregulated and inversely downregulated when both the hsa-miR-422a mimic and inhibitor were administered. Nuclear factor erythroid-2 (NF-E2) was selected as the core transcription factor (TF) via feed forward loop analysis. The luciferase expression was downregulated when both the hsa-miR-422a mimic and siRNA of NF-E2 were treated, compared to the treatment of the hsa-miR-422a mimic alone. The present study suggests that hsa-miR-422a derived from SINE could bind to the exon region as well as the 3'UTR of ARID5B. Additionally, hsa-miR-422a was found to share binding sites in ARID5Bwith several TFs, including NF-E2. The hsa-miR-422a might thus interact with TF to regulate the expression of ARID5B, as demonstrated experimentally. Altogether, hsa-miR-422a acts as a super enhancer miRNA of ARID5Bby collaborating with TF and NF-E2.
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Affiliation(s)
- Woo Ryung Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28199, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28199, Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju 28199, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong Nam Kim
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
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82
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Huang C, Yi H, Zhou Y, Zhang Q, Yao X. Pan-Cancer Analysis Reveals SH3TC2 as an Oncogene for Colorectal Cancer and Promotes Tumorigenesis via the MAPK Pathway. Cancers (Basel) 2022; 14:3735. [PMID: 35954399 PMCID: PMC9367385 DOI: 10.3390/cancers14153735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 12/11/2022] Open
Abstract
SH3 domain and tetrapeptide repeat 2 (SH3TC2) is a protein-encoding gene and has previously been described as a critical signaling hub for neurological disorders. Although increasing evidence supports a vital role of SH3TC2 in the tumorigenesis of various kinds of cancer, no systematic analysis of SH3TC2 is available. The function and mechanism of SH3TC2 in other cancers remain unknown. Thus, this study aimed to analyze SH3TC2 in various kinds of cancer to find its tumorigenic role in one or more specific cancers. In the current study, we analyzed the expression level and prognostic value of SH3TC2 in different tumors in the TCGA-GTEx pan-cancer dataset. Subsequently, the prognostic role and mechanism of SH3TC2 in colorectal cancer (CRC) were further explored via clinical samples and in vitro and in vivo experiments. We observed differential expression of SH3TC2 in colon adenocarcinoma (COAD), acute myeloid leukemia (LAML), READ (rectum adenocarcinoma), SKCM (skin cutaneous melanoma), and TGCT (testicular germ cell tumors). Subsequently, SH3TC2 showed a significant effect on the clinical stage and prognostic value in CRC, LAML, and SKCM. Moreover, we found in the TCGA database and seven GEO datasets that SH3TC2 was significantly highly expressed in tumor tissue. Through enrichment analysis of SH3TC2 and its co-expressed genes, we found that SH3TC2 may play a role in the MAPK signaling pathway. Correlation analysis indicated that SH3TC2 was significantly associated with multiple key factors in the MAPK signaling pathway. Additionally, higher expression of SH3TC2 was found in tumor tissue in our cohort including 40 CRC patients. Overexpression of SH3TC2 may imply poor prognosis. Knockdown of SH3TC2 significantly inhibited tumor invasion, migration, and proliferation. More importantly, knockdown of SH3TC2 inhibited tumor growth in a CRC mouse model. The study preliminarily conducted a pan-cancer study of SH3TC2 and further explored the mechanism of SH3TC2 in CRC. Our research revealed that higher expression of SH3TC2 may promote CRC progression and invasion via the MAPK signaling pathway.
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Affiliation(s)
- Chengzhi Huang
- School of Medicine, South China University of Technology, Guangzhou 510006, China;
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; (H.Y.); (Y.Z.)
- Department of General Surgery, Guangdong Provincial People’s Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou 341000, China
| | - Hui Yi
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; (H.Y.); (Y.Z.)
- Department of General Surgery, Guangdong Provincial People’s Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou 341000, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Department of Pharmacology, The First People’s Hospital of Zhaoqing, Zhaoqing 526000, China
| | - Yue Zhou
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; (H.Y.); (Y.Z.)
- Department of General Surgery, Guangdong Provincial People’s Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou 341000, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Qing Zhang
- Department of General Surgery, Guangdong Provincial People’s Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou 341000, China
- Department of Gastrointestinal and Anorectal Surgery, The First People’s Hospital of Zhaoqing, Zhaoqing 526000, China
| | - Xueqing Yao
- School of Medicine, South China University of Technology, Guangzhou 510006, China;
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; (H.Y.); (Y.Z.)
- Department of General Surgery, Guangdong Provincial People’s Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou 341000, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
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83
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Processed pseudogene insertion in GLB1 causes Morquio B disease by altering intronic splicing regulatory landscape. NPJ Genom Med 2022; 7:44. [PMID: 35882863 PMCID: PMC9325892 DOI: 10.1038/s41525-022-00315-y] [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: 04/05/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022] Open
Abstract
Morquio B disease (MBD) is an ultra-rare lysosomal storage disease, which represents the relatively mild form of GLB1-associated disorders. In this article, we present the unique case of “pure” MBD associated with an insertion of the mobile genetic element from the class of retrotransposons. Using whole-genome sequencing (WGS), we identified an integration of the processed pseudogene NPM1 deep in the intron 5 of GLB1. The patient’s mRNA analysis and the detailed functional analysis revealed the underlying molecular genetic mechanism of pathogenesis, which is an alteration of the GLB1 normal splicing. By co-expression of minigenes and antisense splice-modulating oligonucleotides (ASMOs), we demonstrated that pseudogene-derived splicing regulatory motifs contributed to an activation of the cryptic exon located 36 bp upstream of the integration site. Blocking the cryptic exon with ASMOs incorporated in the modified U7 small nuclear RNA (modU7snRNA) almost completely restored the wild-type splicing in the model cell line, that could be further extended toward the personalized genetic therapy. To our knowledge, this is the second reported case of the processed pseudogene insertion for monogenic disorders. Our data emphasizes the unique role of WGS in identification of such rare and probably underrepresented in literature types of disease-associated genetic variants.
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84
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Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet 2022; 54:1238-1247. [PMID: 35864192 PMCID: PMC9355880 DOI: 10.1038/s41588-022-01132-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 05/26/2022] [Indexed: 12/20/2022]
Abstract
Most endogenous retroviruses (ERVs) in mammals are incapable of retrotransposition; therefore, why ERV derepression is associated with lethality during early development has been a mystery. Here, we report that rapid and selective degradation of the heterochromatin adapter protein TRIM28 triggers dissociation of transcriptional condensates from loci encoding super-enhancer (SE)-driven pluripotency genes and their association with transcribed ERV loci in murine embryonic stem cells. Knockdown of ERV RNAs or forced expression of SE-enriched transcription factors rescued condensate localization at SEs in TRIM28-degraded cells. In a biochemical reconstitution system, ERV RNA facilitated partitioning of RNA polymerase II and the Mediator coactivator into phase-separated droplets. In TRIM28 knockout mouse embryos, single-cell RNA-seq analysis revealed specific depletion of pluripotent lineages. We propose that coding and noncoding nascent RNAs, including those produced by retrotransposons, may facilitate ‘hijacking’ of transcriptional condensates in various developmental and disease contexts. TRIM28 depletion in embryonic stem cells disconnects transcriptional condensates from super-enhancers, which is rescued by knockdown of endogenous retroviruses.
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85
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Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:7802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
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86
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Chiang VSC, DeRosa H, Park JH, Hunter RG. The Role of Transposable Elements in Sexual Development. Front Behav Neurosci 2022; 16:923732. [PMID: 35874645 PMCID: PMC9301316 DOI: 10.3389/fnbeh.2022.923732] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as "junk" or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs' role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.
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Affiliation(s)
| | | | | | - Richard G. Hunter
- College of Liberal Arts, Department of Psychology, Developmental and Brain Sciences Program, University of Massachusetts Boston, Boston, MA, United States
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87
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Fueyo R, Judd J, Feschotte C, Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat Rev Mol Cell Biol 2022; 23:481-497. [PMID: 35228718 PMCID: PMC10470143 DOI: 10.1038/s41580-022-00457-y] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
Abstract
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and engineering have facilitated systematic interrogation of the regulatory activities of TEs. In this Review, we discuss diverse mechanisms by which TEs contribute to transcription regulation. Notably, TEs can donate enhancer and promoter sequences that influence the expression of host genes, modify 3D chromatin architecture and give rise to novel regulatory genes, including non-coding RNAs and transcription factors. We discuss how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development. By virtue of their repetitive and interspersed nature, TEs offer unique opportunities to dissect the effects of mutation and genomic context on the function and evolution of cis-regulatory elements. We argue that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution.
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Affiliation(s)
- Raquel Fueyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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88
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Li W, Pandya D, Pasternack N, Garcia-Montojo M, Henderson L, Kozak CA, Nath A. Retroviral Elements in Pathophysiology and as Therapeutic Targets for Amyotrophic Lateral Sclerosis. Neurotherapeutics 2022; 19:1085-1101. [PMID: 35415778 PMCID: PMC9587200 DOI: 10.1007/s13311-022-01233-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 10/18/2022] Open
Abstract
The study of the role of retroviruses in amyotrophic lateral sclerosis (ALS) dates back to the 1960s shortly after transposable elements themselves were first discovered. It was quickly realized that in wild mice both horizontal and vertical transmissions of retroviral elements were key to the development of an ALS-like syndrome leading to the postulate that endogenous retroviruses (ERVs) contribute significantly to the pathogenicity of this disease. Subsequent studies identified retroviral reverse transcriptase activity in brains of individuals with ALS from Guam. However, except for a single study from the former Soviet Union, ALS could not be transmitted to rhesus macaques. The discovery of an ALS-like syndrome in human immunodeficiency virus (HIV) and human T cell leukemia virus infected individuals led to renewed interest in the field and reverse transcriptase activity was found in the blood and cerebrospinal fluid of individuals with sporadic ALS. However, exogenous retroviruses could not be found in individuals with ALS which further reinforced the possibility of involvement of a human ERV (HERV). The first demonstration of the involvement of a HERV was the discovery of the activation of human endogenous retrovirus-K subtype HML-2 in the brains of individuals with ALS. The envelope protein of HML-2 is neurotoxic and transgenic animals expressing the envelope protein develop an ALS-like syndrome. Activation of HML-2 occurs in the context of generalized transposable element activation and is not specific for ALS. Individuals with HIV-associated ALS show a remarkable response to antiretroviral therapy; however, antiretroviral trials in ALS down-regulate HML-2 without ameliorating the disease. This highlights the need for specific drugs to be developed against HML-2 as a novel therapeutic target for ALS. Other approaches might include antisense oligonucleotides, shRNA targeted against the envelope gene or antibodies that can target the extracellular envelope protein. Future clinical trials in ALS should consider combination therapies to control these ERVs.
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Affiliation(s)
- Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Darshan Pandya
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Lisa Henderson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Christine A Kozak
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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de la Morena-Barrio B, Stephens J, de la Morena-Barrio ME, Stefanucci L, Padilla J, Miñano A, Gleadall N, García JL, López-Fernández MF, Morange PE, Puurunen M, Undas A, Vidal F, Raymond FL, Vicente V, Ouwehand WH, Corral J, Sanchis-Juan A. Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency. Thromb Haemost 2022; 122:1369-1378. [PMID: 35764313 PMCID: PMC9393088 DOI: 10.1055/s-0042-1749345] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The identification of inherited antithrombin deficiency (ATD) is critical to prevent potentially life-threatening thrombotic events. Causal variants in SERPINC1 are identified for up to 70% of cases, the majority being single-nucleotide variants and indels. The detection and characterization of structural variants (SVs) in ATD remain challenging due to the high number of repetitive elements in SERPINC1. Here, we performed long-read whole-genome sequencing on 10 familial and 9 singleton cases with type I ATD proven by functional and antigen assays, who were selected from a cohort of 340 patients with this rare disorder because genetic analyses were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs. This approach resolved, independently of its size or type, all eight SVs detected by multiple ligation-dependent probe amplification, and identified for the first time a complex rearrangement previously misclassified as a deletion. Remarkably, we identified the mechanism explaining ATD in 2 out of 11 cases with previous unknown defect: the insertion of a novel 2.4 kb SINE-VNTR-Alu retroelement, which was characterized by de novo assembly and verified by specific polymerase chain reaction amplification and sequencing in the probands and affected relatives. The nucleotide-level resolution achieved for all SVs allowed breakpoint analysis, which revealed repetitive elements and microhomologies supporting a common replication-based mechanism for all the SVs. Our study underscores the utility of long-read sequencing technology as a complementary method to identify, characterize, and unveil the molecular mechanism of disease-causing SVs involved in ATD, and enlarges the catalogue of genetic disorders caused by retrotransposon insertions.
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Affiliation(s)
- Belén de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Murcia, Murcia, Spain
| | - Jonathan Stephens
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Murcia, Murcia, Spain
| | - Luca Stefanucci
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge, United Kingdom,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - José Padilla
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Murcia, Murcia, Spain
| | - Antonia Miñano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Murcia, Murcia, Spain
| | - Nicholas Gleadall
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Juan Luis García
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | | | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France,C2VN, INRAE, INSERM, Aix-Marseille Université, Marseille, France
| | - Marja Puurunen
- The Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, Massachusetts, United States
| | - Anetta Undas
- Department of Experimental Cardiac Surgery, Anesthesiology and Cardiology, Institute of Cardiology, Jagiellonian University Medical College and John Paul II Hospital, Kraków, Poland
| | - Francisco Vidal
- Banc de Sang i Teixits, Barcelona, Spain,Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain,CIBER de Enfermedades Cardiovasculares, Madrid, Spain
| | - Frances Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom,Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Vicente Vicente
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Murcia, Murcia, Spain
| | - Willem H. Ouwehand
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Murcia, Murcia, Spain,Javier Corral University of Murcia, Centro Regional de HemodonaciónCalle Ronda de Garay s/n, Murcia 30003Spain
| | - Alba Sanchis-Juan
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom,Address for correspondence Alba Sanchis-Juan University of Cambridge, Department of Haematology, NHS Blood and Transplant CentreCambridge, CB2 0PTUnited Kingdom
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Tao J, Wang Q, Mendez-Dorantes C, Burns KH, Chiarle R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat Commun 2022; 13:3685. [PMID: 35760782 PMCID: PMC9237045 DOI: 10.1038/s41467-022-31322-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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91
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Abstract
Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the major open problems that need to be solved, and by discussing these challenges provide a primer to the field. We cover general issues such as population structure, epistasis and gene-environment interactions, data-related issues such as ancestry diversity and rare genetic variants, and specific challenges related to heritability estimates, genetic association studies, and polygenic risk scores. We emphasize the interconnectedness of these problems and suggest promising avenues to address them.
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Affiliation(s)
- Nadav Brandes
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Omer Weissbrod
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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92
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Ma G, Babarinde IA, Zhou X, Hutchins AP. Transposable Elements in Pluripotent Stem Cells and Human Disease. Front Genet 2022; 13:902541. [PMID: 35719395 PMCID: PMC9201960 DOI: 10.3389/fgene.2022.902541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can randomly integrate into other genomic sites. They have successfully replicated and now occupy around 40% of the total DNA sequence in humans. TEs in the genome have a complex relationship with the host cell, being both potentially deleterious and advantageous at the same time. Only a tiny minority of TEs are still capable of transposition, yet their fossilized sequence fragments are thought to be involved in various molecular processes, such as gene transcriptional activity, RNA stability and subcellular localization, and chromosomal architecture. TEs have also been implicated in biological processes, although it is often hard to reveal cause from correlation due to formidable technical issues in analyzing TEs. In this review, we compare and contrast two views of TE activity: one in the pluripotent state, where TEs are broadly beneficial, or at least mechanistically useful, and a second state in human disease, where TEs are uniformly considered harmful.
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93
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Abstract
Adaptive immunity in jawed vertebrates relies on the assembly of antigen receptor genes by the recombination activating gene 1 (RAG1)-RAG2 (collectively RAG) recombinase in a reaction known as V(D)J recombination. Extensive biochemical and structural evidence indicates that RAG and V(D)J recombination evolved from the components of a RAG-like (RAGL) transposable element through a process known as transposon molecular domestication. This Review describes recent advances in our understanding of the functional and structural transitions that occurred during RAG evolution. We use the structures of RAG and RAGL enzymes to trace the evolutionary adaptations that yielded a RAG recombinase with exquisitely regulated cleavage activity and a multilayered array of mechanisms to suppress transposition. We describe how changes in modes of DNA binding, alterations in the dynamics of protein-DNA complexes, single amino acid mutations and a modular design likely enabled RAG family enzymes to survive and spread in the genomes of eukaryotes. These advances highlight the insight that can be gained from viewing evolution of vertebrate immunity through the lens of comparative genome analyses coupled with structural biology and biochemistry.
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94
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Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data. BIOLOGY 2022; 11:biology11060826. [PMID: 35741347 PMCID: PMC9220773 DOI: 10.3390/biology11060826] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 02/08/2023]
Abstract
Simple Summary Transposable elements (TEs) are repetitive sequences comprising more than one third of the human genome with the original ability to change their location within the genome. Owing to their repetitive nature, the quantification of TEs results often challenging. RNA-seq is a useful tool for genome-wide TEs quantification, nevertheless it also presents technical issues, including low reads mappability and erroneous quantification derived from the transcription of TEs fragments embedded in canonical transcripts. Fragments derived from TEs are found within the introns of most genes, which led to the hypothesis that intron retention (IR) can affect the unbiased quantification of TEs expression. Performing meta-analysis of public RNA-seq datasets, here we observe that IR can indeed impact the quantification of TEs by increasing the number of reads mapped on intronic TE copies. Our work highlights a correlation between IR and TEs expression measurement by RNA-seq that should be taken into account to achieve reliable TEs quantification, especially in samples characterized by extensive IR, because differential IR might be confused with differential TEs expression. Abstract Transposable elements (TEs), also known as “jumping genes”, are repetitive sequences with the capability of changing their location within the genome. They are key players in many different biological processes in health and disease. Therefore, a reliable quantification of their expression as transcriptional units is crucial to distinguish between their independent expression and the transcription of their sequences as part of canonical transcripts. TEs quantification faces difficulties of different types, the most important one being low reads mappability due to their repetitive nature preventing an unambiguous mapping of reads originating from their sequences. A large fraction of TEs fragments localizes within introns, which led to the hypothesis that intron retention (IR) can be an additional source of bias, potentially affecting accurate TEs quantification. IR occurs when introns, normally removed from the mature transcript by the splicing machinery, are maintained in mature transcripts. IR is a widespread mechanism affecting many different genes with cell type-specific patterns. We hypothesized that, in an RNA-seq experiment, reads derived from retained introns can introduce a bias in the detection of overlapping, independent TEs RNA expression. In this study we performed meta-analysis using public RNA-seq data from lymphoblastoid cell lines and show that IR can impact TEs quantification using established tools with default parameters. Reads mapped on intronic TEs were indeed associated to the expression of TEs and influence their correct quantification as independent transcriptional units. We confirmed these results using additional independent datasets, demonstrating that this bias does not appear in samples where IR is not present and that differential TEs expression does not impact on IR quantification. We concluded that IR causes the over-quantification of intronic TEs and differential IR might be confused with differential TEs expression. Our results should be taken into account for a correct quantification of TEs expression from RNA-seq data, especially in samples in which IR is abundant.
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95
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Abstract
One of the most fundamental questions in developmental biology is how one fertilized cell can give rise to a fully mature organism and how gene regulation governs this process. Precise spatiotemporal gene expression is required for development and is believed to be achieved through a complex interplay of sequence-specific information, epigenetic modifications, trans-acting factors, and chromatin folding. Here we review the role of chromatin folding during development, the mechanisms governing 3D genome organization, and how it is established in the embryo. Furthermore, we discuss recent advances and debated questions regarding the contribution of the 3D genome to gene regulation during organogenesis. Finally, we describe the mechanisms that can reshape the 3D genome, including disease-causing structural variations and the emerging view that transposable elements contribute to chromatin organization.
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Affiliation(s)
- Juliane Glaser
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
- Charité - Universitätsmedizin Berlin, BCRT - Berlin Institute of Health Center for Regenerative Therapies, 10178 Berlin, Germany
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96
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Pinto A, Cunha C, Chaves R, Butchbach MER, Adega F. Comprehensive In Silico Analysis of Retrotransposon Insertions within the Survival Motor Neuron Genes Involved in Spinal Muscular Atrophy. BIOLOGY 2022; 11:824. [PMID: 35741345 PMCID: PMC9219815 DOI: 10.3390/biology11060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are interspersed repetitive and mobile DNA sequences within the genome. Better tools for evaluating TE-derived sequences have provided insights into the contribution of TEs to human development and disease. Spinal muscular atrophy (SMA) is an autosomal recessive motor neuron disease that is caused by deletions or mutations in the Survival Motor Neuron 1 (SMN1) gene but retention of its nearly perfect orthologue SMN2. Both genes are highly enriched in TEs. To establish a link between TEs and SMA, we conducted a comprehensive, in silico analysis of TE insertions within the SMN1/2 loci of SMA, carrier and healthy genomes. We found an Alu insertion in the promoter region and one L1 element in the 3'UTR that may play an important role in alternative promoter as well as in alternative transcriptional termination. Additionally, several intronic Alu repeats may influence alternative splicing via RNA circularization and causes the presence of new alternative exons. These Alu repeats present throughout the genes are also prone to recombination events that could lead to SMN1 exons deletions and, ultimately, SMA. TE characterization of the SMA genomic region could provide for a better understanding of the implications of TEs on human disease and genomic evolution.
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Affiliation(s)
- Albano Pinto
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Catarina Cunha
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Matthew E. R. Butchbach
- Division of Neurology, Nemours Children’s Hospital Delaware, Wilmington, DE 19803, USA;
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
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97
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Gao D, Caspersen AM, Hu G, Bockelman HE, Chen X. A Novel Mutator-Like Transposable Elements With Unusual Structure and Recent Transpositions in Barley ( Hordeum vulgare). FRONTIERS IN PLANT SCIENCE 2022; 13:904619. [PMID: 35677233 PMCID: PMC9168764 DOI: 10.3389/fpls.2022.904619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Mutator-like transposable elements (MULEs) represent a unique superfamily of DNA transposons as they can capture host genes and cause higher frequency of mutations in some eukaryotes. Despite their essential roles in plant evolution and functional genomics, MULEs are not fully understood yet in many important crops including barley (Hordeum vulgare). In this study, we analyzed the barley genome and identified a new mutator transposon Hvu_Abermu. This transposon is present at extremely high copy number in barley and shows unusual structure as it contains three open reading frames (ORFs) including one ORF (ORF1) encoding mutator transposase protein and one ORF (ORFR) showing opposite transcriptional orientation. We identified homologous sequences of Hvu_Abermu in both monocots and dicots and grouped them into a large mutator family named Abermu. Abermu transposons from different species share significant sequence identity, but they exhibit distinct sequence structures. Unlike the transposase proteins which are highly conserved between Abermu transposons from different organisms, the ORFR-encoded proteins are quite different from distant species. Phylogenetic analysis indicated that Abermu transposons shared closer evolutionary relationships with the maize MuDR transposon than other reported MULEs. We also found phylogenetic incongruence for the Abermu transposons identified in rice and its wild species implying the possibility of horizontal transfer of transposon. Further comparison indicated that over 200 barley genes contain Abermu-related sequences. We analyzed the barley pan genomes and detected polymorphic Hvu_Abermu transposons between the sequenced 23 wild and cultivated barley genomes. Our efforts identified a novel mutator transposon and revealed its recent transposition activity, which may help to develop genetic tools for barley and other crops.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Ann M. Caspersen
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Gongshe Hu
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Harold E. Bockelman
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, United States
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98
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Yandım C, Karakülah G. Repeat expression is linked to patient survival and exhibits single nucleotide variation in pancreatic cancer revealing LTR70:r.879A>G. Gene X 2022; 822:146344. [PMID: 35183687 DOI: 10.1016/j.gene.2022.146344] [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: 11/17/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/04/2022] Open
Abstract
Despite an overwhelming number of cancer literature reporting the links between patient survival and the expression levels of genes or mutations/single nucleotide variations (SNVs) on them, there is only limited information on repeat elements, which make at least half the human genome. Here, we analysed RNA-seq data obtained from primary pancreatic cancer tissues of 51 patients and revealed that two transposons, HERVI-int and X6A_LINE, showed an upregulation trend in the patients who lived shorter, along with 56 other potential repeats which were linked to survival. We also detected expressed single nucleotide variations (SNVs) on repeats, among which LTR70:r.879A>G stands out with the effect of its presence on this particular repeat's expression levels and a significant link to overall patient survival. Interestingly, the expression of LTR70:r.879A>G correlated with different cancer genes in comparison to its reference version highlighting the involvement of BRAF and Fumerate Hydratase with this expressed SNV. This is one of the first studies revealing possible links between repeat expression and survival in cancer and it warrants further research in this avenue.
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Affiliation(s)
- Cihangir Yandım
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330 Balçova, İzmir, Turkey; İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, 35340 İnciraltı, İzmir, Turkey
| | - Gökhan Karakülah
- İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, 35340 İnciraltı, İzmir, Turkey; İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 İnciraltı, İzmir, Turkey.
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99
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Lerat E. Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements. Front Genet 2022; 13:891194. [PMID: 35646069 PMCID: PMC9140218 DOI: 10.3389/fgene.2022.891194] [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: 03/07/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Transposable elements (TEs) are recognized for their great impact on the functioning and evolution of their host genomes. They are associated to various deleterious effects, which has led to the evolution of regulatory epigenetic mechanisms to control their activity. Despite these negative effects, TEs are also important actors in the evolution of genomes by promoting genetic diversity and new regulatory elements. Consequently, it is important to study the epigenetic modifications associated to TEs especially at a locus-specific level to determine their individual influence on gene functioning. To this aim, this short review presents the current bioinformatic tools to achieve this task.
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Affiliation(s)
- Emmanuelle Lerat
- Univ Lyon, Univ Lyon 1, CNRS, VetAgro Sup, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
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Kermi C, Lau L, Asadi Shahmirzadi A, Classon M. Disrupting Mechanisms that Regulate Genomic Repeat Elements to Combat Cancer and Drug Resistance. Front Cell Dev Biol 2022; 10:826461. [PMID: 35602594 PMCID: PMC9114874 DOI: 10.3389/fcell.2022.826461] [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: 11/30/2021] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Despite advancements in understanding cancer pathogenesis and the development of many effective therapeutic agents, resistance to drug treatment remains a widespread challenge that substantially limits curative outcomes. The historical focus on genetic evolution under drug “pressure” as a key driver of resistance has uncovered numerous mechanisms of therapeutic value, especially with respect to acquired resistance. However, recent discoveries have also revealed a potential role for an ancient evolutionary balance between endogenous “viral” elements in the human genome and diverse factors involved in their restriction in tumor evolution and drug resistance. It has long been appreciated that the stability of genomic repeats such as telomeres and centromeres affect tumor fitness, but recent findings suggest that de-regulation of other repetitive genome elements, including retrotransposons, might also be exploited as cancer therapy. This review aims to present an overview of these recent findings.
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