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Chen M, Huang X, Wang C, Wang S, Jia L, Li L. Endogenous retroviral solo-LTRs in human genome. Front Genet 2024; 15:1358078. [PMID: 38606358 PMCID: PMC11007075 DOI: 10.3389/fgene.2024.1358078] [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: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are derived from the infection and integration of exogenetic retroviruses. HERVs account for 8% of human genome, and the majority of HERVs are solitary LTRs (solo-LTRs) due to homologous recombination. Multiple findings have showed that solo-LTRs could provide an enormous reservoir of transcriptional regulatory sequences involved in diverse biological processes, especially carcinogenesis and cancer development. The link between solo-LTRs and human diseases still remains poorly understood. This review focuses on the regulatory modules of solo-LTRs, which contribute greatly to the diversification and evolution of human genes. More importantly, although inactivating mutations, insertions and deletions have been identified in solo-LTRs, the inherited regulatory elements of solo-LTRs initiate the expression of chimeric lncRNA transcripts, which have been reported to play crucial roles in human health and disease. These findings provide valuable insights into the evolutionary and functional mechanisms underlying the presence of HERVs in human genome. Taken together, in this review, we will present evidences showing the regulatory and encoding capacity of solo-LTRs as well as the significant impact on various aspects of human biology.
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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, Hubei, China
| | - Xiaolong Huang
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - 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
| | - Shibo Wang
- 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 Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Simula ER, Zarbo IR, Arru G, Sechi E, Meloni R, Deiana GA, Solla P, Sechi LA. Antibody Response to HERV-K and HERV-W Envelope Epitopes in Patients with Myasthenia Gravis. Int J Mol Sci 2023; 25:446. [PMID: 38203616 PMCID: PMC10778599 DOI: 10.3390/ijms25010446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Myasthenia gravis is an antibody-mediated autoimmune neurological disorder characterized by impaired neuromuscular junction transmission, resulting in muscle weakness. Recently, the involvement of Human Endogenous Retroviruses (HERVs) in the pathophysiology of different immune-mediated and neurodegenerative diseases, such as multiple sclerosis, has been demonstrated. We aimed to investigate potential immune system involvement related to humoral responses targeting specific epitopes of HERV-K and HERV-W envelope proteins in myasthenia gravis. Myasthenia gravis patients were recruited in the Neurology Unit, while healthy controls were selected from the Blood Transfusion Center, both affiliated with AOU Sassari. Highly immunogenic antigens of HERV-K and HERV-W envelope proteins were identified using the Immune Epitope Database (IEDB) online tool. These epitopes were utilized in enzyme-linked immunosorbent assays (ELISA) to detect autoantibodies in serum directed against these sequences. The study involved 39 Healthy Donors and 47 MG patients, further categorized into subgroups based on the presence of autoantibodies: MG-AchR Ab+ (n = 17), MG-MuSK Ab+ (n = 7), double seronegative patients (MG-DSN, n = 18), MG-LRP4 Ab + (n = 4), and one patient with no antibodies data (n = 1). Our findings revealed high levels of autoantibodies in myasthenia gravis patients directed against the HERV-K-env-su(19-37), HERV-K-env-su(109-126), HERV-K-env-su(164-186), HERV-W-env(93-108), HERV-W-env(129-14), and HERV-W-env(248-262) epitopes. Notably, these results remained highly significant even when patients were subdivided into MG-AchR Ab+ and MG-DSN subgroups. Correlation analysis further revealed significant positive associations between the antibody levels against HERV-K and HERV-W families in patients, suggesting a synergistic action of the two HERVs in the pathology context since this correlation is absent in the control group. This study marks the first identification of a specific humoral response directed against defined epitopes of HERV-K and HERV-W envelope proteins in myasthenia gravis patients. These findings lay the foundation for future investigations aimed at elucidating the molecular mechanisms driving this immune response. The detection of these autoantibodies suggests the potential for novel biomarkers, especially within the MG-DSN patient subgroup, addressing the need for new biomarkers in this population.
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Affiliation(s)
- Elena Rita Simula
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy;
| | - Ignazio Roberto Zarbo
- Department of Medicine, Surgery and Pharmacy University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy; (I.R.Z.); (G.A.); (E.S.); (R.M.); (G.A.D.)
| | - Giannina Arru
- Department of Medicine, Surgery and Pharmacy University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy; (I.R.Z.); (G.A.); (E.S.); (R.M.); (G.A.D.)
| | - Elia Sechi
- Department of Medicine, Surgery and Pharmacy University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy; (I.R.Z.); (G.A.); (E.S.); (R.M.); (G.A.D.)
| | - Rossella Meloni
- Department of Medicine, Surgery and Pharmacy University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy; (I.R.Z.); (G.A.); (E.S.); (R.M.); (G.A.D.)
- Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy
| | - Giovanni Andrea Deiana
- Department of Medicine, Surgery and Pharmacy University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy; (I.R.Z.); (G.A.); (E.S.); (R.M.); (G.A.D.)
| | - Paolo Solla
- Department of Medicine, Surgery and Pharmacy University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy; (I.R.Z.); (G.A.); (E.S.); (R.M.); (G.A.D.)
| | - Leonardo Antonio Sechi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy;
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria, 07100 Sassari, Italy
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Tovo PA, Galliano I, Parodi E, Calvi C, Gambarino S, Licciardi F, Dini M, Montanari P, Branca M, Ramenghi U, Bergallo M. Children with Chronic Immune Thrombocytopenia Exhibit High Expression of Human Endogenous Retroviruses TRIM28 and SETDB1. Genes (Basel) 2023; 14:1569. [PMID: 37628621 PMCID: PMC10454145 DOI: 10.3390/genes14081569] [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: 07/11/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Chronic immune thrombocytopenia (CITP) is an autoimmune disease whose underlying biologic mechanisms remain elusive. Human endogenous retroviruses (HERVs) derive from ancestral infections and constitute about 8% of our genome. A wealth of clinical and experimental studies highlights their pivotal pathogenetic role in autoimmune diseases. Epigenetic mechanisms, such as those modulated by TRIM28 and SETDB1, are involved in HERV activation and regulation of immune response. We assessed, through a polymerase chain reaction real-time Taqman amplification assay, the transcription levels of pol genes of HERV-H, HERV-K, and HERV-W; env genes of Syncytin (SYN)1, SYN2, and HERV-W; as well as TRIM28 and SETDB1 in whole blood from 34 children with CITP and age-matched healthy controls (HC). The transcriptional levels of all HERV sequences, with the exception of HERV-W-env, were significantly enhanced in children with CITP as compared to HC. Patients on eltrombopag treatment exhibited lower expression of SYN1, SYN2, and HERV-W-env as compared to untreated patients. The mRNA concentrations of TRIM28 and SETDB1 were significantly higher and were positively correlated with those of HERVs in CITP patients. The over-expressions of HERVs and TRIM28/SETDB1 and their positive correlations in patients with CITP are suggestive clues of their contribution to the pathogenesis of the disease and support innovative interventions to inhibit HERV and TRIM28/SETDB1 expressions in patients unresponsive to standard therapies.
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Affiliation(s)
- Pier-Angelo Tovo
- Department of Public Health and Pediatric Sciences, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (P.-A.T.); (U.R.)
| | - Ilaria Galliano
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Emilia Parodi
- Pediatric and Neonatology Unit, Ordine Mauriziano Hospital, Largo Filippo Turati 62, 10128 Turin, Italy;
| | - Cristina Calvi
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Stefano Gambarino
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Francesco Licciardi
- Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy;
| | - Maddalena Dini
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Paola Montanari
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Margherita Branca
- Postgraduate School of Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy;
| | - Ugo Ramenghi
- Department of Public Health and Pediatric Sciences, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (P.-A.T.); (U.R.)
- Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy;
- Postgraduate School of Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy;
| | - Massimiliano Bergallo
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
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Xu Z, Wei D, Zhang H, Demongeot J. A Novel Mathematical Model That Predicts the Protection Time of SARS-CoV-2 Antibodies. Viruses 2023; 15:v15020586. [PMID: 36851801 PMCID: PMC9962246 DOI: 10.3390/v15020586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Infectious diseases such as SARS-CoV-2 pose a considerable threat to public health. Constructing a reliable mathematical model helps us quantitatively explain the kinetic characteristics of antibody-virus interactions. A novel and robust model is developed to integrate antibody dynamics with virus dynamics based on a comprehensive understanding of immunology principles. This model explicitly formulizes the pernicious effect of the antibody, together with a positive feedback stimulation of the virus-antibody complex on the antibody regeneration. Besides providing quantitative insights into antibody and virus dynamics, it demonstrates good adaptivity in recapturing the virus-antibody interaction. It is proposed that the environmental antigenic substances help maintain the memory cell level and the corresponding neutralizing antibodies secreted by those memory cells. A broader application is also visualized in predicting the antibody protection time caused by a natural infection. Suitable binding antibodies and the presence of massive environmental antigenic substances would prolong the protection time against breakthrough infection. The model also displays excellent fitness and provides good explanations for antibody selection, antibody interference, and self-reinfection. It helps elucidate how our immune system efficiently develops neutralizing antibodies with good binding kinetics. It provides a reasonable explanation for the lower SARS-CoV-2 mortality in the population that was vaccinated with other vaccines. It is inferred that the best strategy for prolonging the vaccine protection time is not repeated inoculation but a directed induction of fast-binding antibodies. Eventually, this model will inform the future construction of an optimal mathematical model and help us fight against those infectious diseases.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou 253023, China
- Correspondence: (Z.X.); (J.D.)
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou 253023, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France
- Correspondence: (Z.X.); (J.D.)
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Modulation of HERV Expression by Four Different Encephalitic Arboviruses during Infection of Human Primary Astrocytes. Viruses 2022; 14:v14112505. [PMID: 36423114 PMCID: PMC9694637 DOI: 10.3390/v14112505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Human retroelements (HERVs) are retroviral origin sequences fixed in the human genome. HERVs induction is associated with neurogenesis, cellular development, immune activation, and neurological disorders. Arboviruses are often associated with the development of encephalitis. The interplay between these viruses and HERVs has not been fully elucidated. In this work, we analyzed RNAseq data derived from infected human primary astrocytes by Zika (ZikV), Mayaro (MayV), Oropouche (OroV) and Chikungunya (ChikV) viruses, and evaluated the modulation of HERVs and their nearby genes. Our data show common HERVs expression modulation by both alphaviruses, suggesting conserved evolutionary routes of transcription regulation. A total of 15 HERVs were co-modulated by the four arboviruses, including the highly upregulated HERV4_4q22. Data on the upregulation of genes nearby to these elements in ChikV, MayV and OroV infections were also obtained, and interaction networks were built. The upregulation of 14 genes common among all viruses was observed in the networks, and 93 genes between MayV and ChikV. These genes are related to cellular processes such as cellular replication, cytoskeleton, cell vesicle traffic and antiviral response. Together, our results support the role of HERVs induction in the transcription regulation process of genes during arboviral infections.
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