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Tavakolian S, Rafiei Atani Z, Zarei A, Goudarzi H, Abedi AR, Faghihloo E. Evaluating of HERV-K Genes Expression in Sperm Samples Collected from Infertile Men Compared to Fertile Individuals: A Case-Control Study. Adv Biomed Res 2025; 14:31. [PMID: 40390817 PMCID: PMC12087934 DOI: 10.4103/abr.abr_530_23] [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: 12/25/2023] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 05/21/2025] Open
Abstract
Background Having detrimental effects on the health-care system, infertility can be related to some risk factors, especially different kinds of viruses. Human endogenous retrovirus-k (HERV-K) env, gag, np9, and rec can be considered as one of these viral agents that are likely to cause male infertility, and we attempted to evaluate it. Materials and Methods This case-control study was conducted on sperm samples of 96 participants in Imam Hossein Hospital, Tehran, Iran, from January 2020 to December 2021. After extracting the RNA form these samples, we evaluated the expression of HERV-K env, np9, rec, and gag using quantitative real-time polymerase chain reaction (qRT-PCR). Results Our data revealed that HERV-K, rec, np9, and env in abnormal samples were higher than normal ones. However, the opposite trend was true for gag expression since a meaningful reduction can be observed in abnormal samples. Conclusions The results of our study suggested that there is a plausible correlation between the expression level of this virus's genes and the progression of infertility. We proposed this marker as a promising biomarker to diagnose infertility. However, further studies are required to support these results.
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Affiliation(s)
- Shaian Tavakolian
- Department of Medical Biology, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Zahra Rafiei Atani
- Department of Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
| | - Amir Zarei
- Department of Clinical Biochemistry, Medical School, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Reza Abedi
- Men’s Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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van der Kuyl AC. Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations. J Mol Evol 2025; 93:62-82. [PMID: 39715846 DOI: 10.1007/s00239-024-10225-5] [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: 04/25/2024] [Accepted: 12/07/2024] [Indexed: 12/25/2024]
Abstract
The time of integration of germline-targeting Long Terminal Repeat (LTR) retroposons, such as endogenous retroviruses (ERVs), can be estimated by assessing the nucleotide divergence between the LTR sequences flanking the viral genes. Due to the viral replication mechanism, both LTRs are identical at the moment of integration, when the provirus becomes part of the host genome. After that time, proviral sequences evolve within the host DNA. When the mutation rate is known, nucleotide divergence between the LTRs would then be a measure of time elapsed since integration. Though frequently used, the approach has been complicated by the choice of host mutation rate and, to a lesser extent, by the method selected to estimate nucleotide divergence. As a result, outcomes can be incompatible with, for instance, speciation events identified from the fossil record. The review will give an overview of research reporting LTR-retroposon dating, and a summary of important factors to consider, including the quality, assembly, and alignment of sequences, the mutation rate of foreign DNA in host genomes, and the choice of a distance estimation method. Primates will here be the focus of the analysis because their genomes, ERVs, and fossil record have been extensively studied. However, most of the factors discussed have a wide applicability in the vertebrate field.
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Affiliation(s)
- Antoinette Cornelia van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam Institute for Immunology & Infectious Diseases, 1100 DD, Amsterdam, The Netherlands.
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3
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Song Y, Wen H, Zhai X, Jia L, Li L. Functional Bidirectionality of ERV-Derived Long Non-Coding RNAs in Humans. Int J Mol Sci 2024; 25:10481. [PMID: 39408810 PMCID: PMC11476766 DOI: 10.3390/ijms251910481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 09/25/2024] [Accepted: 09/26/2024] [Indexed: 10/20/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are widely recognized as the result of exogenous retroviruses infecting the ancestral germline, stabilizing integration and vertical transmission during human genetic evolution. To date, endogenous retroviruses (ERVs) appear to have been selected for human physiological functions with the loss of retrotransposable capabilities. ERV elements were previously regarded as junk DNA for a long time. Since then, the aberrant activation and expression of ERVs have been observed in the development of many kinds of human diseases, and their role has been explored in a variety of human disorders such as cancer. The results show that specific ERV elements play respective crucial roles. Among them, long non-coding RNAs (lncRNAs) transcribed from specific long-terminal repeat regions of ERVs are often key factors. lncRNAs are over 200 nucleotides in size and typically bind to DNA, RNA, and proteins to perform biological functions. Dysregulated lncRNAs have been implicated in a variety of diseases. In particular, studies have shown that the aberrant expression of some ERV-derived lncRNAs has a tumor-suppressive or oncogenic effect, displaying significant functional bidirectionality. Therefore, theses lncRNAs have a promising future as novel biomarkers and therapeutic targets to explore the concise relationship between ERVs and cancers. In this review, we first summarize the role of ERV-derived lncRNAs in physiological regulation, mainly including immunomodulation, the maintenance of pluripotency, and erythropoiesis. In addition, pathological regulation examples of their aberrant activation and expression leading to carcinogenesis are highlighted, and specific mechanisms of occurrence are discussed.
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Affiliation(s)
- Yanmei Song
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory for the Prevention and Control of Emerging Infectious Diseases and Biosafety, Jinan 250012, China; (Y.S.); (H.W.)
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory for the Prevention and Control of Emerging Infectious Diseases and Biosafety, Jinan 250012, China; (Y.S.); (H.W.)
| | - Xiuli Zhai
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230000, China
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100850, China;
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4
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Jia L, Song Y, Chen M, Zhao RY, Li L. Editorial: The evolution, characterization, and role of human endogenous retroviruses in health and diseases. Front Cell Infect Microbiol 2024; 14:1449864. [PMID: 39040603 PMCID: PMC11262060 DOI: 10.3389/fcimb.2024.1449864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/01/2024] [Indexed: 07/24/2024] Open
Affiliation(s)
- Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Yanmei Song
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory for the Prevention and Control of Emerging Infectious Diseases and Biosafety, Jinan, Shandong, China
| | - Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, China
| | - Richard Y. Zhao
- School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
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5
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Chen M, Yang C, Zhai X, Wang C, Liu M, Zhang B, Guo X, Wang Y, Li H, Liu Y, Han J, Wang X, Li J, Jia L, Li L. Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome. Viruses 2024; 16:892. [PMID: 38932184 PMCID: PMC11209481 DOI: 10.3390/v16060892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Endogenous retroviruses (ERVs) are related to long terminal repeat (LTR) retrotransposons, comprising gene sequences of exogenous retroviruses integrated into the host genome and inherited according to Mendelian law. They are considered to have contributed greatly to the evolution of host genome structure and function. We previously characterized HERV-K HML-9 in the human genome. However, the biological function of this type of element in the genome of the chimpanzee, which is the closest living relative of humans, largely remains elusive. Therefore, the current study aims to characterize HML-9 in the chimpanzee genome and to compare the results with those in the human genome. Firstly, we report the distribution and genetic structural characterization of the 26 proviral elements and 38 solo LTR elements of HML-9 in the chimpanzee genome. The results showed that the distribution of these elements displayed a non-random integration pattern, and only six elements maintained a relatively complete structure. Then, we analyze their phylogeny and reveal that the identified elements all cluster together with HML-9 references and with those identified in the human genome. The HML-9 integration time was estimated based on the 2-LTR approach, and the results showed that HML-9 elements were integrated into the chimpanzee genome between 14 and 36 million years ago and into the human genome between 18 and 49 mya. In addition, conserved motifs, cis-regulatory regions, and enriched PBS sequence features in the chimpanzee genome were predicted based on bioinformatics. The results show that pathways significantly enriched for ERV LTR-regulated genes found in the chimpanzee genome are closely associated with disease development, including neurological and neurodevelopmental psychiatric disorders. In summary, the identification, characterization, and genomics of HML-9 presented here not only contribute to our understanding of the role of ERVs in primate evolution but also to our understanding of their biofunctional significance.
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Affiliation(s)
- Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan 430068, China;
| | - Caiqin Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiuli Zhai
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Chunlei Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Mengying Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Bohan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xing Guo
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yanglan Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
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6
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Wang C, Zhai X, Wang S, Zhang B, Yang C, Song Y, Li H, Liu Y, Han J, Wang X, Li J, Chen M, Jia L, Li L. Comprehensive characterization of ERV-K (HML-8) in the chimpanzee genome revealed less genomic activity than humans. Front Cell Infect Microbiol 2024; 14:1349046. [PMID: 38456081 PMCID: PMC10918009 DOI: 10.3389/fcimb.2024.1349046] [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: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024] Open
Abstract
Endogenous retroviruses (ERVs) originate from ancestral germline infections caused by exogenous retroviruses. Throughout evolution, they have become fixed within the genome of the animals into which they were integrated. As ERV elements coevolve with the host, they are normally epigenetically silenced and can become upregulated in a series of physiological and pathological processes. Generally, a detailed ERV profile in the host genome is critical for understanding the evolutionary history and functional performance of the host genome. We previously characterized and cataloged all the ERV-K subtype HML-8 loci in the human genome; however, this has not been done for the chimpanzee, the nearest living relative of humans. In this study, we aimed to catalog and characterize the integration of HML-8 in the chimpanzee genome and compare it with the integration of HML-8 in the human genome. We analyzed the integration of HML-8 and found that HML-8 pervasively invaded the chimpanzee genome. A total of 76 proviral elements were characterized on 23/24 chromosomes, including detailed elements distribution, structure, phylogeny, integration time, and their potential to regulate adjacent genes. The incomplete structure of HML-8 proviral LTRs will undoubtedly affect their activity. Moreover, the results indicated that HML-8 integration occurred before the divergence between humans and chimpanzees. Furthermore, chimpanzees include more HML-8 proviral elements (76 vs. 40) and fewer solo long terminal repeats (LTR) (0 vs. 5) than humans. These results suggested that chimpanzee genome activity is less than the human genome and that humans may have a better ability to shape and screen integrated proviral elements. Our work is informative in both an evolutionary and a functional context for ERVs.
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Affiliation(s)
- Chunlei Wang
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiuli Zhai
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Shibo Wang
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Caiqin Yang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanmei Song
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lin Li
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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7
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Gholami Barzoki M, Shatizadeh Malekshahi S, Heydarifard Z, Mahmodi MJ, Soltanghoraee H. The important biological roles of Syncytin-1 of human endogenous retrovirus W (HERV-W) and Syncytin-2 of HERV-FRD in the human placenta development. Mol Biol Rep 2023; 50:7901-7907. [PMID: 37421503 DOI: 10.1007/s11033-023-08658-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND Human endogenous retroviruses (HERVs) entered the germ line by retroviral infection from a distant ancestor over 30 million years ago and constitute 8% of the human genome. The majorities of HERVs are non-protein coding and lack function because of the accumulation of mutations, insertions, deletions, and/or truncations. However, a small number of HERV genes carried ORFs with beneficial functions for the host. METHODS & RESULTS In this review, we summarize the structural and important biological roles of two HERV gene products termed Syncytin-1 and Syncytin-2 in human placenta development. Indeed, two retroviral gene products that have important roles in mammalian development, Syncytin-1 (HERV-W) and Syncytin-2 (HERV-FRD), are prime examples encoded by env genes and expressed in the placental trophoblasts. Several pivotal studies revealed that Syncytins are fundamental genes implicated in regulating trophoblast fusion and placenta morphogenesis. CONCLUSION Interestingly, it has been suggested that syncytins may also be implicated in non-fusogenic activities leading to apoptosis, proliferation, and immunosuppressive activities.
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Affiliation(s)
- Mehdi Gholami Barzoki
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Zahra Heydarifard
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohamad Javad Mahmodi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Haleh Soltanghoraee
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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8
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Hosseiniporgham S, Sechi LA. Anti-HERV-K Drugs and Vaccines, Possible Therapies against Tumors. Vaccines (Basel) 2023; 11:vaccines11040751. [PMID: 37112663 PMCID: PMC10144246 DOI: 10.3390/vaccines11040751] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
The footprint of human endogenous retroviruses (HERV), specifically HERV-K, has been found in malignancies, such as melanoma, teratocarcinoma, osteosarcoma, breast cancer, lymphoma, and ovary and prostate cancers. HERV-K is characterized as the most biologically active HERV due to possession of open reading frames (ORF) for all Gag, Pol, and Env genes, which enables it to be more infective and obstructive towards specific cell lines and other exogenous viruses, respectively. Some factors might contribute to carcinogenicity and at least one of them has been recognized in various tumors, including overexpression/methylation of long interspersed nuclear element 1 (LINE-1), HERV-K Gag, and Env genes themselves plus their transcripts and protein products, and HERV-K reverse transcriptase (RT). Therapies effective for HERV-K-associated tumors mostly target invasive autoimmune responses or growth of tumors through suppression of HERV-K Gag or Env protein and RT. To design new therapeutic options, more studies are needed to better understand whether HERV-K and its products (Gag/Env transcripts and HERV-K proteins/RT) are the initiators of tumor formation or just the disorder’s developers. Accordingly, this review aims to present evidence that highlights the association between HERV-K and tumorigenicity and introduces some of the available or potential therapies against HERV-K-induced tumors.
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9
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Liu M, Jia L, Guo X, Zhai X, Li H, Liu Y, Han J, Zhang B, Wang X, Li T, Wang Y, Li J, Yu C, Li L. Identification and Characterization of the HERV-K (HML-8) Group of Human Endogenous Retroviruses in the Genome. AIDS Res Hum Retroviruses 2023; 39:176-194. [PMID: 36656667 DOI: 10.1089/aid.2022.0084] [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] [Indexed: 01/20/2023] Open
Abstract
Human endogenous retroviruses (HERVs) can be vertically transmitted in a Mendelian fashion, are stably maintained in the human genome, and are estimated to constitute ∼8% of the genome. HERVs affect human physiology and pathology through their provirus-encoded protein or long terminal repeat (LTR) element effect. Characterization of the genomic distribution is an essential step to understanding the relationships between endogenous retrovirus expression and diseases. However, the poor characterization of human MMTV-like (HML)-8 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, the definition of an accurate and updated HERV-K HML-8 genomic map is urgently needed. In this study, we report the results of a comprehensive analysis of HERV-K HML-8 sequence presence and distribution within the human genome and hominoids, with a detailed description of the different structural and phylogenetic aspects characterizing the group. A total of 40 proviruses and 5 solo LTR elements for human were characterized, which included a detailed description of provirus structure, integration time, potentially regulated genes, transcription factor-binding sites, and primer-binding site features. Besides, 9 chimpanzee sequences, 8 gorilla sequences, and 10 orangutan sequences belonging to the HML-8 subgroup were identified. The integration time results showed that the HML-8 elements were integrated into the primate lineage around 35 and 42 million years ago (mya), during primates evolutionary speciation. Overall, the results clarified the composition of the HML-8 groups, providing an exhaustive background for subsequent functional studies.
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Affiliation(s)
- Mengying Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xing Guo
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China.,Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Xiuli Zhai
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China.,Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Tianyi Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanglan Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Bowles H, Kabiljo R, Al Khleifat A, Jones A, Quinn JP, Dobson RJB, Swanson CM, Al-Chalabi A, Iacoangeli A. An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data. FRONTIERS IN BIOINFORMATICS 2023; 2:1062328. [PMID: 36845320 PMCID: PMC9945273 DOI: 10.3389/fbinf.2022.1062328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/12/2022] [Indexed: 02/10/2023] Open
Abstract
There is a growing interest in the study of human endogenous retroviruses (HERVs) given the substantial body of evidence that implicates them in many human diseases. Although their genomic characterization presents numerous technical challenges, next-generation sequencing (NGS) has shown potential to detect HERV insertions and their polymorphisms in humans. Currently, a number of computational tools to detect them in short-read NGS data exist. In order to design optimal analysis pipelines, an independent evaluation of the available tools is required. We evaluated the performance of a set of such tools using a variety of experimental designs and datasets. These included 50 human short-read whole-genome sequencing samples, matching long and short-read sequencing data, and simulated short-read NGS data. Our results highlight a great performance variability of the tools across the datasets and suggest that different tools might be suitable for different study designs. However, specialized tools designed to detect exclusively human endogenous retroviruses consistently outperformed generalist tools that detect a wider range of transposable elements. We suggest that, if sufficient computing resources are available, using multiple HERV detection tools to obtain a consensus set of insertion loci may be ideal. Furthermore, given that the false positive discovery rate of the tools varied between 8% and 55% across tools and datasets, we recommend the wet lab validation of predicted insertions if DNA samples are available.
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Affiliation(s)
- Harry Bowles
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Renata Kabiljo
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ashley Jones
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
- NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Neurology, King’s College Hospital, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
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11
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Contribution of Retrotransposons to the Pathogenesis of Type 1 Diabetes and Challenges in Analysis Methods. Int J Mol Sci 2023; 24:ijms24043104. [PMID: 36834511 PMCID: PMC9966460 DOI: 10.3390/ijms24043104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Type 1 diabetes (T1D) is one of the most common chronic diseases of the endocrine system, associated with several life-threatening comorbidities. While the etiopathogenesis of T1D remains elusive, a combination of genetic susceptibility and environmental factors, such as microbial infections, are thought to be involved in the development of the disease. The prime model for studying the genetic component of T1D predisposition encompasses polymorphisms within the HLA (human leukocyte antigen) region responsible for the specificity of antigen presentation to lymphocytes. Apart from polymorphisms, genomic reorganization caused by repeat elements and endogenous viral elements (EVEs) might be involved in T1D predisposition. Such elements are human endogenous retroviruses (HERVs) and non-long terminal repeat (non-LTR) retrotransposons, including long and short interspersed nuclear elements (LINEs and SINEs). In line with their parasitic origin and selfish behaviour, retrotransposon-imposed gene regulation is a major source of genetic variation and instability in the human genome, and may represent the missing link between genetic susceptibility and environmental factors long thought to contribute to T1D onset. Autoreactive immune cell subtypes with differentially expressed retrotransposons can be identified with single-cell transcriptomics, and personalized assembled genomes can be constructed, which can then serve as a reference for predicting retrotransposon integration/restriction sites. Here we review what is known to date about retrotransposons, we discuss the involvement of viruses and retrotransposons in T1D predisposition, and finally we consider challenges in retrotransposons analysis methods.
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A Systems Biology Approach on the Regulatory Footprint of Human Endogenous Retroviruses (HERVs). Diseases 2022; 10:diseases10040098. [PMID: 36412592 PMCID: PMC9680359 DOI: 10.3390/diseases10040098] [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: 08/08/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. ENCODE Project has offered a wealth of epigenetic data based on omics technologies. I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. On the one side, HERVs are in 1 out of 9 cCREs (>100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. On the other side, promoter-associated HERV cCREs are present adjacent to (in a 200 bp window) the transcription start sites of 256 human genes. Regulatory network production, followed by centrality analysis led to the discovery of 90 core genes containing HERV-associated promoters. Pathway analysis on the core network genes and their immediate neighbors revealed a regulatory footprint that, among others, is associated with inflammation, chemokine signaling and response to viral infection. Collectively, these results support the concept that the expansion of regulatory sequences derived from HERVs is critical for epigenetic innovation that may have wired together genes into novel transcriptional networks with critical roles in cellular physiology and pathology.
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13
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Jia L, Liu M, Yang C, Li H, Liu Y, Han J, Zhai X, Wang X, Li T, Li J, Zhang B, Yu C, Li L. Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome. Retrovirology 2022; 19:11. [PMID: 35676699 PMCID: PMC9178832 DOI: 10.1186/s12977-022-00596-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs) result from ancestral infections caused by exogenous retroviruses that became incorporated into the germline DNA and evolutionarily fixed in the human genome. HERVs can be transmitted vertically in a Mendelian fashion and be stably maintained in the human genome, of which they are estimated to comprise approximately 8%. HERV-K (HML1-10) transcription has been confirmed to be associated with a variety of diseases, such as breast cancer, lung cancer, prostate cancer, melanoma, rheumatoid arthritis, and amyotrophic lateral sclerosis. However, the poor characterization of HML-9 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, a precise and updated HERV-K HML-9 genomic map is urgently needed to better evaluate the role of these elements in human health. RESULTS We report a comprehensive analysis of the presence and distribution of HERV-K HML-9 elements within the human genome, with a detailed characterization of the structural and phylogenetic properties of the group. A total of 23 proviruses and 47 solo LTR elements were characterized, with a detailed description of the provirus structure, integration time, potential regulated genes, transcription factor binding sites (TFBS), and primer binding site (PBS) features. The integration time results showed that the HML-9 elements found in the human genome integrated into the primate lineage between 17.5 and 48.5 million years ago (mya). CONCLUSION The results provide a clear characterization of HML-9 and a comprehensive background for subsequent functional studies.
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Affiliation(s)
- Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Mengying Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Caiqin Yang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Xiuli Zhai
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Tianyi Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
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