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Trost H, Lopezcolorado FW, Merkell A, Stark JM. Functions of PMS2 and MLH1 important for regulation of divergent repeat-mediated deletions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606388. [PMID: 39149360 PMCID: PMC11326157 DOI: 10.1101/2024.08.05.606388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Repeat-mediated deletions (RMDs) are a type of deletion rearrangement that utilizes two repetitive elements to bridge a DNA double-strand break (DSB) that leads to loss of the intervening sequence and one of the repeats. Sequence divergence between repeats causes RMD suppression and indeed this divergence must be resolved in the RMD products. The mismatch repair factor, MLH1, was shown to be critical for both RMD suppression and a polarity of sequence divergence resolution in RMDs. Here, we sought to study the interrelationship between these two aspects of RMD regulation (i.e., RMD suppression and polar divergence resolution), by examining several mutants of MLH1 and its binding partner PMS2. To begin with, we show that PMS2 is also critical for both RMD suppression and polar resolution of sequence divergence in RMD products. Then, with six mutants of the MLH1-PMS2 heterodimer, we found several different patterns: three mutants showed defects in both functions, one mutant showed loss of RMD suppression but not polar divergence resolution, whereas another mutant showed the opposite, and finally one mutant showed loss of RMD suppression but had a complex effect on polar divergence resolution. These findings indicate that RMD suppression vs. polar resolution of sequence divergence are distinct functions of MLH1-PMS2.
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Affiliation(s)
- Hannah Trost
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Felicia Wednesday Lopezcolorado
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Arianna Merkell
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Jeremy M. Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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2
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Mochizuki AY, Nagaraj CB, Depoorter D, Schieffer KM, Kim SY. Germline PTCH1: c.361_362insAlu alteration identified by comprehensive exome and RNA sequencing in a patient with Gorlin syndrome. Am J Med Genet A 2024:e63788. [PMID: 38864234 DOI: 10.1002/ajmg.a.63788] [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: 02/17/2024] [Revised: 03/15/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
Gorlin syndrome can be caused by pathogenic/likely pathogenic (P/LP) variants in the tumor suppressor gene PTCH1 (9q22.1-q31), which encodes the receptor for the sonic hedgehog (SHH) ligand. We present a 12-month-old boy clinically diagnosed with Gorlin syndrome who was found to have significantly delayed development, palmar pitting, palmar and plantar keratosis, short hands, frontal bossing, coarse face, hypertelorism, a bifid rib, misaligned and missing teeth, and SHH-activated medulloblastoma. Genetic testing, including a pediatric cancer panel and genome sequencing with peripheral blood, failed to identify any P/LP variants in PTCH1. Paired tumor/normal exome sequencing was performed, which identified a germline NM_000264.5 (PTCH1): c.361_362ins? alteration through manual review of sequencing reads. Clinical RNA sequencing further demonstrated an Alu insertion at this region (PTCH1: c.361_362insAlu), providing molecular confirmation of Gorlin syndrome. This finding exemplifies a unique mechanism for PTCH1 disruption in the germline and highlights the importance of comprehensive analysis, including manual review of DNA sequencing reads and the utility of RNA analysis to detect variant types which may not be identified by routine genetic screening techniques.
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Affiliation(s)
- Aaron Y Mochizuki
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Chinmayee B Nagaraj
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Division of Neurology and Rehabilitation Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Douglas Depoorter
- Institute for Genome Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- Institute for Genome Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pathology and Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Sun Young Kim
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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3
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Lee KH, Hwang HJ, Im YJ, Nam AR, Lee JW, Cho JY. New oncogenic functions of LINE1 retroelement as a ceRNA for tumor suppressive microRNA miR-126 on ENPP5. PLoS One 2023; 18:e0286814. [PMID: 37352273 PMCID: PMC10289412 DOI: 10.1371/journal.pone.0286814] [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: 01/30/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
Retroelements (REs) had been considered 'Junk' until the encyclopedia of DNA elements (ENCODE) project demonstrated that most genome is functional. Although the function of retroelements has been reported in diverse cancers including human breast cancer (HBC) and subtypes, only a few studies have suggested the putative functions of REs via their random genome integration. A canine mammary tumor (CMT) has been highlighted due to the similarities in molecular and pathophysiology with HBC. This study investigated the putative roles of REs common in both HBC and CMT. The human LINE and HERV-K sequences harbor many miRNAs responsive elements (MREs) for tumor-suppressive miRNA such as let-7. We also observed that various MREs are exist in the ERV and LINE highly expressed in the transcriptome data of CMT as well as HBC sets. MREs against miR-126 were highly expressed in both HBC and CMT while the levels of miR-126 were down-regulated. Oppositely, the expression of miR-126 target genes was significantly up-regulated in the cancers. Moreover, cancer patients with an increased level of miR-126 showed better overall survival. The expression of ENPP5, a putative miR-126 target gene, was downregulated by miR-126 mimic. Importantly, overexpression of LINE fragment significantly suppressed miR-126 function on the target gene expression. We propose the functional role of REs expression in tumorigenesis as competing endogenous RNAs (ceRNA) against tumor-suppressive miRNAs. This study provided pieces of evidence that LINE expression, even partial and fragmented, have a regulatory function in ENPP5 gene expression via the competition with miR-126.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Hyeon-Ji Hwang
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Yeo-Jin Im
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - A-Reum Nam
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
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4
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Galbraith JD, Hayward A. The influence of transposable elements on animal colouration. Trends Genet 2023:S0168-9525(23)00091-4. [PMID: 37183153 DOI: 10.1016/j.tig.2023.04.005] [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: 01/18/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/16/2023]
Abstract
Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transposition is mutagenic and TEs often contain host regulatory and protein coding sequences. We review cases where TEs influence animal colouration, reporting major patterns and outstanding questions. TE-induced colouration phenotypes typically arise via introduction of novel regulatory sequences and splice sites, affecting pigment cell development or pigment synthesis. We discuss if particular TE types may be more frequently involved in the evolution of colour variation in animals, given that examples involving long terminal repeat (LTR) elements appear to dominate. Currently, examples of TE-induced colouration phenotypes in animals mainly concern model and domesticated insect and mammal species. However, several influential recent examples, coupled with increases in genome sequencing, suggest cases reported from wild species will increase considerably.
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Affiliation(s)
- James D Galbraith
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
| | - Alexander Hayward
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
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Mosaddeghi P, Farahmandnejad M, Zarshenas MM. The role of transposable elements in aging and cancer. Biogerontology 2023:10.1007/s10522-023-10028-z. [PMID: 37017895 DOI: 10.1007/s10522-023-10028-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023]
Abstract
Transposable elements (TEs) constitute a large portion of the human genome. Various mechanisms at the transcription and post-transcription levels developed to suppress TE activity in healthy conditions. However, a growing body of evidence suggests that TE dysregulation is involved in various human diseases, including age-related diseases and cancer. In this review, we explained how sensing TEs by the immune system could induce innate immune responses, chronic inflammation, and following age-related diseases. We also noted that inflammageing and exogenous carcinogens could trigger the upregulation of TEs in precancerous cells. Increased inflammation could enhance epigenetic plasticity and upregulation of early developmental TEs, which rewires the transcriptional networks and gift the survival advantage to the precancerous cells. In addition, upregulated TEs could induce genome instability, activation of oncogenes, or inhibition of tumor suppressors and consequent cancer initiation and progression. So, we suggest that TEs could be considered therapeutic targets in aging and cancer.
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Affiliation(s)
- Pouria Mosaddeghi
- Medicinal Plants Processing Research Center, School of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mitra Farahmandnejad
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Quality Control of Drug Products Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad M Zarshenas
- Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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6
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Burbage M, Rocañín-Arjó A, Baudon B, Arribas YA, Merlotti A, Rookhuizen DC, Heurtebise-Chrétien S, Ye M, Houy A, Burgdorf N, Suarez G, Gros M, Sadacca B, Carrascal M, Garmilla A, Bohec M, Baulande S, Lombard B, Loew D, Waterfall JJ, Stern MH, Goudot C, Amigorena S. Epigenetically controlled tumor antigens derived from splice junctions between exons and transposable elements. Sci Immunol 2023; 8:eabm6360. [PMID: 36735776 DOI: 10.1126/sciimmunol.abm6360] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Oncogenesis often implicates epigenetic alterations, including derepression of transposable elements (TEs) and defects in alternative splicing. Here, we explore the possibility that noncanonical splice junctions between exons and TEs represent a source of tumor-specific antigens. We show that mouse normal tissues and tumor cell lines express wide but distinct ranges of mRNA junctions between exons and TEs, some of which are tumor specific. Immunopeptidome analyses in tumor cell lines identified peptides derived from exon-TE splicing junctions associated to MHC-I molecules. Exon-TE junction-derived peptides were immunogenic in tumor-bearing mice. Both prophylactic and therapeutic vaccinations with junction-derived peptides delayed tumor growth in vivo. Inactivation of the TE-silencing histone 3-lysine 9 methyltransferase Setdb1 caused overexpression of new immunogenic junctions in tumor cells. Our results identify exon-TE splicing junctions as epigenetically controlled, immunogenic, and protective tumor antigens in mice, opening possibilities for tumor targeting and vaccination in patients with cancer.
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Affiliation(s)
- Marianne Burbage
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Ares Rocañín-Arjó
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Blandine Baudon
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Yago A Arribas
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Antonela Merlotti
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Derek C Rookhuizen
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | | | - Mengliang Ye
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Alexandre Houy
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Nina Burgdorf
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Guadalupe Suarez
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Marine Gros
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Andrea Garmilla
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Mylène Bohec
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Sylvain Baulande
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Joshua J Waterfall
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Marc-Henri Stern
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Christel Goudot
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
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7
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Zhao Y, Simon M, Seluanov A, Gorbunova V. DNA damage and repair in age-related inflammation. Nat Rev Immunol 2023; 23:75-89. [PMID: 35831609 PMCID: PMC10106081 DOI: 10.1038/s41577-022-00751-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2022] [Indexed: 02/07/2023]
Abstract
Genomic instability is an important driver of ageing. The accumulation of DNA damage is believed to contribute to ageing by inducing cell death, senescence and tissue dysfunction. However, emerging evidence shows that inflammation is another major consequence of DNA damage. Inflammation is a hallmark of ageing and the driver of multiple age-related diseases. Here, we review the evidence linking DNA damage, inflammation and ageing, highlighting how premature ageing syndromes are associated with inflammation. We discuss the mechanisms by which DNA damage induces inflammation, such as through activation of the cGAS-STING axis and NF-κB activation by ATM. The triggers for activation of these signalling cascades are the age-related accumulation of DNA damage, activation of transposons, cellular senescence and the accumulation of persistent R-loops. We also discuss how epigenetic changes triggered by DNA damage can lead to inflammation and ageing via redistribution of heterochromatin factors. Finally, we discuss potential interventions against age-related inflammation.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA.,Department of Physiology, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
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8
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Trost H, Merkell A, Lopezcolorado FW, Stark J. Resolution of sequence divergence for repeat-mediated deletions shows a polarity that is mediated by MLH1. Nucleic Acids Res 2023; 51:650-667. [PMID: 36620890 PMCID: PMC9881173 DOI: 10.1093/nar/gkac1240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Repeat-mediated deletions (RMDs) are a type of chromosomal rearrangement between two homologous sequences that causes loss of the sequence between the repeats, along with one of the repeats. Sequence divergence between repeats suppresses RMDs; the mechanisms of such suppression and of resolution of the sequence divergence remains poorly understood. We identified RMD regulators using a set of reporter assays in mouse cells that test two key parameters: repeat sequence divergence and the distances between one repeat and the initiating chromosomal break. We found that the mismatch repair factor MLH1 suppresses RMDs with sequence divergence in the same pathway as MSH2 and MSH6, and which is dependent on residues in MLH1 and its binding partner PMS2 that are important for nuclease activity. Additionally, we found that the resolution of sequence divergence in the RMD product has a specific polarity, where divergent bases that are proximal to the chromosomal break end are preferentially removed. Moreover, we found that the domain of MLH1 that forms part of the MLH1-PMS2 endonuclease is important for polarity of resolution of sequence divergence. We also identified distinctions between MLH1 versus TOP3α in regulation of RMDs. We suggest that MLH1 suppresses RMDs with sequence divergence, while also promoting directional resolution of sequence divergence in the RMD product.
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Affiliation(s)
- Hannah Trost
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Arianna Merkell
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- To whom correspondence should be addressed. Tel: +1 626 218-6346; Fax: +1 626 218 8892;
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9
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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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10
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Teresi SJ, Teresi MB, Edger PP. TE Density: a tool to investigate the biology of transposable elements. Mob DNA 2022; 13:11. [PMID: 35413944 PMCID: PMC9004194 DOI: 10.1186/s13100-022-00264-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE's potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs' ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly available computational methods that quantify the presence of TEs relative to genes. RESULTS Here, we have developed a tool to more easily quantify TE presence relative to genes through the use of only a gene and TE annotation, yielding a new metric we call TE Density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome. CONCLUSIONS Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture, comparative genomics, and the tremendous diversity present of the TE world. TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density .
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Affiliation(s)
- Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | | | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan, USA.
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11
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Pinter TB, Ervin CS, Deb A, Penner-Hahn JE, Pecoraro VL. Cu(I) Binding to Designed Proteins Reveals a Putative Copper Binding Site of the Human Line1 Retrotransposon Protein ORF1p. Inorg Chem 2022; 61:5084-5091. [PMID: 35286080 PMCID: PMC10754372 DOI: 10.1021/acs.inorgchem.2c00057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long interspersed nuclear elements-1 (L1) are autonomous retrotransposons that encode two proteins in different open reading frames (ORF1 and ORF2). The ORF1p, which may be an RNA binding and chaperone protein, contains a three-stranded coiled coil (3SCC) domain that facilitates the formation of the biologically active homotrimer. This 3SCC domain is composed of seven amino acid (heptad) repeats as found in native and designed peptides and a stammer that modifies the helical structure. Cysteine residues occur at three hydrophobic positions (2 a and 1 d sites) within this domain. We recently showed that the cysteine layers in ORF1p and model de novo designed peptides bind the toxic metalloid lead(II) with high affinities, a feature that had not been previously recognized. However, there is little understanding of how essential metal ions might interact with this metal binding domain. We have, therefore, investigated the copper(I) binding properties of analogous de novo designed 3SCCs that contain cysteine layers within the hydrophobic core. The results from UV-visible and X-ray absorption spectroscopy show that these designed peptides bind Cu(I) with high affinity in a pH-dependent manner. At pH 9, monomeric trigonal planar Cu(I)S3 centers are formed with 1 equiv of metal, while dinuclear centers form with a second equivalent of metal. At physiologic pH conditions, the dinuclear center forms cooperatively. These data suggest that ORF1p is capable of binding two copper ions to its tris(cysteine) layers. This has major implications for ORF1p coiled coil domain stability and dynamics, ultimately potentially impacting the resulting biological activity.
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Affiliation(s)
- Tyler B.J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- These authors contributed equally to this work
| | - Catherine S. Ervin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- These authors contributed equally to this work
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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12
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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13
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Urazbakhtin S, Smirnova A, Volakhava A, Zerkalenkova E, Salyutina M, Doubek M, Jelinkova H, Khudainazarova N, Volchkov E, Belyaeva L, Komech E, Pavlova S, Lebedev Y, Plevova K, Olshanskaya Y, Komkov A, Mamedov I. The Absence of Retroelement Activity Is Characteristic for Childhood Acute Leukemias and Adult Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:ijms23031756. [PMID: 35163677 PMCID: PMC8835895 DOI: 10.3390/ijms23031756] [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: 01/12/2022] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/06/2023] Open
Abstract
Retroelements (RE) have been proposed as important players in cancerogenesis. Different cancer types are characterized by a different level of tumor-specific RE insertions. In previous studies, small cohorts of hematological malignancies, such as acute myeloid leukemia, multiple myeloma, and chronic lymphocytic leukemia have been characterized by a low level of RE insertional activity. Acute lymphoblastic leukemia (ALL) in adults and childhood acute leukemias have not been studied in this context. We performed a search for new RE insertions (Alu and L1) in 44 childhood ALL, 14 childhood acute myeloid leukemia, and 14 adult ALL samples using a highly sensitive NGS-based approach. First, we evaluated the method sensitivity revealing the 1% detection threshold for the proportion of cells with specific RE insertion. Following this result, we did not identify new tumor-specific RE insertions in the tested cohort of acute leukemia samples at the established level of sensitivity. Additionally, we analyzed the transcription levels of active L1 copies and found them increased. Thus, the increased transcription of active L1 copies is not sufficient for overt elevation of L1 retrotranspositional activity in leukemia.
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Affiliation(s)
- Shamil Urazbakhtin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Anastasia Smirnova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Anastasiya Volakhava
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
| | - Elena Zerkalenkova
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Maria Salyutina
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Michael Doubek
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
- Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
| | - Nelly Khudainazarova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Egor Volchkov
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Laima Belyaeva
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Ekaterina Komech
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Sarka Pavlova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
| | - Yuri Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
- Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (S.U.); (A.S.); (M.S.); (N.K.); (E.K.); (Y.L.); (A.K.)
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; (A.V.); (M.D.); (S.P.); (K.P.)
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (E.Z.); (E.V.); (L.B.); (Y.O.)
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-910-4228-706
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14
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Zhu Y, Jing L, Li X, Zhou G, Zhang Y, Sang Y, Gao L, Liu S, Shi Z, Sun Z, Ge W, Zhou X. Decabromodiphenyl ether-induced PRKACA hypermethylation contributed to glycolipid metabolism disorder via regulating PKA/AMPK pathway in rat and L-02 cells. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 90:103808. [PMID: 35007761 DOI: 10.1016/j.etap.2022.103808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
BDE-209 is the most prevalent congener of polybrominated diphenyl ethers and has high bioaccumulation in humans and animals. BDE-209 has been reported to disrupt glycolipid metabolism, but the mechanisms are still unclear. In this study, we found that BDE-209 induced liver tissue injury and hepatotoxicity, increased the glucose and total cholesterol levels in the serum of rats, and increased glucose and triglyceride levels in L-02 cells. BDE-209 exposure changed the PKA, p-PKA, AMPK, p-AMPK, ACC, and FAS expression in rats' liver and L-02 cells. Moreover, BDE-209 induced PRKACA-1 hypermethylation in L-02 cells. AMPK activator (AICAR) inhibited the changes of p-AMPK, ACC, and FAS expression and elevation of glucose and triglyceride levels induced by BDE-209. DNA methylation inhibitor (5-Aza-CdR) reversed BDE-209 induced alters of PKA/AMPK/ACC/FAS signaling pathway. These results demonstrated that BDE-209 could disrupt the glycolipid metabolism by causing PRKACA-1 hypermethylation to regulate the PKA/AMPK signaling pathway in hepatocytes.
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Affiliation(s)
- Yupeng Zhu
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China; Haidian Maternal&Child Health Hospital, Health Care Department for Women, Beijing 100080, China
| | - Li Jing
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Xiangyang Li
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Guiqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Yue Zhang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Yujian Sang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Leqiang Gao
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Sitong Liu
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China
| | - Zhixiong Shi
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Zhiwei Sun
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China.
| | - Xianqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, 100069 Beijing, China.
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15
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Xu C, Li T, Lei J, Zhang Y, Zhou J, Hu B. The Autophagy Cargo Receptor SQSTM1 Inhibits Infectious Bursal Disease Virus Infection through Selective Autophagic Degradation of Double-Stranded Viral RNA. Viruses 2021; 13:v13122494. [PMID: 34960763 PMCID: PMC8704251 DOI: 10.3390/v13122494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Selective autophagy mediates the degradation of cytoplasmic cargos, such as damaged organelles, invading pathogens, and protein aggregates. However, whether it targets double-stranded RNA (dsRNA) of intracellular pathogens is still largely unknown. Here, we show that selective autophagy regulates the degradation of the infectious bursal disease virus (IBDV) dsRNA genome. The amount of dsRNA decreased greatly in cells that overexpressed the autophagy-required protein VPS34 or autophagy cargo receptor SQSTM1, while it increased significantly in SQSTM1 or VPS34 knockout cells or by treating wild-type cells with the autophagy inhibitor chloroquine or wortmannin. Confocal microscopy and structured illumination microscopy showed SQSTM1 colocalized with dsRNA during IBDV infection. A pull-down assay further confirmed the direct binding of SQSTM1 to dsRNA through amino acid sites R139 and K141. Overexpression of SQSTM1 inhibited the replication of IBDV, while knockout of SQSTM1 promoted IBDV replication. Therefore, our findings reveal the role of SQSTM1 in clearing viral dsRNA through selective autophagy, highlighting the antiviral role of autophagy in the removal of the viral genome.
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Affiliation(s)
- Chenyang Xu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
| | - Tongtong Li
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
| | - Jing Lei
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
| | - Yina Zhang
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (J.Z.)
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (J.Z.)
| | - Boli Hu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (J.Z.)
- Correspondence:
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16
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Abstract
In human cells, each rDNA unit consists of the ~13 kb long ribosomal part and ~30 kb long intergenic spacer (IGS). The ribosomal part, transcribed by RNA polymerase I (pol I), includes genes coding for 18S, 5.8S, and 28S RNAs of the ribosomal particles, as well as their four transcribed spacers. Being highly repetitive, intensively transcribed, and abundantly methylated, rDNA is a very fragile site of the genome, with high risk of instability leading to cancer. Multiple small mutations, considerable expansion or contraction of the rDNA locus, and abnormally enhanced pol I transcription are usual symptoms of transformation. Recently it was found that both IGS and the ribosomal part of the locus contain many functional/potentially functional regions producing non-coding RNAs, which participate in the pol I activity regulation, stress reactions, and development of the malignant phenotype. Thus, there are solid reasons to believe that rDNA locus plays crucial role in carcinogenesis. In this review we discuss the data concerning the human rDNA and its closely associated factors as both targets and drivers of the pathways essential for carcinogenesis. We also examine whether variability in the structure of the locus may be blamed for the malignant transformation. Additionally, we consider the prospects of therapy focused on the activity of rDNA.
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17
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Liao X, Hu K, Salhi A, Zou Y, Wang J, Gao X. msRepDB: a comprehensive repetitive sequence database of over 80 000 species. Nucleic Acids Res 2021; 50:D236-D245. [PMID: 34850956 PMCID: PMC8728181 DOI: 10.1093/nar/gkab1089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).
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Affiliation(s)
- Xingyu Liao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Kang Hu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Adil Salhi
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - You Zou
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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18
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Alekseeva L, Mironova N. Role of Cell-Free DNA and Deoxyribonucleases in Tumor Progression. Int J Mol Sci 2021; 22:12246. [PMID: 34830126 PMCID: PMC8625144 DOI: 10.3390/ijms222212246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.
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Affiliation(s)
| | - Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia;
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19
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Human Recombinant DNase I (Pulmozyme ®) Inhibits Lung Metastases in Murine Metastatic B16 Melanoma Model That Correlates with Restoration of the DNase Activity and the Decrease SINE/LINE and c-Myc Fragments in Blood Cell-Free DNA. Int J Mol Sci 2021; 22:ijms222112074. [PMID: 34769514 PMCID: PMC8585023 DOI: 10.3390/ijms222112074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022] Open
Abstract
Tumor-associated cell-free DNAs (cfDNA) play an important role in the promotion of metastases. Previous studies proved the high antimetastatic potential of bovine pancreatic DNase I and identified short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs)and fragments of oncogenes in cfDNA as the main molecular targets of enzyme in the bloodstream. Here, recombinant human DNase I (commercial name Pulmozyme®), which is used for the treatment of cystic fibrosis in humans, was repurposed for the inhibition of lung metastases in the B16 melanoma model in mice. We found that Pulmozyme® strongly reduced migration and induced apoptosis of B16 cells in vitro and effectively inhibited metastases in lungs and liver in vivo. Pulmozyme® was shown to be two times more effective when administered intranasally (i.n.) than bovine DNase I, but intramuscular (i.m.) administration forced it to exhibit as high an antimetastatic activity as bovine DNase I. Both DNases administered to mice either i.m. or i.n. enhanced the DNase activity of blood serum to the level of healthy animals, significantly decreased cfDNA concentrations, efficiently degraded SINE and LINE repeats and c-Myc fragments in the bloodstream and induced apoptosis and disintegration of neutrophil extracellular traps in metastatic foci; as a result, this manifested as the inhibition of metastases spread. Thus, Pulmozyme®, which is already an approved drug, can be recommended for use in the treatment of lung metastases.
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20
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Stow EC, Kaul T, deHaro DL, Dem MR, Beletsky AG, Morales ME, Du Q, LaRosa AJ, Yang H, Smither E, Baddoo M, Ungerleider N, Deininger P, Belancio VP. Organ-, sex- and age-dependent patterns of endogenous L1 mRNA expression at a single locus resolution. Nucleic Acids Res 2021; 49:5813-5831. [PMID: 34023901 PMCID: PMC8191783 DOI: 10.1093/nar/gkab369] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Expression of L1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability. We used a reported stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. This analysis determined that mRNA expression of L1 loci in rodents exhibits striking organ specificity with less than 0.8% of loci shared between organs of the same organism. This organ specificity in L1 mRNA expression is preserved in male and female mice and across age groups. We discovered notable differences in L1 mRNA expression between sexes with only 5% of expressed L1 loci shared between male and female mice. Moreover, we report that the levels of total L1 mRNA expression and the number and spectrum of expressed L1 loci fluctuate with age as independent variables, demonstrating different patterns in different organs and sexes. Overall, our comparisons between organs and sexes and across ages ranging from 2 to 22 months establish previously unforeseen dynamic changes in L1 mRNA expression in vivo. These findings establish the beginning of an atlas of endogenous L1 mRNA expression across a broad range of biological variables that will guide future studies.
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Affiliation(s)
- Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Dawn L deHaro
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Madeleine R Dem
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Anna G Beletsky
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Maria E Morales
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Qianhui Du
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Alexis J LaRosa
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Hanlin Yang
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Emily Smither
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
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21
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Wong JYY, Cawthon R, Dai Y, Vermeulen R, Bassig BA, Hu W, Duan H, Niu Y, Downward GS, Leng S, Ji BT, Fu W, Xu J, Meliefste K, Zhou B, Yang J, Ren D, Ye M, Jia X, Meng T, Bin P, Hosgood Iii HD, Silverman DT, Rothman N, Zheng Y, Lan Q. Elevated Alu retroelement copy number among workers exposed to diesel engine exhaust. Occup Environ Med 2021; 78:823-828. [PMID: 34039759 DOI: 10.1136/oemed-2021-107462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Millions of workers worldwide are exposed to diesel engine exhaust (DEE), a known genotoxic carcinogen. Alu retroelements are repetitive DNA sequences that can multiply and compromise genomic stability. There is some evidence linking altered Alu repeats to cancer and elevated mortality risks. However, whether Alu repeats are influenced by environmental pollutants is unexplored. In an occupational setting with high DEE exposure levels, we investigated associations with Alu repeat copy number. METHODS A cross-sectional study of 54 male DEE-exposed workers from an engine testing facility and a comparison group of 55 male unexposed controls was conducted in China. Personal air samples were assessed for elemental carbon, a DEE surrogate, using NIOSH Method 5040. Quantitative PCR (qPCR) was used to measure Alu repeat copy number relative to albumin (Alb) single-gene copy number in leucocyte DNA. The unitless Alu/Alb ratio reflects the average quantity of Alu repeats per cell. Linear regression models adjusted for age and smoking status were used to estimate relations between DEE-exposed workers versus unexposed controls, DEE tertiles (6.1-39.0, 39.1-54.5 and 54.6-107.7 µg/m3) and Alu/Alb ratio. RESULTS DEE-exposed workers had a higher average Alu/Alb ratio than the unexposed controls (p=0.03). Further, we found a positive exposure-response relationship (p=0.02). The Alu/Alb ratio was highest among workers exposed to the top tertile of DEE versus the unexposed controls (1.12±0.08 SD vs 1.06±0.07 SD, p=0.01). CONCLUSION Our findings suggest that DEE exposure may contribute to genomic instability. Further investigations of environmental pollutants, Alu copy number and carcinogenesis are warranted.
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Affiliation(s)
- Jason Y Y Wong
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Richard Cawthon
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Yufei Dai
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Bryan A Bassig
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Wei Hu
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Huawei Duan
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yong Niu
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - George S Downward
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Shuguang Leng
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Bu-Tian Ji
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Wei Fu
- Chaoyang Center for Disease Control and Prevention, Chaoyang, Liaoning, China
| | - Jun Xu
- Hong Kong University, Hong Kong, China
| | - Kees Meliefste
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Baosen Zhou
- China Medical University, Shenyang, Liaoning, China
| | - Jufang Yang
- Chaoyang Center for Disease Control and Prevention, Chaoyang, Liaoning, China
| | - Dianzhi Ren
- Chaoyang Center for Disease Control and Prevention, Chaoyang, Liaoning, China
| | - Meng Ye
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaowei Jia
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tao Meng
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping Bin
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - H Dean Hosgood Iii
- Division of Epidemiology, Albert Einstein College of Medicine, Yeshiva University, New York, New York, USA
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Yuxin Zheng
- National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing Lan
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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22
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Morales ME, Kaul T, Walker J, Everett C, White T, Deininger P. Altered DNA repair creates novel Alu/Alu repeat-mediated deletions. Hum Mutat 2021; 42:600-613. [PMID: 33675284 PMCID: PMC8068675 DOI: 10.1002/humu.24193] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/25/2021] [Accepted: 02/24/2021] [Indexed: 12/21/2022]
Abstract
Alu elements are the most abundant source of nonallelic homology that influences genetic instability in the human genome. When there is a DNA double-stranded break, the Alu element's high copy number, moderate length and distance and mismatch between elements uniquely influence recombination processes. We utilize a reporter-gene assay to show the complex influence of Alu mismatches on Alu-related repeat-mediated deletions (RMDs). The Alu/Alu heteroduplex intermediate can result in a nonallelic homologous recombination (HR). Alternatively, the heteroduplex can result in various DNA breaks around the Alu elements caused by competing nucleases. These breaks can undergo Alt-nonhomologous end joining to cause deletions focused around the Alu elements. Formation of these heteroduplex intermediates is largely RAD52 dependent. Cells with low ERCC1 levels utilize more of these alternatives resolutions, while cells with MSH2 defects tend to have more RMDs with a specific increase in the HR events. Therefore, Alu elements are expected to create different forms of deletions in various cancers depending on a number of these DNA repair defects.
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Affiliation(s)
- Maria E Morales
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA
| | - JaNiece Walker
- Department of Biology, Xavier University, New Orleans, Louisiana, USA
| | - Chelsea Everett
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA
| | - Travis White
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA.,Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, USA.,Department of Epidemiology, Tulane University, New Orleans, Louisiana, USA
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23
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24
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Ishak CA, De Carvalho DD. Reactivation of Endogenous Retroelements in Cancer Development and Therapy. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033525] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Domesticated retroelements contribute extensively as regulatory elements within host gene networks. Upon germline integration, retroelement mobilization is restricted through epigenetic silencing, mutational degradation, and innate immune defenses described as the viral mimicry response. Recent discoveries reveal how early events in tumorigenesis reactivate retroelements to facilitate onco-exaptation, replication stress, retrotransposition, mitotic errors, and sterile inflammation, which collectively disrupt genome integrity. The characterization of altered epigenetic homeostasis at retroelements in cancer cells also reveals new epigenetic targets whose inactivation can bolster responses to cancer therapies. Recent discoveries reviewed here frame reactivated retroelements as both drivers of tumorigenesis and therapy responses, where their reactivation by emerging epigenetic therapies can potentiate immune checkpoint blockade, cancer vaccines, and other standard therapies.
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Affiliation(s)
- Charles A. Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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25
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Ho V, Chung L, Singh A, Lea V, Abubakar A, Lim SH, Chua W, Ng W, Lee M, Roberts TL, de Souza P, Lee CS. Aberrant Expression of RAD52, Its Prognostic Impact in Rectal Cancer and Association with Poor Survival of Patients. Int J Mol Sci 2020; 21:ijms21051768. [PMID: 32143539 PMCID: PMC7084626 DOI: 10.3390/ijms21051768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/29/2020] [Accepted: 03/01/2020] [Indexed: 12/18/2022] Open
Abstract
The DNA damage response enables cells to survive and maintain genome integrity. RAD52 is a DNA-binding protein involved in the homologous recombination in DNA repair, and is important for the maintenance of tumour genome integrity. We investigated possible correlations between RAD52 expression and cancer survival and response to preoperative radiotherapy. RAD52 expression was examined in tumour samples from 179 patients who underwent surgery for rectal cancer, including a sub-cohort of 40 patients who were treated with neoadjuvant therapy. A high score for RAD52 expression in the tumour centre was significantly associated with worse disease-free survival (DFS; p = 0.045). In contrast, reduced RAD52 expression in tumour centre samples from patients treated with neoadjuvant therapy (n = 40) significantly correlated with poor DFS (p = 0.025) and overall survival (OS; p = 0.048). Our results suggested that RAD52 may have clinical value as a prognostic marker of tumour response to neoadjuvant radiation and both disease-free status and overall survival in patients with rectal cancer.
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Affiliation(s)
- Vincent Ho
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Correspondence: ; Tel.: +61-2-4620-3845; Fax: +61-2-4520-3116
| | - Liping Chung
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
| | - Amandeep Singh
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia; (A.S.); (V.L.)
| | - Vivienne Lea
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia; (A.S.); (V.L.)
| | - Askar Abubakar
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
| | - Stephanie H. Lim
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- Macarthur Cancer Therapy Centre, Campbelltown Hospital, NSW 2560, Australia
- Discipline of Medical Oncology, School of Medicine, Western Sydney University, Liverpool, NSW 2170, Australia
| | - Wei Chua
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- South Western Sydney Clinical School, University of New South Wales, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Weng Ng
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Mark Lee
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Tara L. Roberts
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- South Western Sydney Clinical School, University of New South Wales, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Paul de Souza
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Discipline of Medical Oncology, School of Medicine, Western Sydney University, Liverpool, NSW 2170, Australia
- Department of Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
| | - Cheok Soon Lee
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (L.C.); (A.A.); (T.L.R.); (P.d.S.); (C.S.L.)
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.H.L.); (W.C.)
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia; (A.S.); (V.L.)
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Discipline of Pathology, School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
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26
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Alekseeva LA, Sen'kova AV, Zenkova MA, Mironova NL. Targeting Circulating SINEs and LINEs with DNase I Provides Metastases Inhibition in Experimental Tumor Models. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:50-61. [PMID: 32146418 PMCID: PMC7058713 DOI: 10.1016/j.omtn.2020.01.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 12/16/2019] [Accepted: 01/23/2020] [Indexed: 12/22/2022]
Abstract
Tumor-associated cell-free DNAs (cfDNAs) are found to play some important roles at different stages of tumor progression; they are involved in the transformation of normal cells and contribute to tumor migration and invasion. DNase I is considered a promising cancer cure, due to its ability to degrade cfDNAs. Previous studies using murine tumor models have proved the high anti-metastatic potential of DNase I. Later circulating cfDNAs, especially tandem repeats associated with short-interspersed nuclear elements (SINEs) and long-interspersed nuclear elements (LINEs), have been found to be the enzyme's main molecular targets. Here, using Lewis lung carcinoma, melanoma B16, and lymphosarcoma RLS40 murine tumor models, we reveal that tumor progression is accompanied by an increase in the level of SINE and LINEs in the pool of circulating cfDNAs. Treatment with DNase I decreased in the number and area of metastases by factor 3-10, and the size of the primary tumor node by factor 1.5-2, which correlated with 5- to 10-fold decreasing SINEs and LINEs. We demonstrated that SINEs and LINEs from cfDNA of tumor-bearing mice are able to penetrate human cells. The results show that SINEs and LINEs could be important players in metastasis, and this allows them to be considered as attractive new targets for anticancer therapy.
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Affiliation(s)
- Ludmila A Alekseeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue, 8, Novosibirsk 630090, Russia
| | - Aleksandra V Sen'kova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue, 8, Novosibirsk 630090, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue, 8, Novosibirsk 630090, Russia
| | - Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue, 8, Novosibirsk 630090, Russia.
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27
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Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 2019; 47:e27. [PMID: 30624635 PMCID: PMC6411935 DOI: 10.1093/nar/gky1301] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.
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Affiliation(s)
- Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clarissa N Pacyna
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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28
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Hu Q, Lu H, Wang H, Li S, Truong L, Li J, Liu S, Xiang R, Wu X. Break-induced replication plays a prominent role in long-range repeat-mediated deletion. EMBO J 2019; 38:e101751. [PMID: 31571254 DOI: 10.15252/embj.2019101751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 09/07/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Repetitive DNA sequences are often associated with chromosomal rearrangements in cancers. Conventionally, single-strand annealing (SSA) is thought to mediate homology-directed repair of double-strand breaks (DSBs) between two repeats, causing repeat-mediated deletion (RMD). In this report, we demonstrate that break-induced replication (BIR) is used predominantly over SSA in mammalian cells for mediating RMD, especially when repeats are far apart. We show that SSA becomes inefficient in mammalian cells when the distance between the DSBs and the repeats is increased to the 1-2 kb range, while BIR-mediated RMD (BIR/RMD) can act over a long distance (e.g., ~ 100-200 kb) when the DSB is close to one repeat. Importantly, oncogene expression potentiates BIR/RMD but not SSA, and BIR/RMD is used more frequently at single-ended DSBs formed at collapsed replication forks than at double-ended DSBs. In contrast to short-range SSA, H2AX is required for long-range BIR/RMD, and sequence divergence strongly suppresses BIR/RMD in a manner partially dependent on MSH2. Our finding that BIR/RMD has a more important role than SSA in mammalian cells has a significant impact on the understanding of repeat-mediated rearrangements associated with oncogenesis.
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Affiliation(s)
- Qing Hu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Hongyan Lu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,School of Medicine, Nankai University, Tianjin, China
| | - Hongjun Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Lan Truong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jun Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,School of Medicine, Nankai University, Tianjin, China
| | - Shuo Liu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,School of Medicine, Nankai University, Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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29
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Navarro FCP, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput Biol 2019; 15:e1007293. [PMID: 31425522 PMCID: PMC6715295 DOI: 10.1371/journal.pcbi.1007293] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/29/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022] Open
Abstract
The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome. Repetitive sequences, such as LINEs, comprise more than half of the human genome. Due to their repetitive nature, LINEs are hard to grasp. In particular, we find that pervasive transcription is a major confounding factor in transcriptome data. We observe that, on average, more than 90% of LINE signal derives from pervasive transcription. To investigate this issue, we developed and validated a new method called TeXP. TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells. By removing the pervasive transcription component, we find that (1) LINE-1 is broadly expressed in healthy somatic tissues; (2) Adult brain show small levels of LINE transcription and; (3) LINE-1 transcription level is correlated with tissue cell turnover. Our method thus offers insights into how repetitive sequences and influenced by pervasive transcription. Moreover, we uncover the activity of LINE-1 in somatic tissues at an unmatched scale.
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Affiliation(s)
- Fabio CP Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jacob Hoops
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Lauren Bellfy
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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30
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Zafon C, Gil J, Pérez-González B, Jordà M. DNA methylation in thyroid cancer. Endocr Relat Cancer 2019; 26:R415-R439. [PMID: 31035251 DOI: 10.1530/erc-19-0093] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
In recent years, cancer genomics has provided new insights into genetic alterations and signaling pathways involved in thyroid cancer. However, the picture of the molecular landscape is not yet complete. DNA methylation, the most widely studied epigenetic mechanism, is altered in thyroid cancer. Recent technological advances have allowed the identification of novel differentially methylated regions, methylation signatures and potential biomarkers. However, despite recent progress in cataloging methylation alterations in thyroid cancer, many questions remain unanswered. The aim of this review is to comprehensively examine the current knowledge on DNA methylation in thyroid cancer and discuss its potential clinical applications. After providing a general overview of DNA methylation and its dysregulation in cancer, we carefully describe the aberrant methylation changes in thyroid cancer and relate them to methylation patterns, global hypomethylation and gene-specific alterations. We hope this review helps to accelerate the use of the diagnostic, prognostic and therapeutic potential of DNA methylation for the benefit of thyroid cancer patients.
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Affiliation(s)
- Carles Zafon
- Diabetes and Metabolism Research Unit (VHIR) and Department of Endocrinology, University Hospital Vall d'Hebron and Autonomous University of Barcelona, Barcelona, Spain
- Consortium for the Study of Thyroid Cancer (CECaT), Catalonia, Spain
| | - Joan Gil
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
| | - Beatriz Pérez-González
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
| | - Mireia Jordà
- Consortium for the Study of Thyroid Cancer (CECaT), Catalonia, Spain
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
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Telonis AG, Loher P, Magee R, Pliatsika V, Londin E, Kirino Y, Rigoutsos I. tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities. Cancer Res 2019; 79:3034-3049. [PMID: 30996049 DOI: 10.1158/0008-5472.can-19-0789] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 01/26/2023]
Abstract
tRNA-derived fragments (tRF) are a class of potent regulatory RNAs. We mined the datasets from The Cancer Genome Atlas (TCGA) representing 32 cancer types with a deterministic and exhaustive pipeline for tRNA fragments. We found that mitochondrial tRNAs contribute disproportionally more tRFs than nuclear tRNAs. Through integrative analyses, we uncovered a multitude of statistically significant and context-dependent associations between the identified tRFs and mRNAs. In many of the 32 cancer types, these associations involve mRNAs from developmental processes, receptor tyrosine kinase signaling, the proteasome, and metabolic pathways that include glycolysis, oxidative phosphorylation, and ATP synthesis. Even though the pathways are common to multiple cancers, the association of specific mRNAs with tRFs depends on and differs from cancer to cancer. The associations between tRFs and mRNAs extend to genomic properties as well; specifically, tRFs are positively correlated with shorter genes that have a higher density in repeats, such as ALUs, MIRs, and ERVLs. Conversely, tRFs are negatively correlated with longer genes that have a lower repeat density, suggesting a possible dichotomy between cell proliferation and differentiation. Analyses of bladder, lung, and kidney cancer data indicate that the tRF-mRNA wiring can also depend on a patient's sex. Sex-dependent associations involve cyclin-dependent kinases in bladder cancer, the MAPK signaling pathway in lung cancer, and purine metabolism in kidney cancer. Taken together, these findings suggest diverse and wide-ranging roles for tRFs and highlight the extensive interconnections of tRFs with key cellular processes and human genomic architecture. SIGNIFICANCE: Across 32 TCGA cancer contexts, nuclear and mitochondrial tRNA fragments exhibit associations with mRNAs that belong to concrete pathways, encode proteins with particular destinations, have a biased repeat content, and are sex dependent.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Rogan Magee
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Venetia Pliatsika
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Eric Londin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Yohei Kirino
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
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Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation. Clin Ther 2019; 41:675-698. [PMID: 30910331 DOI: 10.1016/j.clinthera.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Studies to determine epigenetic changes associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain scarce; however, current evidence clearly shows that methylation patterns of genomic DNA and noncoding RNA profiles of immune cells differ between patients and healthy subjects, suggesting an active role of these epigenetic mechanisms in the disease. The present study compares and contrasts the available ME/CFS epigenetic data in an effort to evidence overlapping pathways capable of explaining at least some of the dysfunctional immune parameters linked to this disease. METHODS A systematic search of the literature evaluating the ME/CFS epigenome landscape was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Differential DNA methylation and noncoding RNA differential expression patterns associated with ME/CFS were used to screen for the presence of transposable elements using the Dfam browser, a search program nurtured with the Repbase repetitive sequence database and the RepeatMasker annotation tool. FINDINGS Unexpectedly, particular associations of transposable elements and ME/CFS epigenetic hallmarks were uncovered. A model for the disease emerged involving transcriptional induction of endogenous dormant transposons and structured cellular RNA interactions, triggering the activation of the innate immune system without a concomitant active infection. IMPLICATIONS Repetitive sequence filters (ie, RepeatMasker) should be avoided when analyzing transcriptomic data to assess the potential participation of repetitive sequences ("junk repetitive DNA"), representing >45% of the human genome, in the onset and evolution of ME/CFS. In addition, transposable element screenings aimed at designing cost-effective, focused empirical assays that can confirm or disprove the suspected involvement of transposon transcriptional activation in this disease, following the pilot strategy presented here, will require databases gathering large ME/CFS epigenetic datasets.
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Rozek LS, Virani S, Bellile EL, Taylor JMG, Sartor MA, Zarins KR, Virani A, Cote C, Worden FP, Mark MEP, McLean SA, Duffy SA, Yoo GH, Saba NF, Shin DM, Kucuk O, Wolf GT. Soy Isoflavone Supplementation Increases Long Interspersed Nucleotide Element-1 (LINE-1) Methylation in Head and Neck Squamous Cell Carcinoma. Nutr Cancer 2019; 71:772-780. [PMID: 30862188 PMCID: PMC6513708 DOI: 10.1080/01635581.2019.1577981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/13/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022]
Abstract
AIM Soy isoflavones have been suggested as epigenetic modulating agents with effects that could be important in carcinogenesis. Hypomethylation of LINE-1 has been associated with head and neck squamous cell carcinoma (HNSCC) development from oral premalignant lesions and with poor prognosis. To determine if neoadjuvant soy isoflavone supplementation could modulate LINE-1 methylation in HNSCC, we undertook a clinical trial. METHODS Thirty-nine patients received 2-3 weeks of soy isoflavone supplements (300 mg/day) orally prior to surgery. Methylation of LINE-1, and 6 other genes was measured by pyrosequencing in biopsy, resection, and whole blood (WB) specimens. Changes in methylation were tested using paired t tests and ANOVA. Median follow up was 45 months. RESULTS LINE-1 methylation increased significantly after soy isoflavone (P < 0.005). Amount of change correlated positively with days of isoflavone taken (P = 0.04). Similar changes were not seen in corresponding WB samples. No significant changes in tumor or blood methylation levels were seen in the other candidate genes. CONCLUSION This is the first demonstration of in vivo increases in tissue-specific global methylation associated with soy isoflavone intake in patients with HNSCC. Prior associations of LINE-1 hypomethylation with genetic instability, carcinogenesis, and prognosis suggest that soy isoflavones maybe potential chemopreventive agents in HNSCC.
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Affiliation(s)
- Laura S Rozek
- a University of Michigan , Ann Arbor , Michigan, USA
| | - Shama Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - A Virani
- a University of Michigan , Ann Arbor , Michigan, USA
| | - C Cote
- a University of Michigan , Ann Arbor , Michigan, USA
| | | | | | | | | | - George H Yoo
- c Karmanos Cancer Institute , Wayne State University , Detroit , Michigan 48201, USA
| | - Nabil F Saba
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Dong M Shin
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
| | - Omer Kucuk
- d Winship Cancer Institute , Emory University , Atlanta , Georgia, USA
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Mustafin RN. Functional Dualism of Transposon Transcripts in Evolution of Eukaryotic Genomes. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360418070019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Transposons, p53 and Genome Security. Trends Genet 2018; 34:846-855. [PMID: 30195581 DOI: 10.1016/j.tig.2018.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/31/2018] [Accepted: 08/07/2018] [Indexed: 12/16/2022]
Abstract
p53, the most commonly mutated tumor suppressor, is a transcription factor known to regulate proliferation, senescence, and apoptosis. Compelling studies have found that p53 may prevent oncogenesis through effectors that are unrelated to these canonical processes and recent findings have uncovered ancient roles for p53 in the containment of mobile elements. Together, these developments raise the possibility that some p53-driven cancers could result from unrestrained transposons. Here, we explore evidence linking conserved features of p53 biology to the control of transposons. We also show how p53-deficient cells can be exploited to probe the behavior of transposons and illustrate how unrestrained transposons incited by p53 loss might contribute to human malignancies.
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Russell SJ, Stalker L, LaMarre J. PIWIs, piRNAs and Retrotransposons: Complex battles during reprogramming in gametes and early embryos. Reprod Domest Anim 2018; 52 Suppl 4:28-38. [PMID: 29052331 DOI: 10.1111/rda.13053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Gamete and embryo development are indispensable processes for successful reproduction. Cells involved in these processes acquire pluripotency, the ability to differentiate into multiple different cell types, through a series of events known as reprogramming that lead to profound changes in histone and DNA methylation. While essential for pluripotency, this epigenetic remodelling removes constraints that normally limit the expression of genomic sequences known as transposable elements (TEs). Unconstrained TE expression can lead to many deleterious consequences including infertility, so organisms have evolved complex and potent mechanistic arsenals to target and suppress TE expression during reprogramming. This review will focus on the control of transposable elements in gametes and embryos, and one important TE suppressing system known as the PIWI pathway. This broadly conserved, small RNA-targeted silencing mechanism appears critical for fertility in many species and may participate in multiple aspects of gene regulation in reproduction and other contexts.
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Affiliation(s)
- S J Russell
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - L Stalker
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - J LaMarre
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
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Li S, Wehrenberg B, Waldman BC, Waldman AS. Mismatch tolerance during homologous recombination in mammalian cells. DNA Repair (Amst) 2018; 70:25-36. [PMID: 30103093 DOI: 10.1016/j.dnarep.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
We investigated the homology dependency of recombination in thymidine kinase (tk)-deficient mouse fibroblasts. Cells were transfected with DNA constructs harboring a herpes tk gene (the "recipient") rendered non-functional by an oligonucleotide containing the recognition site for endonuclease I-SceI. Constructs also contained a "donor" tk sequence that could restore function to the recipient gene through spontaneous gene conversion or via repair of a double-strand break (DSB) at the I-SceI site. Recombination events were recoverable by selection for tk-positive clones. Three different donors were used containing 16, 25, or 33 mismatches relative to the recipient. The mismatches were clustered, forming an interval of "homeology" relative to the recipient sequences. We show that when homeologous sequences were surrounded by high homology, mismatches were frequently included in gene conversion events. Notably, conversion tracts from spontaneous recombination included either all or none of the mismatches, suggesting that recombination must begin and end in high homology. This requirement was relaxed for events that occurred near an induced DSB, as a significant number of these latter conversion tracts had one end positioned within homeology. Knock-down of mismatch repair showed that incorporation of mismatches into gene conversion tracts can involve repair of mismatched heteroduplex intermediates, indicating that mismatch repair does not necessarily impede homeologous genetic exchange. Our results illustrate (1) genetic exchange between homeologous sequences in a mammalian genome is enabled by nearby homology, (2) proximity to a DSB impacts the homology requirements for where genetic exchange may begin and end, and (3) mismatch correction and previously documented anti-recombination activity are separable functions of the mismatch repair machinery in mammalian cells.
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Affiliation(s)
- Shen Li
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Bryan Wehrenberg
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Barbara C Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Alan S Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA.
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Enigma of Retrotransposon Biology in Mammalian Early Embryos and Embryonic Stem Cells. Stem Cells Int 2018; 2018:6239245. [PMID: 30123290 PMCID: PMC6079326 DOI: 10.1155/2018/6239245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/05/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022] Open
Abstract
Retrotransposons comprise a significant fraction of mammalian genome with unclear functions. Increasing evidence shows that they are not just remnants of ancient retroviruses but play important roles in multiple biological processes. Retrotransposons are epigenetically silenced in most somatic tissues and become reactivated in early embryos. Notably, abundant retrotransposon expression in mouse embryonic stem cells (ESCs) marks transient totipotency status, while retrotransposon enrichment in human ESCs indicates naive-like status. Some retrotransposon elements retained the capacity to retrotranspose, such as LINE1, producing genetic diversity or disease. Some other retrotransposons reside in the vicinity of endogenous genes and are capable of regulating nearby genes and cell fate, possibly through providing alternative promoters, regulatory modules, or orchestrating high-order chromatin assembly. In addition, retrotransposons may mediate epigenetic memory, regulate gene expression posttranscriptionally, defend virus infection, and so on. In this review, we summarize expression patterns and regulatory functions of different retrotransposons in early embryos and ESCs, as well as document molecular mechanisms controlling retrotransposon expression and their potential functions. Further investigations on the regulatory network of retrotransposons in early embryogenesis and ESCs will provide valuable insights and a deeper understanding of retrotransposon biology. Additionally, endeavors made to unveil the roles of these mysterious elements may facilitate stem cell status conversion and manipulation of pluripotency.
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Mustafin RN, Khusnutdinova EK. Epigenetic Hypothesis of the Role of Peptides in Aging. ADVANCES IN GERONTOLOGY 2018. [DOI: 10.1134/s2079057018030128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rota F, Conti A, Campo L, Favero C, Cantone L, Motta V, Polledri E, Mercadante R, Dieci G, Bollati V, Fustinoni S. Epigenetic and Transcriptional Modifications in Repetitive Elements in Petrol Station Workers Exposed to Benzene and MTBE. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E735. [PMID: 29649143 PMCID: PMC5923777 DOI: 10.3390/ijerph15040735] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/30/2018] [Accepted: 04/08/2018] [Indexed: 12/19/2022]
Abstract
Benzene, a known human carcinogen, and methyl tert-butyl ether (MTBE), not classifiable as to its carcinogenicity, are fuel-related pollutants. This study investigated the effect of these chemicals on epigenetic and transcriptional alterations in DNA repetitive elements. In 89 petrol station workers and 90 non-occupationally exposed subjects the transcriptional activity of retrotransposons (LINE-1, Alu), the methylation on repeated-element DNA, and of H3K9 histone, were investigated in peripheral blood lymphocytes. Median work shift exposure to benzene and MTBE was 59 and 408 µg/m³ in petrol station workers, and 4 and 3.5 µg/m³, in controls. Urinary benzene (BEN-U), S-phenylmercapturic acid, and MTBE were significantly higher in workers than in controls, while trans,trans-muconic acid (tt-MA) was comparable between the two groups. Increased BEN-U was associated with increased Alu-Y and Alu-J expression; moreover, increased tt-MA was associated with increased Alu-Y and Alu-J and LINE-1 (L1)-5'UTR expression. Among repetitive element methylation, only L1-Pa5 was hypomethylated in petrol station workers compared to controls. While L1-Ta and Alu-YD6 methylation was not associated with benzene exposure, a negative association with urinary MTBE was observed. The methylation status of histone H3K9 was not associated with either benzene or MTBE exposure. Overall, these findings only partially support previous observations linking benzene exposure with global DNA hypomethylation.
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Affiliation(s)
- Federica Rota
- EPIGET, Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy.
| | - Anastasia Conti
- Department of Life Sciences, University of Parma, 43124 Parma, Italy.
- Present address: San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), 20132 Milan, Italy.
| | - Laura Campo
- Occupational Medicine Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy.
| | - Chiara Favero
- EPIGET, Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy.
| | - Laura Cantone
- EPIGET, Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy.
| | - Valeria Motta
- EPIGET, Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy.
| | - Elisa Polledri
- Occupational Medicine Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy.
| | - Rosa Mercadante
- EPIGET, Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy.
| | - Giorgio Dieci
- Department of Life Sciences, University of Parma, 43124 Parma, Italy.
| | - Valentina Bollati
- EPIGET, Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy.
- Occupational Medicine Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy.
| | - Silvia Fustinoni
- EPIGET, Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy.
- Occupational Medicine Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy.
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Mendez-Dorantes C, Bhargava R, Stark JM. Repeat-mediated deletions can be induced by a chromosomal break far from a repeat, but multiple pathways suppress such rearrangements. Genes Dev 2018; 32:524-536. [PMID: 29636371 PMCID: PMC5959236 DOI: 10.1101/gad.311084.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/20/2018] [Indexed: 12/20/2022]
Abstract
Here, Mendez-Dorantes et al. investigated how far a chromosomal double-strand break (DSB) can be positioned from a repeat sequence to induce repeat-mediated rearrangements in mammalian cells. Using a novel reporter assay in mouse embryonic stem cells, they found that a DSB separated from the 3′ repeat by 28.4 kb can still substantially induce RMDs, indicating that a DSB is sufficient to induce RMDs at a relatively far distance. Chromosomal deletion rearrangements mediated by repetitive elements often involve repeats separated by several kilobases and sequences that are divergent. While such rearrangements are likely induced by DNA double-strand breaks (DSBs), it has been unclear how the proximity of DSBs relative to repeat sequences affects the frequency of such events. We generated a reporter assay in mouse cells for a deletion rearrangement involving repeats separated by 0.4 Mb. We induced this repeat-mediated deletion (RMD) rearrangement with two DSBs: the 5′ DSB that is just downstream from the first repeat and the 3′ DSB that is varying distances upstream of the second repeat. Strikingly, we found that increasing the 3′ DSB/repeat distance from 3.3 kb to 28.4 kb causes only a modest decrease in rearrangement frequency. We also found that RMDs are suppressed by KU70 and RAD51 and promoted by RAD52, CtIP, and BRCA1. In addition, we found that 1%–3% sequence divergence substantially suppresses these rearrangements in a manner dependent on the mismatch repair factor MSH2, which is dominant over the suppressive role of KU70. We suggest that a DSB far from a repeat can stimulate repeat-mediated rearrangements, but multiple pathways suppress these events.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, City of Hope, Duarte, California 91010, USA.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
| | - Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, City of Hope, Duarte, California 91010, USA.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, City of Hope, Duarte, California 91010, USA.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
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Mustafin RN, Khusnutdinova EK. The Role of Transposable Elements in Emergence of Metazoa. BIOCHEMISTRY (MOSCOW) 2018; 83:185-199. [PMID: 29625540 DOI: 10.1134/s000629791803001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Systems initially emerged for protecting genomes against insertions of transposable elements and represented by mechanisms of splicing regulation, RNA-interference, and epigenetic factors have played a key role in the evolution of animals. Many studies have shown inherited transpositions of mobile elements in embryogenesis and preservation of their activities in certain tissues of adult organisms. It was supposed that on the emergence of Metazoa the self-regulation mechanisms of transposons related with the gene networks controlling their activity could be involved in intercellular cell coordination in the cascade of successive divisions with differentiated gene expression for generation of tissues and organs. It was supposed that during evolution species-specific features of transposons in the genomes of eukaryotes could form the basis for creation of dynamically related complexes of systems for epigenetic regulation of gene expression. These complexes could be produced due to the influence of noncoding transposon-derived RNAs on DNA methylation, histone modifications, and processing of alternative splicing variants, whereas the mobile elements themselves could be directly involved in the regulation of gene expression in cis and in trans. Transposons are widely distributed in the genomes of eukaryotes; therefore, their activation can change the expression of specific genes. In turn, this can play an important role in cell differentiation during ontogenesis. It is supposed that transposons can form a species-specific pattern for control of gene expression, and that some variants of this pattern can be favorable for adaptation. The presented data indicate the possible influence of transposons in karyotype formation. It is supposed that transposon localization relative to one another and to protein-coding genes can influence the species-specific epigenetic regulation of ontogenesis.
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43
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Mustafin RN, Khusnutdinova EK. The Role of Transposons in Epigenetic Regulation of Ontogenesis. Russ J Dev Biol 2018. [DOI: 10.1134/s1062360418020066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Larsen PA, Hunnicutt KE, Larsen RJ, Yoder AD, Saunders AM. Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease. Chromosome Res 2018; 26:93-111. [PMID: 29460123 PMCID: PMC5857278 DOI: 10.1007/s10577-018-9573-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/14/2018] [Accepted: 01/15/2018] [Indexed: 12/28/2022]
Abstract
Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potentially vulnerable to the epigenetic dysregulation of Alu elements operating across the suite of nuclear-encoded mitochondrial genes that are critical for both mitochondrial and CNS function. Here, we highlight the beneficial neurological aspects of Alu elements as well as their potential to cause disease by disrupting key cellular processes across the CNS. We identify at least 37 neurological and neurodegenerative disorders wherein deleterious Alu activity has been implicated as a contributing factor for the manifestation of disease, and for many of these disorders, this activity is operating on genes that are essential for proper mitochondrial function. We conclude that the epigenetic dysregulation of Alu elements can ultimately disrupt mitochondrial homeostasis within the CNS. This mechanism is a plausible source for the incipient neuronal stress that is consistently observed across a spectrum of sporadic neurological and neurodegenerative disorders.
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Affiliation(s)
- Peter A Larsen
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Duke Lemur Center, Duke University, Durham, NC, 27708, USA.
- Department of Biology, Duke University, 130 Science Drive, Box 90338, Durham, NC, 27708, USA.
| | | | - Roxanne J Larsen
- Duke University School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Duke Lemur Center, Duke University, Durham, NC, 27708, USA
| | - Ann M Saunders
- Zinfandel Pharmaceuticals Inc, Chapel Hill, NC, 27709, USA
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Transposable elements and the multidimensional genome. Chromosome Res 2018; 26:1-3. [DOI: 10.1007/s10577-018-9575-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 01/08/2023]
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46
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Tremblay R, Dufort I, Sirard MA. Metabolic stress induces modifications in the epigenetic program of preimplantation bovine embryos. Mol Reprod Dev 2018; 85:117-127. [PMID: 29240275 DOI: 10.1002/mrd.22941] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/04/2017] [Indexed: 12/16/2022]
Abstract
The mammalian embryo is sensitive to and adapts to its metabolic environment. The mother's metabolic health and nutrient availability, for example, can modulate the oviductal fluid composition and thus embryo development. In this project, we induced energetic stress in bovine embryos during early culture to observe the epigenetic responses associated with metabolic stress, using a treatment paradigm known to decrease blastocyst rates. Embryos were generated using oocytes from slaughtered cows, and then exposed to an elevated glucose concentration (5 vs. 0.2 mM in control conditions) for the first 3 days post-fertilization, followed by normal media until the blastocyst stage. The EmbryoGENE platform was then used to identify DNA methylation differences between the two treatments. Probes (450,000) were then analyzed based on their genome location and methylation differences. Our results revealed that elevated glucose led to hypomethylation close to telomeric regions and methylation changes on genomic regions associated with energy metabolism.
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Affiliation(s)
- Rachele Tremblay
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Faculté des sciences de l'agriculture et de l'alimentation, Département des sciences animales, Pavillon des services, Université Laval, Québec, Québec, Canada
| | - Isabelle Dufort
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Faculté des sciences de l'agriculture et de l'alimentation, Département des sciences animales, Pavillon des services, Université Laval, Québec, Québec, Canada
| | - Marc-Andre Sirard
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Faculté des sciences de l'agriculture et de l'alimentation, Département des sciences animales, Pavillon des services, Université Laval, Québec, Québec, Canada
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High homology is not required at the site of strand invasion during recombinational double-strand break repair in mammalian chromosomes. DNA Repair (Amst) 2017; 60:1-8. [PMID: 29055804 DOI: 10.1016/j.dnarep.2017.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/22/2017] [Accepted: 10/11/2017] [Indexed: 12/23/2022]
Abstract
We investigated the impact of sequence divergence on DNA double-strand break (DSB) repair occurring via recombination in cultured thymidine kinase deficient mouse fibroblasts. We stably transfected cells with a DNA construct harboring a herpes thymidine kinase (tk) gene (the "recipient") rendered nonfunctional by insertion of an oligonucleotide containing the recognition site for endonuclease I-SceI. The construct also contained a closely linked truncated "donor" tk sequence. The donor could potentially restore function to the recipient gene via recombination provoked by induction of a DSB at the I-SceI site in the recipient. Repair events were recoverable by selection for tk-positive clones. The donor contained 33 mismatches relative to the recipient. The mismatches were clustered, forming a localized segment of DNA sequence displaying about 20% divergence relative to the recipient, and the mismatched segment was surrounded by regions of high homology. When the donor was aligned with the recipient, the DSB site in the recipient aligned opposite the mismatched segment, allowing us to potentially capture recombinational repair events initiating between diverged sequences. Previous work demonstrated that mammalian cells effectively avoid recombination between 20% diverged sequences. In the current study we asked whether flanking regions of high homology would enable genetic exchange between highly diverged sequences or, instead, would rejection of exchange between diverged sequences remain unchanged. We found that by surrounding mismatches with high homology, suppression of recombination between diverged sequences was overcome. Strikingly, we recovered a high frequency of gene conversion tracts positioned entirely within the mismatched sequences. We infer that such events were enabled by homologous pairing interactions between sequences surrounding the site of strand invasion. Our results suggest a search for high homology prior to recombination that is not mediated by an invading DNA terminus.
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Ye L, Jiao N, Tang X, Chen Y, Ye X, Ren L, Hu F, Wang S, Wen M, Zhang C, Tao M, Liu S. Chimeras Linked to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:401-409. [PMID: 28681105 DOI: 10.1007/s10126-017-9764-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/09/2017] [Indexed: 06/07/2023]
Abstract
The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species, and therefore, it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs benefit from the intervention of recombinases. In addition, TRs and TEs can also result in insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.
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Affiliation(s)
- Lihai Ye
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Ni Jiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Xiaojun Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Yiyi Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Xiaolan Ye
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China.
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Stefanovski D, Tang G, Wawrowsky K, Boston RC, Lambrecht N, Tajbakhsh J. Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers. Oncotarget 2017; 8:57278-57301. [PMID: 28915670 PMCID: PMC5593641 DOI: 10.18632/oncotarget.18985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/02/2017] [Indexed: 11/29/2022] Open
Abstract
Background Prostate cancer (PCa) management can benefit from novel concepts/biomarkers for reducing the current 20-30% chance of false-negative diagnosis with standard histopathology of biopsied tissue. Method We explored the potential of selected epigenetic markers in combination with validated histopathological markers, 3D high-content imaging, cell-by-cell analysis, and probabilistic classification in generating novel detailed maps of biomarker heterogeneity in patient tissues, and PCa diagnosis. We used consecutive biopsies/radical prostatectomies from five patients for building a database of ∼140,000 analyzed cells across all tissue compartments and for model development; and from five patients and the two well-characterized HPrEpiC primary and LNCaP cancer cell types for model validation. Results Principal component analysis presented highest covariability for the four biomarkers 4′,6-diamidino-2-phenylindole, 5-methylcytosine, 5-hydroxymethylcytosine, and alpha-methylacyl-CoA racemase in the epithelial tissue compartment. The panel also showed best performance in discriminating between normal and cancer-like cells in prostate tissues with a sensitivity and specificity of 85%, correctly classified 87% of HPrEpiC as healthy and 99% of LNCaP cells as cancer-like, identified a majority of aberrant cells within histopathologically benign tissues at baseline diagnosis of patients that were later diagnosed with adenocarcinoma. Using k-nearest neighbor classifier with cells from an initial patient biopsy, the biomarkers were able to predict cancer stage and grade of prostatic tissue that occurred at later prostatectomy with 79% accuracy. Conclusion Our approach showed favorable diagnostic values to identify the portion and pathological category of aberrant cells in a small subset of sampled tissue cells, correlating with the degree of malignancy beyond baseline.
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Affiliation(s)
- Darko Stefanovski
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George Tang
- Translational Cytomics Group, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kolja Wawrowsky
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Raymond C Boston
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nils Lambrecht
- Pathology and Laboratory Medicine Service, Veterans Affairs Medical Center, Long Beach, CA, USA.,Department of Pathology and Laboratory Medicine, University of California Irvine, Orange, CA, USA
| | - Jian Tajbakhsh
- Translational Cytomics Group, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Groh S, Schotta G. Silencing of endogenous retroviruses by heterochromatin. Cell Mol Life Sci 2017; 74:2055-2065. [PMID: 28160052 PMCID: PMC11107624 DOI: 10.1007/s00018-017-2454-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/14/2016] [Accepted: 01/03/2017] [Indexed: 02/05/2023]
Abstract
Endogenous retroviruses (ERV) are an abundant class of repetitive elements in mammalian genomes. To ensure genomic stability, ERVs are largely transcriptionally silent. However, these elements also feature physiological roles in distinct developmental contexts, under which silencing needs to be partially relieved. ERV silencing is mediated through a heterochromatic structure, which is established by histone modification and DNA methylation machineries. This heterochromatic structure is largely refractory to transcriptional stimulation, however, challenges to the heterochromatic state, such as DNA replication, require re-establishment of the heterochromatic state in competition with transcriptional activators. In this review, we discuss the major pathways leading to efficient establishment of robust and inaccessible heterochromatin across ERVs.
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Affiliation(s)
- Sophia Groh
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152, Planegg-Martinsried, Germany
| | - Gunnar Schotta
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152, Planegg-Martinsried, Germany.
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