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Prokopov D, Tunbak H, Leddy E, Drylie B, Camera F, Deniz Ö. Transposable elements as genome regulators in normal and malignant haematopoiesis. Blood Cancer J 2025; 15:87. [PMID: 40328728 PMCID: PMC12056191 DOI: 10.1038/s41408-025-01295-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 04/16/2025] [Accepted: 04/23/2025] [Indexed: 05/08/2025] Open
Abstract
Transposable elements (TEs) constitute over half of the human genome and have played a profound role in genome evolution. While most TEs have lost the ability to transpose, many retain functional elements that serve as drivers of genome innovation, including the emergence of novel genes and regulatory elements. Recent advances in experimental and bioinformatic methods have provided new insights into their roles in human biology, both in health and disease. In this review, we discuss the multifaceted roles of TEs in haematopoiesis, highlighting their contributions to both normal and pathological contexts. TEs influence gene regulation by reshaping gene-regulatory networks, modulating transcriptional activity, and creating novel regulatory elements. These activities play key roles in maintaining normal haematopoietic processes and supporting cellular regeneration. However, in haematological malignancies, TE reactivation can disrupt genomic integrity, induce structural variations, and dysregulate transcriptional programmes, thereby driving oncogenesis. By examining the impact of TE activity on genome regulation and variation, we highlight their pivotal roles in both normal haematopoietic processes and haematological cancers.
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Affiliation(s)
- Dmitry Prokopov
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- QMUL Centre for Epigenetics, Queen Mary University of London, London, UK
| | - Hale Tunbak
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- QMUL Centre for Epigenetics, Queen Mary University of London, London, UK
| | - Eve Leddy
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- QMUL Centre for Epigenetics, Queen Mary University of London, London, UK
| | - Bryce Drylie
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- QMUL Centre for Epigenetics, Queen Mary University of London, London, UK
| | - Francesco Camera
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
- QMUL Centre for Epigenetics, Queen Mary University of London, London, UK
| | - Özgen Deniz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
- QMUL Centre for Epigenetics, Queen Mary University of London, London, UK.
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2
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Michel M, Heidary M, Mechri A, Da Silva K, Gorse M, Dixon V, von Grafenstein K, Bianchi C, Hego C, Rampanou A, Lamy C, Kamal M, Le Tourneau C, Séné M, Bièche I, Reyes C, Gentien D, Stern MH, Lantz O, Cabel L, Pierga JY, Bidard FC, Azencott CA, Proudhon C. Noninvasive Multicancer Detection Using DNA Hypomethylation of LINE-1 Retrotransposons. Clin Cancer Res 2025; 31:1275-1291. [PMID: 39620930 PMCID: PMC11959274 DOI: 10.1158/1078-0432.ccr-24-2669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/20/2024] [Accepted: 11/22/2024] [Indexed: 04/02/2025]
Abstract
PURPOSE The detection of ctDNA, which allows noninvasive tumor molecular profiling and disease follow-up, promises optimal and individualized management of patients with cancer. However, detecting small fractions of tumor DNA released when the tumor burden is reduced remains a challenge. EXPERIMENTAL DESIGN We implemented a new, highly sensitive strategy to detect bp resolution methylation patterns from plasma DNA and assessed the potential of hypomethylation of long interspersed nuclear element-1 retrotransposons as a noninvasive multicancer detection biomarker. The Detection of Long Interspersed Nuclear Element Altered Methylation ON plasma DNA method targets 30 to 40,000 young long interspersed nuclear element-1 retrotransposons scattered throughout the genome, covering about 100,000 CpG sites and is based on a reference-free analysis pipeline. RESULTS Resulting machine learning-based classifiers showed powerful correct classification rates discriminating healthy and tumor plasmas from six types of cancers (colorectal, breast, lung, ovarian, and gastric cancers and uveal melanoma, including localized stages) in two independent cohorts (AUC = 88%-100%, N = 747). The Detection of Long Interspersed Nuclear Element Altered Methylation ON plasma DNA method can also be used to perform copy number alteration analysis that improves cancer detection. CONCLUSIONS This should lead to the development of more efficient noninvasive diagnostic tests adapted to all patients with cancer, based on the universality of these factors. See related commentary by Szymanski et al., p. 1179.
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Affiliation(s)
- Marc Michel
- Inserm U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
- CBIO-Center for Computational Biology, Mines Paris, PSL Research University, Paris, France
- INSERM U900, Institut Curie, PSL Research University, Paris, France
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Maryam Heidary
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Anissa Mechri
- Inserm U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - Kévin Da Silva
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - Marine Gorse
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - Victoria Dixon
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - Klaus von Grafenstein
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - Charline Bianchi
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - Caroline Hego
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Aurore Rampanou
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Constance Lamy
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | | | - Mathieu Séné
- Pharmacogenomics Unit, Genetics Department, Institut Curie, Paris, France
| | - Ivan Bièche
- Pharmacogenomics Unit, Genetics Department, Institut Curie, Paris, France
| | - Cécile Reyes
- Genomics Platform, Translational Research Department, Research Center, Institut Curie, PSL Research University, Paris, France
| | - David Gentien
- Genomics Platform, Translational Research Department, Research Center, Institut Curie, PSL Research University, Paris, France
| | - Marc-Henri Stern
- Inserm U830, Institut Curie, PSL Research University, Paris, France
| | - Olivier Lantz
- Inserm U932, Institut Curie, PSL Research University, Paris, France
- Laboratory of Clinical Immunology, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Luc Cabel
- Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, France
- CNRS UMR144, Institut Curie, PSL Research University, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
- Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, France
- Université Paris Cité, Paris, France
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
- Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, France
- UVSQ, Université Paris-Saclay, Saint Cloud, France
| | - Chloé-Agathe Azencott
- CBIO-Center for Computational Biology, Mines Paris, PSL Research University, Paris, France
- INSERM U900, Institut Curie, PSL Research University, Paris, France
| | - Charlotte Proudhon
- Inserm U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
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de Santiago PR, Sato S, Zhang SJ, Dougher MC, Devins KM, Bilecz AJ, Rayamajhi S, Mingo G, Rendulich HS, Feng Y, Wu C, Taylor MS, Zhuravlev Y, Jung E, Omran DK, Wang TL, Shih IM, Schwartz LE, Kim S, Morgan MA, Tanyi JL, Burns KH, Lengyel E, Parra-Herran C, Godwin AK, Walt DR, Drapkin R. LINE-1 ORF1p expression occurs in clear cell ovarian carcinoma precursors and is a candidate blood biomarker. NPJ Precis Oncol 2025; 9:62. [PMID: 40050409 PMCID: PMC11885553 DOI: 10.1038/s41698-025-00849-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 02/24/2025] [Indexed: 03/09/2025] Open
Abstract
Long interspersed element 1 (LINE-1) retrotransposons are repetitive sequences that can move within the genome by an autonomous mechanism. To limit their mutagenic potential, benign cells restrict LINE-1 expression through molecular mechanisms such as DNA methylation and histone modification, but these mechanisms are usually impaired in cancer. Clear cell ovarian carcinoma (CCOC) represents 5-10% of ovarian cancers and is thought to arise from endometriosis. Women with advanced CCOC face poor prognoses, highlighting the importance of understanding early disease pathogenesis. In our study, 33 of 40 cases (over 82%) of CCOC tumors express ORF1p, a LINE-1-encoded protein. We found that LINE-1 de-repression is an early event in CCOC, as ORF1p is enhanced during the transition from typical to atypical endometriosis and persists in invasive cancer. Finally, using single-molecule array (Simoa) assays, we detected ORF1p in patient blood, suggesting it as a potential minimally invasive biomarker for this disease.
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Affiliation(s)
- Pamela R de Santiago
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sho Sato
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie J Zhang
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Meaghan C Dougher
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Kyle M Devins
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Agnes J Bilecz
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Sagar Rayamajhi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Gabriel Mingo
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hannah S Rendulich
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi Feng
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Connie Wu
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yelena Zhuravlev
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Euihye Jung
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dalia K Omran
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tian-Li Wang
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ie-Ming Shih
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lauren E Schwartz
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Kim
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Mark A Morgan
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Janos L Tanyi
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen H Burns
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Carlos Parra-Herran
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA.
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Matsuo M, Cristofari G. LINE-1, the NORth star of nucleolar organization. Genes Dev 2025; 39:183-185. [PMID: 39794124 PMCID: PMC11789626 DOI: 10.1101/gad.352583.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2025]
Abstract
Long interspersed element-1 (LINE-1) retrotransposons are abundant transposable elements in mammals and significantly influence chromosome structure, chromatin organization, and 3D genome architecture. In this issue of Genes & Development, Ataei et al. (doi:10.1101/gad.351979.124) identify a homininae-specific LINE-1 element within nucleolar organizer regions (NORs) that is specifically transcribed in naïve human embryonic stem cells. Deletion or silencing of this element disrupts nucleolar organization and function and alters cellular identity. These findings provide novel insights into the role of retrotransposons in genome organization and suggest that individual LINE-1 elements may have evolved specialized roles.
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Affiliation(s)
- Misaki Matsuo
- Institute for Research on Cancer and Aging of Nice (IRCAN), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), University Cote d'Azur, Nice 06107, France
| | - Gael Cristofari
- Institute for Research on Cancer and Aging of Nice (IRCAN), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), University Cote d'Azur, Nice 06107, France
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5
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Mangoni D, Mazzetti A, Ansaloni F, Simi A, Tartaglia GG, Pandolfini L, Gustincich S, Sanges R. From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs. Bioessays 2025; 47:e2400125. [PMID: 39520370 PMCID: PMC11755705 DOI: 10.1002/bies.202400125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 10/16/2024] [Accepted: 10/23/2024] [Indexed: 11/16/2024]
Abstract
Transposable elements (TEs) are mobile genomic elements constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages of mammalian development, suggesting potential benefits for the host. Among TEs, the long interspersed nuclear element (LINE-1 or L1) has been found to be active in neurons. This activity prompted extensive research into its possible role in cognition. So far, no specific cause-effect relationship between L1 retrotransposition and brain functions has been conclusively identified. Nevertheless, accumulating evidence suggests that interactions between L1 RNAs and RNA/DNA binding proteins encode specific messages that cells utilize to activate or repress entire transcriptional programs. We summarize recent findings highlighting the activity of L1 RNAs at the non-coding level during early embryonic and brain development. We propose a hypothesis suggesting a mutualistic relationship between L1 mRNAs and the host cell. In this scenario, cells tolerate a certain rate of retrotransposition to leverage the regulatory effects of L1s as non-coding RNAs on potentiating their mitotic potential. In turn, L1s benefit from the cell's proliferative state to increase their chance to mobilize.
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Affiliation(s)
- Damiano Mangoni
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Aurora Mazzetti
- Area of NeuroscienceInternational School for Advanced Studies (SISSA)TriesteItaly
| | - Federico Ansaloni
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Alessandro Simi
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, RNA Systems BiologyIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Luca Pandolfini
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Stefano Gustincich
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Remo Sanges
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
- Area of NeuroscienceInternational School for Advanced Studies (SISSA)TriesteItaly
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6
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Morandini F, Lu JY, Rechsteiner C, Shadyab AH, Casanova R, Snively BM, Seluanov A, Gorbunova V. Transposable element 5mC methylation state of blood cells predicts age and disease. NATURE AGING 2025; 5:193-204. [PMID: 39604704 PMCID: PMC11839465 DOI: 10.1038/s43587-024-00757-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024]
Abstract
Transposable elements (TEs) are DNA sequences that expand selfishly in the genome, possibly causing severe cellular damage. While normally silenced, TEs have been shown to activate during aging. DNA 5-methylcytosine (5mC) is one of the main epigenetic modifications by which TEs are silenced and has been used to train highly accurate age predictors. Yet, one common criticism of such predictors is that they lack interpretability. In this study, we investigate the changes in TE 5mC methylation that occur during aging in human blood using published methylation array data. We find that evolutionarily young long interspersed nuclear elements 1 (L1s), the only known TEs capable of autonomous transposition in humans, undergo the fastest loss of 5mC methylation, suggesting an active mechanism of de-repression. The same young L1s also showed preferential gain in chromatin accessibility but not expression. The long terminal repeat retrotransposons THE1A and THE1C also showed very rapid 5mC loss. We then show that accurate age predictors can be trained on both 5mC methylation of individual TE copies and average methylation of TE families genome wide. Lastly, we show that while old L1s gradually lose 5mC during the entire lifespan, demethylation of young L1s only happens late in life and is associated with cancer.
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Affiliation(s)
| | - Jinlong Y Lu
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science and Division of Geriatrics, Gerontology, and Palliative Care, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ramon Casanova
- Division of Public Health Sciences, Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Beverly M Snively
- Division of Public Health Sciences, Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA.
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA.
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.
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Akhatova A, Jones C, Coward K, Yeste M. How do lifestyle and environmental factors influence the sperm epigenome? Effects on sperm fertilising ability, embryo development, and offspring health. Clin Epigenetics 2025; 17:7. [PMID: 39819375 PMCID: PMC11740528 DOI: 10.1186/s13148-025-01815-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 01/08/2025] [Indexed: 01/19/2025] Open
Abstract
Recent studies support the influence of paternal lifestyle and diet before conception on the health of the offspring via epigenetic inheritance through sperm DNA methylation, histone modification, and small non-coding RNA (sncRNA) expression and regulation. Smoking may induce DNA hypermethylation in genes related to anti-oxidation and insulin resistance. Paternal diet and obesity are associated with greater risks of metabolic dysfunction in offspring via epigenetic alterations in the sperm. Metabolic changes, such as high blood glucose levels and increased body weight, are commonly observed in the offspring of fathers subjected to chronic stress, in addition to an enhanced risk of depressive-like behaviour and increased sensitivity to stress in both the F0 and F1 generations. DNA methylation is correlated with alterations in sperm quality and the ability to fertilise oocytes, possibly via a differentially regulated MAKP81IP3 signalling pathway. Paternal exposure to toxic endocrine-disrupting chemicals (EDCs) is also linked to the transgenerational transmission of increased predisposition to disease, infertility, testicular disorders, obesity, and polycystic ovarian syndrome (PCOS) in females through epigenetic changes during gametogenesis. As the success of assisted reproductive technology (ART) is also affected by paternal diet, BMI, and alcohol consumption, its outcomes could be improved by modifying factors that are dependent on male lifestyle choices and environmental factors. This review discusses the importance of epigenetic signatures in sperm-including DNA methylation, histone retention, and sncRNA-for sperm functionality, early embryo development, and offspring health. We also discuss the mechanisms by which paternal lifestyle and environmental factors (obesity, smoking, EDCs, and stress) may impact the sperm epigenome.
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Affiliation(s)
- Ayazhan Akhatova
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- School of Medicine, Nazarbayev University, Zhanybek-Kerey Khan Street 5/1, 010000, Astana, Kazakhstan
| | - Celine Jones
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Kevin Coward
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, 17003, Girona, Spain.
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, 17003, Girona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.
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8
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Chour M, Porteu F, Depil S, Alcazer V. Endogenous retroelements in hematological malignancies: From epigenetic dysregulation to therapeutic targeting. Am J Hematol 2025; 100:116-130. [PMID: 39387681 PMCID: PMC11625990 DOI: 10.1002/ajh.27501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 09/30/2024] [Accepted: 10/02/2024] [Indexed: 10/15/2024]
Abstract
Endogenous retroelements (EREs), which comprise half of the human genome, play a pivotal role in genome dynamics. Some EREs retained the ability to encode proteins, although most degenerated or served as a source for novel genes and regulatory elements during evolution. Despite ERE repression mechanisms developed to maintain genome stability, widespread pervasive ERE activation is observed in cancer including hematological malignancies. Challenging the perception of noncoding DNA as "junk," EREs are underestimated contributors to cancer driver mechanisms as well as antitumoral immunity by providing innate immune ligands and tumor antigens. This review highlights recent progress in understanding ERE co-option events in cancer and focuses on the controversial debate surrounding their causal role in shaping malignant phenotype. We provide insights into the rapidly evolving landscape of ERE research in hematological malignancies and their clinical implications in these cancers.
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Affiliation(s)
- Mohamed Chour
- Département de Biologie, Master Biosciences‐SantéÉcole Normale Supérieure de LyonLyonFrance
- Centre International de Recherche en InfectiologieINSERM U1111 CNRS UMR530LyonFrance
| | - Françoise Porteu
- Institut Gustave RoussyINSERM U1287 Université Paris SaclayVillejuifFrance
| | - Stéphane Depil
- Centre de Recherche en Cancérologie de LyonUMR INSERM U1052 CNRS 5286 Université Claude Bernard Lyon 1 Centre Léon BérardLyonFrance
- ErVimmuneLyonFrance
- Centre Léon BérardLyonFrance
- Université Claude Bernard Lyon 1LyonFrance
| | - Vincent Alcazer
- Centre International de Recherche en InfectiologieINSERM U1111 CNRS UMR530LyonFrance
- Université Claude Bernard Lyon 1LyonFrance
- Service d'hématologie CliniqueCentre Hospitalier Lyon Sud, Hospices Civils de LyonPierre‐BéniteFrance
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9
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Arkhipova IR, Burns KH, Lesage P. Controlling and controlled elements: highlights of the year in mobile DNA research. Mob DNA 2024; 15:27. [PMID: 39741304 PMCID: PMC11689530 DOI: 10.1186/s13100-024-00340-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Accepted: 12/26/2024] [Indexed: 01/02/2025] Open
Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Pascale Lesage
- CNRS, Institute for Research Saint Louis, Université Paris Cité (IRSL), Inserm, Paris, France
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10
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Gorse M, Bianchi C, Proudhon C. [Epigenetics and cancer: the role of DNA methylation]. Med Sci (Paris) 2024; 40:925-934. [PMID: 39705563 DOI: 10.1051/medsci/2024180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2024] Open
Abstract
Alterations in DNA methylation profiles are typically found in cancer cells, combining genome-wide hypomethylation with hypermethylation of specific regions, such as CpG islands, which are normally unmethylated. Driving effects in cancer development have been associated with alteration of DNA methylation in certain regions, inducing, for example, the repression of tumor suppressor genes or the activation of oncogenes and retrotransposons. These alterations represent prime candidates for the development of specific markers for the detection, diagnosis and prognosis of cancer. In particular, these markers, distributed along the genome, provide a wealth of information that offers potential for innovation in the field of liquid biopsy, in particular thanks to the emergence of artificial intelligence for diagnostic purposes. This could overcome the limitations related to sensitivities and specificities, which remain too low for the most difficult applications in oncology: the detection of cancers at an early stage, the monitoring of residual disease and the analysis of brain tumors. In addition, targeting the enzymatic processes that control the epigenome offers new therapeutic strategies that could reverse the regulatory anomalies of these altered epigenomes.
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Affiliation(s)
- Marine Gorse
- Université de Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) UMR_S 1085, Rennes, France
| | - Charline Bianchi
- Université de Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) UMR_S 1085, Rennes, France
| | - Charlotte Proudhon
- Université de Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) UMR_S 1085, Rennes, France
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11
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Pandiloski N, Horváth V, Karlsson O, Koutounidou S, Dorazehi F, Christoforidou G, Matas-Fuentes J, Gerdes P, Garza R, Jönsson ME, Adami A, Atacho DAM, Johansson JG, Englund E, Kokaia Z, Jakobsson J, Douse CH. DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor. Nat Commun 2024; 15:7534. [PMID: 39214989 PMCID: PMC11364546 DOI: 10.1038/s41467-024-50765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. How HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains largely unknown. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding, and simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.
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Affiliation(s)
- Ninoslav Pandiloski
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Vivien Horváth
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ofelia Karlsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Symela Koutounidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Fereshteh Dorazehi
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Georgia Christoforidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jon Matas-Fuentes
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
| | - Patricia Gerdes
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann A M Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
| | - Elisabet Englund
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Zaal Kokaia
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Laboratory of Stem Cells and Restorative Neurology, Department of Clinical Sciences, BMC B10, Lund University, Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Christopher H Douse
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden.
- Lund Stem Cell Center, Lund University, Lund, Sweden.
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12
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Bodea GO, Botto JM, Ferreiro ME, Sanchez-Luque FJ, de Los Rios Barreda J, Rasmussen J, Rahman MA, Fenlon LR, Jansz N, Gubert C, Gerdes P, Bodea LG, Ajjikuttira P, Da Costa Guevara DJ, Cumner L, Bell CC, Kozulin P, Billon V, Morell S, Kempen MJHC, Love CJ, Saha K, Palmer LM, Ewing AD, Jhaveri DJ, Richardson SR, Hannan AJ, Faulkner GJ. LINE-1 retrotransposons contribute to mouse PV interneuron development. Nat Neurosci 2024; 27:1274-1284. [PMID: 38773348 PMCID: PMC11239520 DOI: 10.1038/s41593-024-01650-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/14/2024] [Indexed: 05/23/2024]
Abstract
Retrotransposons are mobile DNA sequences duplicated via transcription and reverse transcription of an RNA intermediate. Cis-regulatory elements encoded by retrotransposons can also promote the transcription of adjacent genes. Somatic LINE-1 (L1) retrotransposon insertions have been detected in mammalian neurons. It is, however, unclear whether L1 sequences are mobile in only some neuronal lineages or therein promote neurodevelopmental gene expression. Here we report programmed L1 activation by SOX6, a transcription factor critical for parvalbumin (PV) interneuron development. Mouse PV interneurons permit L1 mobilization in vitro and in vivo, harbor unmethylated L1 promoters and express full-length L1 mRNAs and proteins. Using nanopore long-read sequencing, we identify unmethylated L1s proximal to PV interneuron genes, including a novel L1 promoter-driven Caps2 transcript isoform that enhances neuron morphological complexity in vitro. These data highlight the contribution made by L1 cis-regulatory elements to PV interneuron development and transcriptome diversity, uncovered due to L1 mobility in this milieu.
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Affiliation(s)
- Gabriela O Bodea
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia.
| | - Juan M Botto
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Maria E Ferreiro
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine 'López-Neyra', Spanish National Research Council, Granada, Spain
| | | | - Jay Rasmussen
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Muhammed A Rahman
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Laura R Fenlon
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Carolina Gubert
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Patricia Gerdes
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Prabha Ajjikuttira
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Darwin J Da Costa Guevara
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Linda Cumner
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Charles C Bell
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Peter Kozulin
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Victor Billon
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
| | - Santiago Morell
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Marie-Jeanne H C Kempen
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Chloe J Love
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Karabi Saha
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Lucy M Palmer
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Adam D Ewing
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Dhanisha J Jhaveri
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Sandra R Richardson
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia.
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13
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Deaville LA, Berrens RV. Technology to the rescue: how to uncover the role of transposable elements in preimplantation development. Biochem Soc Trans 2024; 52:1349-1362. [PMID: 38752836 PMCID: PMC11346443 DOI: 10.1042/bst20231262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024]
Abstract
Transposable elements (TEs) are highly expressed in preimplantation development. Preimplantation development is the phase when the cells of the early embryo undergo the first cell fate choice and change from being totipotent to pluripotent. A range of studies have advanced our understanding of TEs in preimplantation, as well as their epigenetic regulation and functional roles. However, many questions remain about the implications of TE expression during early development. Challenges originate first due to the abundance of TEs in the genome, and second because of the limited cell numbers in preimplantation. Here we review the most recent technological advancements promising to shed light onto the role of TEs in preimplantation development. We explore novel avenues to identify genomic TE insertions and improve our understanding of the regulatory mechanisms and roles of TEs and their RNA and protein products during early development.
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Affiliation(s)
- Lauryn A. Deaville
- Institute for Developmental and Regenerative Medicine, Oxford University, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Oxford OX3 7TY, U.K
- Department of Paediatrics, Oxford University, Level 2, Children's Hospital, John Radcliffe Headington, Oxford OX3 9DU, U.K
- MRC Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DS, U.K
| | - Rebecca V. Berrens
- Institute for Developmental and Regenerative Medicine, Oxford University, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Oxford OX3 7TY, U.K
- Department of Paediatrics, Oxford University, Level 2, Children's Hospital, John Radcliffe Headington, Oxford OX3 9DU, U.K
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14
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Lee M, Ahmad SF, Xu J. Regulation and function of transposable elements in cancer genomes. Cell Mol Life Sci 2024; 81:157. [PMID: 38556602 PMCID: PMC10982106 DOI: 10.1007/s00018-024-05195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/02/2024]
Abstract
Over half of human genomic DNA is composed of repetitive sequences generated throughout evolution by prolific mobile genetic parasites called transposable elements (TEs). Long disregarded as "junk" or "selfish" DNA, TEs are increasingly recognized as formative elements in genome evolution, wired intimately into the structure and function of the human genome. Advances in sequencing technologies and computational methods have ushered in an era of unprecedented insight into how TE activity impacts human biology in health and disease. Here we discuss the current views on how TEs have shaped the regulatory landscape of the human genome, how TE activity is implicated in human cancers, and how recent findings motivate novel strategies to leverage TE activity for improved cancer therapy. Given the crucial role of methodological advances in TE biology, we pair our conceptual discussions with an in-depth review of the inherent technical challenges in studying repeats, specifically related to structural variation, expression analyses, and chromatin regulation. Lastly, we provide a catalog of existing and emerging assays and bioinformatic software that altogether are enabling the most sophisticated and comprehensive investigations yet into the regulation and function of interspersed repeats in cancer genomes.
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Affiliation(s)
- Michael Lee
- Department of Pediatrics, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Syed Farhan Ahmad
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA
| | - Jian Xu
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA.
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