1
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Goldbach-Mansky R, Alehashemi S, de Jesus AA. Emerging concepts and treatments in autoinflammatory interferonopathies and monogenic systemic lupus erythematosus. Nat Rev Rheumatol 2025; 21:22-45. [PMID: 39623155 DOI: 10.1038/s41584-024-01184-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2024] [Indexed: 12/22/2024]
Abstract
Over the past two decades, the number of genetically defined autoinflammatory interferonopathies has steadily increased. Aicardi-Goutières syndrome and proteasome-associated autoinflammatory syndromes (PRAAS, also known as CANDLE) are caused by genetic defects that impair homeostatic intracellular nucleic acid and protein processing respectively. Research into these genetic defects revealed intracellular sensors that activate type I interferon production. In SAVI and COPA syndrome, genetic defects that cause chronic activation of the dinucleotide sensor stimulator of interferon genes (STING) share features of lung inflammation and fibrosis; and selected mutations that amplify interferon-α/β receptor signalling cause central nervous system manifestations resembling Aicardi-Goutières syndrome. Research into the monogenic causes of childhood-onset systemic lupus erythematosus (SLE) demonstrates the pathogenic role of autoantibodies to particle-bound extracellular nucleic acids that distinguishes monogenic SLE from the autoinflammatory interferonopathies. This Review introduces a classification for autoinflammatory interferonopathies and discusses the divergent and shared pathomechanisms of interferon production and signalling in these diseases. Early success with drugs that block type I interferon signalling, new insights into the roles of cytoplasmic DNA or RNA sensors, pathways in type I interferon production and organ-specific pathology of the autoinflammatory interferonopathies and monogenic SLE, reveal novel drug targets that could personalize treatment approaches.
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Affiliation(s)
- Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Sara Alehashemi
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adriana A de Jesus
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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2
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Sun S, You E, Hong J, Hoyos D, Del Priore I, Tsanov KM, Mattagajasingh O, Di Gioacchino A, Marhon SA, Chacon-Barahona J, Li H, Jiang H, Hozeifi S, Rosas-Bringas O, Xu KH, Song Y, Lang ER, Rojas AS, Nieman LT, Patel BK, Murali R, Chanda P, Karacay A, Vabret N, De Carvalho DD, Zenklusen D, LaCava J, Lowe SW, Ting DT, Iacobuzio-Donahue CA, Solovyov A, Greenbaum BD. Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms. Immunity 2024; 57:2879-2894.e11. [PMID: 39577413 DOI: 10.1016/j.immuni.2024.10.015] [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: 11/16/2023] [Revised: 06/28/2024] [Accepted: 10/29/2024] [Indexed: 11/24/2024]
Abstract
To thrive, cancer cells must navigate acute inflammatory signaling accompanying oncogenic transformation, such as via overexpression of repeat elements. We examined the relationship between immunostimulatory repeat expression, tumor evolution, and the tumor-immune microenvironment. Integration of multimodal data from a cohort of pancreatic ductal adenocarcinoma (PDAC) patients revealed expression of specific Alu repeats predicted to form double-stranded RNAs (dsRNAs) and trigger retinoic-acid-inducible gene I (RIG-I)-like-receptor (RLR)-associated type-I interferon (IFN) signaling. Such Alu-derived dsRNAs also anti-correlated with pro-tumorigenic macrophage infiltration in late stage tumors. We defined two complementary pathways whereby PDAC may adapt to such anti-tumorigenic signaling. In mutant TP53 tumors, ORF1p from long interspersed nuclear element (LINE)-1 preferentially binds Alus and decreases their expression, whereas adenosine deaminases acting on RNA 1 (ADAR1) editing primarily reduces dsRNA formation in wild-type TP53 tumors. Depletion of either LINE-1 ORF1p or ADAR1 reduced tumor growth in vitro. The fact that tumors utilize multiple pathways to mitigate immunostimulatory repeats implies the stress from their expression is a fundamental phenomenon to which PDAC, and likely other tumors, adapt.
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Affiliation(s)
- Siyu Sun
- Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eunae You
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Jungeui Hong
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Hoyos
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Isabella Del Priore
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Om Mattagajasingh
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Andrea Di Gioacchino
- Laboratoire de Physique de l'Ecole Normale Supérieure, Sorbonne Université, Université de Paris, Paris, France
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jonathan Chacon-Barahona
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Hao Li
- Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Samira Hozeifi
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Omar Rosas-Bringas
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Katherine H Xu
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Yuhui Song
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Evan R Lang
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Alexandra S Rojas
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Linda T Nieman
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Bidish K Patel
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Rajmohan Murali
- Last Wish Program and Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pharto Chanda
- Last Wish Program and Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ali Karacay
- Last Wish Program and Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicolas Vabret
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Daniel Zenklusen
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - John LaCava
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David T Ting
- Massachusetts General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Last Wish Program and Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Solovyov
- Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin D Greenbaum
- Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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3
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Saha K, Nielsen G, Nandani R, Zhang Y, Kong L, Ye P, An W. YY1 is a transcriptional activator of the mouse LINE-1 Tf subfamily. Nucleic Acids Res 2024; 52:12878-12894. [PMID: 39460630 PMCID: PMC11602158 DOI: 10.1093/nar/gkae949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 09/07/2024] [Accepted: 10/08/2024] [Indexed: 10/28/2024] Open
Abstract
Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element in human and mouse genomes. L1 transcription is controlled by an internal RNA polymerase II promoter in the 5' untranslated region (5'UTR) of a full-length L1. It has been shown that transcription factor YY1 binds to a conserved sequence at the 5' end of the human L1 5'UTR and primarily dictates where transcription initiates. Putative YY1-binding motifs have been predicted in the 5'UTRs of two distinct mouse L1 subfamilies, Tf and Gf. Using site-directed mutagenesis, in vitro binding and gene knockdown assays, we experimentally tested the role of YY1 in mouse L1 transcription. Our results indicate that Tf, but not Gf subfamily, harbors functional YY1-binding sites in 5'UTR monomers and YY1 functions as a transcriptional activator for the mouse Tf subfamily. Activation of Tf transcription by YY1 during early embryogenesis is also supported by a reanalysis of published zygotic knockdown data. Furthermore, YY1-binding motifs are solely responsible for the synergistic interaction between Tf monomers, consistent with a model wherein distant monomers act as enhancers for mouse L1 transcription. The abundance of YY1-binding sites in Tf elements also raise important implications for gene regulation across the genome.
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Affiliation(s)
- Karabi Saha
- Department of Pharmaceutical Sciences, South Dakota State University, 1055 Campanile Ave, Brookings, SD 57007, USA
| | - Grace I Nielsen
- Department of Pharmaceutical Sciences, South Dakota State University, 1055 Campanile Ave, Brookings, SD 57007, USA
| | - Raj Nandani
- Department of Pharmaceutical Sciences, South Dakota State University, 1055 Campanile Ave, Brookings, SD 57007, USA
| | - Yizi Zhang
- Department of Pharmaceutical Sciences, South Dakota State University, 1055 Campanile Ave, Brookings, SD 57007, USA
| | - Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, 1055 Campanile Ave, Brookings, SD 57007, USA
| | - Ping Ye
- Department of Pharmaceutical Sciences, South Dakota State University, 1055 Campanile Ave, Brookings, SD 57007, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, 1055 Campanile Ave, Brookings, SD 57007, USA
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4
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Nelson B, Faquin W. Cancer-aiding elements begin illuminating the genome's "dark matter": Within what was once deemed useless junk, virus-like retrotransposons, long noncoding RNAs, and other exotic molecules have emerged as beacons for cancer researchers. Cancer Cytopathol 2024; 132:671-672. [PMID: 39487955 DOI: 10.1002/cncy.22917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2024]
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5
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Feng S, Marhon SA, Sokolowski DJ, D'Costa A, Soares F, Mehdipour P, Ishak C, Loo Yau H, Ettayebi I, Patel PS, Chen R, Liu J, Zuzarte PC, Ho KC, Ho B, Ning S, Huang A, Arrowsmith CH, Wilson MD, Simpson JT, De Carvalho DD. Inhibiting EZH2 targets atypical teratoid rhabdoid tumor by triggering viral mimicry via both RNA and DNA sensing pathways. Nat Commun 2024; 15:9321. [PMID: 39472584 PMCID: PMC11522499 DOI: 10.1038/s41467-024-53515-8] [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: 03/01/2023] [Accepted: 10/12/2024] [Indexed: 11/02/2024] Open
Abstract
Inactivating mutations in SMARCB1 confer an oncogenic dependency on EZH2 in atypical teratoid rhabdoid tumors (ATRTs), but the underlying mechanism has not been fully elucidated. We found that the sensitivity of ATRTs to EZH2 inhibition (EZH2i) is associated with the viral mimicry response. Unlike other epigenetic therapies targeting transcriptional repressors, EZH2i-induced viral mimicry is not triggered by cryptic transcription of endogenous retroelements, but rather mediated by increased expression of genes enriched for intronic inverted-repeat Alu (IR-Alu) elements. Interestingly, interferon-stimulated genes (ISGs) are highly enriched for dsRNA-forming intronic IR-Alu elements, suggesting a feedforward loop whereby these activated ISGs may reinforce dsRNA formation and viral mimicry. EZH2i also upregulates the expression of full-length LINE-1s, leading to genomic instability and cGAS/STING signaling in a process dependent on reverse transcriptase activity. Co-depletion of dsRNA sensing and cytoplasmic DNA sensing completely rescues the viral mimicry response to EZH2i in SMARCB1-deficient tumors.
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Affiliation(s)
- Shengrui Feng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- The First Affiliated Hospital of University of South China, Hengyang, Hunan, China.
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dustin J Sokolowski
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Alister D'Costa
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Fraser Soares
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Parinaz Mehdipour
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Charles Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen Loo Yau
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Ilias Ettayebi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Raymond Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jiming Liu
- The Cardiac Development and Early Intervention Unit, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, China
| | | | - King Ching Ho
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | - Ben Ho
- Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Shiyao Ning
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Annie Huang
- The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Jared T Simpson
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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6
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Martinez JC, Morandini F, Fitzgibbons L, Sieczkiewicz N, Bae SJ, Meadow ME, Hillpot E, Cutting J, Paige V, Biashad SA, Simon M, Sedivy J, Seluanov A, Gorbunova V. cGAS deficient mice display premature aging associated with de-repression of LINE1 elements and inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617645. [PMID: 39416083 PMCID: PMC11482887 DOI: 10.1101/2024.10.10.617645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Aging-associated inflammation, or 'inflammaging" is a driver of multiple age-associated diseases. Cyclic GMP-AMP Synthase (cGAS) is a cytosolic DNA sensor that functions to activate interferon response upon detecting viral DNA in the cytoplasm. cGAS contributes to inflammaging by responding to endogenous signals such as damaged DNA or LINE1 (L1) cDNA which forms in aged cells. While cGAS knockout mice are viable their aging has not been examined. Unexpectedly, we found that cGAS knockout mice exhibit accelerated aging phenotype associated with induction of inflammation. Transcription of L1 elements was increased in both cGAS knockout mice and in cGAS siRNA knockdown cells associated with high levels of cytoplasmic L1 DNA and expression of ORF1 protein. Cells from cGAS knockout mice showed increased chromatin accessibility and decreased DNA methylation on L1 transposons. Stimulated emission depletion microscopy (STED) showed that cGAS forms nuclear condensates that co-localize with H3K9me3 heterochromatin marks, and H3K9me3 pattern is disrupted in cGAS knockout cells. Taken together these results suggest a previously undescribed role for cGAS in maintaining heterochromatin on transposable elements. We propose that loss of cGAS leads to loss of chromatin organization, de-repression of transposable elements and induction of inflammation resulting in accelerated aging.
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Affiliation(s)
- John C Martinez
- Translational Biomedical Sciences Program, University of Rochester, NY, 14627, USA
- Department of Biology, University of Rochester, NY, 14627, USA
| | | | | | | | - Sung Jae Bae
- Department of Biology, University of Rochester, NY, 14627, USA
| | | | - Eric Hillpot
- Department of Biology, University of Rochester, NY, 14627, USA
| | - Joseph Cutting
- Department of Biology, University of Rochester, NY, 14627, USA
| | - Victoria Paige
- Department of Biology, University of Rochester, NY, 14627, USA
| | | | - Matthew Simon
- Department of Biology, University of Rochester, NY, 14627, USA
| | - John Sedivy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, RI, 02912, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, NY, 14627, USA
- Department of Medicine, University of Rochester, NY, 14627, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, NY, 14627, USA
- Department of Medicine, University of Rochester, NY, 14627, USA
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7
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Kraft K, Murphy SE, Jones MG, Shi Q, Bhargava-Shah A, Luong C, Hung KL, He BJ, Li R, Park SK, Weiser NE, Luebeck J, Bafna V, Boeke JD, Mischel PS, Boettiger AN, Chang HY. Enhancer activation from transposable elements in extrachromosomal DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611262. [PMID: 39282372 PMCID: PMC11398463 DOI: 10.1101/2024.09.04.611262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Extrachromosomal DNA (ecDNA) is a hallmark of aggressive cancer, contributing to both oncogene amplification and tumor heterogeneity. Here, we used Hi-C, super-resolution imaging, and long-read sequencing to explore the nuclear architecture of MYC-amplified ecDNA in colorectal cancer cells. Intriguingly, we observed frequent spatial proximity between ecDNA and 68 repetitive elements which we called ecDNA-interacting elements or EIEs. To characterize a potential regulatory role of EIEs, we focused on a fragment of the L1M4a1#LINE/L1 which we found to be co-amplified with MYC on ecDNA, gaining enhancer-associated chromatin marks in contrast to its normally silenced state. This EIE, in particular, existed as a naturally occurring structural variant upstream of MYC, gaining oncogenic potential in the transcriptionally permissive ecDNA environment. This EIE sequence is sufficient to enhance MYC expression and is required for cancer cell fitness. These findings suggest that silent repetitive genomic elements can be reactivated on ecDNA, leading to functional cooption and amplification. Repeat element activation on ecDNA represents a mechanism of accelerated evolution and tumor heterogeneity and may have diagnostic and therapeutic potential.
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Affiliation(s)
- Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sedona E. Murphy
- Present address: Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Matthew G. Jones
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aarohi Bhargava-Shah
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Christy Luong
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford, CA 94305, USA
| | - King L. Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Britney J. He
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung K. Park
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Natasha E. Weiser
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Paul S. Mischel
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | | | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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8
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Potapov V, Krudup S, Maguire S, Unlu I, Guan S, Buss JA, Smail BA, van Eeuwen T, Taylor MS, Burns KH, Ong JL, Trachman RJ. Discrete measurements of RNA polymerase and reverse transcriptase fidelity reveal evolutionary tuning. RNA (NEW YORK, N.Y.) 2024; 30:1246-1258. [PMID: 38942481 PMCID: PMC11331410 DOI: 10.1261/rna.080002.124] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Direct methods for determining the fidelity of DNA polymerases are robust, with relatively little sample manipulation before sequencing. In contrast, methods for measuring RNA polymerase and reverse transcriptase fidelities are complicated by additional preparation steps that introduce ambiguity and error. Here, we describe a sequencing method, termed Roll-Seq, for simultaneously determining the individual fidelities of RNA polymerases and reverse transcriptases (RT) using Pacific Biosciences single molecule real-time sequencing. By using reverse transcriptases with high rolling-circle activity, Roll-Seq generates long concatemeric cDNA from a circular RNA template. To discern the origin of a mutation, errors are recorded and determined to occur within a single concatemer (reverse transcriptase error) or all concatemers (RNA polymerase error) over the cDNA strand. We used Roll-Seq to measure the fidelities of T7 RNA polymerases, a Group II intron-encoded RT (Induro), and two LINE RTs (Fasciolopsis buski R2-RT and human LINE-1). Substitution rates for Induro and R2-RT are the same for cDNA and second-strand synthesis while LINE-1 has 2.5-fold lower fidelity when performing second-strand synthesis. Deletion and insertion rates increase for all RTs during second-strand synthesis. In addition, we find that a structured RNA template impacts fidelity for both RNA polymerase and RT. The accuracy and precision of Roll-Seq enable this method to be applied as a complementary analysis to structural and mechanistic characterization of RNA polymerases and reverse transcriptases or as a screening method for RNAP and RT fidelity.
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Affiliation(s)
| | - Stanislas Krudup
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
- École Supérieure de Biotechnologie de Strasbourg, 67400 Strasbourg, France
| | - Sean Maguire
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Irem Unlu
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Jackson A Buss
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
| | - Benedict A Smail
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Martin S Taylor
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Pathology, Mass General Brigham and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jennifer L Ong
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA
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9
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Shi G, Pang Q, Lin Z, Zhang X, Huang K. Repetitive Sequence Stability in Embryonic Stem Cells. Int J Mol Sci 2024; 25:8819. [PMID: 39201503 PMCID: PMC11354519 DOI: 10.3390/ijms25168819] [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: 07/10/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Repetitive sequences play an indispensable role in gene expression, transcriptional regulation, and chromosome arrangements through trans and cis regulation. In this review, focusing on recent advances, we summarize the epigenetic regulatory mechanisms of repetitive sequences in embryonic stem cells. We aim to bridge the knowledge gap by discussing DNA damage repair pathway choices on repetitive sequences and summarizing the significance of chromatin organization on repetitive sequences in response to DNA damage. By consolidating these insights, we underscore the critical relationship between the stability of repetitive sequences and early embryonic development, seeking to provide a deeper understanding of repetitive sequence stability and setting the stage for further research and potential therapeutic strategies in developmental biology and regenerative medicine.
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Affiliation(s)
- Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Qianwen Pang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Zhancheng Lin
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Xinyi Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Kaimeng Huang
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA;
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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10
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Faulkner GJ. Two HUSH complexes connect a direct LINE to innate immunity. Mol Cell 2024; 84:2801-2803. [PMID: 39121841 DOI: 10.1016/j.molcel.2024.07.010] [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: 07/12/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 08/12/2024]
Abstract
In this issue of Molecular Cell, Danac et al.1 identify a second HUSH complex, HUSH2, that represses interferon-stimulated genes and, by competing for subunits with the canonical HUSH complex, couples LINE-1 (L1) retrotransposon transcription with immune activation.
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Affiliation(s)
- Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, St. Lucia, QLD 4067, Australia.
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11
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Wu MJ, Kondo H, Kammula AV, Shi L, Xiao Y, Dhiab S, Xu Q, Slater CJ, Avila OI, Merritt J, Kato H, Kattel P, Sussman J, Gritti I, Eccleston J, Sun Y, Cho HM, Olander K, Katsuda T, Shi DD, Savani MR, Smith BC, Cleary JM, Mostoslavsky R, Vijay V, Kitagawa Y, Wakimoto H, Jenkins RW, Yates KB, Paik J, Tassinari A, Saatcioglu DH, Tron AE, Haas W, Cahill D, McBrayer SK, Manguso RT, Bardeesy N. Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity. Science 2024; 385:eadl6173. [PMID: 38991060 PMCID: PMC11602233 DOI: 10.1126/science.adl6173] [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: 11/17/2023] [Accepted: 05/09/2024] [Indexed: 07/13/2024]
Abstract
Isocitrate dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores antitumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. IDH1-mutant solid tumors show selective hypermethylation and silencing of the cytoplasmic double-stranded DNA (dsDNA) sensor CGAS, compromising innate immune signaling. mIDH1 inhibition restores DNA demethylation, derepressing CGAS and transposable element (TE) subclasses. dsDNA produced by TE-reverse transcriptase (TE-RT) activates cGAS, triggering viral mimicry and stimulating antitumor immunity. In summary, we demonstrate that mIDH1 epigenetically suppresses innate immunity and link endogenous RT activity to the mechanism of action of a US Food and Drug Administration-approved oncology drug.
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Affiliation(s)
- Meng-Ju Wu
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Hiroshi Kondo
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Ashwin V. Kammula
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Lei Shi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Yi Xiao
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofiene Dhiab
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Qin Xu
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Chloe J. Slater
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Universite Paris-Saclay, Institut Gustave Roussy, INSERM U1015, Villejuif, France
- Servier Pharmaceuticals LLC, Boston, MA, USA
| | - Omar I. Avila
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Joshua Merritt
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Hiroyuki Kato
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Prabhat Kattel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jonathan Sussman
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ilaria Gritti
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jason Eccleston
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yi Sun
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
| | - Hyo Min Cho
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Kira Olander
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Takeshi Katsuda
- Abramson Family Cancer Research Institute and Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Diana D. Shi
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Radiation Oncology, Dana-Farber/Brigham and Women’s Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Milan R. Savani
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bailey C. Smith
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James M Cleary
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Raul Mostoslavsky
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Vindhya Vijay
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Yosuke Kitagawa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Russell W. Jenkins
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Kathleen B. Yates
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine, Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | | | | | | | - Wilhelm Haas
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Daniel Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert T. Manguso
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Nabeel Bardeesy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
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12
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Hernandez CM, Duran-Chaparro DC, van Eeuwen T, Rout MP, Holt LJ. Development and Characterization of 50 nanometer diameter Genetically Encoded Multimeric Nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602291. [PMID: 39005449 PMCID: PMC11245105 DOI: 10.1101/2024.07.05.602291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The mechanisms that regulate the physical properties of the cell interior remain poorly understood, especially at the mesoscale (10nm-100nm). Changes in these properties have been suggested to be crucial for both normal physiology and disease. Many crucial macromolecules and molecular assemblies such as ribosomes, RNA polymerase, and biomolecular condensates span the mesoscale size range. Therefore, we need better tools to study the cellular environment at this scale. A recent approach has been to use genetically encoded multimeric nanoparticles (GEMs), which consist of self-assembling scaffold proteins fused to fluorescent tags. After translation of the fusion protein, the monomers self-assemble into bright and stable nanoparticles of defined geometry that can be visualized by fluorescence microscopy. Physical properties of the cell can then be inferred through analysis of the motion of these particles, an approach called nanorheology. Previously, 40nm-GEMs elucidated TORC1 kinase as a regulator of cytoplasmic crowding. However, extremely sensitive microscopes were required. Here, we describe the development and characterization of a 50 nm diameter GEM that is brighter and probes a larger length scale. 50nm-GEMs will make high-throughput nanorheology accessible to a broader range of researchers and reveal new insights into the biophysical properties of cells.
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Affiliation(s)
- Cindy M Hernandez
- Institute for Systems Genetics, New York University School of Medicine, New York, 435 E 30th Street NY 10016, United States
| | - David C Duran-Chaparro
- Institute for Systems Genetics, New York University School of Medicine, New York, 435 E 30th Street NY 10016, United States
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY10065
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY10065
| | - Liam J Holt
- Institute for Systems Genetics, New York University School of Medicine, New York, 435 E 30th Street NY 10016, United States
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13
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Talley MJ, Longworth MS. Retrotransposons in embryogenesis and neurodevelopment. Biochem Soc Trans 2024; 52:1159-1171. [PMID: 38716891 PMCID: PMC11346457 DOI: 10.1042/bst20230757] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024]
Abstract
Retrotransposable elements (RTEs) are genetic elements that can replicate and insert new copies into different genomic locations. RTEs have long been identified as 'parasitic genes', as their mobilization can cause mutations, DNA damage, and inflammation. Interestingly, high levels of retrotransposon activation are observed in early embryogenesis and neurodevelopment, suggesting that RTEs may possess functional roles during these stages of development. Recent studies demonstrate that RTEs can function as transcriptional regulatory elements through mechanisms such as chromatin organization and noncoding RNAs. It is clear, however, that RTE expression and activity must be restrained at some level during development, since overactivation of RTEs during neurodevelopment is associated with several developmental disorders. Further investigation is needed to understand the importance of RTE expression and activity during neurodevelopment and the balance between RTE-regulated development and RTE-mediated pathogenesis.
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Affiliation(s)
- Mary Jo Talley
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
| | - Michelle S. Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, U.S.A
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14
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D'Ordine AM, Jogl G, Sedivy JM. Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease. Nat Commun 2024; 15:3883. [PMID: 38719805 PMCID: PMC11078990 DOI: 10.1038/s41467-024-48066-x] [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: 07/12/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We characterize structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be used for further pharmacological development and as tools to better understand the life cycle of this element and its impact on disease processes.
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Affiliation(s)
- Alexandra M D'Ordine
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
- Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
- Center on the Biology of Aging, Brown University, Providence, RI, USA.
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
- Center on the Biology of Aging, Brown University, Providence, RI, USA.
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15
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Baril T, Galbraith J, Hayward A. Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline. Mol Biol Evol 2024; 41:msae068. [PMID: 38577785 PMCID: PMC11003543 DOI: 10.1093/molbev/msae068] [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: 11/24/2023] [Revised: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above while scoring highly in benchmarking for TE annotation and classification and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focused on further quality control and tailored analyses in future releases.
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Affiliation(s)
- Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - James Galbraith
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
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16
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Zehrbach NM, Oh N, Ishak CA. Insights into LINE-1 reverse transcription guide therapy development. Trends Cancer 2024; 10:286-288. [PMID: 38499453 DOI: 10.1016/j.trecan.2024.02.010] [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: 01/15/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
Subsets of long interspersed nuclear element 1 (LINE-1) retrotransposons can 'retrotranspose' throughout the human genome at a cost to host cell fitness, as observed in some cancers. Pharmacological inhibition of LINE-1 retrotransposition requires a comprehensive understanding of the LINE-1 ORF2p reverse transcriptase. Two recent publications, by Thawani et al. and Baldwin et al., report structures of LINE-1 ORF2p and address long-standing mechanistic gaps regarding LINE-1 retrotransposition. Both studies will be critical to design new specific inhibitors of the LINE-1 ORF2p reverse transcriptase.
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Affiliation(s)
- Nicholas M Zehrbach
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nakyung Oh
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles A Ishak
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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17
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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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18
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Chow TW, Raupp M, Reynolds MW, Li S, Kaeser GE, Chun J. Nucleoside Reverse Transcriptase Inhibitor Exposure Is Associated with Lower Alzheimer's Disease Risk: A Retrospective Cohort Proof-of-Concept Study. Pharmaceuticals (Basel) 2024; 17:408. [PMID: 38675371 PMCID: PMC11053431 DOI: 10.3390/ph17040408] [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: 02/12/2024] [Revised: 03/02/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Brain somatic gene recombination (SGR) and the endogenous reverse transcriptases (RTs) that produce it have been implicated in the etiology of Alzheimer's disease (AD), suggesting RT inhibitors as novel prophylactics or therapeutics. This retrospective, proof-of-concept study evaluated the incidence of AD in people with human immunodeficiency virus (HIV) with or without exposure to nucleoside RT inhibitors (NRTIs) using de-identified medical claims data. Eligible participants were aged ≥60 years, without pre-existing AD diagnoses, and pursued medical services in the United States from October 2015 to September 2016. Cohorts 1 (N = 46,218) and 2 (N = 32,923) had HIV. Cohort 1 had prescription claims for at least one NRTI within the exposure period; Cohort 2 did not. Cohort 3 (N = 150,819) had medical claims for the common cold without evidence of HIV or antiretroviral therapy. The cumulative incidence of new AD cases over the ensuing 2.75-year observation period was lowest in patients with NRTI exposure and highest in controls. Age- and sex-adjusted hazard ratios showed a significantly decreased risk for AD in Cohort 1 compared with Cohorts 2 (HR 0.88, p < 0.05) and 3 (HR 0.84, p < 0.05). Sub-grouping identified a decreased AD risk in patients with NRTI exposure but without protease inhibitor (PI) exposure. Prospective clinical trials and the development of next-generation agents targeting brain RTs are warranted.
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Affiliation(s)
- Tiffany W. Chow
- IQVIA, Durham, NC 27703, USA; (T.W.C.); (M.R.)
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Raupp
- IQVIA, Durham, NC 27703, USA; (T.W.C.); (M.R.)
| | | | - Siying Li
- IQVIA, Durham, NC 27703, USA; (T.W.C.); (M.R.)
| | - Gwendolyn E. Kaeser
- Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jerold Chun
- Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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19
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Kines KJ, Sokolowski M, DeFreece C, Shareef A, deHaro DL, Belancio VP. Large Deletions, Cleavage of the Telomeric Repeat Sequence, and Reverse Transcriptase-Mediated DNA Damage Response Associated with Long Interspersed Element-1 ORF2p Enzymatic Activities. Genes (Basel) 2024; 15:143. [PMID: 38397133 PMCID: PMC10887698 DOI: 10.3390/genes15020143] [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: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
L1 elements can cause DNA damage and genomic variation via retrotransposition and the generation of endonuclease-dependent DNA breaks. These processes require L1 ORF2p protein that contains an endonuclease domain, which cuts genomic DNA, and a reverse transcriptase domain, which synthesizes cDNA. The complete impact of L1 enzymatic activities on genome stability and cellular function remains understudied, and the spectrum of L1-induced mutations, other than L1 insertions, is mostly unknown. Using an inducible system, we demonstrate that an ORF2p containing functional reverse transcriptase is sufficient to elicit DNA damage response even in the absence of the functional endonuclease. Using a TK/Neo reporter system that captures misrepaired DNA breaks, we demonstrate that L1 expression results in large genomic deletions that lack any signatures of L1 involvement. Using an in vitro cleavage assay, we demonstrate that L1 endonuclease efficiently cuts telomeric repeat sequences. These findings support that L1 could be an unrecognized source of disease-promoting genomic deletions, telomere dysfunction, and an underappreciated source of chronic RT-mediated DNA damage response in mammalian cells. Our findings expand the spectrum of biological processes that can be triggered by functional and nonfunctional L1s, which have impactful evolutionary- and health-relevant consequences.
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Affiliation(s)
- Kristine J. Kines
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Cecily DeFreece
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Afzaal Shareef
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Dawn L. deHaro
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
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20
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Saha K, Nielsen GI, Nandani R, Kong L, Ye P, An W. YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573552. [PMID: 38260579 PMCID: PMC10802269 DOI: 10.1101/2024.01.03.573552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element (TE) in the human genome. The first step of L1 replication is transcription, which is controlled by an internal RNA polymerase II promoter in the 5' untranslated region (UTR) of a full-length L1. It has been shown that transcription factor YY1 binds to a conserved sequence motif at the 5' end of the human L1 5'UTR and dictates where transcription initiates but not the level of transcription. Putative YY1-binding motifs have been predicted in the 5'UTRs of two distinct mouse L1 subfamilies, Tf and Gf. Using site-directed mutagenesis, in vitro binding, and gene knockdown assays, we experimentally tested the role of YY1 in mouse L1 transcription. Our results indicate that Tf, but not Gf subfamily, harbors functional YY1-binding sites in its 5'UTR monomers. In contrast to its role in human L1, YY1 functions as a transcriptional activator for the mouse Tf subfamily. Furthermore, YY1-binding motifs are solely responsible for the synergistic interaction between monomers, consistent with a model wherein distant monomers act as enhancers for mouse L1 transcription. The abundance of YY1-binding sites in Tf elements also raise important implications for gene regulation at the genomic level.
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Affiliation(s)
- Karabi Saha
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Grace I. Nielsen
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Raj Nandani
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Ping Ye
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
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Luqman-Fatah A, Nishimori K, Amano S, Fumoto Y, Miyoshi T. Retrotransposon life cycle and its impacts on cellular responses. RNA Biol 2024; 21:11-27. [PMID: 39396200 PMCID: PMC11485995 DOI: 10.1080/15476286.2024.2409607] [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] [Revised: 08/30/2024] [Accepted: 09/16/2024] [Indexed: 10/14/2024] Open
Abstract
Approximately 45% of the human genome is comprised of transposable elements (TEs), also known as mobile genetic elements. However, their biological function remains largely unknown. Among them, retrotransposons are particularly abundant, and some of the copies are still capable of mobilization within the genome through RNA intermediates. This review focuses on the life cycle of human retrotransposons and summarizes their regulatory mechanisms and impacts on cellular processes. Retrotransposons are generally epigenetically silenced in somatic cells, but are transcriptionally reactivated under certain conditions, such as tumorigenesis, development, stress, and ageing, potentially leading to genetic instability. We explored the dual nature of retrotransposons as genomic parasites and regulatory elements, focusing on their roles in genetic diversity and innate immunity. Furthermore, we discuss how host factors regulate retrotransposon RNA and cDNA intermediates through their binding, modification, and degradation. The interplay between retrotransposons and the host machinery provides insight into the complex regulation of retrotransposons and the potential for retrotransposon dysregulation to cause aberrant responses leading to inflammation and autoimmune diseases.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kei Nishimori
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shota Amano
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yukiko Fumoto
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomoichiro Miyoshi
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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