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Wang YN, Chen XL, Yang J, Gong XX, Zhang HF, Zhang YM, Zeng DF, Chen PS, Chen HB. Reduced syncytin-1 regulates trophoblast invasion and apoptosis in preeclampsia. Placenta 2024; 155:32-41. [PMID: 39121585 DOI: 10.1016/j.placenta.2024.07.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/08/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024]
Abstract
INTRODUCTION Preeclampsia is a pregnancy-specific disorder characterized by de novo development of hypertension and proteinuria over 20 weeks gestation that has been associated with the dysfunction of trophoblasts. Current evidence suggests that syncytin-1 plays an important role in the non-fusogenic biological activity of trophoblasts, except for specific fusogenic function. However, the underlying mechanism remains unclear. METHODS The expression and location of syncytin-1 in normal and the late-onset preeclampsia placentas were detected by quantitative real-time PCR, western blotting and immunofluorescence. Morphological and apoptosis analysis were processed in placentas. The ex vivo extravillous explant culture model was used to explore the effect of syncytin-1 on EVT outgrowths. Real-time quantitative PCR and immunoblotting were used to calculate syncytin-1 levels in the trophoblast cells before and after syncytin-1 knockdown or overexpression. CCK-8 assay was used to detect the cell viability. TUNEL staining and immunoblotting were processed in trophoblast cells. Transwell assays and wound healing assays were utilize to assess the invasion and migration of trophoblastic cells. Conditional knockout of syncytin-a mouse model was conducted to present the change of placentas in vivo. The ex vivo extravillous explant culture model was used to explore the effect of syncytin-1 on EVT outgrowths. Western blotting was used to identify the key proteins of PI3K/Akt pathways and invasion-related proteins in trophoblast cells. RESULTS AND DISCUSSION Here, reduced syncytin-1 was identified in the late-onset preeclampsia placentas. Reduced syncytin-1 may attenuates the EMT process by promoting apoptosis, inhibiting proliferation and invasion by suppressed PI3K/Akt pathway in trophoblast cells. Our findings provide novel insights into the non-fusogenic biological function of reduced syncytin-1 that may be involves in the pathogenesis of preeclampsia.
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Affiliation(s)
- Ya-Nan Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China; Department of Histology and Embryology, Shantou University Medical College, China
| | - Xue-Ling Chen
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Ju Yang
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Xing-Xing Gong
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Hai-Feng Zhang
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Yan-Mei Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China
| | - Dan-Feng Zeng
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China
| | - Pei-Shan Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China.
| | - Hai-Bin Chen
- Department of Histology and Embryology, Shantou University Medical College, China
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Zhang D, Wu X, Xue X, Li W, Zhou P, Lv Z, Zhao K, Zhu F. Ancient dormant virus remnant ERVW-1 drives ferroptosis via degradation of GPX4 and SLC3A2 in schizophrenia. Virol Sin 2024; 39:31-43. [PMID: 37690733 PMCID: PMC10877354 DOI: 10.1016/j.virs.2023.09.001] [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: 05/04/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of retroviral infections in human germline cells from millions of years ago. Among these, ERVW-1 (also known as HERV-W-ENV, ERVWE1, or ENVW) encodes the envelope protein of the HERV-W family, which contributes to the pathophysiology of schizophrenia. Additionally, neuropathological studies have revealed cell death and disruption of iron homeostasis in the brains of individuals with schizophrenia. Here, our bioinformatics analysis showed that differentially expressed genes in the human prefrontal cortex RNA microarray dataset (GSE53987) were mainly related to ferroptosis and its associated pathways. Clinical data demonstrated significantly lower expression levels of ferroptosis-related genes, particularly Glutathione peroxidase 4 (GPX4) and solute carrier family 3 member 2 (SLC3A2), in schizophrenia patients compared to normal controls. Further in-depth analyses revealed a significant negative correlation between ERVW-1 expression and the levels of GPX4/SLC3A2 in schizophrenia. Studies indicated that ERVW-1 increased iron levels, malondialdehyde (MDA), and transferrin receptor protein 1 (TFR1) expression while decreasing glutathione (GSH) levels and triggering the loss of mitochondrial membrane potential, suggesting that ERVW-1 can induce ferroptosis. Ongoing research has shown that ERVW-1 reduced the expression of GPX4 and SLC3A2 by inhibiting their promoter activities. Moreover, Ferrostatin-1 (Fer-1), the ferroptosis inhibitor, reversed the iron accumulation and mitochondrial membrane potential loss, as well as restored the expressions of ferroptosis markers GSH, MDA, and TFR1 induced by ERVW-1. In conclusion, ERVW-1 could promote ferroptosis by downregulating the expression of GPX4 and SLC3A2, revealing a novel mechanism by which ERVW-1 contributes to neuronal cell death in schizophrenia.
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Affiliation(s)
- Dongyan Zhang
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xiulin Wu
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xing Xue
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenshi Li
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ping Zhou
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zhao Lv
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Kexin Zhao
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fan Zhu
- State Key Laboratory of Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China; Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan, 430071, China.
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Katoh H, Honda T. Roles of Human Endogenous Retroviruses and Endogenous Virus-Like Elements in Cancer Development and Innate Immunity. Biomolecules 2023; 13:1706. [PMID: 38136578 PMCID: PMC10741599 DOI: 10.3390/biom13121706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections in the host genome. Although mutations and silencing mechanisms impair their original role in viral replication, HERVs are believed to play roles in various biological processes. Long interspersed nuclear elements (LINEs) are non-LTR retrotransposons that have a lifecycle resembling that of retroviruses. Although LINE expression is typically silenced in somatic cells, it also contributes to various biological processes. The aberrant expression of HERVs and LINEs is closely associated with the development of cancer and/or immunological diseases, suggesting that they are integrated into various pathways related to the diseases. HERVs/LINEs control gene expression depending on the context as promoter/enhancer elements. Some RNAs and proteins derived from HERVs/LINEs have oncogenic potential, whereas others stimulate innate immunity. Non-retroviral endogenous viral elements (nrEVEs) are a novel type of virus-like element in the genome. nrEVEs may also be involved in host immunity. This article provides a current understanding of how these elements impact cellular physiology in cancer development and innate immunity, and provides perspectives for future studies.
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Affiliation(s)
- Hirokazu Katoh
- Department of Virology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Tomoyuki Honda
- Department of Virology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
- Department of Virology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
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Wu X, Liu L, Xue X, Li X, Zhao K, Zhang J, Li W, Yao W, Ding S, Jia C, Zhu F. Captive ERVWE1 triggers impairment of 5-HT neuronal plasticity in the first-episode schizophrenia by post-transcriptional activation of HTR1B in ALKBH5-m6A dependent epigenetic mechanisms. Cell Biosci 2023; 13:213. [PMID: 37990254 PMCID: PMC10664518 DOI: 10.1186/s13578-023-01167-4] [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: 07/27/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Abnormalities in the 5-HT system and synaptic plasticity are hallmark features of schizophrenia. Previous studies suggest that the human endogenous retrovirus W family envelope (ERVWE1) is an influential risk factor for schizophrenia and inversely correlates with 5-HT4 receptor in schizophrenia. To our knowledge, no data describes the effect of ERVWE1 on 5-HT neuronal plasticity. N6-methyladenosine (m6A) regulates gene expression and impacts synaptic plasticity. Our research aims to systematically investigate the effects of ERVWE1 on 5-HT neuronal plasticity through m6A modification in schizophrenia. RESULTS HTR1B, ALKBH5, and Arc exhibited higher levels in individuals with first-episode schizophrenia compared to the controls and showed a strong positive correlation with ERVWE1. Interestingly, HTR1B was also correlated with ALKBH5 and Arc. Further analyses confirmed that ALKBH5 may be an independent risk factor for schizophrenia. In vitro studies, we discovered that ERVWE1 enhanced HTR1B expression, thereby activating the ERK-ELK1-Arc pathway and reducing the complexity and spine density of 5-HT neurons. Furthermore, ERVWE1 reduced m6A levels through ALKBH5 demethylation. ERVWE1 induced HTR1B upregulation by improving its mRNA stability in ALKBH5-m6A-dependent epigenetic mechanisms. Importantly, ALKBH5 mediated the observed alterations in 5-HT neuronal plasticity induced by ERVWE1. CONCLUSIONS Overall, HTR1B, Arc, and ALKBH5 levels were increased in schizophrenia and positively associated with ERVWE1. Moreover, ALKBH5 was a novel risk gene for schizophrenia. ERVWE1 impaired 5-HT neuronal plasticity in ALKBH5-m6A dependent mechanism by the HTR1B-ERK-ELK1-Arc pathway, which may be an important contributor to aberrant synaptic plasticity in schizophrenia.
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Affiliation(s)
- Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | | | - Xing Xue
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xuhang Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Kexin Zhao
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jiahang Zhang
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenshi Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wei Yao
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Shuang Ding
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Chen Jia
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan, 430071, China.
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Sano R, Fukuda H, Kubo R, Oishi T, Miyabe-Nishiwaki T, Kaneko A, Masato H, Takahashi Y, Hayakawa A, Yazawa S, Kominato Y. Emergence of an erythroid cell-specific regulatory region in ABO intron 1 attributable to A- or B-antigen expression on erythrocytes in Hominoidea. Sci Rep 2023; 13:4947. [PMID: 36973299 PMCID: PMC10043005 DOI: 10.1038/s41598-023-31961-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
A- and B-antigens are present on red blood cells (RBCs) as well as other cells and secretions in Hominoidea including humans and apes such as chimpanzees and gibbons, whereas expression of these antigens on RBCs is subtle in monkeys such as Japanese macaques. Previous studies have indicated that H-antigen expression has not completely developed on RBCs in monkeys. Such antigen expression requires the presence of H-antigen and A- or B-transferase expression in cells of erythroid lineage, although whether or not ABO gene regulation is associated with the difference of A- or B-antigen expression between Hominoidea and monkeys has not been examined. Since it has been suggested that ABO expression on human erythrocytes is dependent upon an erythroid cell-specific regulatory region or the + 5.8-kb site in intron 1, we compared the sequences of ABO intron 1 among non-human primates, and demonstrated the presence of sites orthologous to the + 5.8-kb site in chimpanzees and gibbons, and their absence in Japanese macaques. In addition, luciferase assays revealed that the former orthologues enhanced promoter activity, whereas the corresponding site in the latter did not. These results suggested that the A- or B-antigens on RBCs might be ascribed to emergence of the + 5.8-kb site or the corresponding regions in ABO through genetic evolution.
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Affiliation(s)
- Rie Sano
- Department of Legal Medicine, Gunma University Graduate School of Medicine, 3-39-22 Showa-Machi, Maebashi, 371-8511, Japan.
| | - Haruki Fukuda
- Department of Legal Medicine, Gunma University Graduate School of Medicine, 3-39-22 Showa-Machi, Maebashi, 371-8511, Japan
| | - Rieko Kubo
- Department of Legal Medicine, Gunma University Graduate School of Medicine, 3-39-22 Showa-Machi, Maebashi, 371-8511, Japan
| | - Takao Oishi
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan
| | | | - Akihisa Kaneko
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan
| | | | - Yoichiro Takahashi
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Akira Hayakawa
- Department of Legal Medicine, Gunma University Graduate School of Medicine, 3-39-22 Showa-Machi, Maebashi, 371-8511, Japan
| | - Shin Yazawa
- Department of General Surgical Science, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Yoshihiko Kominato
- Department of Legal Medicine, Gunma University Graduate School of Medicine, 3-39-22 Showa-Machi, Maebashi, 371-8511, Japan
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Pandit R, Ipinmoroti AO, Crenshaw BJ, Li T, Matthews QL. Canine Coronavirus Infection Modulates the Biogenesis and Composition of Cell-Derived Extracellular Vesicles. Biomedicines 2023; 11:biomedicines11030976. [PMID: 36979955 PMCID: PMC10046050 DOI: 10.3390/biomedicines11030976] [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: 12/17/2022] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Coronavirus (CoV) has persistently become a global health concern causing various diseases in a wide variety of hosts, including humans, birds, and companion animals. However, the virus-mediated responses in animal hosts have not been studied extensively due to pathogenesis complexity and disease developments. Extracellular vesicles (EVs) are widely explored in viral infections for their intercellular communication, nanocarrier, and immunomodulatory properties. We proposed that coronavirus hijacks the host exosomal pathway and modulates the EV biogenesis, composition, and protein trafficking in the host. In the present study, Crandell-Rees feline kidney (CRFK) cells were infected with canine coronavirus (CCoV) in an exosome-free medium at the multiplicity of infection (MOI) of 400 infectious units (IFU) at various time points. The cell viability was significantly decreased over time, as determined by the 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Post-infection EVs were isolated, and transmission electron microscopy (TEM) showed the presence of small EVs (sEVs) after infection. NanoSight particle tracking analysis (NTA) revealed that EV sizes averaged between 100 and 200 nm at both incubation times; however, the mean size of infection-derived EVs was significantly decreased at 48 h when compared to uninfected control EVs. Quantitative analysis of protein levels performed by dot blot scanning showed that the expression levels of ACE-2, annexin-V, flotillin-1, TLR-7, LAMP, TNF-α, caspase-1, caspase-8, and others were altered in EVs after infection. Our findings suggested that coronavirus infection impacts cell viability, modulates EV biogenesis, and alters cargo composition and protein trafficking in the host, which could impact viral progression and disease development. Future experiments with different animal CoVs will provide a detailed understanding of host EV biology in infection pathogenesis and progression. Hence, EVs could offer a diagnostic and therapeutic tool to study virus-mediated host responses that could be extended to study the interspecies jump of animal CoVs to cause infection in humans.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Ayodeji O Ipinmoroti
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Brennetta J Crenshaw
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Ting Li
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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7
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Li X, Wu X, Li W, Yan Q, Zhou P, Xia Y, Yao W, Zhu F. HERV-W ENV Induces Innate Immune Activation and Neuronal Apoptosis via linc01930/cGAS Axis in Recent-Onset Schizophrenia. Int J Mol Sci 2023; 24:ijms24033000. [PMID: 36769337 PMCID: PMC9917391 DOI: 10.3390/ijms24033000] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Schizophrenia is a severe neuropsychiatric disorder affecting about 1% of individuals worldwide. Increased innate immune activation and neuronal apoptosis are common findings in schizophrenia. Interferon beta (IFN-β), an essential cytokine in promoting and regulating innate immune responses, causes neuronal apoptosis in vitro. However, the precise pathogenesis of schizophrenia is unknown. Recent studies indicate that a domesticated endogenous retroviral envelope glycoprotein of the W family (HERV-W ENV, also called ERVWE1 or syncytin 1), derived from the endogenous retrovirus group W member 1 (ERVWE1) locus on chromosome 7q21.2, has a high level in schizophrenia. Here, we found an increased serum IFN-β level in schizophrenia and showed a positive correlation with HERV-W ENV. In addition, serum long intergenic non-protein coding RNA 1930 (linc01930), decreased in schizophrenia, was negatively correlated with HERV-W ENV and IFN-β. In vitro experiments showed that linc01930, mainly in the nucleus and with noncoding functions, was repressed by HERV-W ENV through promoter activity suppression. Further studies indicated that HERV-W ENV increased IFN-β expression and neuronal apoptosis by restraining the expression of linc01930. Furthermore, HERV-W ENV enhanced cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes protein (STING) expression and interferon regulatory factor 3 (IRF3) phosphorylation in neuronal cells. Notably, cGAS interacted with HERV-W ENV and triggered IFN-β expression and neuronal apoptosis caused by HERV-W ENV. Moreover, Linc01930 participated in the increased neuronal apoptosis and expression level of cGAS and IFN-β induced by HERV-W ENV. To summarize, our results suggested that linc01930 and IFN-β might be novel potential blood-based biomarkers in schizophrenia. The totality of these results also showed that HERV-W ENV facilitated antiviral innate immune response, resulting in neuronal apoptosis through the linc01930/cGAS/STING pathway in schizophrenia. Due to its monoclonal antibody GNbAC1 application in clinical trials, we considered HERV-W ENV might be a reliable therapeutic choice for schizophrenia.
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Affiliation(s)
- Xuhang Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
| | - Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
| | - Wenshi Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
| | - Qiujin Yan
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
| | - Ping Zhou
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
| | - Yaru Xia
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
| | - Wei Yao
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan 430071, China
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan 430071, China
- Correspondence:
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8
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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.
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9
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Yao W, Zhou P, Yan Q, Wu X, Xia Y, Li W, Li X, Zhu F. ERVWE1 Reduces Hippocampal Neuron Density and Impairs Dendritic Spine Morphology through Inhibiting Wnt/JNK Non-Canonical Pathway via miR-141-3p in Schizophrenia. Viruses 2023; 15:168. [PMID: 36680208 PMCID: PMC9863209 DOI: 10.3390/v15010168] [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: 11/01/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancestral germline infections by exogenous retroviruses. Human endogenous retroviruses W family envelope gene (HERV-W env, also called ERVWE1), located on chromosome 7q21-22, encodes an envelope glycoprotein from the HERV-W family. Mounting evidence suggests that aberrant expression of ERVWE1 involves the etiology of schizophrenia. Moreover, the genetic and morphological studies indicate that dendritic spine deficits may contribute to the onset of schizophrenia. Here, we reported that ERVWE1 changed the density and morphology of the dendritic spine through inhibiting Wingless-type (Wnt)/c-Jun N-terminal kinases (JNK) non-canonical pathway via miR-141-3p in schizophrenia. In this paper, we found elevated levels of miR-141-3p and a significant positive correlation with ERVWE1 in schizophrenia. Moreover, serum Wnt5a and actin-related protein 2 (Arp2) levels decreased and demonstrated a significant negative correlation with ERVWE1 in schizophrenia. In vitro experiments disclosed that ERVWE1 up-regulated miR-141-3p expression by interacting with transcription factor (TF) Yin Yang 1 (YY1). YY1 modulated miR-141-3p expression by binding to its promoter. The luciferase assay revealed that YY1 enhanced the promoter activity of miR-141-3p. Using the miRNA target prediction databases and luciferase reporter assays, we demonstrated that miR-141-3p targeted Wnt5a at its 3' untranslated region (3' UTR). Furthermore, ERVWE1 suppressed the expression of Arp2 through non-canonical pathway, Wnt5a/JNK signaling pathway. In addition, ERVWE1 inhibited Wnt5a/JNK/Arp2 signal pathway through miR-141-3p. Finally, functional assays showed that ERVWE1 induced the abnormalities in hippocampal neuron morphology and spine density through inhibiting Wnt/JNK non-canonical pathway via miR-141-3p in schizophrenia. Our findings indicated that miR-141-3p, Wnt5a, and Arp2 might be potential clinical blood-based biomarkers or therapeutic targets for schizophrenia. Our work also provided new insight into the role of ERVWE1 in schizophrenia pathogenesis.
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Affiliation(s)
- Wei Yao
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Ping Zhou
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Qiujin Yan
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yaru Xia
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Wenshi Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xuhang Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan 430071, China
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Lee DH, Bae WH, Ha H, Park EG, Lee YJ, Kim WR, Kim HS. Z-DNA-Containing Long Terminal Repeats of Human Endogenous Retrovirus Families Provide Alternative Promoters for Human Functional Genes. Mol Cells 2022; 45:522-530. [PMID: 35950452 PMCID: PMC9385571 DOI: 10.14348/molcells.2022.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/16/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022] Open
Abstract
Transposable elements (TEs) account for approximately 45% of the human genome. TEs have proliferated randomly and integrated into functional genes during hominoid radiation. They appear as right-handed B-DNA double helices and slightly elongated left-handed Z-DNAs. Human endogenous retrovirus (HERV) families are widely distributed in human chromosomes at a ratio of 8%. They contain a 5'-long terminal repeat (LTR)-gag-pol-env-3'-LTR structure. LTRs contain the U3 enhancer and promoter region, transcribed R region, and U5 region. LTRs can influence host gene expression by acting as regulatory elements. In this review, we describe the alternative promoters derived from LTR elements that overlap Z-DNA by comparing Z-hunt and DeepZ data for human functional genes. We also present evidence showing the regulatory activity of LTR elements containing Z-DNA in GSDML. Taken together, the regulatory activity of LTR elements with Z-DNA allows us to understand gene function in relation to various human diseases.
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Affiliation(s)
- Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Hongseok Ha
- Division of Life Sciences, Korea University, Seoul 02841, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46231, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
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11
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p53 Binding Sites in Long Terminal Repeat 5Hs (LTR5Hs) of Human Endogenous Retrovirus K Family (HML-2 Subgroup) Play Important Roles in the Regulation of LTR5Hs Transcriptional Activity. Microbiol Spectr 2022; 10:e0048522. [PMID: 35867400 PMCID: PMC9430305 DOI: 10.1128/spectrum.00485-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) are distributed throughout the human genome and provide favorable conditions to regulate the expression of their adjacent genes. HML-2 is the most biologically active subgroup of the HERV-K family, and expression of its members has been associated with many cancer types. The LTRs of HML-2 have been classified into three subgroups (LTR5A, LTR5B, and LTR5Hs) based on phylogenetic analyses. The current study aimed to explore the LTR transcriptional activity differences among the three subtypes and further explore the underlying factors. A total of 43 LTR5A elements, 62 LTR5B elements, and 194 LTR5Hs elements were selected. A phylogenetic tree showed that the LTR5Hs group was clearly separated from the LTR5A and LTR5B groups. A luciferase reporter assay indicated that LTR5Hs had the strongest promoter activity, followed by LTR5A and LTR5B. To investigate the underlying factors, LTR5Hs was divided into 4 sections, and the homologous fragments in LTR5B were replaced successively. Replacement of the third section (−263 to 0) significantly increased LTR5B activity. Subsequent mutation experiments revealed that the increased transcriptional activity was induced by the TATA box and the two p53 binding sites within the section. Further interference with TP53 significantly decreased LTR5Hs transcriptional activity. Chromatin immunoprecipitation (ChIP) and CUT&Tag experiments finally confirmed the direct binding of the p53 protein with the two LTR5Hs p53 binding sites. Overall, the two p53 binding sites in the third section (−263 to 0) of LTR5Hs were revealed to play critical roles in the difference in transcriptional activity among the three subtypes. IMPORTANCE Human endogenous retroviruses (HERVs) were integrated into the human genome in ancient times and have been coevolving with the host. Since the Human Genome Project, HERVs have attracted increasing attention. Many studies have focused on their characterization, evolution, and biological function. In particular, the expression of HERV-K has been associated with many diseases, such as germ cell tumors, neurotoxicity, ovarian cancer, prostate cancer, and melanoma. Indeed, two HML-2-produced proteins, Np9 and Rec, are associated with certain cancers. However, their roles in these disease associations remain unclear. The current work focused on subgroup HML-2 of HERV-K, which is recognized as the most biologically active subgroup, and aimed to explore the mechanistic basis of transcriptional activity. The results revealed that p53 deeply determined the activity of HML-2 LTR5Hs. p53 is a rather important tumor suppressor protein. It can regulate the expression of genes related to cell cycle arrest, organic processes, and apoptosis in response to cellular stress and is critical for the control of homeostasis. Previous ChIP and expression studies of individual genes suggested that p53 sites in HERV LTRs may be part of the p53 transcription program and directly regulate p53 target genes in a species-specific manner. However, the exact function of p53 in the regulation of HERV LTR expression is largely elusive. Our results clearly demonstrated the interaction between LTR5Hs of HML-2 and p53. They are of great significance for the future comprehensive study of the physiological and pathological functions of LTRs of HERVs.
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Bu C, Wang Z, Ren Y, Chen D, Jiang SW. Syncytin-1 nonfusogenic activities modulate inflammation and contribute to preeclampsia pathogenesis. Cell Mol Life Sci 2022; 79:290. [PMID: 35536515 PMCID: PMC11073204 DOI: 10.1007/s00018-022-04294-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/23/2022] [Accepted: 04/06/2022] [Indexed: 11/03/2022]
Abstract
Maternal cellular and humoral immune responses to the allogeneic fetoplacental unit are a normal part of pregnancy adaptation. Overactive or dysregulated immune responses that often manifest as inflammation are considered a key element for the development of preeclampsia. Infiltration and activation of macrophages, nature killer cells, and T lymphocytes are frequently observed in the decidua and placenta associated with preeclampsia. In addition to local inflammation, systemic inflammatory changes including increased levels of TNF-α and interleukins (ILs) are detected in the maternal circulation. Syncytin-1 is an endogenous retroviral envelope protein that mediates the fusion of trophoblasts to form syncytiotrophoblasts, a cellular component carrying out most of placental barrier, exchange, and endocrine functions. In addition to these well-defined fusogenic functions that are known for their close association with preeclampsia, multiple studies indicated that syncytin-1 possesses nonfusogenic activities such as those for cell cycle and apoptosis regulation. Moreover, syncytin-1 expressed by trophoblasts and various types of immune cells may participate in regulation of inflammation in preeclamptic placenta and decidua. This review concentrates on the triangular relationship among inflammation, syncytin-1 nonfusogenic functions, and preeclampsia pathogenesis. Data regarding the reciprocal modulations of inflammation and poor vascularization/hypoxia are summarized. The impacts of syncytin-A (the mouse counterpart of human syncytin-1) gene knockout on placental vascularization and their implications for preeclampsia are discussed. Syncytin-1 expression in immune cells and its significance for inflammation are analyzed in the context of preeclampsia development. Finally, the involvements of syncytin-1 nonfusogenic activities in neuroinflammation and multiple sclerosis are compared to findings from preeclampsia.
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Affiliation(s)
- Chaozhi Bu
- Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China
| | - Zhiwei Wang
- Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, 222000, Jiangsu, China
| | - Yongwei Ren
- Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China
| | - Daozhen Chen
- Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China.
| | - Shi-Wen Jiang
- Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China.
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13
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Shah AH, Govindarajan V, Doucet-O'Hare TT, Rivas S, Ampie L, DeMarino C, Banasavadi-Siddegowda YK, Zhang Y, Johnson KR, Almsned F, Gilbert MR, Heiss JD, Nath A. Differential expression of an endogenous retroviral element [HERV-K(HML-6)] is associated with reduced survival in glioblastoma patients. Sci Rep 2022; 12:6902. [PMID: 35477752 PMCID: PMC9046263 DOI: 10.1038/s41598-022-10914-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/04/2022] [Indexed: 11/09/2022] Open
Abstract
Comprising approximately 8% of our genome, Human Endogenous RetroViruses (HERVs) represent a class of germline retroviral infections that are regulated through epigenetic modifications. In cancer cells, which often have epigenetic dysregulation, HERVs have been implicated as potential oncogenic drivers. However, their role in gliomas is not known. Given the link between HERV expression in cancer cell lines and the distinct epigenetic dysregulation in gliomas, we utilized a tailored bioinformatic pipeline to characterize and validate the glioma retrotranscriptome and correlate HERV expression with locus-specific epigenetic modifications. We identified robust overexpression of multiple HERVs in our cell lines, including a retroviral transcript, HML-6, at 19q13.43b in glioblastoma cells. HERV expression inversely correlated with loci-specific DNA methylation. HML-6 contains an intact open reading frame encoding a small envelope protein, ERVK3-1. Increased expression of ERVK3-1 in GBM patients is associated with a poor prognosis independent of IDH-mutational status. Our results suggest that not only is HML-6 uniquely overexpressed in highly invasive cell lines and tissue samples, but also its gene product, ERVK3-1, may be associated with reduced survival in GBM patients. These results may have implications for both the tumor biology of GBM and the role of ERVK3-1 as a potential therapeutic target.
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Affiliation(s)
- Ashish H Shah
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA.
| | - Vaidya Govindarajan
- Department of Neurosurgery, University of Miami School of Medicine, Miami, FL, USA
| | - Tara T Doucet-O'Hare
- Center for Cancer Research (CCR), National Institutes of Health, National Cancer Institute (NCI), Neuro-Oncology Branch (NOB), Bethesda, MD, USA
| | - Sarah Rivas
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Leo Ampie
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Catherine DeMarino
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | | | - Yong Zhang
- Bioinformatics Section, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Kory R Johnson
- Bioinformatics Section, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Fahad Almsned
- Bioinformatics Section, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Mark R Gilbert
- Center for Cancer Research (CCR), National Institutes of Health, National Cancer Institute (NCI), Neuro-Oncology Branch (NOB), Bethesda, MD, USA
| | - John D Heiss
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Avindra Nath
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
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Carter T, Singh M, Dumbovic G, Chobirko JD, Rinn JL, Feschotte C. Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. eLife 2022; 11:76257. [PMID: 35179489 PMCID: PMC8912925 DOI: 10.7554/elife.76257] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/17/2022] [Indexed: 12/05/2022] Open
Abstract
The human endogenous retrovirus type-H (HERVH) family is expressed in the preimplantation embryo. A subset of these elements are specifically transcribed in pluripotent stem cells where they appear to exert regulatory activities promoting self-renewal and pluripotency. How HERVH elements achieve such transcriptional specificity remains poorly understood. To uncover the sequence features underlying HERVH transcriptional activity, we performed a phyloregulatory analysis of the long terminal repeats (LTR7) of the HERVH family, which harbor its promoter, using a wealth of regulatory genomics data. We found that the family includes at least eight previously unrecognized subfamilies that have been active at different timepoints in primate evolution and display distinct expression patterns during human embryonic development. Notably, nearly all HERVH elements transcribed in ESCs belong to one of the youngest subfamilies we dubbed LTR7up. LTR7 sequence evolution was driven by a mixture of mutational processes, including point mutations, duplications, and multiple recombination events between subfamilies, that led to transcription factor binding motif modules characteristic of each subfamily. Using a reporter assay, we show that one such motif, a predicted SOX2/3 binding site unique to LTR7up, is essential for robust promoter activity in induced pluripotent stem cells. Together these findings illuminate the mechanisms by which HERVH diversified its expression pattern during evolution to colonize distinct cellular niches within the human embryo.
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Affiliation(s)
- Thomas Carter
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States [US]
| | - Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Gabrijela Dumbovic
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Jason D Chobirko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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15
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Kozlov AP. Mammalian tumor-like organs. 1. The role of tumor-like normal organs and atypical tumor organs in the evolution of development (carcino-evo-devo). Infect Agent Cancer 2022; 17:2. [PMID: 35012580 PMCID: PMC8751115 DOI: 10.1186/s13027-021-00412-0] [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: 07/02/2021] [Accepted: 12/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Earlier I hypothesized that hereditary tumors might participate in the evolution of multicellular organisms. I formulated the hypothesis of evolution by tumor neofunctionalization, which suggested that the evolutionary role of hereditary tumors might consist in supplying evolving multicellular organisms with extra cell masses for the expression of evolutionarily novel genes and the origin of new cell types, tissues, and organs. A new theory—the carcino-evo-devo theory—has been developed based on this hypothesis. Main text My lab has confirmed several non-trivial predictions of this theory. Another non-trivial prediction is that evolutionarily new organs if they originated from hereditary tumors or tumor-like structures, should recapitulate some tumor features in their development. This paper reviews the tumor-like features of evolutionarily novel organs. It turns out that evolutionarily new organs such as the eutherian placenta, mammary gland, prostate, the infantile human brain, and hoods of goldfishes indeed have many features of tumors. I suggested calling normal organs, which have many tumor features, the tumor-like organs. Conclusion Tumor-like organs might originate from hereditary atypical tumor organs and represent the part of carcino-evo-devo relationships, i.e., coevolution of normal and neoplastic development. During subsequent evolution, tumor-like organs may lose the features of tumors and the high incidence of cancer and become normal organs without (or with almost no) tumor features.
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Affiliation(s)
- A P Kozlov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3, Gubkina Street, Moscow, Russia, 117971. .,Peter the Great St. Petersburg Polytechnic University, 29, Polytekhnicheskaya Street, St. Petersburg, Russia, 195251.
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16
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Ko EJ, Cha HJ. The Roles of Human Endogenous Retroviruses (HERVs) in Inflammation. KOSIN MEDICAL JOURNAL 2021. [DOI: 10.7180/kmj.2021.36.2.69] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are ancient, currently inactive, and non-infectious due to recombination, deletions, and mutations in the host genome. However, HERV-derived elements are involved in physiological phenomena including inflammatory response. In recent studies, HERV-derived elements were involved directly in various inflammatory diseases including autoimmune diseases such as rheumatoid arthritis (RA), multiple sclerosis, amyotrophic lateral sclerosis (ALS), and Sjogren’s syndrome. Regarding the involvement of HERV-derived elements in inflammation, two possible mechanisms have been proposed. First, HERV-derived elements cause nonspecific innate immune processes. Second, HERV-derived RNA or proteins might stimulate selective signaling mechanisms. However, it is unknown how silent HERV elements are activated in the inflammatory response and what factors and signaling mechanisms are involved with HERV-derived elements. In this review, we introduce HERV-related autoimmune diseases and propose the possible action mechanisms of HERV-derived elements in the inflammatory response at the molecular level.
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Zhou Y, Liu L, Liu Y, Zhou P, Yan Q, Yu H, Chen X, Zhu F. Implication of human endogenous retrovirus W family envelope in hepatocellular carcinoma promotes MEK/ERK-mediated metastatic invasiveness and doxorubicin resistance. Cell Death Discov 2021; 7:177. [PMID: 34238921 PMCID: PMC8266889 DOI: 10.1038/s41420-021-00562-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/06/2021] [Accepted: 06/13/2021] [Indexed: 02/06/2023] Open
Abstract
Human endogenous retrovirus (HERVs), originating from exogenous retroviral infections of germ cells millions of years ago, have the potential for human diseases. Syncytin-1, an envelope protein encoded by the HERV W family, participates in the contexts of schizophrenia, multiple sclerosis, diabetes, and several types of cancers. Nevertheless, there is no report on the expression pattern and potential mechanism of Syncytin-1 in HCC. Here we found Syncytin-1 expression was up-regulated in HCC compared to adjacent non-tumorous tissues, especially in advanced HCC. Syncytin-1 was an independent risk factor to predict vascular invasion, metastasis, larger tumor size, and poor prognosis in HCC patients. Further analysis discovered that Syncytin-1 overexpression positively associated with HCC patients with serum HBsAg positive. Functional experiments in vitro and in vivo demonstrated that Syncytin-1 enhanced cell proliferation, metastasis, and tumorigenicity in HCC. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the mitogen-activated protein kinase (MEK)/extracellular signal-regulated protein kinase (ERK) pathway was involved in HCC. Our clinical data indicated that the levels of phosphorylation MEK1/2 and ERK1/2 were increased in HCC comparing with adjacent non-tumorous tissues. It showed the linear correlation between Syncytin-1 expression and upregulated MEK1/2 and ERK1/2 phosphorylation levels in HCC. Furthermore, Syncytin-1 activated MEK/ERK pathway in HCC cells. In-depth research showed that the inflammation-activated MEK/ERK pathway was essential in Syncytin-1 promoted hepatocarcinogenesis. Syncytin-1 suppressed doxorubicin-induced apoptosis via MEK/ERK cascade. In conclusion, Syncytin-1 promoted HCC progression and doxorubicin resistance via the inflammation-activated MEK/ERK pathway. Our findings revealed that Syncytin-1 was a potential prognostic biomarker and therapeutic target for HCC.
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Affiliation(s)
- Yan Zhou
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, 430071, Wuhan, P. R. China
| | - Lijuan Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, 430071, Wuhan, P. R. China
| | - Youyi Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, 430071, Wuhan, P. R. China
- Wuxi School of Medicine, Jiangnan University, 214000, Wuxi, P. R. China
| | - Ping Zhou
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, 430071, Wuhan, P. R. China
| | - Qiujin Yan
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, 430071, Wuhan, P. R. China
| | - Honglian Yu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, 430071, Wuhan, P. R. China
- Department of Biochemistry and Collaborative Innovation Center, Jining Medical University, 272067, Jining, P. R. China
| | - Xiaobei Chen
- Department of Infectious Diseases, Renmin Hospital, Wuhan University, 430071, Wuhan, P. R. China
| | - Fan Zhu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, 430071, Wuhan, P. R. China.
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18
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Shah AH, Gilbert M, Ivan ME, Komotar RJ, Heiss J, Nath A. The role of human endogenous retroviruses in gliomas: from etiological perspectives and therapeutic implications. Neuro Oncol 2021; 23:1647-1655. [PMID: 34120190 DOI: 10.1093/neuonc/noab142] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Accounting for approximately 8% of the human genome, Human Endogenous Retroviruses (HERVs) have been implicated in a variety of cancers including gliomas. In normal cells, tight epigenetic regulation of HERVs prevent aberrant expression; however, in cancer cells, HERVs expression remains pervasive, suggesting a role of HERVs in oncogenic transformation. HERVs may contribute to oncogenesis in several ways including insertional mutagenesis, chromosomal rearrangements, proto-oncogene formation, and maintenance of stemness. On the other hand, recent data has suggested that reversing epigenetic silencing of HERVs may induce robust anti-tumor immune responses, suggesting HERVs' potential therapeutic utility in gliomas. By reversing epigenetic modifications that silence HERVs, DNA methyltransferase and histone deacetylase inhibitors may stimulate a viral-mimicry cascade via HERV-derived dsRNA formation that induce interferon-mediated apoptosis. Leveraging this anti-tumor autoimmune response may be a unique avenue to target certain subsets of epigenetically-dysregulated gliomas. Nevertheless, the role of HERVs in gliomas as either arbitrators of oncogenesis or forerunners of the innate anti-tumor immune response remains unclear. Here, we review the role of HERVs in gliomas, their potential dichotomous function in propagating oncogenesis and stimulating the anti-tumor immune response and identify future directions for research.
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Affiliation(s)
- Ashish H Shah
- Department of Neurological Surgery, University of Miami Miller School of Medicine
| | - Mark Gilbert
- Neuro-oncology Branch, National Cancer Institute, National Institute of Health
| | - Michael E Ivan
- Department of Neurological Surgery, University of Miami Miller School of Medicine
| | - Ricardo J Komotar
- Department of Neurological Surgery, University of Miami Miller School of Medicine
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Dolci M, Favero C, Tarantini L, Villani S, Bregni M, Signorini L, Della Valle A, Crivelli F, D'Alessandro S, Ferrante P, Bollati V, Delbue S. Human endogenous retroviruses env gene expression and long terminal repeat methylation in colorectal cancer patients. Med Microbiol Immunol 2020; 209:189-199. [PMID: 32040616 DOI: 10.1007/s00430-020-00662-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Human endogenous retroviruses (HERV) are remnants of exogenous retroviral infections, representing 8% of the human genome. Their regulation is based on the DNA methylation of promoters, the long terminal repeats (LTRs). Transcripts from HERV have been associated with cancers, but reports concerning HERV expression in colorectal cancer remain sporadic. Sixty-three patients with advanced stages of colorectal cancer were enrolled in this study. The expressions of HERV env gene, and HERV-H, -K, -R and -P LTRs and Alu, LINE-1 methylation levels, were investigated in the tumor, normal adjacent tissues, and, where possible, blood and plasmatic extracellular vesicles (EVs). Associations among HERV env expression, methylation status and clinical characteristics were evaluated. No differences were observed in HERV env gene expression levels among the clinical specimens, while Alu, LINE-1, HERV-H and -K LTRs were demethylated in the tumor compared to the normal adjacent tissues (p < 0.05).The HERV env gene was expressed in the EVs at of 54% (-H), 38% (-K), 31% (-R) patients. Association was not found between HERV env expression and LTR methylation, but significant higher expression of HERV-P and -R env was found in tumor tissues arising from the right colon. Our findings do not demonstrate significant overexpression of the studied HERV in colorectal cancer, but their association with tumor localization and specificity of the changes in DNA methylation of retroelements are shown. HERV sequences were packaged in the EVs and might be transferred from one cell to another.
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Affiliation(s)
- Maria Dolci
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal, 36, 20133, Milan, Italy
| | - Chiara Favero
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, University of Milan, Via San Barnaba 8, Milan, Italy
| | - Letizia Tarantini
- Department of Preventive Medicine, Fondazione IRCSS Ca' Granda, Ospedale Maggiore Policlinico, Via San Barnaba 8, Milan, Italy
| | - Sonia Villani
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal, 36, 20133, Milan, Italy
| | - Marco Bregni
- Hematology Unit, ASST Valle Olona, Ospedale di Circolo di Busto Arsizio, Via Arnaldo da Brescia 3, Busto Arsizio, Italy
| | - Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal, 36, 20133, Milan, Italy
| | - Alberto Della Valle
- General Surgery Unit, Istituto Clinico Città Studi, Via Jommelli 19, Milan, Italy
| | - Filippo Crivelli
- Pathology Unit, ASST Valle Olona, Ospedale di Circolo di Busto Arsizio, Via Arnaldo da Brescia 3, Busto Arsizio, Italy
| | - Sarah D'Alessandro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal, 36, 20133, Milan, Italy
| | - Pasquale Ferrante
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal, 36, 20133, Milan, Italy
| | - Valentina Bollati
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, University of Milan, Via San Barnaba 8, Milan, Italy.,Department of Preventive Medicine, Fondazione IRCSS Ca' Granda, Ospedale Maggiore Policlinico, Via San Barnaba 8, Milan, Italy
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal, 36, 20133, Milan, Italy.
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Silveira MM, Vargas LN, Bayão HXS, Schumann NAB, Caetano AR, Rumpf R, Franco MM. DNA methylation of the endogenous retrovirus Fematrin-1 in fetal placenta is associated with survival rate of cloned calves. Placenta 2019; 88:52-60. [PMID: 31671312 DOI: 10.1016/j.placenta.2019.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The expression of retroviral envelope proteins in the placenta facilitates generation of the multinuclear syncytiotrophoblast as an outer cellular layer of the placenta by fusion of the trophoblastic cells. This process is essential for placenta development in eutherians and for successful pregnancy. METHODS We tested the hypothesis that alterations in DNA methylation and gene expression profiles of the endogenous retroviruses (ERVs) and genes related to epigenetic reprogramming in placenta of cloned calves result in abnormal offspring phenotypes. The fetal cotyledons in 13 somatic cell nuclear transfer (SCNT) pregnancies were collected. DNA methylation level of Fematrin-1 was analyzed using bisulfite PCR and mRNA levels of Fematrin-1, Syncytin-Rum1, DNMT1, DNMT3A, DNMT3B, TET1, TET2 and TET3 measured by RT-qPCR. RESULTS Methylation of Fematrin-1 in placenta of control animals produced by artificial insemination (AI) was similar to live SCNT-produced calves, but hypermethylated than dead SCNT-produced calves. The levels of mRNA differed between SCNT-produced calves and AI animals for all genes, except TET3. However, no differences were observed between the live and dead cloned calves for all genes. Moreover, no differences were found between mRNA levels of Fematrin-1 and Syncytin-Rum1. DISCUSSION Our results suggest that this altered DNA methylation, deregulation in the expression of ERVs and in the genes of epigenetic machinery in fetal cotyledons of cloned calves may be associated with abnormal placentogenesis found in SCNT-produced animals. Further studies characterizing other mechanisms involved in the regulation of ERVs are important to support the development of new strategies to improve the efficiency of cloning.
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Affiliation(s)
- Márcia Marques Silveira
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil; Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
| | - Luna Nascimento Vargas
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil; Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
| | | | - Naiara Araújo Borges Schumann
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil; Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
| | | | - Rodolfo Rumpf
- GENEAL Genetics and Animal Biotechnology, Uberaba, Minas Gerais, Brazil.
| | - Maurício Machaim Franco
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil; Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil; Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil; School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
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21
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Kong Q, Quan X, Du J, Tai Y, Liu W, Zhang J, Zhang X, Mu Y, Liu Z. Endo-siRNAs regulate early embryonic development by inhibiting transcription of long terminal repeat sequence in pig†. Biol Reprod 2019; 100:1431-1439. [PMID: 30883641 DOI: 10.1093/biolre/ioz042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/21/2019] [Accepted: 03/16/2019] [Indexed: 11/12/2022] Open
Abstract
Activity of some endogenous retroviruses (ERVs) has been proven to be important for development of early mammalian embryo. However, abnormal activation of ERVs can also cause genetic diseases due to their ability to retrotranspose, so the regulatory mechanism to limit transcription of ERVs needs to be clarified. Endogenous small interfering RNA (endo-siRNA) has been reported to protect cells against transposable elements (TEs). Here, we determined the role of ERVs long terminal repeat sequences (LTRs) derived endo-siRNAs (LTR-siRNAs) on inhibition of the activity of ERVs during early embryonic development in pig. Seven most highly expressed LTR-siRNAs were identified in porcine zygote by high-throughput small RNA sequencing. We verified that the biogenesis of the LTR-siRNAs was DICER-dependent and they were generated from double-stranded RNA (dsRNA) formed by sense and antisense transcripts of LTRs. And, the expression of sense and antisense of LTRs might be due to the loss of DNA methylation at some LTR loci. Furthermore, we showed that the LTR-siRNAs could regulate early embryonic development by repression of LTRs expression at a post-transcriptional level. So, we propose here, during early embryonic development when epigenetic reprogramming occurs, the endo-siRNA pathway acts as a sophisticated balance of regulatory mechanism for ERV activity.
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Affiliation(s)
- Qingran Kong
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Xue Quan
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Jiawei Du
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Yurong Tai
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Wanxin Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Jiaming Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Xiaolei Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
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22
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Daskalakis M, Brocks D, Sheng YH, Islam MS, Ressnerova A, Assenov Y, Milde T, Oehme I, Witt O, Goyal A, Kühn A, Hartmann M, Weichenhan D, Jung M, Plass C. Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors. Cell Cycle 2018; 17:811-822. [PMID: 29633898 DOI: 10.1080/15384101.2018.1442623] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Inhibitors of DNA methyltransferases (DNMTis) or histone deacetylases (HDACis) are epigenetic drugs which are investigated since decades. Several have been approved and are applied in the treatment of hematopoietic and lymphatic malignancies, although their mode of action has not been fully understood. Two recent findings improved mechanistic insights: i) activation of human endogenous retroviral elements (HERVs) with concomitant synthesis of double-stranded RNAs (dsRNAs), and ii) massive activation of promoters from long terminal repeats (LTRs) which originated from past HERV invasions. These dsRNAs activate an antiviral response pathway followed by apoptosis. LTR promoter activation leads to synthesis of non-annotated transcripts potentially encoding novel or cryptic proteins. Here, we discuss the current knowledge of the molecular effects exerted by epigenetic drugs with a focus on DNMTis and HDACis. We highlight the role in LTR activation and provide novel data from both in vitro and in vivo epigenetic drug treatment.
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Affiliation(s)
- Michael Daskalakis
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - David Brocks
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yi-Hua Sheng
- b School of Pharmacy, College of Medicine , National Taiwan University , Taipei , Taiwan
| | - Md Saiful Islam
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alzbeta Ressnerova
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Yassen Assenov
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Till Milde
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ina Oehme
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Olaf Witt
- c Translational Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ) , Germany.,d CCU Pediatric Oncology , German Cancer Research Center (DKFZ) , Heidelberg , Germany.,e Department of Pediatric Oncology, Hematology and Immunology , University Hospital, and Clinical Cooperation Unit Pediatric Oncology, DKFZ , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
| | - Ashish Goyal
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Alexander Kühn
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Mark Hartmann
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,g Regulation of Cellular Differentiation Group , German Cancer Research Center , Heidelberg , Germany
| | - Dieter Weichenhan
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany
| | - Manfred Jung
- h Institute of Pharmaceutical Sciences, University of Freiburg , Germany
| | - Christoph Plass
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center , Heidelberg , Germany.,f German Cancer Research Consortium (DKTK) , Heidelberg , Germany
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23
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Nguyen NPD, Deshpande V, Luebeck J, Mischel PS, Bafna V. ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res 2018; 46:3309-3325. [PMID: 29579309 PMCID: PMC6283451 DOI: 10.1093/nar/gky180] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/12/2018] [Accepted: 03/05/2018] [Indexed: 12/20/2022] Open
Abstract
The integration of viral sequences into the host genome is an important driver of tumorigenesis in many viral mediated cancers, notably cervical cancer and hepatocellular carcinoma. We present ViFi, a computational method that combines phylogenetic methods with reference-based read mapping to detect viral integrations. In contrast with read-based reference mapping approaches, ViFi is faster, and shows high precision and sensitivity on both simulated and biological data, even when the integrated virus is a novel strain or highly mutated. We applied ViFi to matched genomic and mRNA data from 68 cervical cancer samples from TCGA and found high concordance between the two. Surprisingly, viral integration resulted in a dramatic transcriptional upregulation in all proximal elements, including LINEs and LTRs that are not normally transcribed. This upregulation is highly correlated with the presence of a viral gene fused with a downstream human element. Moreover, genomic rearrangements suggest the formation of apparent circular extrachromosomal (ecDNA) human-viral structures. Our results suggest the presence of apparent small circular fusion viral/human ecDNA, which correlates with indiscriminate and unregulated expression of proximal genomic elements, potentially contributing to the pathogenesis of HPV-associated cervical cancers. ViFi is available at https://github.com/namphuon/ViFi.
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Affiliation(s)
- Nam-phuong D Nguyen
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Viraj Deshpande
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
- Department of Pathology, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Vineet Bafna
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
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24
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Grandi N, Cadeddu M, Blomberg J, Mayer J, Tramontano E. HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini. BMC Evol Biol 2018; 18:6. [PMID: 29351742 PMCID: PMC5775608 DOI: 10.1186/s12862-018-1125-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/14/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. RESULTS We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini), Tarsiiformes and to the most primitive Prosimians. Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae, Platyrrhini parvorder), identified as ERV1-1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae, representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians. CONCLUSIONS Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.
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Affiliation(s)
- Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jens Mayer
- Institute of Human Genetics, University of Saarland, Homburg, Germany
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy
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25
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Wang X, Huang J, Zhu F. Human Endogenous Retroviral Envelope Protein Syncytin-1 and Inflammatory Abnormalities in Neuropsychological Diseases. Front Psychiatry 2018; 9:422. [PMID: 30245643 PMCID: PMC6137383 DOI: 10.3389/fpsyt.2018.00422] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/17/2018] [Indexed: 12/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) comprise approximately 8% of the human genome. Recent studies have considered HERVs as potential pathogenic factors. The majority of HERV genes are mutated and not capable of encoding functional proteins; regardless, some HERV genes, such as HERV-W envelope (env) glycoprotein, are known to have intact open reading frames. The HERV-W element on 7q21.2, which encodes a protein referred to as Syncytin-1, participates in human placental morphogenesis and can activate a pro-inflammatory and autoimmune cascade. Neuropsychological disorders are typically linked to inflammatory abnormalities. In this study, we review that Syncytin-1 has been increasingly involved in the development of neuropsychological disorders, such as schizophrenia and multiple sclerosis (MS). This study also presents inflammation imbalances in schizophrenia and MS. More importantly, we discuss the potential role and molecular mechanisms by which Syncytin-1 regulates inflammatory abnormalities in neuropsychological diseases. In summary, Syncytin-1 activity may represent a novel molecular pathogenic mechanism in neuropyschological diseases, such as schizophrenia and MS.
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Affiliation(s)
- Xiuling Wang
- Department of Medical Microbiology, School of Medicine Wuhan University, Wuhan, China.,Department of Medical Laboratory, The Central Hospital of Wuhan Huazhong University of Science and Technology, Wuhan, China
| | - Jin Huang
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan Huazhong University of Science and Technology, Wuhan, China
| | - Fan Zhu
- Department of Medical Microbiology, School of Medicine Wuhan University, Wuhan, China.,Hubei Province Key Laboratory of Allergy and Immunology Wuhan University, Wuhan, China
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26
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Díaz-Carballo D, Klein J, Acikelli AH, Wilk C, Saka S, Jastrow H, Wennemuth G, Dammann P, Giger-Pabst U, Khosrawipour V, Rassow J, Nienen M, Strumberg D. Cytotoxic stress induces transfer of mitochondria-associated human endogenous retroviral RNA and proteins between cancer cells. Oncotarget 2017; 8:95945-95964. [PMID: 29221178 PMCID: PMC5707072 DOI: 10.18632/oncotarget.21606] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 08/25/2017] [Indexed: 12/24/2022] Open
Abstract
About 8 % of the human genome consists of human endogenous retroviruses (HERVs), which are relicts of ancient exogenous retroviral infections incurred during evolution. Although the majority of HERVs have functional gene defects or epigenetic modifications, many of them are still able to produce retroviral proteins that have been proposed to be involved in cellular transformation and cancer development. We found that, in chemo-resistant U87RETO glioblastoma cells, cytotoxic stress induced by etoposide promotes accumulation and large-scale fission of mitochondria, associated with the detection of HERV-WE1 (syncytin-1) and HERV-FRD1 (syncytin-2) in these organelles. In addition, mitochondrial preparations also contained the corresponding receptors, i.e. ASCT2 and MFSD2. We clearly demonstrated that mitochondria associated with HERV-proteins were shuttled between adjacent cancer cells not only via tunneling tubes, but also by direct cellular uptake across the cell membrane. Furthermore, anti-syncytin-1 and anti-syncytin-2 antibodies were able to specifically block this direct cellular uptake of mitochondria even more than antibodies targeting the cognate receptors. Here, we suggest that the association of mitochondria with syncytin-1/syncytin-2 together with their respective receptors could represent a novel mechanism of cell-to-cell transfer. In chemotherapy-refractory cancer cells, this might open up attractive avenues to novel mitochondria-targeting therapies.
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Affiliation(s)
- David Díaz-Carballo
- Institute for Molecular Oncology and Experimental Therapeutics, Department of Hematology and Medical Oncology, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Jacqueline Klein
- Institute for Molecular Oncology and Experimental Therapeutics, Department of Hematology and Medical Oncology, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Ali H Acikelli
- Institute for Molecular Oncology and Experimental Therapeutics, Department of Hematology and Medical Oncology, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Camilla Wilk
- Institute for Molecular Oncology and Experimental Therapeutics, Department of Hematology and Medical Oncology, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Sahitya Saka
- Institute for Molecular Oncology and Experimental Therapeutics, Department of Hematology and Medical Oncology, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Holger Jastrow
- Institute of Anatomy and Experimental Morphology, University of Duisburg-Essen, Essen, Germany
| | - Gunther Wennemuth
- Institute of Anatomy and Experimental Morphology, University of Duisburg-Essen, Essen, Germany
| | - Phillip Dammann
- Central Animal Laboratory, University of Duisburg-Essen, Essen, Germany
| | - Urs Giger-Pabst
- Department of Surgery, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Veria Khosrawipour
- Department of Surgery, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Joachim Rassow
- Institute of Biochemistry and Pathobiochemistry, Department of Cellular Biochemistry, Ruhr-University of Bochum, Bochum, Germany
| | - Mikalai Nienen
- Department of Nephrology, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
| | - Dirk Strumberg
- Institute for Molecular Oncology and Experimental Therapeutics, Department of Hematology and Medical Oncology, Marienhospital Herne, Ruhr-University of Bochum, Bochum, Germany
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27
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Liu C, Liu L, Wang X, Liu Y, Wang M, Zhu F. HBV X Protein induces overexpression of HERV-W env through NF-κB in HepG2 cells. Virus Genes 2017. [PMID: 28639221 DOI: 10.1007/s11262-017-1479-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Human endogenous retrovirus W family (HERV-W) envelope (env) at chromosome 7 is highly expressed in the placenta and possesses fusogenic activity in trophoblast development. HERV-W env has been found to be overexpressed in some cancers and immune diseases. Viral transactivators can induce the overexpression of HERV-W env in human cell lines. Hepatitis B virus X protein (HBx) is believed to be a multifunctional oncogenic protein. Here, we reported that HBx could increase the promoter activity of HERV-W env and upregulate the mRNA levels of non-spliced and spliced HERV-W env and also its protein in human hepatoma HepG2 cells. Interestingly, we found that the inhibition of nuclear factor κB (NF-κB) using shRNA targeting NF-κB/p65 or PDTC (an inhibitor of NF-κB) could attenuate the upregulation of HERV-W env induced by HBx. These suggested that HBx might upregulate the expression of HERV-W env through NF-κB in HepG2 cells. This study might provide a new insight in HBV-associated liver diseases including HCC.
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Affiliation(s)
- Cong Liu
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Lijuan Liu
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Xiuling Wang
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Youyi Liu
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Miao Wang
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Fan Zhu
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, 430071, People's Republic of China. .,Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, 430071, Hubei Province, People's Republic of China.
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28
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Becker J, Pérot P, Cheynet V, Oriol G, Mugnier N, Mommert M, Tabone O, Textoris J, Veyrieras JB, Mallet F. A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray. BMC Genomics 2017; 18:286. [PMID: 28390408 PMCID: PMC5385096 DOI: 10.1186/s12864-017-3669-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/28/2017] [Indexed: 02/07/2023] Open
Abstract
Background Human endogenous retroviruses (HERVs) have received much attention for their implications in the etiology of many human diseases and their profound effect on evolution. Notably, recent studies have highlighted associations between HERVs expression and cancers (Yu et al., Int J Mol Med 32, 2013), autoimmunity (Balada et al., Int Rev Immunol 29:351–370, 2010) and neurological (Christensen, J Neuroimmune Pharmacol 5:326–335, 2010) conditions. Their repetitive nature makes their study particularly challenging, where expression studies have largely focused on individual loci (De Parseval et al., J Virol 77:10414–10422, 2003) or general trends within families (Forsman et al., J Virol Methods 129:16–30, 2005; Seifarth et al., J Virol 79:341–352, 2005; Pichon et al., Nucleic Acids Res 34:e46, 2006). Methods To refine our understanding of HERVs activity, we introduce here a new microarray, HERV-V3. This work was made possible by the careful detection and annotation of genomic HERV/MaLR sequences as well as the development of a new hybridization model, allowing the optimization of probe performances and the control of cross-reactions. Results HERV-V3 offers an almost complete coverage of HERVs and their ancestors (mammalian apparent LTR-retrotransposons, MaLRs) at the locus level along with four other repertoires (active LINE-1 elements, lncRNA, a selection of 1559 human genes and common infectious viruses). We demonstrate that HERV-V3 analytical performances are comparable with commercial Affymetrix arrays, and that for a selection of tissue/pathological specific loci, the patterns of expression measured on HERV-V3 is consistent with those reported in the literature. Conclusions Given its large HERVs/MaLRs coverage and additional repertoires, HERV-V3 opens the door to multiple applications such as enhancers and alternative promoters identification, biomarkers identification as well as the characterization of genes and HERVs/MaLRs modulation caused by viral infection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3669-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jérémie Becker
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Philippe Pérot
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Valérie Cheynet
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Guy Oriol
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Nathalie Mugnier
- Bioinformatics Research Department, bioMerieux, 376 Chemin de l'Orme, 69280, Marcy l'Etoile, France
| | - Marine Mommert
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France.,EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Olivier Tabone
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Julien Textoris
- EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Jean-Baptiste Veyrieras
- Bioinformatics Research Department, bioMerieux, 376 Chemin de l'Orme, 69280, Marcy l'Etoile, France
| | - François Mallet
- Joint research unit, Hospice Civils de Lyon, bioMerieux, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France. .,EA 7426 Pathophysiology of Injury-induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.
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29
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Kozlov AP. Expression of evolutionarily novel genes in tumors. Infect Agent Cancer 2016; 11:34. [PMID: 27437030 PMCID: PMC4949931 DOI: 10.1186/s13027-016-0077-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023] Open
Abstract
The evolutionarily novel genes originated through different molecular mechanisms are expressed in tumors. Sometimes the expression of evolutionarily novel genes in tumors is highly specific. Moreover positive selection of many human tumor-related genes in primate lineage suggests their involvement in the origin of new functions beneficial to organisms. It is suggested to consider the expression of evolutionarily young or novel genes in tumors as a new biological phenomenon, a phenomenon of TSEEN (tumor specifically expressed, evolutionarily novel) genes.
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Affiliation(s)
- A. P. Kozlov
- The Biomedical Center and Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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30
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Trela M, Nelson PN, Rylance PB. The role of molecular mimicry and other factors in the association of Human Endogenous Retroviruses and autoimmunity. APMIS 2016; 124:88-104. [PMID: 26818264 DOI: 10.1111/apm.12487] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/26/2015] [Indexed: 02/02/2023]
Abstract
Human Endogenous Retroviruses (HERVs) have been implicated in autoimmune and other diseases. Molecular mimicry has been postulated as a potential mechanism of autoimmunity. Exogenous viruses have also been reported to be associated with the same diseases, as have genetic and environmental factors. If molecular mimicry were to be shown to be an initiating mechanism of some autoimmune diseases, then therapeutic options of blocking antibodies and peptides might be of benefit in halting diseases at the outset. Bioinformatic and molecular modelling techniques have been employed to investigate molecular mimicry and the evidence for the association of HERVs and autoimmunity is reviewed. The most convincing evidence for molecular mimicry is in rheumatoid arthritis, where HERV K-10 shares amino acid sequences with IgG1Fc, a target for rheumatoid factor. Systemic lupus erythematosus is an example of a condition associated with several autoantibodies, and several endogenous and exogenous viruses have been reported to be associated with the disease. The lack of a clear link between one virus and this condition, and the spectrum of clinical manifestations, suggests that genetic, environmental and the inflammatory response to a virus or viruses might also be major factors in the pathogenesis of lupus and other autoimmune conditions. Where there are strong associations between a virus and an autoimmune condition, such as in hepatitis C and cryoglobulinaemia, the use of bioinformatics and molecular modelling can also be utilized to help to understand the role of molecular mimicry in how HERVs might trigger disease.
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Affiliation(s)
- Malgorzata Trela
- Immunology Research Group, Research Institute in Healthcare Sciences, University of Wolverhampton, Wolverhampton, UK
| | - Paul N Nelson
- Immunology Research Group, Research Institute in Healthcare Sciences, University of Wolverhampton, Wolverhampton, UK
| | - Paul B Rylance
- Royal Wolverhampton NHS Trust, New Cross Hospital, Wolverhampton, UK
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31
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Garazha A, Ivanova A, Suntsova M, Malakhova G, Roumiantsev S, Zhavoronkov A, Buzdin A. New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome. Cell Cycle 2016; 14:1476-84. [PMID: 25853282 PMCID: PMC4612461 DOI: 10.1080/15384101.2015.1022696] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of “domestication” of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.
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Affiliation(s)
- Andrew Garazha
- a Group for Genomic Regulation of Cell Signaling Systems ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry ; Moscow , Russia
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32
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Identification of a new subclass of ALK-negative ALCL expressing aberrant levels of ERBB4 transcripts. Blood 2015; 127:221-32. [PMID: 26463425 DOI: 10.1182/blood-2014-12-614503] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 10/06/2015] [Indexed: 11/20/2022] Open
Abstract
Anaplastic large-cell lymphoma (ALCL) is a clinical and biological heterogeneous disease that includes systemic anaplastic lymphoma kinase (ALK)-positive and ALK-negative entities. To discover biomarkers and/or genes involved in ALK-negative ALCL pathogenesis, we applied the cancer outlier profile analysis algorithm to a gene expression profiling data set including 249 cases of T-cell non-Hodgkin lymphoma and normal T cells. Ectopic coexpression of ERBB4 and COL29A1 genes was detected in 24% of ALK-negative ALCL patients. RNA sequencing and 5' RNA ligase-mediated rapid amplification of complementary DNA ends identified 2 novel ERBB4-truncated transcripts displaying intronic transcription start sites. By luciferase assays, we defined that the expression of ERBB4-aberrant transcripts is promoted by endogenous intronic long terminal repeats. ERBB4 expression was confirmed at the protein level by western blot analysis and immunohistochemistry. Lastly, we demonstrated that ERBB4-truncated forms show oncogenic potentials and that ERBB4 pharmacologic inhibition partially controls ALCL cell growth and disease progression in an ERBB4-positive patient-derived tumorgraft model. In conclusion, we identified a new subclass of ALK-negative ALCL characterized by aberrant expression of ERBB4-truncated transcripts carrying intronic 5' untranslated regions.
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33
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Suntsova M, Garazha A, Ivanova A, Kaminsky D, Zhavoronkov A, Buzdin A. Molecular functions of human endogenous retroviruses in health and disease. Cell Mol Life Sci 2015; 72:3653-75. [PMID: 26082181 PMCID: PMC11113533 DOI: 10.1007/s00018-015-1947-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/29/2015] [Accepted: 06/03/2015] [Indexed: 12/13/2022]
Abstract
Human endogenous retroviruses (HERVs) and related genetic elements form 504 distinct families and occupy ~8% of human genome. Recent success of high-throughput experimental technologies facilitated understanding functional impact of HERVs for molecular machinery of human cells. HERVs encode active retroviral proteins, which may exert important physiological functions in the body, but also may be involved in the progression of cancer and numerous human autoimmune, neurological and infectious diseases. The spectrum of related malignancies includes, but not limits to, multiple sclerosis, psoriasis, lupus, schizophrenia, multiple cancer types and HIV. In addition, HERVs regulate expression of the neighboring host genes and modify genomic regulatory landscape, e.g., by providing regulatory modules like transcription factor binding sites (TFBS). Indeed, recent bioinformatic profiling identified ~110,000 regulatory active HERV elements, which formed at least ~320,000 human TFBS. These and other peculiarities of HERVs might have played an important role in human evolution and speciation. In this paper, we focus on the current progress in understanding of normal and pathological molecular niches of HERVs, on their implications in human evolution, normal physiology and disease. We also review the available databases dealing with various aspects of HERV genetics.
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Affiliation(s)
- Maria Suntsova
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia.
| | - Andrew Garazha
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia.
| | - Alena Ivanova
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
| | - Dmitry Kaminsky
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
| | - Alex Zhavoronkov
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
- Department of Translational and Regenerative Medicine, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow, 141700, Russia.
| | - Anton Buzdin
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, 1, Akademika Kurchatova sq., Moscow, 123182, Russia.
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34
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Díaz-Carballo D, Acikelli AH, Klein J, Jastrow H, Dammann P, Wyganowski T, Guemues C, Gustmann S, Bardenheuer W, Malak S, Tefett NS, Khosrawipour V, Giger-Pabst U, Tannapfel A, Strumberg D. Therapeutic potential of antiviral drugs targeting chemorefractory colorectal adenocarcinoma cells overexpressing endogenous retroviral elements. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:81. [PMID: 26260344 PMCID: PMC4542094 DOI: 10.1186/s13046-015-0199-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/30/2015] [Indexed: 12/31/2022]
Abstract
Background Endoretroviruses account for circa 8 % of all transposable elements found in the genome of humans and other animals. They represent a genetic footprint of ancestral germ-cell infections of exoviruses that is transmittable to the progeny by Mendelian segregation. Traces of human endogenous retroviruses are physiologically expressed in ovarial, testicular and placental tissues as well as in stem cells. In addition, a number of these fossil viral elements have also been related to carcinogenesis. However, a relation between endoretroviruses expression and chemoresistance has not been reported yet. Methods Twenty colorectal carcinoma patient samples were scrutinized for HERV-WE1 and HERV-FRD1 endoretroviruses using immunohistochemical approaches. In order to search for differential expression of these elements in chemotherapy refractory cells, a resistant HCT8 colon carcinoma subline was developed by serial etoposide exposure. Endoretroviral elements were detected by immunocytochemical staining, qPCR and ELISA. IC50-values of antiviral and cytostatic drugs in HCT8 cells were determined by MTT proliferation assay. The antivirals-cytostatics interaction was evaluated by the isobologram method. Results In this work, we show for the first time that HERV-WE1, HERV-FRD1, HERV-31, and HERV-V1 are a) simultaneously expressed in treatment-naïve colon carcinoma cells and b) upregulated after cytostatic exposure, suggesting that these retroviral elements are intimately related to chemotherapy resistance. We found a number of antiviral drugs to have cytotoxic activity and the ability to force the downregulation of HERV proteins in vitro. We also demonstrate that the use of different antiviral compounds alone or in combination with anticancer agents results in a synergistic antiproliferative effect and downregulation of different endoretroviral elements in highly chemotherapy-resistant colorectal tumor cells. Conclusions Enhanced HERV-expression is associated with chemoresistance in colon carcinomas which can be overcome by antiviral drugs alone or in combination with anticancer drugs. Therefore, the introduction of antiviral compounds to the current chemotherapy regimens potentially improves patient outcomes. Electronic supplementary material The online version of this article (doi:10.1186/s13046-015-0199-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Díaz-Carballo
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany.
| | - Ali Haydar Acikelli
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Jacqueline Klein
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Holger Jastrow
- Institute of Anatomy and Experimental Morphology, University of Duisburg-Essen, Medical School, Essen, Germany
| | - Philipp Dammann
- Central Animal Laboratory, University of Duisburg-Essen, Medical School, Essen, Germany
| | - Thomas Wyganowski
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Cihan Guemues
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Sebastian Gustmann
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Walter Bardenheuer
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Sascha Malak
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Nora Sophia Tefett
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
| | - Veria Khosrawipour
- Department of Visceral Surgery, Marienhospital Herne, Ruhr University of Bochum, Medical School, Herne, Germany
| | - Urs Giger-Pabst
- Department of Visceral Surgery, Marienhospital Herne, Ruhr University of Bochum, Medical School, Herne, Germany
| | - Andrea Tannapfel
- Institute of Pathology, Ruhr-University of Bochum, Medical School, Bochum, Germany
| | - Dirk Strumberg
- Institute for Molecular Oncology and Experimental Therapeutics, Division of Oncology and Hematology, Marienhospital Herne, Ruhr University of Bochum, Medical School, Marienhospital Herne, Duengelstr. 33, 44623, Herne, Germany
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