1
|
Pizzioli E, Minutolo A, Balestrieri E, Matteucci C, Magiorkinis G, Horvat B. Crosstalk between human endogenous retroviruses and exogenous viruses. Microbes Infect 2024:105427. [PMID: 39349096 DOI: 10.1016/j.micinf.2024.105427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 09/11/2024] [Accepted: 09/26/2024] [Indexed: 10/02/2024]
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections of human germ-line cells, which are mostly silenced during evolution, but could be de-repressed and play a pathological role. Infection with some exogenous viruses, including herpesviruses, HIV-1 and SARS-CoV-2, was demonstrated to induce the expression of HERV RNAs and proteins.
Collapse
Affiliation(s)
- Edoardo Pizzioli
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, France
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, France.
| |
Collapse
|
2
|
Kitsou K, Katzourakis A, Magiorkinis G. Limitations of current high-throughput sequencing technologies lead to biased expression estimates of endogenous retroviral elements. NAR Genom Bioinform 2024; 6:lqae081. [PMID: 38984066 PMCID: PMC11231582 DOI: 10.1093/nargab/lqae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/09/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
Human endogenous retroviruses (HERVs), the remnants of ancient germline retroviral integrations, comprise almost 8% of the human genome. The elucidation of their biological roles is hampered by our inability to link HERV mRNA and protein production with specific HERV loci. To solve the riddle of the integration-specific RNA expression of HERVs, several bioinformatics approaches have been proposed; however, no single process seems to yield optimal results due to the repetitiveness of HERV integrations. The performance of existing data-bioinformatics pipelines has been evaluated against real world datasets whose true expression profile is unknown, thus the accuracy of widely-used approaches remains unclear. Here, we simulated mRNA production from specific HERV integrations to evaluate second and third generation sequencing technologies along with widely used bioinformatic approaches to estimate the accuracy in describing integration-specific expression. We demonstrate that, while a HERV-family approach offers accurate results, per-integration analyses of HERV expression suffer from substantial expression bias, which is only partially mitigated by algorithms developed for calculating the per-integration HERV expression, and is more pronounced in recent integrations. Hence, this bias could erroneously result into biologically meaningful inferences. Finally, we demonstrate the merits of accurate long-read high-throughput sequencing technologies in the resolution of per-locus HERV expression.
Collapse
Affiliation(s)
- Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens 11527, Greece
| | | | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens 11527, Greece
| |
Collapse
|
3
|
Jarosz AS, Halo JV. Transcription of Endogenous Retroviruses: Broad and Precise Mechanisms of Control. Viruses 2024; 16:1312. [PMID: 39205286 PMCID: PMC11359688 DOI: 10.3390/v16081312] [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: 06/24/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous retroviruses (ERVs) are the remnants of retroviral germline infections and are highly abundant in the genomes of vertebrates. At one time considered to be nothing more than inert 'junk' within genomes, ERVs have been tolerated within host genomes over vast timescales, and their study continues to reveal complex co-evolutionary histories within their respective host species. For example, multiple instances have been characterized of ERVs having been 'borrowed' for normal physiology, from single copies to ones involved in various regulatory networks such as innate immunity and during early development. Within the cell, the accessibility of ERVs is normally tightly controlled by epigenetic mechanisms such as DNA methylation or histone modifications. However, these silencing mechanisms of ERVs are reversible, and epigenetic alterations to the chromatin landscape can thus lead to their aberrant expression, as is observed in abnormal cellular environments such as in tumors. In this review, we focus on ERV transcriptional control and draw parallels and distinctions concerning the loss of regulation in disease, as well as their precise regulation in early development.
Collapse
Affiliation(s)
- Abigail S. Jarosz
- Science and Mathematics Division, Lorrain County Community College, Lorrain, OH 44035, USA;
| | - Julia V. Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| |
Collapse
|
4
|
Williams ZH, Imedio AD, Gaucherand L, Lee DC, Mostafa SM, Phelan JP, Coffin JM, Johnson WE. Recombinant origin and interspecies transmission of a HERV-K(HML-2)-related primate retrovirus with a novel RNA transport element. eLife 2024; 13:e80216. [PMID: 39037763 PMCID: PMC11379458 DOI: 10.7554/elife.80216] [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: 05/24/2022] [Accepted: 07/20/2024] [Indexed: 07/23/2024] Open
Abstract
HERV-K(HML-2), the youngest clade of human endogenous retroviruses (HERVs), includes many intact or nearly intact proviruses, but no replication competent HML-2 proviruses have been identified in humans. HML-2-related proviruses are present in other primates, including rhesus macaques, but the extent and timing of HML-2 activity in macaques remains unclear. We have identified 145 HML-2-like proviruses in rhesus macaques, including a clade of young, rhesus-specific insertions. Age estimates, intact open reading frames, and insertional polymorphism of these insertions are consistent with recent or ongoing infectious activity in macaques. 106 of the proviruses form a clade characterized by an ~750 bp sequence between env and the 3' long terminal repeat (LTR), derived from an ancient recombination with a HERV-K(HML-8)-related virus. This clade is found in Old World monkeys (OWM), but not great apes, suggesting it originated after the ape/OWM split. We identified similar proviruses in white-cheeked gibbons; the gibbon insertions cluster within the OWM recombinant clade, suggesting interspecies transmission from OWM to gibbons. The LTRs of the youngest proviruses have deletions in U3, which disrupt the Rec Response Element (RcRE), required for nuclear export of unspliced viral RNA. We show that the HML-8-derived region functions as a Rec-independent constitutive transport element (CTE), indicating the ancestral Rec-RcRE export system was replaced by a CTE mechanism.
Collapse
Affiliation(s)
| | | | - Lea Gaucherand
- Molecular Microbiology Program, Tufts University Graduate School of Biomedical Sciences, Boston, United States
| | - Derek C Lee
- Department of Biology, Boston College, Boston, United States
| | - Salwa Mohd Mostafa
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, United States
| | - James P Phelan
- Molecular Microbiology Program, Tufts University Graduate School of Biomedical Sciences, Boston, United States
| | - John M Coffin
- Molecular Microbiology Program, Tufts University Graduate School of Biomedical Sciences, Boston, United States
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, United States
| | | |
Collapse
|
5
|
Pasternack N, Doucet-O'Hare T, Johnson K, Paulsen O, Nath A. Endogenous retroviruses are dysregulated in ALS. iScience 2024; 27:110147. [PMID: 38989463 PMCID: PMC11233923 DOI: 10.1016/j.isci.2024.110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/25/2024] [Accepted: 05/27/2024] [Indexed: 07/12/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a universally fatal neurodegenerative disease with no cure. Human endogenous retroviruses (HERVs) have been implicated in its pathogenesis but their relevance to ALS is not fully understood. We examined bulk RNA-seq data from almost 2,000 ALS and unaffected control samples derived from the cortex and spinal cord. Using different methods of feature selection, including differential expression analysis and machine learning, we discovered that transcription of HERV-K loci 1q22 and 8p23.1 were significantly upregulated in the spinal cord of individuals with ALS. Additionally, we identified a subset of ALS patients with upregulated HERV-K expression in the cortex and spinal cord. We also found the expression of HERV-K loci 19q11 and 8p23.1 was correlated with protein coding genes previously implicated in ALS and dysregulated in ALS patients in this study. These results clarify the association of HERV-K and ALS and highlight specific genes in the pathobiology of late-stage ALS.
Collapse
Affiliation(s)
- Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Tara Doucet-O'Hare
- Neuro-Oncology Branch Stem Cell Team, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kory Johnson
- Bioinformatics Unit, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ole Paulsen
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| |
Collapse
|
6
|
Perron H. A tale of a hidden family of genetic immigrants. Microbes Infect 2024:105387. [PMID: 38944111 DOI: 10.1016/j.micinf.2024.105387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Though not usual for the editors of a scientific journal to ask that a story be told to its readers, this special issue is offering an opportunity to pay tribute to all those who have made it possible for a long scientific journey to open up many research avenues, to access the discoveries of what was not known and to the understanding of what was unveiled in the field of human endogenous retroviruses. In particular, and beyond a simple fortuitous association, to show their pathogenic involvement in certain diseases whose causality has been the subject of numerous and variable hypotheses.
Collapse
Affiliation(s)
- Hervé Perron
- GeNeuro, 3 chemin du Pré-Fleuri, 1228 Plan-les-ouates, Geneva, Switzerland; Geneuro-Innovation, 60A, Avenue Rockefeller, 69008 Lyon, France.
| |
Collapse
|
7
|
Moadab F, Sohrabi S, Wang X, Najjar R, Wolters JC, Jiang H, Miao W, Romero D, Zaller DM, Tran M, Bays A, Taylor MS, Kapeller R, LaCava J, Mustelin T. Subcellular location of L1 retrotransposon-encoded ORF1p, reverse transcription products, and DNA sensors in lupus granulocytes. Mob DNA 2024; 15:14. [PMID: 38937837 PMCID: PMC11212426 DOI: 10.1186/s13100-024-00324-x] [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: 02/14/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with an unpredictable course of recurrent exacerbations alternating with more stable disease. SLE is characterized by broad immune activation and autoantibodies against double-stranded DNA and numerous proteins that exist in cells as aggregates with nucleic acids, such as Ro60, MOV10, and the L1 retrotransposon-encoded ORF1p. RESULTS Here we report that these 3 proteins are co-expressed and co-localized in a subset of SLE granulocytes and are concentrated in cytosolic dots that also contain DNA: RNA heteroduplexes and the DNA sensor ZBP1, but not cGAS. The DNA: RNA heteroduplexes vanished from the neutrophils when they were treated with a selective inhibitor of the L1 reverse transcriptase. We also report that ORF1p granules escape neutrophils during the extrusion of neutrophil extracellular traps (NETs) and, to a lesser degree, from neutrophils dying by pyroptosis, but not apoptosis. CONCLUSIONS These results bring new insights into the composition of ORF1p granules in SLE neutrophils and may explain, in part, why proteins in these granules become targeted by autoantibodies in this disease.
Collapse
Affiliation(s)
- Fatemeh Moadab
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sepideh Sohrabi
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Xiaoxing Wang
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Rayan Najjar
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Justina C Wolters
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | | | | | | | - Megan Tran
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Alison Bays
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA.
- University of Washington, 750 Republican Street, Room E507, Seattle, WA, 98109, USA.
| |
Collapse
|
8
|
Kojima S. Investigating mobile element variations by statistical genetics. Hum Genome Var 2024; 11:23. [PMID: 38816353 PMCID: PMC11140006 DOI: 10.1038/s41439-024-00280-1] [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: 01/31/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
The integration of structural variations (SVs) in statistical genetics provides an opportunity to understand the genetic factors influencing complex human traits and disease. Recent advances in long-read technology and variant calling methods for short reads have improved the accurate discovery and genotyping of SVs, enabling their use in expression quantitative trait loci (eQTL) analysis and genome-wide association studies (GWAS). Mobile elements are DNA sequences that insert themselves into various genome locations. Insertional polymorphisms of mobile elements between humans, called mobile element variations (MEVs), contribute to approximately 25% of human SVs. We recently developed a variant caller that can accurately identify and genotype MEVs from biobank-scale short-read whole-genome sequencing (WGS) datasets and integrate them into statistical genetics. The use of MEVs in eQTL analysis and GWAS has a minimal impact on the discovery of genome loci associated with gene expression and disease; most disease-associated haplotypes can be identified by single nucleotide variations (SNVs). On the other hand, it helps make hypotheses about causal variants or effector variants. Focusing on MEVs, we identified multiple MEVs that contribute to differential gene expression and one of them is a potential cause of skin disease, emphasizing the importance of the integration of MEVs in medical genetics. Here, I will provide an overview of MEVs, MEV calling from WGS, and the integration of MEVs in statistical genetics. Finally, I will discuss the unanswered questions about MEVs, such as rare variants.
Collapse
Affiliation(s)
- Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
| |
Collapse
|
9
|
Chen G, Yu D, Yang Y, Li X, Wang X, Sun D, Lu Y, Ke R, Zhang G, Cui J, Feng S. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nat Commun 2024; 15:3151. [PMID: 38605055 PMCID: PMC11009239 DOI: 10.1038/s41467-024-47501-3] [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: 09/29/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.
Collapse
Affiliation(s)
- Guangji Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- BGI Research, Wuhan, China
| | - Dan Yu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Yang
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Danyang Sun
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yanlin Lu
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Center for Genomic Research, International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jie Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Institute of Infection and Health Research, Fudan University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, 200052, China.
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| |
Collapse
|
10
|
da Silva AL, Guedes BLM, Santos SN, Correa GF, Nardy A, Nali LHDS, Bachi ALL, Romano CM. Beyond pathogens: the intriguing genetic legacy of endogenous retroviruses in host physiology. Front Cell Infect Microbiol 2024; 14:1379962. [PMID: 38655281 PMCID: PMC11035796 DOI: 10.3389/fcimb.2024.1379962] [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: 01/31/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
The notion that viruses played a crucial role in the evolution of life is not a new concept. However, more recent insights suggest that this perception might be even more expansive, highlighting the ongoing impact of viruses on host evolution. Endogenous retroviruses (ERVs) are considered genomic remnants of ancient viral infections acquired throughout vertebrate evolution. Their exogenous counterparts once infected the host's germline cells, eventually leading to the permanent endogenization of their respective proviruses. The success of ERV colonization is evident so that it constitutes 8% of the human genome. Emerging genomic studies indicate that endogenous retroviruses are not merely remnants of past infections but rather play a corollary role, despite not fully understood, in host genetic regulation. This review presents some evidence supporting the crucial role of endogenous retroviruses in regulating host genetics. We explore the involvement of human ERVs (HERVs) in key physiological processes, from their precise and orchestrated activities during cellular differentiation and pluripotency to their contributions to aging and cellular senescence. Additionally, we discuss the costs associated with hosting a substantial amount of preserved viral genetic material.
Collapse
Affiliation(s)
- Amanda Lopes da Silva
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Luiz Miranda Guedes
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Samuel Nascimento Santos
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Giovanna Francisco Correa
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ariane Nardy
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | | | - Andre Luis Lacerda Bachi
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Camila Malta Romano
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| |
Collapse
|
11
|
Liang B, Yan T, Wei H, Zhang D, Li L, Liu Z, Li W, Zhang Y, Jiang N, Meng Q, Jiang G, Hu Y, Leng J. HERVK-mediated regulation of neighboring genes: implications for breast cancer prognosis. Retrovirology 2024; 21:4. [PMID: 38388382 PMCID: PMC10885364 DOI: 10.1186/s12977-024-00636-z] [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: 08/23/2023] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the remnants of ancient retroviral infections integrated into the human genome. Although most HERVs are silenced or rendered inactive by various regulatory mechanisms, they retain the potential to influence the nearby genes. We analyzed the regulatory map of 91 HERV-Ks on neighboring genes in human breast cancer and investigated the impact of HERV-Ks on the tumor microenvironment (TME) and prognosis of breast cancer. Nine RNA-seq datasets were obtained from GEO and NCBI SRA. Differentially expressed genes and HERV-Ks were analyzed using DESeq2. Validation of high-risk prognostic candidate genes using TCGA data. These included Overall survival (multivariate Cox regression model), immune infiltration analysis (TIMER), tumor mutation burden (maftools), and drug sensitivity analysis (GSCA). A total of 88 candidate genes related to breast cancer prognosis were screened, of which CD48, SLAMF7, SLAMF1, IGLL1, IGHA1, and LRRC8A were key genes. Functionally, these six key genes were significantly enriched in some immune function-related pathways, which may be associated with poor prognosis for breast cancer (p = 0.00016), and the expression levels of these genes were significantly correlated with the sensitivity of breast cancer treatment-related drugs. Mechanistically, they may influence breast cancer development by modulating the infiltration of various immune cells into the TME. We further experimentally validated these genes to confirm the results obtained from bioinformatics analysis. This study represents the first report on the regulatory potential of HERV-K in the neighboring breast cancer genome. We identified three key HERV-Ks and five neighboring genes that hold promise as novel targets for future interventions and treatments for breast cancer.
Collapse
Affiliation(s)
- Boying Liang
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Nanning, China
| | - Tengyue Yan
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Huilin Wei
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Die Zhang
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Lanxiang Li
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zengjing Liu
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Wen Li
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Yuluan Zhang
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Nili Jiang
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Qiuxia Meng
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Guiyang Jiang
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Yanling Hu
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China.
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China.
- Genomic Experimental Center, Guangxi Medical University, Nanning, China.
| | - Jing Leng
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Nanning, China.
| |
Collapse
|
12
|
Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
Collapse
Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
| |
Collapse
|
13
|
Cherkasova EA, Chen L, Childs RW. Mechanistic regulation of HERV activation in tumors and implications for translational research in oncology. Front Cell Infect Microbiol 2024; 14:1358470. [PMID: 38379771 PMCID: PMC10877039 DOI: 10.3389/fcimb.2024.1358470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Transcription of distinct loci of human endogenous retroviruses (HERVs) and in some cases, translation of these transcripts have been consistently observed in many types of cancer. It is still debated whether HERV activation serves as a trigger for carcinogenesis or rather occurs as a consequence of epigenetic alterations and other molecular sequelae that characterize cellular transformation. Here we review the known molecular and epigenetic mechanisms of HERV activation in cancer cells as well as its potential contribution to carcinogenesis. Further, we describe the use of HERV expression in cancer diagnostic and characterize the potential of HERV-derived antigens to serve as novel targets for cancer immunotherapy. We believe this review, which summarizes both what is known as well as unknown in this rapidly developing field, will boost interest in research on the therapeutic potential of targeting HERV elements in tumors and the impact of HERV activation in oncogenesis.
Collapse
Affiliation(s)
| | | | - Richard W. Childs
- Laboratory of Transplantation Immunotherapy, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
14
|
Ramirez P, Sun W, Kazempour Dehkordi S, Zare H, Fongang B, Bieniek KF, Frost B. Nanopore-based DNA long-read sequencing analysis of the aged human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark loci," are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements ("jumping genes") as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer's disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer's disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer's disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer's disease neuropathology.
Collapse
Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri
| | - Shiva Kazempour Dehkordi
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| |
Collapse
|
15
|
DeMarino C, Nath A, Zhuang Z, Doucet-O’Hare TT. Does the interplay between human endogenous retrovirus K and extracellular vesicles contribute to aging? EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2023; 4:548-56. [PMID: 38606283 PMCID: PMC11007738 DOI: 10.20517/evcna.2023.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
The role of extracellular vesicles (EVs), including retroviral-like particles (RVLPs), in pathogenic processes is currently a subject of active investigation. Several studies have identified mechanistic links between the increased presence of EVs and the process of senescence. A recent study reveals that the reverse transcribed complementary DNA (cDNA) of a human endogenous retroviral sequence can activate the innate immune system and result in tissue damage and/or the spread of cellular senescence to distant tissues. Several studies have linked EVs to age-related diseases, such as Alzheimer's disease and Parkinson's disease, and have included isolation of EVs from individuals with these diseases. Loss of epigenetic regulation, immune activation, and environmental stimuli can all lead to the expression of endogenous retroviruses and the incorporation of their proteins and transcripts into EVs. In addition, EVs disseminating these endogenous retroviral components have now been shown to act in a paracrine manner in multiple human diseases. Further investigation of the connection between EVs containing endogenous retroviral protein products or nucleotides should be pursued in models of age-related diseases.
Collapse
Affiliation(s)
- Catherine DeMarino
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Zhengping Zhuang
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | | |
Collapse
|
16
|
Shin W, Mun S, Han K. Human Endogenous Retrovirus-K (HML-2)-Related Genetic Variation: Human Genome Diversity and Disease. Genes (Basel) 2023; 14:2150. [PMID: 38136972 PMCID: PMC10742618 DOI: 10.3390/genes14122150] [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: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs) comprise a significant portion of the human genome, making up roughly 8%, a notable comparison to the 2-3% represented by coding sequences. Numerous studies have underscored the critical role and importance of HERVs, highlighting their diverse and extensive influence on the evolution of the human genome and establishing their complex correlation with various diseases. Among HERVs, the HERV-K (HML-2) subfamily has recently attracted significant attention, integrating into the human genome after the divergence between humans and chimpanzees. Its insertion in the human genome has received considerable attention due to its structural and functional characteristics and the time of insertion. Originating from ancient exogenous retroviruses, these elements succeeded in infecting germ cells, enabling vertical transmission and existing as proviruses within the genome. Remarkably, these sequences have retained the capacity to form complete viral sequences, exhibiting activity in transcription and translation. The HERV-K (HML-2) subfamily is the subject of active debate about its potential positive or negative effects on human genome evolution and various pathologies. This review summarizes the variation, regulation, and diseases in human genome evolution arising from the influence of HERV-K (HML-2).
Collapse
Affiliation(s)
- Wonseok Shin
- NGS Clinical Laboratory, Division of Cancer Research, Dankook University Hospital, Cheonan 31116, Republic of Korea;
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
| | - Seyoung Mun
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
| | - Kyudong Han
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Republic of Korea
- R&D Center, HuNBiome Co., Ltd., Seoul 08507, Republic of Korea
| |
Collapse
|
17
|
Dubowsky M, Theunissen F, Carr JM, Rogers ML. The Molecular Link Between TDP-43, Endogenous Retroviruses and Inflammatory Neurodegeneration in Amyotrophic Lateral Sclerosis: a Potential Target for Triumeq, an Antiretroviral Therapy. Mol Neurobiol 2023; 60:6330-6345. [PMID: 37450244 PMCID: PMC10533598 DOI: 10.1007/s12035-023-03472-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease (MND), is a progressive neurological disorder, characterised by the death of upper and lower motor neurons. The aetiology of ALS remains unknown, and treatment options are limited. Endogenous retroviruses (ERVs), specifically human endogenous retrovirus type K (HERV-K), have been proposed to be involved in the propagation of neurodegeneration in ALS. ERVs are genomic remnants of ancient viral infection events, with most being inactive and not retaining the capacity to encode a fully infectious virus. However, some ERVs retain the ability to be activated and transcribed, and ERV transcripts have been found to be elevated within the brain tissue of MND patients. A hallmark of ALS pathology is altered localisation of the transactive response (TAR) DNA binding protein 43 kDa (TDP-43), which is normally found within the nucleus of neuronal and glial cells and is involved in RNA regulation. In ALS, TDP-43 aggregates within the cytoplasm and facilitates neurodegeneration. The involvement of ERVs in ALS pathology is thought to occur through TDP-43 and neuroinflammatory mediators. In this review, the proposed involvement of TDP-43, HERV-K and immune regulators on the onset and progression of ALS will be discussed. Furthermore, the evidence supporting a therapy based on targeting ERVs in ALS will be reviewed.
Collapse
Affiliation(s)
- Megan Dubowsky
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia.
| | - Frances Theunissen
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Jillian M Carr
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Mary-Louise Rogers
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| |
Collapse
|
18
|
Ferlita AL, Nigita G, Tsyba L, Palamarchuk A, Alaimo S, Pulvirenti A, Balatti V, Rassenti L, Tsichlis PN, Kipps T, Pekarsky Y, Croce CM. Expression signature of human endogenous retroviruses in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 2023; 120:e2307593120. [PMID: 37871223 PMCID: PMC10622969 DOI: 10.1073/pnas.2307593120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is one of the most diagnosed forms of leukemia worldwide and it is usually classified into two forms: indolent and aggressive. These two forms are characterized by distinct molecular features that drive different responses to treatment and clinical outcomes. In this context, a better understanding of the molecular landscape of the CLL forms may potentially lead to the development of new drugs or the identification of novel biomarkers. Human endogenous retroviruses (HERVs) are a class of transposable elements that have been associated with the development of different human cancers, including different forms of leukemias. However, no studies about HERVs in CLL have ever been reported so far. Here, we present the first locus-specific profiling of HERV expression in both the aggressive and indolent forms of CLL. Our analyses revealed several dysregulations in HERV expression occurring in CLL and some of them were specific for either the aggressive or indolent form of CLL. Such results were also validated by analyzing an external cohort of CLL patients and by RT-qPCR. Moreover, in silico analyses have shown relevant signaling pathways associated with them suggesting a potential involvement of the dysregulated HERVs in these pathways and consequently in CLL development.
Collapse
Affiliation(s)
- Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Liudmyla Tsyba
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Alexey Palamarchuk
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania95123, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania95123, Italy
| | - Veronica Balatti
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Laura Rassenti
- Department of Medicine, University of California San Diego, La JollaCA92093
| | - Philip N. Tsichlis
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Thomas Kipps
- Department of Medicine, University of California San Diego, La JollaCA92093
| | - Yuri Pekarsky
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| |
Collapse
|
19
|
Lyons DE, Kumar P, Roan NR, Defechereux PA, Feschotte C, Lange UC, Murthy N, Sameshima P, Verdin E, Ake JA, Parsons MS, Nath A, Gianella S, Smith DM, Kallas EG, Villa TJ, Strange R, Mwesigwa B, Furler O’Brien RL, Nixon DF, Ndhlovu LC, Valente ST, Ott M. HIV-1 Remission: Accelerating the Path to Permanent HIV-1 Silencing. Viruses 2023; 15:2171. [PMID: 38005849 PMCID: PMC10674359 DOI: 10.3390/v15112171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Despite remarkable progress, a cure for HIV-1 infection remains elusive. Rebound competent latent and transcriptionally active reservoir cells persevere despite antiretroviral therapy and rekindle infection due to inefficient proviral silencing. We propose a novel "block-lock-stop" approach, entailing long term durable silencing of viral expression towards an irreversible transcriptionally inactive latent provirus to achieve long term antiretroviral free control of the virus. A graded transformation of remnant HIV-1 in PLWH from persistent into silent to permanently defective proviruses is proposed, emulating and accelerating the natural path that human endogenous retroviruses (HERVs) take over millions of years. This hypothesis was based on research into delineating the mechanisms of HIV-1 latency, lessons from latency reversing agents and advances of Tat inhibitors, as well as expertise in the biology of HERVs. Insights from elite controllers and the availability of advanced genome engineering technologies for the direct excision of remnant virus set the stage for a rapid path to an HIV-1 cure.
Collapse
Affiliation(s)
- Danielle E. Lyons
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA;
| | - Nadia R. Roan
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Patricia A. Defechereux
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | | | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA;
- Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - Pauline Sameshima
- Faculty of Education, Lakehead University, Thunder Bay, ON P7B 5E1, Canada;
| | - Eric Verdin
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Julie A. Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (M.S.P.)
| | - Matthew S. Parsons
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (M.S.P.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD 20824, USA;
| | - Sara Gianella
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Davey M. Smith
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Esper G. Kallas
- Department of Infectious and Parasitic Diseases, University of Sao Paulo, São Paulo 04023-900, Brazil
| | - Thomas J. Villa
- HOPE Martin Delaney Collaboratory for HIV Cure Research Community Engagement Ambassador, Washinton, DC 20004, USA (R.S.)
- National HIV & Aging Advocacy Network, Washington, DC 20004, USA
| | - Richard Strange
- HOPE Martin Delaney Collaboratory for HIV Cure Research Community Engagement Ambassador, Washinton, DC 20004, USA (R.S.)
| | - Betty Mwesigwa
- Research Department, Makerere University Walter Reed Project, Kampala P.O Box 7062, Uganda
| | - Robert L. Furler O’Brien
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Susana T. Valente
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
20
|
Ko EJ, Kim MH, Kim DY, An H, Leem SH, Choi YH, Kim HS, Cha HJ. The Role of Human Endogenous Retrovirus (HERV)-K119 env in THP-1 Monocytic Cell Differentiation. Int J Mol Sci 2023; 24:15566. [PMID: 37958549 PMCID: PMC10648273 DOI: 10.3390/ijms242115566] [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: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Human endogenous retrovirus (HERV)-K was reportedly inserted into the human genome millions of years ago and is closely related to various diseases, including cancer and immune regulation. In our previous studies, CRISPR-Cas9-enabled knockout (KO) of the HERV-K env gene was found to potentially reduce cell proliferation, cell migration, and invasion in colorectal and ovarian cancer cell lines. The immune response involves the migration and invasion of cells and is similar to cancer; however, in certain ways, it is completely unlike cancer. Therefore, we induced HERV-K119 env gene KO in THP-1, a monocytic cell that can be differentiated into a macrophage, to investigate the role of HERV-K119 env in immune regulation. Cell migration and invasion were noted to be significantly increased in HERV-K119 env KO THP-1 cells than in MOCK, and these results were contrary to those of cancer cells. To identify the underlying mechanism of HERV-K119 env KO in THP-1 cells, transcriptome analysis and cytokine array analysis were conducted. Semaphorin7A (SEMA7A), which induces the production of cytokines in macrophages and monocytic cells and plays an important role in immune effector cell activation during an inflammatory immune response, was significantly increased in HERV-K119 env KO THP-1 cells. We also found that HERV-K119 env KO THP-1 cells expressed various macrophage-specific surface markers, suggesting that KO of HERV-K119 env triggers the differentiation of THP-1 cells from monocytic cells into macrophages. In addition, analysis of the expression of M1 and M2 macrophage markers showed that M1 macrophage marker cluster of differentiation 32 (CD32) was significantly increased in HERV-K119 env KO cells. These results suggest that HERV-K119 env is implicated in the differentiation of monocytic cells into M1 macrophages and plays important roles in the immune response.
Collapse
Affiliation(s)
- Eun-Ji Ko
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
| | - Min-Hye Kim
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea;
| | - Do-Ye Kim
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
| | - Hyojin An
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
| | - Sun-Hee Leem
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dongeui University, Busan 47227, Republic of Korea;
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 49241, Republic of Korea;
| | - Hee-Jae Cha
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
- Institute for Medical Science, Kosin University College of Medicine, Busan 49267, Republic of Korea
| |
Collapse
|
21
|
Guzmán-Solís AA, Navarro MA, Ávila-Arcos MC, Blanco-Melo D. A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History. Annu Rev Virol 2023; 10:49-75. [PMID: 37268008 DOI: 10.1146/annurev-virology-111821-123859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.
Collapse
Affiliation(s)
- Axel A Guzmán-Solís
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miguel Alejandro Navarro
- Licenciatura en Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México;
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México;
| | - Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA;
| |
Collapse
|
22
|
Gimenez J, Spalloni A, Cappelli S, Ciaiola F, Orlando V, Buratti E, Longone P. TDP-43 Epigenetic Facets and Their Neurodegenerative Implications. Int J Mol Sci 2023; 24:13807. [PMID: 37762112 PMCID: PMC10530927 DOI: 10.3390/ijms241813807] [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: 07/06/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
Since its initial involvement in numerous neurodegenerative pathologies in 2006, either as a principal actor or as a cofactor, new pathologies implicating transactive response (TAR) DNA-binding protein 43 (TDP-43) are regularly emerging also beyond the neuronal system. This reflects the fact that TDP-43 functions are particularly complex and broad in a great variety of human cells. In neurodegenerative diseases, this protein is often pathologically delocalized to the cytoplasm, where it irreversibly aggregates and is subjected to various post-translational modifications such as phosphorylation, polyubiquitination, and cleavage. Until a few years ago, the research emphasis has been focused particularly on the impacts of this aggregation and/or on its widely described role in complex RNA splicing, whether related to loss- or gain-of-function mechanisms. Interestingly, recent studies have strengthened the knowledge of TDP-43 activity at the chromatin level and its implication in the regulation of DNA transcription and stability. These discoveries have highlighted new features regarding its own transcriptional regulation and suggested additional mechanistic and disease models for the effects of TPD-43. In this review, we aim to give a comprehensive view of the potential epigenetic (de)regulations driven by (and driving) this multitask DNA/RNA-binding protein.
Collapse
Affiliation(s)
- Juliette Gimenez
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Alida Spalloni
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Sara Cappelli
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Francesca Ciaiola
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
- Department of Systems Medicine, University of Roma Tor Vergata, 00133 Rome, Italy
| | - Valerio Orlando
- KAUST Environmental Epigenetics Program, Biological Environmental Sciences and Engineering Division BESE, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Emanuele Buratti
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Patrizia Longone
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| |
Collapse
|
23
|
Kyriakou E, Magiorkinis G. Interplay between endogenous and exogenous human retroviruses. Trends Microbiol 2023; 31:933-946. [PMID: 37019721 DOI: 10.1016/j.tim.2023.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/07/2023]
Abstract
In humans, retroviruses thrive more as symbionts than as parasites. Apart from the only two modern exogenous human retroviruses (human T-cell lymphotropic and immunodeficiency viruses; HTLV and HIV, respectively), ~8% of the human genome is occupied by ancient retroviral DNA [human endogenous retroviruses (HERVs)]. Here, we review the recent discoveries about the interactions between the two groups, the impact of infection by exogenous retroviruses on the expression of HERVs, the effect of HERVs on the pathogenicity of HIV and HTLV and on the severity of the diseases caused by them, and the antiviral protection that HERVs can allegedly provide to the host. Tracing the crosstalk between contemporary retroviruses and their endogenized ancestors will provide better understanding of the retroviral world.
Collapse
Affiliation(s)
- Eleni Kyriakou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
| |
Collapse
|
24
|
Alkailani MI, Gibbings D. The Regulation and Immune Signature of Retrotransposons in Cancer. Cancers (Basel) 2023; 15:4340. [PMID: 37686616 PMCID: PMC10486412 DOI: 10.3390/cancers15174340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Advances in sequencing technologies and the bioinformatic analysis of big data facilitate the study of jumping genes' activity in the human genome in cancer from a broad perspective. Retrotransposons, which move from one genomic site to another by a copy-and-paste mechanism, are regulated by various molecular pathways that may be disrupted during tumorigenesis. Active retrotransposons can stimulate type I IFN responses. Although accumulated evidence suggests that retrotransposons can induce inflammation, the research investigating the exact mechanism of triggering these responses is ongoing. Understanding these mechanisms could improve the therapeutic management of cancer through the use of retrotransposon-induced inflammation as a tool to instigate immune responses to tumors.
Collapse
Affiliation(s)
- Maisa I. Alkailani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
| |
Collapse
|
25
|
Wang J, Han GZ. Genome mining shows that retroviruses are pervasively invading vertebrate genomes. Nat Commun 2023; 14:4968. [PMID: 37591904 PMCID: PMC10435555 DOI: 10.1038/s41467-023-40732-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Endogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
Collapse
Affiliation(s)
- Jianhua Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
| |
Collapse
|
26
|
Stricker E, Peckham-Gregory EC, Scheurer ME. CancerHERVdb: Human Endogenous Retrovirus (HERV) Expression Database for Human Cancer Accelerates Studies of the Retrovirome and Predictions for HERV-Based Therapies. J Virol 2023; 97:e0005923. [PMID: 37255431 PMCID: PMC10308937 DOI: 10.1128/jvi.00059-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
In this study, we sought to create a database summarizing the expression of human endogenous retroviruses (HERVs) in various human cancers. HERVs are suitable therapeutic targets due to their abundance in the human genome, overexpression in various malignancies, and involvement in various cancer pathways. We identified articles on HERVs from PubMed and then prescreened and automatically categorized them using the portable document format (PDF) data extractor (PDE) R package. We discovered 196 primary research articles with HERV expression data from cancer tissues or cancer cell lines. HERV RNA and protein expression was reported in brain, breast, cervical, colorectal, endocrine, gastrointestinal, kidney/renal/pelvis, liver, lung, genital, oral cavity, pharynx, ovary, pancreas, prostate, skin, testicular, urinary/bladder, and uterus cancers, leukemias, lymphomas, and myelomas. Additionally, we discovered reports of HERV RNA-only overexpression in soft tissue cancers including heart, thyroid, bone, and joint cancers. The CancerHERVdb database is hosted in the form of interactive visualizations of the expression data and a summary data table at https://erikstricker.shinyapps.io/cancerHERVdb/. The user can filter the findings according to cancer type, HERV family, HERV gene, or a combination thereof and easily export the results with the corresponding reference list. In our report, we provide examples of potential uses of the CancerHERVdb, such as identification of cancers suitable for off-target treatment with the multiple sclerosis-associated retrovirus (MSRV)-Env-targeting antibody GNbAC1 (now named temelimab) currently in phase 2b clinical trials for multiple sclerosis or the discovery of cancers overexpressing HERV-H long terminal repeat-associating 2 (HHLA2), a newly emerging immune checkpoint. In summary, the CancerHERVdb allows cross-study comparisons, encourages data exploration, and informs about potential off-target effects of HERV-targeting treatments. IMPORTANCE Human endogenous retroviruses (HERVs), which in the past have inserted themselves in various regions of the human genome, are to various degrees activated in virtually every cancer type. While a centralized naming system and resources summarizing HERV levels in cancers are lacking, the CancerHERVdb database provides a consolidated resource for cross-study comparisons, data exploration, and targeted searches of HERV activation. The user can access data extracted from hundreds of articles spanning 25 human cancer categories. Therefore, the CancerHERVdb database can aid in the identification of prognostic and risk markers, drivers of cancer, tumor-specific targets, multicancer spanning signals, and targets for immune therapies. Consequently, the CancerHERVdb database is of direct relevance for clinical as well as basic research.
Collapse
Affiliation(s)
- Erik Stricker
- Baylor College of Medicine, Department of Molecular Virology and Microbiology, Houston, Texas, USA
- Baylor College of Medicine, Department of Pediatrics, Houston, Texas, USA
| | | | | |
Collapse
|
27
|
Petrone V, Fanelli M, Giudice M, Toschi N, Conti A, Maracchioni C, Iannetta M, Resta C, Cipriani C, Miele MT, Amati F, Andreoni M, Sarmati L, Rogliani P, Novelli G, Garaci E, Rasi G, Sinibaldi-Vallebona P, Minutolo A, Matteucci C, Balestrieri E, Grelli S. Expression profile of HERVs and inflammatory mediators detected in nasal mucosa as a predictive biomarker of COVID-19 severity. Front Microbiol 2023; 14:1155624. [PMID: 37283924 PMCID: PMC10239953 DOI: 10.3389/fmicb.2023.1155624] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction Our research group and others demonstrated the implication of the human endogenous retroviruses (HERVs) in SARS-CoV-2 infection and their association with disease progression, suggesting HERVs as contributing factors in COVID-19 immunopathology. To identify early predictive biomarkers of the COVID-19 severity, we analyzed the expression of HERVs and inflammatory mediators in SARS-CoV-2-positive and -negative nasopharyngeal/oropharyngeal swabs with respect to biochemical parameters and clinical outcome. Methods Residuals of swab samples (20 SARS-CoV-2-negative and 43 SARS-CoV-2-positive) were collected during the first wave of the pandemic and expression levels of HERVs and inflammatory mediators were analyzed by qRT-Real time PCR. Results The results obtained show that infection with SARS-CoV-2 resulted in a general increase in the expression of HERVs and mediators of the immune response. In particular, SARS-CoV-2 infection is associated with increased expression of HERV-K and HERV-W, IL-1β, IL-6, IL-17, TNF-α, MCP-1, INF-γ, TLR-3, and TLR-7, while lower levels of IL-10, IFN-α, IFN-β, and TLR-4 were found in individuals who underwent hospitalization. Moreover, higher expression of HERV-W, IL-1β, IL-6, IFN-α, and IFN-β reflected the respiratory outcome of patients during hospitalization. Interestingly, a machine learning model was able to classify hospitalized vs not hospitalized patients with good accuracy based on the expression levels of HERV-K, HERV-W, IL-6, TNF-a, TLR-3, TLR-7, and the N gene of SARS-CoV-2. These latest biomarkers also correlated with parameters of coagulation and inflammation. Discussion Overall, the present results suggest HERVs as contributing elements in COVID-19 and early genomic biomarkers to predict COVID-19 severity and disease outcome.
Collapse
Affiliation(s)
- Vita Petrone
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Marialaura Fanelli
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Martina Giudice
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Martinos Center for Biomedical Imaging and Harvard Medical School, Boston, MA, United States
| | - Allegra Conti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | | | - Marco Iannetta
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Resta
- Respiratory Medicine Unit, Policlinic of Tor Vergata, Rome, Italy
| | - Chiara Cipriani
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Martino Tony Miele
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Amati
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Loredana Sarmati
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Paola Rogliani
- Respiratory Medicine Unit, Policlinic of Tor Vergata, Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Neuromed IRCCS Institute, Pozzilli, IS, Italy
- University of Nevada, Department of Pharmacology, Reno, NV, United States
| | | | - Guido Rasi
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- National Research Council, Institute of Translational Pharmacology, Rome, Italy
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- Virology Unit, Policlinic of Tor Vergata, Rome, Italy
| |
Collapse
|
28
|
Ishihara S. Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing. Sci Rep 2023; 13:7380. [PMID: 37149699 PMCID: PMC10164170 DOI: 10.1038/s41598-023-34520-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel long terminal repeat (LTR) loci derived from ERVs (ERV-LTRs) absent in the reference genome using whole-genome sequencing data of red junglefowl, gray junglefowl, Ceylon junglefowl, and green junglefowl. In total, 835 ERV-LTR loci were identified across the four Gallus species. The numbers of ERV-LTRs loci detected in red junglefowl and its subspecies gray junglefowl, Ceylon junglefowl, and green junglefowl were 362, 216, 193, and 128, respectively. The phylogenetic tree was congruent with previously reported trees, suggesting the potential for inferring relationships among past junglefowl populations from the identified ERV-LTR loci. Of the detected loci, 306 ERV-LTRs were identified near or within the genes, and some were associated with cell adhesion. The detected ERV-LTR sequences were classified as endogenous avian retrovirus family, avian leukosis virus subgroup E, Ovex-1, and murine leukemia virus-related ERVs. In addition, the sequence of the EAV family was divided into four patterns by combining the U3, R, and U5 regions. These findings contribute to a more comprehensive understanding of the characteristics of junglefowl ERVs.
Collapse
Affiliation(s)
- Shinya Ishihara
- Department of Animal Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan.
| |
Collapse
|
29
|
Copley KE, Shorter J. Repetitive elements in aging and neurodegeneration. Trends Genet 2023; 39:381-400. [PMID: 36935218 PMCID: PMC10121923 DOI: 10.1016/j.tig.2023.02.008] [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: 12/14/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 03/19/2023]
Abstract
Repetitive elements (REs), such as transposable elements (TEs) and satellites, comprise much of the genome. Here, we review how TEs and (peri)centromeric satellite DNA may contribute to aging and neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Alterations in RE expression, retrotransposition, and chromatin microenvironment may shorten lifespan, elicit neurodegeneration, and impair memory and movement. REs may cause these phenotypes via DNA damage, protein sequestration, insertional mutagenesis, and inflammation. We discuss several TE families, including gypsy, HERV-K, and HERV-W, and how TEs interact with various factors, including transactive response (TAR) DNA-binding protein 43 kDa (TDP-43) and the siRNA and piwi-interacting (pi)RNA systems. Studies of TEs in neurodegeneration have focused on Drosophila and, thus, further examination in mammals is needed. We suggest that therapeutic silencing of REs could help mitigate neurodegenerative disorders.
Collapse
Affiliation(s)
- Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
30
|
Stricker E, Peckham-Gregory EC, Scheurer ME. HERVs and Cancer-A Comprehensive Review of the Relationship of Human Endogenous Retroviruses and Human Cancers. Biomedicines 2023; 11:936. [PMID: 36979914 PMCID: PMC10046157 DOI: 10.3390/biomedicines11030936] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Genomic instability and genetic mutations can lead to exhibition of several cancer hallmarks in affected cells such as sustained proliferative signaling, evasion of growth suppression, activated invasion, deregulation of cellular energetics, and avoidance of immune destruction. Similar biological changes have been observed to be a result of pathogenic viruses and, in some cases, have been linked to virus-induced cancers. Human endogenous retroviruses (HERVs), once external pathogens, now occupy more than 8% of the human genome, representing the merge of genomic and external factors. In this review, we outline all reported effects of HERVs on cancer development and discuss the HERV targets most suitable for cancer treatments as well as ongoing clinical trials for HERV-targeting drugs. We reviewed all currently available reports of the effects of HERVs on human cancers including solid tumors, lymphomas, and leukemias. Our review highlights the central roles of HERV genes, such as gag, env, pol, np9, and rec in immune regulation, checkpoint blockade, cell differentiation, cell fusion, proliferation, metastasis, and cell transformation. In addition, we summarize the involvement of HERV long terminal repeat (LTR) regions in transcriptional regulation, creation of fusion proteins, expression of long non-coding RNAs (lncRNAs), and promotion of genome instability through recombination.
Collapse
Affiliation(s)
- Erik Stricker
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
| | | | - Michael E. Scheurer
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
| |
Collapse
|
31
|
Bowles H, Kabiljo R, Al Khleifat A, Jones A, Quinn JP, Dobson RJB, Swanson CM, Al-Chalabi A, Iacoangeli A. An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data. FRONTIERS IN BIOINFORMATICS 2023; 2:1062328. [PMID: 36845320 PMCID: PMC9945273 DOI: 10.3389/fbinf.2022.1062328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/12/2022] [Indexed: 02/10/2023] Open
Abstract
There is a growing interest in the study of human endogenous retroviruses (HERVs) given the substantial body of evidence that implicates them in many human diseases. Although their genomic characterization presents numerous technical challenges, next-generation sequencing (NGS) has shown potential to detect HERV insertions and their polymorphisms in humans. Currently, a number of computational tools to detect them in short-read NGS data exist. In order to design optimal analysis pipelines, an independent evaluation of the available tools is required. We evaluated the performance of a set of such tools using a variety of experimental designs and datasets. These included 50 human short-read whole-genome sequencing samples, matching long and short-read sequencing data, and simulated short-read NGS data. Our results highlight a great performance variability of the tools across the datasets and suggest that different tools might be suitable for different study designs. However, specialized tools designed to detect exclusively human endogenous retroviruses consistently outperformed generalist tools that detect a wider range of transposable elements. We suggest that, if sufficient computing resources are available, using multiple HERV detection tools to obtain a consensus set of insertion loci may be ideal. Furthermore, given that the false positive discovery rate of the tools varied between 8% and 55% across tools and datasets, we recommend the wet lab validation of predicted insertions if DNA samples are available.
Collapse
Affiliation(s)
- Harry Bowles
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Renata Kabiljo
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ashley Jones
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
- NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Neurology, King’s College Hospital, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
| |
Collapse
|
32
|
Abdullah U, Saleh N, Shaw P, Jalal N. COVID-19: The Ethno-Geographic Perspective of Differential Immunity. Vaccines (Basel) 2023; 11:319. [PMID: 36851197 PMCID: PMC9966855 DOI: 10.3390/vaccines11020319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the agent behind the worst global pandemic of the 21st century (COVID-19), is primarily a respiratory-disease-causing virus called SARS-CoV-2 that is responsible for millions of new cases (incidence) and deaths (mortalities) worldwide. Many factors have played a role in the differential morbidity and mortality experienced by nations and ethnicities against SARS-CoV-2, such as the quality of primary medical health facilities or enabling economies. At the same time, the most important variable, i.e., the subsequent ability of individuals to be immunologically sensitive or resistant to the infection, has not been properly discussed before. Despite having excellent medical facilities, an astounding issue arose when some developed countries experienced higher morbidity and mortality compared with their relatively underdeveloped counterparts. Hence, this investigative review attempts to analyze the issue from an angle of previously undiscussed genetic, epigenetic, and molecular immune resistance mechanisms in correlation with the pathophysiology of SARS-CoV-2 and varied ethnicity-based immunological responses against it. The biological factors discussed here include the overall landscape of human microbiota, endogenous retroviral genes spliced into the human genome, and copy number variation, and how they could modulate the innate and adaptive immune systems that put a certain ethnic genetic architecture at a higher risk of SARS-CoV-2 infection than others. Considering an array of these factors in their entirety may help explain the geographic disparity of disease incidence, severity, and subsequent mortality associated with the disease while at the same time encouraging scientists to design new experimental approaches to investigation.
Collapse
Affiliation(s)
- Usman Abdullah
- Department of Biomedical Sciences, Pak-Austria Fachhochschule, Mang, Haripur 22621, Pakistan
| | - Ned Saleh
- Synsal Inc., San Jose, CA 95138, USA
| | - Peter Shaw
- Oujiang Lab, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou 325000, China
| | - Nasir Jalal
- Department of Biomedical Sciences, Pak-Austria Fachhochschule, Mang, Haripur 22621, Pakistan
- Oujiang Lab, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou 325000, China
| |
Collapse
|
33
|
Endogenous Retroviruses as Modulators of Innate Immunity. Pathogens 2023; 12:pathogens12020162. [PMID: 36839434 PMCID: PMC9963469 DOI: 10.3390/pathogens12020162] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Endogenous retroviruses (ERVs), or LTR retrotransposons, are a class of transposable elements that are highly represented in mammalian genomes. Human ERVs (HERVs) make up roughly 8.3% of the genome and over the course of evolution, HERV elements underwent positive selection and accrued mutations that rendered them non-infectious; thereby, the genome could co-opt them into constructive roles with important biological functions. In the past two decades, with the help of advances in sequencing technology, ERVs are increasingly considered to be important components of the innate immune response. While typically silenced, expression of HERVs can be induced in response to traumatic, toxic, or infection-related stress, leading to a buildup of viral transcripts and under certain circumstances, proteins, including functionally active reverse transcriptase and viral envelopes. The biological activity of HERVs in the context of the innate immune response can be based on the functional effect of four major viral components: (1) HERV LTRs, (2) HERV-derived RNAs, (3) HERV-derived RNA:DNA duplexes and cDNA, and (4) HERV-derived proteins and ribonucleoprotein complexes. In this review, we will discuss the implications of HERVs in all four contexts in relation to innate immunity and their association with various pathological disease states.
Collapse
|
34
|
Chen X, Bourque G, Goubert C. Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments. Methods Mol Biol 2023; 2607:63-83. [PMID: 36449158 DOI: 10.1007/978-1-0716-2883-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Transposable element (TE) insertions are a major source of structural variation in the human genome. Due to the repetitive nature and biological importance of TEs, many bioinformatic tools have been developed to identify and genotype TE insertion polymorphisms using high-throughput short-reads. In this chapter, we outline recently developed methods to characterize TE insertion polymorphisms in human populations. We also provide detailed protocols to tackle this question primarily using three software: MELT2, ERVcaller, and TypeREF.
Collapse
Affiliation(s)
- Xun Chen
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
- Human Genetics, McGill University, Montreal, QC, Canada
| | - Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
| |
Collapse
|
35
|
Fan TJ, Cui J. Human Endogenous Retroviruses in Diseases. Subcell Biochem 2023; 106:403-439. [PMID: 38159236 DOI: 10.1007/978-3-031-40086-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Human endogenous retroviruses (HERVs), which are conserved sequences of ancient retroviruses, are widely distributed in the human genome. Although most HERVs have been rendered inactive by evolution, some have continued to exhibit important cytological functions. HERVs in the human genome perform dual functions: on the one hand, they are involved in important physiological processes such as placental development and immune regulation; on the other hand, their aberrant expression is closely associated with the pathological processes of several diseases, such as cancers, autoimmune diseases, and viral infections. HERVs can also regulate a variety of host cellular functions, including the expression of protein-coding genes and regulatory elements that have evolved from HERVs. Here, we present recent research on the roles of HERVs in viral infections and cancers, including the dysregulation of HERVs in various viral infections, HERV-induced epigenetic modifications of histones (such as methylation and acetylation), and the potential mechanisms of HERV-mediated antiviral immunity. We also describe therapies to improve the efficacy of vaccines and medications either by directly or indirectly targeting HERVs, depending on the HERV.
Collapse
Affiliation(s)
- Tian-Jiao Fan
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
36
|
Remnants of SIRE1 retrotransposons in human genome? J Genet 2022. [DOI: 10.1007/s12041-022-01398-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
37
|
Lou C, Qiang R, Wu H, Zhang L, Li W, Jia T, Liu X. Expression of LINE-1 retrotransposon in early human spontaneous abortion tissues. Medicine (Baltimore) 2022; 101:e31964. [PMID: 36626466 PMCID: PMC9750690 DOI: 10.1097/md.0000000000031964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The aim of this study is to investigate a new mechanism that may affect spontaneous abortions (SA): Can long interspersed nuclear element-1 (LINE-1) insertions in embryo cells lead to early SA? METHODS The method involves prospective study on new mechanism of human early SA. Twenty SA tissues and 10 induced abortion (IA) tissues were utilized for this experiment. Western Blot, Immunohistochemistry (IHC), and reverse transcription-polymerase chain reaction were used to analyze different LINE-1 proteins and mRNA expression between early SA tissues and early IA tissues. SPSS software version 21.0 was used for statistical analysis. RESULTS Western Blot demonstrated that the LINE-1 protein expression in SA tissues (Mean: 60.2%) is higher than in IA tissues (Mean: 30.3%) in 91% of the compared samples. reverse transcription-polymerase chain reaction showed that LINE-1 mRNA expression in SA tissues (Mean: 64.2%) is higher than in IA tissues (Mean: 29.2%) in 6 primer pairs in 89% of the compared samples. IHC showed that the LINE-1 protein expression in SA tissues (Mean: 59.2%) is higher than in IA tissues (Mean: 28.8%) in 83% of the compared samples. CONCLUSIONS Expression of LINE-1 in early SA tissues is higher than in IA tissues, LINE-1 may lead to early SA and LINE-1 plays a role in early SA, this shows that a new mechanism may be involved in SA.
Collapse
Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Hanzhi Wu
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Liping Zhang
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Wei Li
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Ting Jia
- Department of Genetics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Xing Liu
- Department of Obstetrics, Northwest Women’s and Children’s Hospital, Xi’an, Shaanxi Province, China
- * Correspondence: Xing Liu, Department of Obstetrics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province, China (e-mail: )
| |
Collapse
|
38
|
Cipriani C, Giudice M, Petrone V, Fanelli M, Minutolo A, Miele MT, Toschi N, Maracchioni C, Siracusano M, Benvenuto A, Coniglio A, Curatolo P, Mazzone L, Sandro G, Garaci E, Sinibaldi-Vallebona P, Matteucci C, Balestrieri E. Modulation of human endogenous retroviruses and cytokines expression in peripheral blood mononuclear cells from autistic children and their parents. Retrovirology 2022; 19:26. [PMID: 36451209 PMCID: PMC9709758 DOI: 10.1186/s12977-022-00603-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Putative pathogenic effects mediated by human endogenous retroviruses (HERVs) in neurological and psychiatric disorders in humans have been extensively described. HERVs may alter the development of the brain by means of several mechanisms, including modulation of gene expression, alteration of DNA stability, and activation of immune system. We recently demonstrated that autistic children and their mothers share high expression levels of some HERVs and cytokines in peripheral blood mononuclear cells (PBMCs) ex vivo, suggesting a close mother-child association in Autism Spectrum Disorder (ASD). RESULTS In the present study, PBMCs from autistic children and their parents were exposed to stimulating factors (Interleukin-2/Phytohaemagglutinin) or drugs, as Valproic acid and Efavirenz. The results show that HERVs and cytokines expression can be modulated in vitro by different stimuli in PBMCs from autistic children and their mothers, while no significant changes were found in PBMCs ASD fathers or in controls individuals. In particular, in vitro exposure to interleukin-2/Phytohaemagglutinin or valproic acid induces the expression of several HERVs and cytokines while Efavirenz inhibits them. CONCLUSION Herein we show that autistic children and their mothers share an intrinsic responsiveness to in vitro microenvironmental changes in expressing HERVs and pro-inflammatory cytokines. Remarkably, the antiretroviral drug Efavirenz restores the expression of specific HERV families to values similar to those of the controls, also reducing the expression of proinflammatory cytokines but keeping the regulatory ones high. Our findings open new perspectives to study the role of HERVs in the biological mechanisms underlying Autism.
Collapse
Affiliation(s)
- Chiara Cipriani
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Martina Giudice
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Vita Petrone
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Marialaura Fanelli
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Antonella Minutolo
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Martino T. Miele
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Nicola Toschi
- grid.6530.00000 0001 2300 0941Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy ,grid.38142.3c000000041936754XMartinos Center for Biomedical Imaging and Harvard Medical School, Boston, USA
| | - Christian Maracchioni
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Martina Siracusano
- grid.6530.00000 0001 2300 0941Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Arianna Benvenuto
- grid.413009.fChild Neurology and Psychiatry Unit, System Medicine Department, Tor Vergata University Hospital of Rome, 00133 Rome, Italy
| | - Antonella Coniglio
- grid.413009.fChild Neurology and Psychiatry Unit, System Medicine Department, Tor Vergata University Hospital of Rome, 00133 Rome, Italy
| | - Paolo Curatolo
- grid.413009.fChild Neurology and Psychiatry Unit, System Medicine Department, Tor Vergata University Hospital of Rome, 00133 Rome, Italy
| | - Luigi Mazzone
- grid.413009.fChild Neurology and Psychiatry Unit, System Medicine Department, Tor Vergata University Hospital of Rome, 00133 Rome, Italy
| | - Grelli Sandro
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy ,Virology Unit, Policlinic of Tor Vergata, 00133 Rome, Italy
| | - Enrico Garaci
- University San Raffaele, Rome, Italy ,grid.18887.3e0000000417581884IRCCS San Raffaele Pisana, 00133 Rome, Italy
| | - Paola Sinibaldi-Vallebona
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy ,grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Claudia Matteucci
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Emanuela Balestrieri
- grid.6530.00000 0001 2300 0941Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| |
Collapse
|
39
|
Kabiljo R, Bowles H, Marriott H, Jones AR, Bouton CR, Dobson RJ, Quinn JP, Al Khleifat A, Swanson CM, Al-Chalabi A, Iacoangeli A. RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data. iScience 2022; 25:105289. [PMID: 36339261 PMCID: PMC9626663 DOI: 10.1016/j.isci.2022.105289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 12/02/2022] Open
Abstract
Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training. Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.
Collapse
Affiliation(s)
- Renata Kabiljo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Harry Bowles
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Heather Marriott
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Clement R. Bouton
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Richard J.B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust, London, UK
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
| |
Collapse
|
40
|
Burn A, Roy F, Freeman M, Coffin JM. Widespread expression of the ancient HERV-K (HML-2) provirus group in normal human tissues. PLoS Biol 2022; 20:e3001826. [PMID: 36256614 PMCID: PMC9578601 DOI: 10.1371/journal.pbio.3001826] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, yet their activity in nondiseased tissue is largely unknown. Using the GTEx RNA-seq dataset from normal tissue sampled at autopsy, we characterized individual expression of the recent HERV-K (HML-2) provirus group across 13,000 different samples of 54 different tissues from 948 individuals. HML-2 transcripts could be identified in every tissue sampled and were elevated in the cerebellum, pituitary, testis, and thyroid. A total of 37 different individual proviruses were expressed in 1 or more tissues, representing all 3 LTR5 subgroups. Nine proviruses were identified as having long terminal repeat (LTR)-driven transcription, 7 of which belonged to the most recent LTR5HS subgroup. Proviruses of different subgroups displayed a bias in tissue expression, which may be associated with differences in transcription factor binding sites in their LTRs. Provirus expression was greater in evolutionarily older proviruses with an earliest shared ancestor of gorilla or older. HML-2 expression was significantly affected by biological sex in 1 tissue, while age and timing of death (Hardy score) had little effect. Proviruses containing intact gag, pro, and env open reading frames (ORFs) were expressed in the dataset, with almost every tissue measured potentially expressing at least 1 intact ORF (gag). Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, but what is their activity in normal tissue? This study uses unique patterns of HERV-K RNA expression in the large GEx dataset from non-diseased tissue sites to provide new insights into both the coevolution of HERV-K with our primate ancestors and their current role in human biology.
Collapse
Affiliation(s)
- Aidan Burn
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Farrah Roy
- Immuneering Corporation, Cambridge, Massachusetts, United States of America
| | - Michael Freeman
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - John M. Coffin
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
41
|
Molecular diversity and phenotypic pleiotropy of ancient genomic regulatory loci derived from human endogenous retrovirus type H (HERVH) promoter LTR7 and HERVK promoter LTR5_Hs and their contemporary impacts on pathophysiology of Modern Humans. Mol Genet Genomics 2022; 297:1711-1740. [PMID: 36121513 PMCID: PMC9483895 DOI: 10.1007/s00438-022-01954-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022]
Abstract
Timelines of population-level effects of viruses on humans varied from the evolutionary scale of million years to contemporary spread of viral infections. Correspondingly, these events are exemplified by: (i) emergence of human endogenous retroviruses (HERVs) from ancient germline infections leading to stable integration of viral genomes into human chromosomes; and (ii) wide-spread viral infections reaching a global pandemic state such as the COVID-19 pandemic. Despite significant efforts, understanding of HERV’s roles in governance of genomic regulatory networks, their impacts on primate evolution and development of human-specific physiological and pathological phenotypic traits remains limited. Remarkably, present analyses revealed that expression of a dominant majority of genes (1696 of 1944 genes; 87%) constituting high-confidence down-steam regulatory targets of defined HERV loci was significantly altered in cells infected with the SARS-CoV-2 coronavirus, a pathogen causing the global COVID-19 pandemic. This study focused on defined sub-sets of DNA sequences derived from HERVs that are expressed at specific stages of human preimplantation embryogenesis and exert regulatory actions essential for self-renewal and pluripotency. Evolutionary histories of LTR7/HERVH and LTR5_Hs/HERVK were charted based on evidence of the earliest presence and expansion of highly conserved (HC) LTR sequences. Sequence conservation analyses of most recent releases 17 primate species’ genomes revealed that LTR7/HERVH have entered germlines of primates in Africa after the separation of the New World Monkey lineage, while LTR5_Hs/HERVK successfully colonized primates’ germlines after the segregation of Gibbons’ species. Subsequently, both LTR7 and LTR5_Hs undergo a marked ~ fourfold–fivefold expansion in genomes of Great Apes. Timelines of quantitative expansion of both LTR7 and LTR5_Hs loci during evolution of Great Apes appear to replicate the consensus evolutionary sequence of increasing cognitive and behavioral complexities of non-human primates, which seems particularly striking for LTR7 loci and 11 distinct LTR7 subfamilies. Consistent with previous reports, identified in this study, 351 human-specific (HS) insertions of LTR7 (175 loci) and LTR5_Hs (176 loci) regulatory sequences have been linked to genes implicated in establishment and maintenance of naïve and primed pluripotent states and preimplantation embryogenesis phenotypes. Unexpectedly, HS-LTRs manifest regulatory connectivity to genes encoding markers of 12 distinct cells’ populations of fetal gonads, as well as genes implicated in physiology and pathology of human spermatogenesis, including Y-linked spermatogenic failure, oligo- and azoospermia. Granular interrogations of genes linked with 11 distinct LTR7 subfamilies revealed that mammalian offspring survival (MOS) genes seem to remain one of consistent regulatory targets throughout ~ 30 MYA of the divergent evolution of LTR7 loci. Differential GSEA of MOS versus non-MOS genes identified clearly discernable dominant enrichment patterns of phenotypic traits affected by MOS genes linked with LTR7 (562 MOS genes) and LTR5_Hs (126 MOS genes) regulatory loci across the large panel of genomics and proteomics databases reflecting a broad spectrum of human physiological and pathological traits. GSEA of LTR7-linked MOS genes identified more than 2200 significantly enriched records of human common and rare diseases and gene signatures of 466 significantly enriched records of Human Phenotype Ontology traits, including Autosomal Dominant (92 genes) and Autosomal Recessive (93 genes) Inheritance. LTR7 regulatory elements appear linked with genes implicated in functional and morphological features of central nervous system, including synaptic transmission and protein–protein interactions at synapses, as well as gene signatures differentially regulated in cells of distinct neurodevelopmental stages and morphologically diverse cell types residing and functioning in human brain. These include Neural Stem/Precursor cells, Radial Glia cells, Bergman Glia cells, Pyramidal cells, Tanycytes, Immature neurons, Interneurons, Trigeminal neurons, GABAergic neurons, and Glutamatergic neurons. GSEA of LTR7-linked genes identified significantly enriched gene sets encoding markers of more than 80 specialized types of neurons and markers of 521 human brain regions, most prominently, subiculum and dentate gyrus. Identification and characterization of 1944 genes comprising high-confidence down-steam regulatory targets of LTR7 and/or LTR5_Hs loci validated and extended these observations by documenting marked enrichments for genes implicated in neoplasm metastasis, intellectual disability, autism, multiple cancer types, Alzheimer’s, schizophrenia, and other brain disorders. Overall, genes representing down-stream regulatory targets of ancient retroviral LTRs exert the apparently cooperative and exceedingly broad phenotypic impacts on human physiology and pathology. This is exemplified by altered expression of 93% high-confidence LTR targets in cells infected by contemporary viruses, revealing a convergence of virus-inflicted aberrations on genomic regulatory circuitry governed by ancient retroviral LTR elements and interference with human cells’ differentiation programs.
Collapse
|
42
|
Li W, Pandya D, Pasternack N, Garcia-Montojo M, Henderson L, Kozak CA, Nath A. Retroviral Elements in Pathophysiology and as Therapeutic Targets for Amyotrophic Lateral Sclerosis. Neurotherapeutics 2022; 19:1085-1101. [PMID: 35415778 PMCID: PMC9587200 DOI: 10.1007/s13311-022-01233-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 10/18/2022] Open
Abstract
The study of the role of retroviruses in amyotrophic lateral sclerosis (ALS) dates back to the 1960s shortly after transposable elements themselves were first discovered. It was quickly realized that in wild mice both horizontal and vertical transmissions of retroviral elements were key to the development of an ALS-like syndrome leading to the postulate that endogenous retroviruses (ERVs) contribute significantly to the pathogenicity of this disease. Subsequent studies identified retroviral reverse transcriptase activity in brains of individuals with ALS from Guam. However, except for a single study from the former Soviet Union, ALS could not be transmitted to rhesus macaques. The discovery of an ALS-like syndrome in human immunodeficiency virus (HIV) and human T cell leukemia virus infected individuals led to renewed interest in the field and reverse transcriptase activity was found in the blood and cerebrospinal fluid of individuals with sporadic ALS. However, exogenous retroviruses could not be found in individuals with ALS which further reinforced the possibility of involvement of a human ERV (HERV). The first demonstration of the involvement of a HERV was the discovery of the activation of human endogenous retrovirus-K subtype HML-2 in the brains of individuals with ALS. The envelope protein of HML-2 is neurotoxic and transgenic animals expressing the envelope protein develop an ALS-like syndrome. Activation of HML-2 occurs in the context of generalized transposable element activation and is not specific for ALS. Individuals with HIV-associated ALS show a remarkable response to antiretroviral therapy; however, antiretroviral trials in ALS down-regulate HML-2 without ameliorating the disease. This highlights the need for specific drugs to be developed against HML-2 as a novel therapeutic target for ALS. Other approaches might include antisense oligonucleotides, shRNA targeted against the envelope gene or antibodies that can target the extracellular envelope protein. Future clinical trials in ALS should consider combination therapies to control these ERVs.
Collapse
Affiliation(s)
- Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Darshan Pandya
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Lisa Henderson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Christine A Kozak
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
| |
Collapse
|
43
|
Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome. Sci Rep 2022; 12:10485. [PMID: 35729348 PMCID: PMC9213404 DOI: 10.1038/s41598-022-14654-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/09/2022] [Indexed: 11/09/2022] Open
Abstract
The Vietnamese native pig (VnP)-a porcine breed with a small body-has proven suitable as a biomedical animal model. Here, we demonstrate that, compared to other breeds, VnPs have fewer copies of porcine endogenous retroviruses (PERVs), which pose a risk for xenotransplantation of pig organs to humans. More specifically, we sought to characterize non-reference PERVs (nrPERVs) that were previously unidentified in the reference genome. To this end, we used whole-genome sequencing data to identify nrPERV loci with long terminal repeat (LTR) sequences in VnPs. RetroSeq was used to estimate nrPERV loci based on the most current porcine reference genome (Sscrofa11.1). LTRs were detected using de novo sequencing read assembly near the loci containing the target site duplication sequences in the inferred regions. A total of 21 non-reference LTR loci were identified and separated into two subtypes based on phylogenetic analysis. Moreover, PERVs within the detected LTR loci were identified, the presence of which was confirmed using conventional PCR and Sanger sequencing. These novel loci represent previously unknown PERVs as they have not been identified in the porcine reference genome. Thus, our RetroSeq method accurately detects novel PERV loci, and can be applied for development of a useful biomedical model.
Collapse
|
44
|
Ito J, Seita Y, Kojima S, Parrish NF, Sasaki K, Sato K. A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells. PLoS Genet 2022; 18:e1009846. [PMID: 35551519 PMCID: PMC9128956 DOI: 10.1371/journal.pgen.1009846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/24/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
Mammalian germ cells stem from primordial germ cells (PGCs). Although the gene regulatory network controlling the development of germ cells such as PGCs is critical for ensuring gamete integrity, substantial differences exist in this network among mammalian species, suggesting that this network has been modified during mammalian evolution. Here, we show that a hominoid-specific group of endogenous retroviruses, LTR5_Hs, discloses enhancer-like signatures in human in vitro-induced PGCs, PGC-like cells (PGCLCs). Human PGCLCs exhibit a transcriptome signature similar to that of naïve-state pluripotent cells. LTR5_Hs are epigenetically activated in both PGCLCs and naïve pluripotent cells, and the expression of genes in the vicinity of LTR5_Hs is coordinately upregulated in these cell types, contributing to the establishment of the transcriptome similarity between these cell types. LTR5_Hs are preferentially bound by transcription factors that are highly expressed in both PGCLCs and naïve pluripotent cells (KLF4, TFAP2C, NANOG, and CBFA2T2), suggesting that these transcription factors contribute to the epigenetic activation of LTR5_Hs in these cells. Comparative transcriptome analysis between humans and macaques suggests that the expression of many genes in PGCLCs and naïve pluripotent cells is upregulated by LTR5_Hs insertions in the hominoid lineage. Together, this study suggests that LTR5_Hs insertions may have finetuned the gene regulatory network shared between PGCLCs and naïve pluripotent cells and coordinately altered the gene expression in these cells during hominoid evolution. To ensure the health of the next generation and the continuation of a species, the development of germ cells, including primordial germ cells (PGCs), is strictly controlled by a complex gene regulatory network. Nevertheless, the gene regulatory network controlling the germ cell development has been substantially diversified during mammalian or even primate evolution. Here, our integrated analyses using multiomics and comparative genomics resources suggest that hominoid-specific insertions of endogenous retroviruses are epigenetically activated in both in vitro-induced PGCs and naïve pluripotent cells and may have coordinately altered the expression of the adjacent genes in these cells. This study provides evidence suggesting that the gene regulatory network shared between PGCs and naïve pluripotent cells may have been rewired by ERV insertions during hominoid evolution.
Collapse
Affiliation(s)
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasunari Seita
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Bell Research Center for Reproductive Health and Cancer, Nagoya, Aichi, Japan
| | - Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan
| | - Kotaro Sasaki
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (KS); (KS)
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- * E-mail: (KS); (KS)
| |
Collapse
|
45
|
Marchi E, Jones M, Klenerman P, Frater J, Magiorkinis G, Belshaw R. BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations. BMC Bioinformatics 2022; 23:134. [PMID: 35428171 PMCID: PMC9013057 DOI: 10.1186/s12859-022-04621-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/28/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Retroviruses replicate by integrating a DNA copy into a host chromosome. Detecting novel retroviral integrations (ones not in the reference genome sequence of the host) from genomic NGS data is bioinformatically challenging and frequently produces many false positives. One common method of confirmation is visual inspection of an alignment of the chimaeric (split) reads that span a putative novel retroviral integration site. We perceived the need for a program that would facilitate this by producing a multiple alignment containing both the viral and host regions that flank an integration. RESULTS BreakAlign is a Perl program that uses blastn to produce such a multiple alignment. In addition to the NGS dataset and a reference viral sequence, the program requires either (a) the ~ 500nt host genome sequence that spans the putative integration or (b) coordinates of this putative integration in an installed copy of the reference human genome (multiple integrations can be processed automatically). BreakAlign is freely available from https://github.com/marchiem/breakalign and is accompanied by example files allowing a test run. CONCLUSION BreakAlign will confirm and facilitate characterisation of both (a) germline integrations of endogenous retroviruses and (b) somatic integrations of exogenous retroviruses such as HIV and HTLV. Although developed for use with genomic short-read NGS (second generation) data and retroviruses, it should also be useful for long-read (third generation) data and any mobile element with at least one conserved flanking region.
Collapse
Affiliation(s)
- Emanuele Marchi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Mathew Jones
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Robert Belshaw
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.
| |
Collapse
|
46
|
Abstract
Human endogenous retroviruses (HERVs) occupy approximately 8% of the human genome. HERVs, transcribed in early embryos, are epigenetically silenced in somatic cells, except under pathological conditions. HERV-K is thought to protect embryos from exogenous viral infection. However, uncontrolled HERV-K expression in somatic cells has been implicated in several diseases. Here, we show that SOX2, which plays a key role in maintaining the pluripotency of stem cells, is critical for HERV-K LTR5Hs. HERV-K undergoes retrotransposition within producer cells in the absence of Env expression. Furthermore, we identified new HERV-K integration sites in long-term culture of induced pluripotent stem cells that express SOX2. These results suggest that the strict dependence of HERV-K on SOX2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos. IMPORTANCE Human endogenous retroviruses (HERVs) account for approximately 8% of the human genome; however, the physiological role of HERV-K remains unknown. This study found that HERV-K LTR5Hs and LTR5B were transactivated by SOX2, which is essential for maintaining and reestablishing pluripotency. HERV-K can undergo retrotransposition within producer cells without env expression, and new integration sites may affect cell proliferation. In induced pluripotent stem cells (iPSCs), genomic impairment due to HERV-K retrotransposition has been identified, but it is a rare event. Considering the retention of SOX2-responsive elements in the HERV-K long terminal repeat (LTR) for over 20 million years, we conclude that HERV-K may play important physiological roles in SOX2-expressing cells.
Collapse
|
47
|
Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T, He S. Characterizing mobile element insertions in 5675 genomes. Nucleic Acids Res 2022; 50:2493-2508. [PMID: 35212372 PMCID: PMC8934628 DOI: 10.1093/nar/gkac128] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36 699 non-reference MEIs constructed from 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that LINE-1 insertions were highly enriched in centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.
Collapse
Affiliation(s)
- Yiwei Niu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyi Teng
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yirong Shi
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Li
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiheng Tang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Kang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
48
|
Yang C, Guo X, Li J, Han J, Jia L, Wen HL, Sun C, Wang X, Zhang B, Li J, Chi Y, An T, Wang Y, Wang Z, Li H, Li L. Significant Upregulation of HERV-K (HML-2) Transcription Levels in Human Lung Cancer and Cancer Cells. Front Microbiol 2022; 13:850444. [PMID: 35359739 PMCID: PMC8960717 DOI: 10.3389/fmicb.2022.850444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the second most common cancer worldwide and the leading cause of cancer death in the world. Therefore, there is an urgent need to develop new and effective biomarkers for diagnosis and treatment. Under this circumstance, human endogenous retroviruses (HERVs) were recently introduced as novel biomarkers for cancer diagnosis. This study focused on the correlation between lung cancer and HERV-K (HML-2) transcription levels. At the cellular level, different types of lung cancer cells and human normal lung epithelial cells were used to analyze the transcription levels of the HERV-K (HML-2) gag, pol, and env genes by RT–qPCR. At the level of lung cancer patients, blood samples with background information from 734 lung cancer patients and 96 healthy persons were collected to analyze the transcription levels of HERV-K (HML-2) gag, pol, and env genes. The results showed that the transcriptional levels of the HERV-K (HML-2) gag, pol, and env genes in lung cancer cells and lung cancer patient blood samples were significantly higher than those in the healthy controls, which was also verified by RNAScope ISH technology. In addition, we also found that there was a correlation between the abnormal transcription levels of HERV-K (HML-2) genes in lung cancer patients and the clinicopathological parameters of lung cancer. We also identified the distribution locations of the gag, pol, and env primer sequences on each chromosome and analyzed the function of these loci. In conclusion, HERV-K (HML-2) genes may be a potential biomarker for the diagnosis of lung cancer.
Collapse
Affiliation(s)
- Caiqin Yang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Xin Guo
- Department of Nutrition and Food Hygiene, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jianjie Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jingwan Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Lei Jia
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Hong-Ling Wen
- Key Laboratory for the Prevention and Control of Infectious Diseases, Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chengxi Sun
- Department of Clinical Laboratory, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaolin Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Bohan Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Jingyun Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Yujia Chi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Tongtong An
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuyan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ziping Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- *Correspondence: Ziping Wang,
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
- Hanping Li,
| | - Lin Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
- Lin Li,
| |
Collapse
|
49
|
Latifi T, Zebardast A, Marashi SM. The role of human endogenous retroviruses (HERVs) in Multiple Sclerosis and the plausible interplay between HERVs, Epstein-Barr virus infection, and vitamin D. Mult Scler Relat Disord 2022; 57:103318. [PMID: 35158423 DOI: 10.1016/j.msard.2021.103318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/19/2021] [Accepted: 10/06/2021] [Indexed: 12/30/2022]
Abstract
Multiple Sclerosis (MS) is one of the chronic inflammatory diseases with neurological disability in the central nervous system (CNS). Although the exact cause of MS is still largely unknown, both genetic and environmental factors are thought to play a role in disease risk. Human Endogenous Retroviruses (HERVs) are endogenous viral elements of the human genome whose expression is associated with MS. HERVs are normally silenced or expressed at low levels, although their expression is higher in MS than in the healthy population. Several studies highlighted the plausible interaction between HERVs and other MS risk factors, including viral infection like Epstein-Barr viruses and vitamin D deficiency which may lead to high expression of HERVs in these patients. Understanding how HERVs act in this scenario can improve our understanding towards MS etiology and may lead to the development of antiretroviral therapies in these patients. Here in this review, we try to examine the different HERVs expression implicated in MS and their association with EBV infection and vitamin D status.
Collapse
Affiliation(s)
- Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Arghavan Zebardast
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
50
|
Wang X, Hefton A, Ni K, Ukadike KC, Bowen MA, Eckert M, Stevens A, Lood C, Mustelin T. Autoantibodies Against Unmodified and Citrullinated Human Endogenous Retrovirus K Envelope Protein in Patients With Rheumatoid Arthritis. J Rheumatol Suppl 2022; 49:26-35. [PMID: 34334364 PMCID: PMC8963793 DOI: 10.3899/jrheum.201492] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Autoantibodies against proteins encoded by human endogenous retrovirus K (HERV-K) have been reported in patients with rheumatoid arthritis (RA), but their relevance, if any, has remained unresolved. We revisited this question and tested if such autoantibodies may react with citrullinated epitopes on the envelope (Env) protein of HERV-K. METHODS Immunoblotting and ELISAs were conducted with unmodified Env protein and with Env citrullinated by protein arginine deiminase 4 (PAD4). Sera from 100 patients with RA, plasma from 32 patients with juvenile idiopathic arthritis (JIA), and healthy adult and pediatric controls were included. Antibody reactivity was evaluated for correlations with clinical and laboratory variables of the patients. RESULTS We replicated and expanded upon published data suggesting that patients with RA or JIA have autoantibodies against HERV-K Env, some with high titers. Anti-HERV-K antibodies correlated with cigarette smoking and with circulating myeloperoxidase-DNA complexes indicative of nonapoptotic neutrophil cell death. Further, most of the patients with RA, but not those with JIA, had autoantibodies that reacted more strongly with Env that was citrullinated by PAD4. These anticitrullinated Env autoantibodies correlated with seropositivity and tended to be higher in patients with erosive disease. CONCLUSION Our data suggest that anti-HERV-K immunity is elevated in RA and JIA and may have a connection with pathogenic protein citrullination in RA.
Collapse
Affiliation(s)
- Xiaoxing Wang
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Amanda Hefton
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kathryn Ni
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kennedy C. Ukadike
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Michael A. Bowen
- M.A. Bowen, PhD, Product and Process Development, Allogene Therapeutics, San Francisco, California
| | - Mary Eckert
- M. Eckert, BS, Seattle Children’s Research Institute, Seattle, Washington
| | - Anne Stevens
- A. Stevens, MD, Professor, Seattle Children’s Research Institute, Seattle, Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, and Janssen Research & Development, LLC, Wayne, Pennsylvania, USA
| | - Christian Lood
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Tomas Mustelin
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| |
Collapse
|