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Stricker E, Peckham-Gregory EC, Scheurer ME. HERVs and Cancer-A Comprehensive Review of the Relationship of Human Endogenous Retroviruses and Human Cancers. Biomedicines 2023; 11:936. [PMID: 36979914 PMCID: PMC10046157 DOI: 10.3390/biomedicines11030936] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Genomic instability and genetic mutations can lead to exhibition of several cancer hallmarks in affected cells such as sustained proliferative signaling, evasion of growth suppression, activated invasion, deregulation of cellular energetics, and avoidance of immune destruction. Similar biological changes have been observed to be a result of pathogenic viruses and, in some cases, have been linked to virus-induced cancers. Human endogenous retroviruses (HERVs), once external pathogens, now occupy more than 8% of the human genome, representing the merge of genomic and external factors. In this review, we outline all reported effects of HERVs on cancer development and discuss the HERV targets most suitable for cancer treatments as well as ongoing clinical trials for HERV-targeting drugs. We reviewed all currently available reports of the effects of HERVs on human cancers including solid tumors, lymphomas, and leukemias. Our review highlights the central roles of HERV genes, such as gag, env, pol, np9, and rec in immune regulation, checkpoint blockade, cell differentiation, cell fusion, proliferation, metastasis, and cell transformation. In addition, we summarize the involvement of HERV long terminal repeat (LTR) regions in transcriptional regulation, creation of fusion proteins, expression of long non-coding RNAs (lncRNAs), and promotion of genome instability through recombination.
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Affiliation(s)
- Erik Stricker
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
| | | | - Michael E. Scheurer
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
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Akula S, Paivandy A, Fu Z, Thorpe M, Pejler G, Hellman L. How Relevant Are Bone Marrow-Derived Mast Cells (BMMCs) as Models for Tissue Mast Cells? A Comparative Transcriptome Analysis of BMMCs and Peritoneal Mast Cells. Cells 2020; 9:cells9092118. [PMID: 32957735 PMCID: PMC7564378 DOI: 10.3390/cells9092118] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 01/09/2023] Open
Abstract
Bone marrow-derived mast cells (BMMCs) are often used as a model system for studies of the role of MCs in health and disease. These cells are relatively easy to obtain from total bone marrow cells by culturing under the influence of IL-3 or stem cell factor (SCF). After 3 to 4 weeks in culture, a nearly homogenous cell population of toluidine blue-positive cells are often obtained. However, the question is how relevant equivalents these cells are to normal tissue MCs. By comparing the total transcriptome of purified peritoneal MCs with BMMCs, here we obtained a comparative view of these cells. We found several important transcripts that were expressed at very high levels in peritoneal MCs, but were almost totally absent from the BMMCs, including the major chymotryptic granule protease Mcpt4, the neurotrophin receptor Gfra2, the substance P receptor Mrgprb2, the metalloprotease Adamts9 and the complement factor 2 (C2). In addition, there were a number of other molecules that were expressed at much higher levels in peritoneal MCs than in BMMCs, including the transcription factors Myb and Meis2, the MilR1 (Allergin), Hdc (Histidine decarboxylase), Tarm1 and the IL-3 receptor alpha chain. We also found many transcripts that were highly expressed in BMMCs but were absent or expressed at low levels in the peritoneal MCs. However, there were also numerous MC-related transcripts that were expressed at similar levels in the two populations of cells, but almost absent in peritoneal macrophages and B cells. These results reveal that the transcriptome of BMMCs shows many similarities, but also many differences to that of tissue MCs. BMMCs can thereby serve as suitable models in many settings concerning the biology of MCs, but our findings also emphasize that great care should be taken when extrapolating findings from BMMCs to the in vivo function of tissue-resident MCs.
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Affiliation(s)
- Srinivas Akula
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
| | - Aida Paivandy
- Department of Medical Biochemistry and Microbiology, Uppsala University, The Biomedical Center, Box 589, SE-751 23 Uppsala, Sweden; (A.P.); (G.P.)
| | - Zhirong Fu
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
| | - Michael Thorpe
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
| | - Gunnar Pejler
- Department of Medical Biochemistry and Microbiology, Uppsala University, The Biomedical Center, Box 589, SE-751 23 Uppsala, Sweden; (A.P.); (G.P.)
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, SE-75007 Uppsala, Sweden
| | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
- Correspondence: ; Tel.: +46-(0)18-471-4532; Fax: +46-(0)18-471-4862
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Akula S, Paivandy A, Fu Z, Thorpe M, Pejler G, Hellman L. Quantitative In-Depth Analysis of the Mouse Mast Cell Transcriptome Reveals Organ-Specific Mast Cell Heterogeneity. Cells 2020; 9:cells9010211. [PMID: 31947690 PMCID: PMC7016716 DOI: 10.3390/cells9010211] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/19/2022] Open
Abstract
Mast cells (MCs) are primarily resident hematopoietic tissue cells that are localized at external and internal surfaces of the body where they act in the first line of defense. MCs are found in all studied vertebrates and have also been identified in tunicates, an early chordate. To obtain a detailed insight into the biology of MCs, here we analyzed the transcriptome of MCs from different mouse organs by RNA-seq and PCR-based transcriptomics. We show that MCs at different tissue locations differ substantially in their levels of transcripts coding for the most abundant MC granule proteins, even within the connective tissue type, or mucosal MC niches. We also demonstrate that transcript levels for the major granule proteins, including the various MC-restricted proteases and the heparin core protein, can be several orders of magnitude higher than those coding for various surface receptors and enzymes involved in protease activation, as well as enzymes involved in the synthesis of heparin, histamine, leukotrienes, and prostaglandins. Interestingly, our analyses revealed an almost complete absence in MCs of transcripts coding for cytokines at baseline conditions, indicating that cytokines are primarily produced by activated MCs. Bone marrow-derived MCs (BMMCs) are often used as equivalents of tissue MCs. Here, we show that these cells differ substantially from tissue MCs with regard to their transcriptome. Notably, they showed a transcriptome indicative of relatively immature cells, both with respect to the expression of granule proteases and of various enzymes involved in the processing/synthesis of granule compounds, indicating that care should be taken when extrapolating findings from BMMCs to the in vivo function of tissue-resident MCs. Furthermore, the latter finding indicates that the development of fully mature tissue-resident MCs requires a cytokine milieu beyond what is needed for in vitro differentiation of BMMCs. Altogether, this study provides a comprehensive quantitative view of the transcriptome profile of MCs resident at different tissue locations that builds nicely on previous studies of both the mouse and human transcriptome, and form a solid base for future evolutionary studies of the role of MCs in vertebrate immunity.
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Affiliation(s)
- Srinivas Akula
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
| | - Aida Paivandy
- Department of Medical Biochemistry and Microbiology, BMC, Box 589, SE-751 23 Uppsala, Sweden; (A.P.); (G.P.)
| | - Zhirong Fu
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
| | - Michael Thorpe
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
| | - Gunnar Pejler
- Department of Medical Biochemistry and Microbiology, BMC, Box 589, SE-751 23 Uppsala, Sweden; (A.P.); (G.P.)
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden; (S.A.); (Z.F.); (M.T.)
- Correspondence: ; Tel.: +46-(0)18-471-4532; Fax: +46-(0)18-471-4862
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Bustamante Rivera YY, Brütting C, Schmidt C, Volkmer I, Staege MS. Endogenous Retrovirus 3 - History, Physiology, and Pathology. Front Microbiol 2018; 8:2691. [PMID: 29379485 PMCID: PMC5775217 DOI: 10.3389/fmicb.2017.02691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/26/2017] [Indexed: 01/05/2023] Open
Abstract
Endogenous viral elements (EVE) seem to be present in all eukaryotic genomes. The composition of EVE varies between different species. The endogenous retrovirus 3 (ERV3) is one of these elements that is present only in humans and other Catarrhini. Conservation of ERV3 in most of the investigated Catarrhini and the expression pattern in normal tissues suggest a putative physiological role of ERV3. On the other hand, ERV3 has been implicated in the pathogenesis of auto-immunity and cancer. In the present review we summarize knowledge about this interesting EVE. We propose the model that expression of ERV3 (and probably other EVE loci) under pathological conditions might be part of a metazoan SOS response.
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Affiliation(s)
| | - Christine Brütting
- Department of Paediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany.,Department of Neurology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Caroline Schmidt
- Department of Paediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ines Volkmer
- Department of Paediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin S Staege
- Department of Paediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
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Kewitz S, Staege MS. Expression and Regulation of the Endogenous Retrovirus 3 in Hodgkin's Lymphoma Cells. Front Oncol 2013; 3:179. [PMID: 23847767 PMCID: PMC3706881 DOI: 10.3389/fonc.2013.00179] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/25/2013] [Indexed: 11/13/2022] Open
Abstract
Human endogenous retroviruses (ERV) are an integral part of our genome. Expression of ERV is usually switched off but reactivation of ERV has been observed in varying human diseases including cancer. Recently, reactivation of ERV associated promoters in Hodgkin's lymphoma (HL) cells has been described. Despite relatively good prognosis, not all patients with HL can be cured with the established therapy and this therapy is associated with severe late side effects. Therefore, new targets are required for the development of future treatment strategies. Reactivated ERV might represent such target structures. Therefore, we asked which ERV loci are expressed in HL cells. Using DNA microarray analysis, we found no evidence for a general activation of ERV transcription in HL cells. In contrast, we observed down-regulation of ERV3, an ERV with potential tumor suppressor function, in HL cells in comparison to normal blood cells. Interestingly, ERV3 was also differentially expressed in published DNA microarray data from resting versus cycling B cells. Treatment of HL cells with the histone deacetylase inhibitor vorinostat strongly up-regulated ERV3 expression. In addition, we observed up-regulation in HL cells after treatment with hypoxia-mimetic cobalt(II) chloride. Like vorinostat, cobalt(II) chloride inhibited cell growth of HL cells. Our results suggest that cell cycle inhibition of HL cells is accompanied by up-regulation of ERV3.
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Affiliation(s)
- Stefanie Kewitz
- Department of Pediatrics, Martin-Luther-University Halle-Wittenberg , Halle , Germany
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Perron H, Lang A. The human endogenous retrovirus link between genes and environment in multiple sclerosis and in multifactorial diseases associating neuroinflammation. Clin Rev Allergy Immunol 2010; 39:51-61. [PMID: 19697163 DOI: 10.1007/s12016-009-8170-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Endogenous retroviruses represent about 8% of the human genome and belong to the superfamily of transposable and retrotransposable genetic elements. Altogether, these mobile genetic elements and their numerous inactivated "junk" sequences represent nearly one half of the human DNA. Nonetheless, a significant part of this "non-conventional" genome has retained potential activity. Epigenetic control is notably involved in silencing most of these genetic elements but certain environmental factors such as viruses are known to dysregulate their expression in susceptible cells. More particularly, embryonal cells with limited gene methylation are most susceptible to uncontrolled activation of these mobile genetic elements by, e.g., viral infections. In particular, certain viruses transactivate promoters from endogenous retroviral family type W (HERV-W). HERV-W RNA was first isolated in circulating viral particles (Multiple Sclerosis-associated RetroViral element, MSRV) that have been associated with the evolution and prognosis of multiple sclerosis. HERV-W elements encode a powerful immunopathogenic envelope protein (ENV) that activates a pro-inflammatory and autoimmune cascade through interaction with Toll-like receptor 4 on immune cells. This ENV protein has repeatedly been detected in MS brain lesions and may be involved in other diseases. Epigenetic factors controlling HERV-W ENV protein expression then reveal critical. This review addresses the gene-environment epigenetic interface of such HERV-W elements and its potential involvement in disease.
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Affiliation(s)
- Hervé Perron
- GeNeuro, 18, Chemin des Aulx, 1228, Plan-Les Ouates, Geneva, Switzerland.
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Abrarova ND, Stoukacheva EA, Pleshkan VV, Vinogradova TV, Sverdlov ED. Functional analysis of the HERV-K LTR residing in the KIAA1245/NBPF subfamily genes. Mol Biol 2010. [DOI: 10.1134/s0026893310040084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Huh JW, Ha HS, Kim DS, Kim HS. Placenta-restricted expression of LTR-derived NOS3. Placenta 2008; 29:602-8. [PMID: 18474398 DOI: 10.1016/j.placenta.2008.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 03/25/2008] [Accepted: 04/04/2008] [Indexed: 10/22/2022]
Abstract
Domestication events of long terminal repeat (LTR) sequences of the human endogenous retrovirus (HERV) family have been considered to be a new mechanism for the generation of alternative splicing in the human genome. We investigated an LTR10A belonging to the HERV-I family at the human endothelial nitric oxide synthase (NOS3) gene locus. The LTR10A element was located upstream of the original promoter sequences of NOS3. Expression analysis using RT-PCR and reporter gene assays in HCT116 and COS7 cells indicated placenta-specific expression of NOS3 driven by the LTR10A-derived promoter. The placenta-restricted expression was also determined to be associated with hypomethylation of the LTR10A element by methylation analysis using sodium bisulfite DNA sequencing. Furthermore, treatment of brain-derived cell lines with demethylation reagents did not restore expression of the LTR-derived NOS3 gene transcript. Taken together, the integration event of an LTR10A element in the upstream region of NOS3 led to the generation of a placenta-specific alternative transcript governed by cooperative mechanisms of epigenetic control (DNA methylation) and transcriptional regulation (interaction between cis- and trans-acting elements).
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Affiliation(s)
- J-W Huh
- Division of Biological Sciences, College of Natural Sciences, Pusan National University, Changjeon-dong, Busan, Republic of Korea
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Abstract
Endogenous retroviruses (ERVs) integrated into human genome after cross-species infectious events millions of years ago. Few of the ERVs retain the basic structure of the integrated proviral form of infectious retroviruses. Human endogenous retroviruses (HERVs) represent a key molecular link between the host genome and infectious viral particles. They constitute a large reservoir of viral genes that could be activated by various factors such as mutations or carcinogenic chemical exposures and so forth. Endogenous retroviruses are transmitted genetically in a Mendelian fashion through the germline as proviral DNA. Expression pattern of HERVs can influence the outcome of their presence in many forms, which can be either beneficial or detrimental to the host. ERVs have been reported to play a role in both human physiology and human pathology. Along with their expression in many disease conditions, they have also been reported to be expressed on normal peripheral blood lymphocytes, salivary glands and keratinocytes.
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Affiliation(s)
- Sunit Kumar Singh
- Center for Cellular and Molecular Biology, Section of Infectious Diseases, Hyderabad, India.
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Wentzensen N, Coy JF, Knaebel HP, Linnebacher M, Wilz B, Gebert J, von Knebel Doeberitz M. Expression of an endogenous retroviral sequence from the HERV-H group in gastrointestinal cancers. Int J Cancer 2007; 121:1417-23. [PMID: 17546591 DOI: 10.1002/ijc.22826] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human endogenous retroviruses (HERVs) account for approximately 8% of the human genome. Since the majority of HERV elements have accumulated inactivating mutations in the viral genes, only few expressed viral open reading frames (ORFs) have been described. In this study, we have analyzed the expression of a HERV-H copy located on Xp22.3 encompassing a potential ORF immediately downstream of the viral promoter. Conventional and real time RT-PCR based expression analysis of this specific HERV-H sequence showed overexpression in 16 of 34 (47%) colorectal, 25 of 63 (40%) gastric and 2 of 12 (17%) pancreatic cancers, whereas no overexpression was detected in bronchial and cervical cancers. Normal human testis, placenta and breast tissue did not show expression of this sequence. CpG methylation analysis of the viral promoter revealed a loss of methylation in cell lines expressing the HERV-H sequence as compared to nonexpressing cell lines and lymphocyte DNA derived from healthy individuals. Further investigations of the HERV-H long terminal repeat and the HERV-H RNA are necessary to assess the functional relevance of the HERV-H expression.
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Affiliation(s)
- Nicolas Wentzensen
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.
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Illarionova AE, Vinogradova TV, Sverdlov ED. Only those genes of the KIAA1245 gene subfamily that contain HERV(K) LTRs in their introns are transcriptionally active. Virology 2006; 358:39-47. [PMID: 16997346 DOI: 10.1016/j.virol.2006.06.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 04/13/2006] [Accepted: 06/21/2006] [Indexed: 11/26/2022]
Abstract
Insertion of LTRs into some genome locations might seriously affect regulation of the neighboring genes expression. This hypothesis is widely accepted but, however, not confirmed directly. Earlier, we have identified a family of closely related genes highly similar to the KIAA1245 mRNA counterpart. This family included a subfamily of genes some of which contained and the others lacked an LTR in their structure. We compared transcription of several closely related genes of the subfamily differing in the presence or absence of LTRs. Only LTR-containing genes were transcribed in transformed cell lines, tumorous and embryonic human tissues, whereas LTR-lacking genes remained silent. Since the genes were in the same intracellular microenvironment, we suggested that this effect was most probably due to intrinsic cis-characteristics of integrated LTRs and confirmed this by demonstrating high enhancer activity of KIAA1245 LTRs. The expression of the LTR-containing genes in embryonic tissues might suggest their involvement in evolutionary events during primate speciation.
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Affiliation(s)
- A E Illarionova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, Moscow 117997, Russia
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Hamilton AT, Huntley S, Tran-Gyamfi M, Baggott DM, Gordon L, Stubbs L. Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res 2006; 16:584-94. [PMID: 16606703 PMCID: PMC1457049 DOI: 10.1101/gr.4843906] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Most genes are conserved in mammals, but certain gene families have acquired large numbers of lineage-specific loci through repeated rounds of gene duplication, divergence, and loss that have continued in each mammalian group. One such family encodes KRAB-zinc finger (KRAB-ZNF) proteins, which function as transcriptional repressors. One particular subfamily of KRAB-ZNF genes, including ZNF91, has expanded specifically in primates to comprise more than 110 loci in the human genome. Genes of the ZNF91 subfamily reside in large gene clusters near centromeric regions of human chromosomes 19 and 7 with smaller clusters or isolated copies in other locations. Phylogenetic analysis indicates that many of these genes arose before the split between the New and Old World monkeys, but the ZNF91 subfamily has continued to expand and diversify throughout the evolution of apes and humans. Paralogous loci are distinguished by divergence within their zinc finger arrays, indicating selection for proteins with different regulatory targets. In addition, many loci produce multiple alternatively spliced transcripts encoding proteins that may serve separate and perhaps even opposing regulatory roles because of the modular motif structure of KRAB-ZNF genes. The tissue-specific expression patterns and rapid structural divergence of ZNF91 subfamily genes suggest a role in determining gene expression differences between species and the evolution of novel primate traits.
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Affiliation(s)
- Aaron T. Hamilton
- Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Stuart Huntley
- Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Mary Tran-Gyamfi
- Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Daniel M. Baggott
- Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Laurie Gordon
- Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Lisa Stubbs
- Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
- Corresponding author.E-mail ; fax (925) 422-2099
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Kim HS, Yi JM, Hirai H, Huh JW, Jeong MS, Jang SB, Kim CG, Saitou N, Hyun BH, Lee WH. Human Endogenous Retrovirus (HERV)-R family in primates: Chromosomal location, gene expression, and evolution. Gene 2006; 370:34-42. [PMID: 16443335 DOI: 10.1016/j.gene.2005.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 10/31/2005] [Accepted: 11/02/2005] [Indexed: 11/24/2022]
Abstract
Hitherto, full-length endogenous retrovirus (HERV)-R has been located at human chromosome 7q11.2, and mRNA and envelope proteins have been detected in placenta and a variety of other cell types. In the present study, using a probe derived from the gorilla fosmid library, we detected the paralogous locus (7q31.3) of the HERV-R env gene in human chromosome 7q11.2, and also determined the chromosomal location in apes and Old World monkeys. The HERV-R gene was not detected in New World monkeys or prosimians with FISH and PCR analyses. We determined the sequences of the HERV-R env genes obtained from the genomic DNA of primates using PCR and sequencing tools. Except for a HERV-R env sequence derived from gorilla DNA, the functional domains of putative envelope proteins are conserved, suggesting that those domains could have a functional capacity in the primate genome. In addition, we investigated the env gene expression of HERV-R in various human tissues and cancer cells. An RT-PCR approach indicated that the env gene was expressed in several human tissues (brain, prostate, testis, kidney, placenta, thymus, and uterus) and cancer cells (RT4, BT-474, MCF7, OVCAR-3, LOX-IMVI, and AZ521). Taken together, our data could be of great use for understanding the evolutionary dynamics of HERV-R through primate radiation as well as the implications of its functional role in human tissues and cancers cells.
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Affiliation(s)
- Heui-Soo Kim
- Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea.
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Lavie L, Kitova M, Maldener E, Meese E, Mayer J. CpG methylation directly regulates transcriptional activity of the human endogenous retrovirus family HERV-K(HML-2). J Virol 2005; 79:876-83. [PMID: 15613316 PMCID: PMC538560 DOI: 10.1128/jvi.79.2.876-883.2005] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A significant proportion of the human genome consists of stably inherited retroviral sequences. Most human endogenous retroviruses (HERVs) became defective over time. The HERV-K(HML-2) family is exceptional because of its coding capacity and the possible involvement in germ cell tumor (GCT) development. HERV-K(HML-2) transcription is strongly upregulated in GCTs. However, regulation of HERV-K(HML-2) transcription remains poorly understood. We investigated in detail the role of CpG methylation on the transcriptional activity of HERV-K(HML-2) long terminal repeats (LTRs). We find that CpG sites in various HERV-K(HML-2) proviral 5' LTRs are methylated at different levels in the cell line Tera-1. Methylation levels correlate with previously observed transcriptional activities of these proviruses. CpG-mediated silencing of HERV-K(HML-2) LTRs is further corroborated by transcriptional inactivity of in vitro-methylated 5' LTR reporter plasmids. However, CpG methylation levels do not solely regulate HERV-K(HML-2) 5' LTR activity, as evidenced by different LTR activities in the cell line T47D. A significant number of mutated CpG sites in evolutionary old HERV-K(HML-2) 5' LTRs suggests that CpG methylation had already silenced HERV-K(HML-2) proviruses millions of years ago. Direct silencing of HERV-K(HML-2) expression by CpG methylation enlightens upregulated HERV-K(HML-2) expression in usually hypomethylated GCT tissue.
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Affiliation(s)
- Laurence Lavie
- Department of Human Genetics, Building 60, University of Saarland, Medical Faculty, 66421 Hamburg, Germany.
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Thomas RM, Haleem K, Siddique AB, Simmons WJ, Sen N, Zhang DJ, Tsiagbe VK. Regulation of mouse mammary tumor virus env transcriptional activator initiated mammary tumor virus superantigen transcripts in lymphomas of SJL/J mice: role of Ikaros, demethylation, and chromatin structural change in the transcriptional activation of mammary tumor virus superantigen. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:218-27. [PMID: 12496403 DOI: 10.4049/jimmunol.170.1.218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mammary tumor virus (Mtv29)-encoded superantigen expressed by SJL/J mouse B cell lymphomas stimulates CD4+V16+ T cells and thereby acquires T cell help necessary for lymphoma growth. Mtv29 mouse mammary tumor virus env transcriptional activator (META) env-controlled Mtv29 superantigen (vSAg29) mRNA transcripts (1.8 kb) are not expressed in normal B or other somatic cells. Real-time PCR-based assays with DNA from normal SJL liver and vSAg29- lymphoma (cNJ101), digested with methylation-sensitive enzymes, showed hypermethylation at AvaI, FspI, HpaII, ThaI, and the distal HgaI sites of the META env, but vSAg29+ lymphoma cells showed significant demethylation at AvaI, HpaII, and the distal HgaI sites. The distal HgaI site that is adjacent to an Ikaros binding site is significantly demethylated in the META env DNA from primary lymphomas. Gel shift assays showed binding of Ikaros to a sequence representing this region in the META env. SJL lymphomas expressed the Ikaros isoform Ik6 that was absent in normal B cells. vSAg29+ cells exhibited increased DNaseI accessibility to chromatin at the vSAg29 initiation site. Treatment of cNJ101 cells with a demethylating agent, 5-azacytidine, and a histone deacetylase inhibitor, trichostatin A, caused hypomethylation at AvaI, HpaII, and distal HgaI sites and led to chromatin structural change at the vSAg29 initiation site, accompanied by the expression of vSAg29 transcripts. This enabled cNJ101 cells to stimulate SJL lymphoma-responsive CD4+V16+ T hybridoma cells. Thus, demethylation at the distal HgaI site of the Mtv29 META env permits vSAg29 expression, which may have an impact on the development of germinal center-derived B cell lymphomas of SJL/J mice.
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MESH Headings
- Animals
- Azacitidine/pharmacology
- Chromatin/chemistry
- Chromatin/enzymology
- Chromatin/metabolism
- DNA Methylation
- DNA-Binding Proteins
- Deoxyribonuclease I/metabolism
- Female
- Genes, env/physiology
- Hydroxamic Acids/pharmacology
- Ikaros Transcription Factor
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/virology
- Mammary Tumor Virus, Mouse/genetics
- Mammary Tumor Virus, Mouse/immunology
- Mice
- Promoter Regions, Genetic/immunology
- RNA, Messenger/biosynthesis
- Retroviridae Infections/genetics
- Retroviridae Infections/immunology
- Superantigens/genetics
- Superantigens/metabolism
- Trans-Activators/metabolism
- Trans-Activators/physiology
- Transcription Factors/physiology
- Transcription, Genetic/immunology
- Transcriptional Activation/immunology
- Tumor Cells, Cultured
- Tumor Virus Infections/genetics
- Tumor Virus Infections/immunology
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Affiliation(s)
- Rajan M Thomas
- Department of Pathology and Comprehensive Kaplan Cancer Center, New York University School of Medicine, New York, NY 10016, USA
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16
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Andersson AC, Venables PJW, Tönjes RR, Scherer J, Eriksson L, Larsson E. Developmental expression of HERV-R (ERV3) and HERV-K in human tissue. Virology 2002; 297:220-5. [PMID: 12083821 DOI: 10.1006/viro.2002.1428] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The human endogenous retroviruses (HERVs), ERV3 (HERV-R) and HERV-K, are both known to be transcriptionally active in human placenta. In the case of ERV3 there is also indirect evidence for its participation in cellular differentiation. In this study we examined the expression of ERV3 (HERV-R) and HERV-K in human normal fetal tissues by in situ hybridization. The highest level of ERV3 env expression was detected in primitive adrenal cortex. Elevated levels of expression were also found in the following developing tissues: kidneys (tubules), tongue, heart, liver, and central nervous system. Tissue-specific expression was found for HERV-K rec (former cORF) but not for pol/int transcripts. The highest rec expression was found in placenta and levels slightly higher than sense control were found in the rest of the tissues examined. Pol/Int was not possible to quantitate. It appears that ERV3 is expressed in an organ-specific way during embryogenesis and might suggest a possible role in the development and differentiation of human tissues.
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17
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Anway MD, Johnston DS, Crawford D, Griswold MD. Identification of a novel retrovirus expressed in rat Sertoli cells and granulosa cells. Biol Reprod 2001; 65:1289-96. [PMID: 11566755 DOI: 10.1095/biolreprod65.4.1289] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR) was used to identify a novel retrovirus, designated SC1, that is expressed at high levels in rat granulosa cells and prepubertal Sertoli cells. The initial DDRT-PCR screen was performed using RNA from cultured prepubertal rat Sertoli cell, liver, and brain samples. SC1 was detected in the prepubertal rat Sertoli cell samples but not in those from liver and brain. SC1 cDNA was 6 kilobases in length and contained regions encoding for the gag, pol, and env retroviral proteins. Northern blot analysis failed to detect expression of the SC1 gene in total RNA isolated from adult brain, heart, spleen, lung, liver, skeletal muscle, kidney, prostate, and epididymis. Similarly, Northern blot analysis of testes from rats at various ages of development showed that high-level expression of the SC1 gene was limited to prepubertal testis samples. In situ hybridization analysis localized the SC1 mRNA to the seminiferous tubules of prepubertal testes and at a much lower level in Sertoli cells of adult testes. Northern blot analysis of total RNA isolated from Sertoli cells from 20-, 27-, and 35-day-old rat Sertoli cells and type A spermatogonia, pachytene spermatocytes, and round spermatids showed expression of the SC1 gene to be restricted to 20- and 27-day-old Sertoli cells, with no expression detected in germ cells. Furthermore, Northern blot analysis also showed expression of the SC1 gene in rat ovaries, and the level of expression was affected during eCG/hCG-induced ovulation. Expression of SC1 mRNA was localized by in situ hybridization of eCG-treated ovaries to the granulosa cell layer in developing follicles. Southern blot analysis showed SC1 to be endogenous in the rat and absent in mouse and human cell genomes. Transient transfection assays using the SC1 promoter region showed high promoter activity in MSC-1 and cultured prepubertal rat Sertoli cells, and no activity in 3T3 or MCF-7 cell lines.
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Affiliation(s)
- M D Anway
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
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18
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Schön U, Seifarth W, Baust C, Hohenadl C, Erfle V, Leib-Mösch C. Cell type-specific expression and promoter activity of human endogenous retroviral long terminal repeats. Virology 2001; 279:280-91. [PMID: 11145909 DOI: 10.1006/viro.2000.0712] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Evolution over millions of years has adapted several thousand copies of retrovirus-like elements and over 10 times as many solitary long terminal repeats (LTRs) to their present location in the human genome. Transcription of these human endogenous retroviruses (HERVs) has been detected in various cells and tissues, and in some cases their transcriptional control elements have been recruited by cellular genes. We used a retroviral pol-specific expression array to obtain a HERV transcription profile in a variety of human cells such as epidermal keratinocytes, liver cells, kidney cells, pancreatic cells, lymphocytes, and lung fibroblasts. This rapid screening test revealed a distinct HERV pol-expression pattern in each cell type tested so far. About 40 different U3/R regulatory sequences from the HERV-H and HERV-W families were then amplified from actively transcribed 3'HERV LTRs of various cell lines and tissues. Their promoter activities were compared with LTR sequences of other known HERV families in 12 human cell lines using a transient luciferase reporter system. Expression of the isolated HERV LTRs varied significantly in these cell lines, in some cases showing strict cell type specificity. These results suggest that endogenous retroviral LTRs may be a valuable source of transcriptional regulatory elements for the construction of targeted retroviral expression vectors.
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Affiliation(s)
- U Schön
- Institute of Molecular Virology, Oberschleissheim, D-85764, Germany.
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