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Tam PLF, Leung D. The Molecular Impacts of Retrotransposons in Development and Diseases. Int J Mol Sci 2023; 24:16418. [PMID: 38003607 PMCID: PMC10671454 DOI: 10.3390/ijms242216418] [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: 10/07/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Retrotransposons are invasive genetic elements that constitute substantial portions of mammalian genomes. They have the potential to influence nearby gene expression through their cis-regulatory sequences, reverse transcription machinery, and the ability to mold higher-order chromatin structures. Due to their multifaceted functions, it is crucial for host fitness to maintain strict regulation of these parasitic sequences to ensure proper growth and development. This review explores how subsets of retrotransposons have undergone evolutionary exaptation to enhance the complexity of mammalian genomes. It also highlights the significance of regulating these elements, drawing on recent studies conducted in human and murine systems.
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Affiliation(s)
- Phoebe Lut Fei Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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2
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Zhang M, Zheng S, Liang JQ. Transcriptional and reverse transcriptional regulation of host genes by human endogenous retroviruses in cancers. Front Microbiol 2022; 13:946296. [PMID: 35928153 PMCID: PMC9343867 DOI: 10.3389/fmicb.2022.946296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) originated from ancient retroviral infections of germline cells millions of years ago and have evolved as part of the host genome. HERVs not only retain the capacity as retroelements but also regulate host genes. The expansion of HERVs involves transcription by RNA polymerase II, reverse transcription, and re-integration into the host genome. Fast progress in deep sequencing and functional analysis has revealed the importance of domesticated copies of HERVs, including their regulatory sequences, transcripts, and proteins in normal cells. However, evidence also suggests the involvement of HERVs in the development and progression of many types of cancer. Here we summarize the current state of knowledge about the expression of HERVs, transcriptional regulation of host genes by HERVs, and the functions of HERVs in reverse transcription and gene editing with their reverse transcriptase.
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Affiliation(s)
- Mengwen Zhang
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Ministry of Education Key Laboratory of Cancer Prevention and Intervention, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
| | - Shu Zheng
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Ministry of Education Key Laboratory of Cancer Prevention and Intervention, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Shu Zheng,
| | - Jessie Qiaoyi Liang
- Department of Medicine and Therapeutics, Faculty of Medicine, Center for Gut Microbiota Research, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Jessie Qiaoyi Liang,
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3
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Di Giorgio E, Xodo LE. Endogenous Retroviruses (ERVs): Does RLR (RIG-I-Like Receptors)-MAVS Pathway Directly Control Senescence and Aging as a Consequence of ERV De-Repression? Front Immunol 2022; 13:917998. [PMID: 35757716 PMCID: PMC9218063 DOI: 10.3389/fimmu.2022.917998] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Bi-directional transcription of Human Endogenous Retroviruses (hERVs) is a common feature of autoimmunity, neurodegeneration and cancer. Higher rates of cancer incidence, neurodegeneration and autoimmunity but a lower prevalence of autoimmune diseases characterize elderly people. Although the re-expression of hERVs is commonly observed in different cellular models of senescence as a result of the loss of their epigenetic transcriptional silencing, the hERVs modulation during aging is more complex, with a peak of activation in the sixties and a decline in the nineties. What is clearly accepted, instead, is the impact of the re-activation of dormant hERV on the maintenance of stemness and tissue self-renewing properties. An innate cellular immunity system, based on the RLR-MAVS circuit, controls the degradation of dsRNAs arising from the transcription of hERV elements, similarly to what happens for the accumulation of cytoplasmic DNA leading to the activation of cGAS/STING pathway. While agonists and inhibitors of the cGAS-STING pathway are considered promising immunomodulatory molecules, the effect of the RLR-MAVS pathway on innate immunity is still largely based on correlations and not on causality. Here we review the most recent evidence regarding the activation of MDA5-RIG1-MAVS pathway as a result of hERV de-repression during aging, immunosenescence, cancer and autoimmunity. We will also deal with the epigenetic mechanisms controlling hERV repression and with the strategies that can be adopted to modulate hERV expression in a therapeutic perspective. Finally, we will discuss if the RLR-MAVS signalling pathway actively modulates physiological and pathological conditions or if it is passively activated by them.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, University of Udine, Udine, Italy
| | - Luigi E Xodo
- Laboratory of Biochemistry, Department of Medicine, University of Udine, Udine, Italy
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4
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Activation of lnc-ALVE1-AS1 inhibited ALV-J replication through triggering the TLR3 pathway in chicken macrophage like cell line. Vet Res Commun 2022; 47:431-443. [PMID: 35715584 DOI: 10.1007/s11259-022-09960-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/14/2022] [Indexed: 11/27/2022]
Abstract
Endogenous retroviruses (ERVs) are remnants of the historical retroviral infections, and their derived transcripts with viral signatures are important sources of long noncoding RNAs (lncRNAs). We have previously shown that the chicken ERV-derived lncRNA lnc-ALVE1-AS1 exerts antiviral innate immunity in chicken embryo fibroblasts. However, it is not clear whether this endogenous retroviral RNA has a similar function in immune cells. Here, we found that lnc-ALVE1-AS1 was persistently inhibited in chicken macrophages after avian leukosis virus subgroup J (ALV-J) infection. Furthermore, overexpression of lnc-ALVE1-AS1 significantly inhibited the replication of exogenous ALV-J, whereas knockdown of lnc-ALVE1-AS1 promoted the replication of ALV-J in chicken macrophages. This phenomenon is attributed to the induction of antiviral innate immunity by lnc-ALVE1-AS1 in macrophages, whereas knockdown of lnc-ALVE1-AS1 had the opposite effect. Mechanistically, lnc-ALVE1-AS1 can be sensed by the cytosolic pattern recognition receptor TLR3 and trigger the type I interferons response. The present study provides novel insights into the antiviral defense of ERV-derived lncRNAs in macrophages and offers new strategies for future antiviral solutions.
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5
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Nojima T, Proudfoot NJ. Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 2022; 23:389-406. [DOI: 10.1038/s41580-021-00447-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
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6
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Manning JM, Manning LR, Dumoulin A, Padovan JC, Chait B. Embryonic and Fetal Human Hemoglobins: Structures, Oxygen Binding, and Physiological Roles. Subcell Biochem 2020; 94:275-296. [PMID: 32189304 DOI: 10.1007/978-3-030-41769-7_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
During the past two decades, significant advances have been made in our understanding of the human fetal and embryonic hemoglobins made possible by the availability of pure, highly characterized materials and novel methods, e.g., nano gel filtration, to study their properties and to correct some misconceptions. For example, whereas the structures of the human adult, fetal, and embryonic hemoglobins are very similar, it has generally been assumed that functional differences between them are due to primary sequence effects. However, more recent studies indicate that the strengths of the interactions between their subunits are very different leading to changes in their oxygen binding properties compared to adult hemoglobin. Fetal hemoglobin in the oxy conformation is a much stronger tetramer than adult hemoglobin and dissociates to dimers 70-times less than adult hemoglobin. This property may form the basis for its protective effect against malaria. A major source of the increased strength of fetal hemoglobin resides within the A-helix of its gamma subunit as demonstrated in studies with the hybrid hemoglobin Felix and related hybrids. Re-activating fetal hemoglobin synthesis in vivo is currently a major focus of clinical efforts designed to treat sickle cell anemia since it inhibits the aggregation of sickle hemoglobin. The mechanisms for both the increased oxygen affinity of fetal hemoglobin and its decreased response to DPG have been clarified. Acetylated fetal hemoglobin, which makes up 10-20% of total fetal hemoglobin, has a significantly weakened tetramer structure suggesting a similar role for other kinds of protein acetylation. Embryonic hemoglobins have the weakest tetramer and dimer structures. In general, the progressively increasing strength of the subunit interfaces of the hemoglobin family during development from the embryonic to the fetal and ultimately to the adult types correlates with their temporal appearance and disappearance in vivo, i.e., ontogeny.
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Affiliation(s)
- James M Manning
- Department of Biology, Northeastern University, Boston, MA, 02115, USA.
| | - Lois R Manning
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Antoine Dumoulin
- Department of Developability, Pierre Fabre Research Centre, Castres, 81106, France
| | - Julio C Padovan
- Laboratory of Gaseous Ion Chemistry, Rockefeller University, New York, NY, 10065, USA
| | - Brian Chait
- Laboratory of Gaseous Ion Chemistry, Rockefeller University, New York, NY, 10065, USA
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7
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Ribeiro ML, Reyes-Garau D, Armengol M, Fernández-Serrano M, Roué G. Recent Advances in the Targeting of Epigenetic Regulators in B-Cell Non-Hodgkin Lymphoma. Front Genet 2019; 10:986. [PMID: 31681423 PMCID: PMC6807552 DOI: 10.3389/fgene.2019.00986] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
Abstract
In the last 10 years, major advances have been made in the diagnosis and development of selective therapies for several blood cancers, including B-cell non-Hodgkin lymphoma (B-NHL), a heterogeneous group of malignancies arising from the mature B lymphocyte compartment. However, most of these entities remain incurable and current treatments are associated with variable efficacy, several adverse events, and frequent relapses. Thus, new diagnostic paradigms and novel therapeutic options are required to improve the prognosis of patients with B-NHL. With the recent deciphering of the mutational landscapes of B-cell disorders by high-throughput sequencing, it came out that different epigenetic deregulations might drive and/or promote B lymphomagenesis. Consistently, over the last decade, numerous epigenetic drugs (or epidrugs) have emerged in the clinical management of B-NHL patients. In this review, we will present an overview of the most relevant epidrugs tested and/or used so far for the treatment of different subtypes of B-NHL, from first-generation epigenetic therapies like histone acetyl transferases (HDACs) or DNA-methyl transferases (DNMTs) inhibitors to new agents showing selectivity for proteins that are mutated, translocated, and/or overexpressed in these diseases, including EZH2, BET, and PRMT. We will dissect the mechanisms of action of these epigenetic inhibitors, as well as the molecular processes underlying their lack of efficacy in refractory patients. This review will also provide a summary of the latest strategies being employed in preclinical and clinical settings, and will point out the most promising lines of investigation in the field.
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Affiliation(s)
- Marcelo L Ribeiro
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain.,Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista, São Paulo, Brazil
| | - Diana Reyes-Garau
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Marc Armengol
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Miranda Fernández-Serrano
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Gaël Roué
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
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8
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Dimopoulos K, Grønbæk K. Epigenetic therapy in hematological cancers. APMIS 2019; 127:316-328. [DOI: 10.1111/apm.12906] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/22/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Konstantinos Dimopoulos
- Department of Hematology Rigshospitalet University Hospital Copenhagen Copenhagen Denmark
- Biotech Research and Innovation Centre (BRIC) Novo Nordisk Foundation Center for Stem Cell Biology DanStem Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Kirsten Grønbæk
- Department of Hematology Rigshospitalet University Hospital Copenhagen Copenhagen Denmark
- Biotech Research and Innovation Centre (BRIC) Novo Nordisk Foundation Center for Stem Cell Biology DanStem Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
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9
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OAS-RNase L innate immune pathway mediates the cytotoxicity of a DNA-demethylating drug. Proc Natl Acad Sci U S A 2019; 116:5071-5076. [PMID: 30814222 PMCID: PMC6421468 DOI: 10.1073/pnas.1815071116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Drugs that cause epigenetic modification of DNA, such as 5-azacytidine (AZA), are used clinically to treat myelodysplastic syndromes and acute myeloid leukemia. In addition, AZA is being investigated for use against a range of different types of solid tumors, including lung and colorectal cancers. Treatment with AZA causes demethylation of DNA, thus increasing RNA synthesis, including the synthesis of double-stranded RNA, which is otherwise produced in virus-infected cells. We determined that cell death in response to AZA requires the antiviral enzyme RNase L. The results identify a drug target for enhancing the anticancer activity and reducing the toxicity of AZA and related drugs. Drugs that reverse epigenetic silencing, such as the DNA methyltransferase inhibitor (DNMTi) 5-azacytidine (AZA), have profound effects on transcription and tumor cell survival. AZA is an approved drug for myelodysplastic syndromes and acute myeloid leukemia, and is under investigation for different solid malignant tumors. AZA treatment generates self, double-stranded RNA (dsRNA), transcribed from hypomethylated repetitive elements. Self dsRNA accumulation in DNMTi-treated cells leads to type I IFN production and IFN-stimulated gene expression. Here we report that cell death in response to AZA treatment occurs through the 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway. OASs are IFN-induced enzymes that synthesize the RNase L activator 2-5A in response to dsRNA. Cells deficient in RNase L or OAS1 to 3 are highly resistant to AZA, as are wild-type cells treated with a small-molecule inhibitor of RNase L. A small-molecule inhibitor of c-Jun NH2-terminal kinases (JNKs) also antagonizes RNase L-dependent cell death in response to AZA, consistent with a role for JNK in RNase L-induced apoptosis. In contrast, the rates of AZA-induced and RNase L-dependent cell death were increased by transfection of 2-5A, by deficiencies in ADAR1 (which edits and destabilizes dsRNA), PDE12 or AKAP7 (which degrade 2-5A), or by ionizing radiation (which induces IFN-dependent signaling). Finally, OAS1 expression correlates with AZA sensitivity in the NCI-60 set of tumor cell lines, suggesting that the level of OAS1 can be a biomarker for predicting AZA sensitivity of tumor cells. These studies may eventually lead to pharmacologic strategies for regulating the antitumor activity and toxicity of AZA and related drugs.
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10
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Osorio-Montalvo P, Sáenz-Carbonell L, De-la-Peña C. 5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis. Int J Mol Sci 2018; 19:E3182. [PMID: 30332727 PMCID: PMC6214027 DOI: 10.3390/ijms19103182] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023] Open
Abstract
Somatic embryogenesis (SE) is a widely studied process due to its biotechnological potential to generate large quantities of plants in short time frames and from different sources of explants. The success of SE depends on many factors, such as the nature of the explant, the microenvironment generated by in vitro culture conditions, and the regulation of gene expression, among others. Epigenetics has recently been identified as an important factor influencing SE outcome. DNA methylation is one of the most studied epigenetic mechanisms due to its essential role in gene expression, and its participation in SE is crucial. DNA methylation levels can be modified through the use of drugs such as 5-Azacytidine (5-AzaC), an inhibitor of DNA methylation, which has been used during SE protocols. The balance between hypomethylation and hypermethylation seems to be the key to SE success. Here, we discuss the most prominent recent research on the role of 5-AzaC in the regulation of DNA methylation, highlighting its importance during the SE process. Also, the molecular implications that this inhibitor might have for the increase or decrease in the embryogenic potential of various explants are reviewed.
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Affiliation(s)
- Pedro Osorio-Montalvo
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
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11
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Bergallo M, Daprà V, Ponti R, Quaglino P, Novelli M, Fava P, Montanari P, Calvi C, Galliano I, Fierro M. HERV-E expression in peripheral mononuclear cells of patients with psoriasis. Ital J Dermatol Venerol 2018; 156:42-45. [PMID: 30251805 DOI: 10.23736/s2784-8671.18.06133-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Psoriasis is a common inflammatory skin disease characterized by uncontrolled proliferation of keratinocytes and recruitment of T lymphocytes into the skin. Possible triggers for psoriasis have been attributed to drugs or pathogens such as bacteria and possibly virus. Human endogenous retroviruses (HERVs) might play a role in triggering these antiviral immune responses, since the role of HERVs in the pathogenesis of autoimmune diseases has generated considerable interest. Some studies have also reported an association of HERV-E and psoriasis. None of them investigate the HERV-E expression in peripheral blood of psoriasis. All these considerations have prompted us to perform a survey for HERV-E expression in PBMC from psoriatic patients. METHODS Peripheral blood mononuclear cells from 69 psoriatic patients were analyzed. Total RNA was extracted and amplified with reverse transcription polymerase chain reaction. Results were compared with those obtained in a cohort of 20 healthy donors. RESULTS HERV E was expressed in all samples analyzed but the level of expression was much lower in the psoriasis that in HC P<0.0001. CONCLUSIONS The reasons for the unexpected, low levels of HERV expression in psoriatic patients are unclear and might be in part a consequence of antiviral defense mechanisms.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy -
| | - Valentina Daprà
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Renata Ponti
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Pietro Quaglino
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mauro Novelli
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo Fava
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Mariateresa Fierro
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
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12
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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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13
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Silverman LR. The Role of Methyltransferase Inhibitors in the Management of the Myelodysplastic Syndromes. Cancer Control 2017; 11:11-5. [PMID: 15625532 DOI: 10.1177/10732748040110s604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Lewis R Silverman
- Division of Hematology/Oncology, Mount Sinai School of Medicine, New York, NY 10029, USA.
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14
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Tie CHC, Rowe HM. Epigenetic control of retrotransposons in adult tissues: implications for immune regulation. Curr Opin Virol 2017; 25:28-33. [DOI: 10.1016/j.coviro.2017.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/26/2017] [Accepted: 06/19/2017] [Indexed: 12/29/2022]
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15
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Wang Y, Zhang Y, Guo Y, Kang XF. Fast and precise detection of DNA methylation with tetramethylammonium-filled nanopore. Sci Rep 2017; 7:183. [PMID: 28298646 PMCID: PMC5428259 DOI: 10.1038/s41598-017-00317-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/21/2017] [Indexed: 11/22/2022] Open
Abstract
The tremendous demand for detecting methylated DNA has stimulated intensive studies on developing fast single-molecule techniques with excellent sensitivity, reliability, and selectivity. However, most of these methods cannot directly detect DNA methylation at single-molecule level, which need either special recognizing elements or chemical modification of DNA. Here, we report a tetramethylammonium-based nanopore (termed TMA-NP) sensor that can quickly and accurately detect locus-specific DNA methylation, without bisulfite conversion, chemical modification or enzyme amplification. In the TMA-NP sensor, TMA-Cl is utilized as a nanopore-filling electrolyte to record the ion current change in a single nanopore triggered by methylated DNA translocation through the pore. Because of its methyl-philic nature, TMA can insert into the methylcytosine-guanine (mC-G) bond and then effectively unfasten and reduce the mC-G strength by 2.24 times. Simultaneously, TMA can increase the stability of A-T to the same level as C-G. The abilities of TMA (removing the base pair composition dependence of DNA strands, yet highly sensing for methylated base sites) endow the TMA-NP sensor with high selectivity and high precision. Using nanopore to detect dsDNA stability, the methylated and unmethylated bases are easily distinguished. This simple single-molecule technique should be applicable to the rapid analysis in epigenetic research.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, P. R. China
| | - Yani Zhang
- College of Life Sciences, Northwest University, Xi'an, 710069, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, P. R. China.
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16
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A New Molecular Mechanism Underlying the Antitumor Effect of DNA Methylation Inhibitors via an Antiviral Immune Response. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:227-242. [DOI: 10.1016/bs.apcsb.2016.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Saliba AN, Alameddine RS, Harb AR, Taher AT. Globin gene regulation for treating β-thalassemias: progress, obstacles and future. Expert Opin Orphan Drugs 2015. [DOI: 10.1517/21678707.2015.1074071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Lessard S, Beaudoin M, Benkirane K, Lettre G. Comparison of DNA methylation profiles in human fetal and adult red blood cell progenitors. Genome Med 2015; 7:1. [PMID: 25606059 PMCID: PMC4298057 DOI: 10.1186/s13073-014-0122-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/09/2014] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation is an epigenetic modification that plays an important role during mammalian development. Around birth in humans, the main site of red blood cell production moves from the fetal liver to the bone marrow. DNA methylation changes at the β-globin locus and a switch from fetal to adult hemoglobin production characterize this transition. Understanding this globin switch may improve the treatment of patients with sickle cell disease and β-thalassemia, two of the most common Mendelian diseases in the world. The goal of our study was to describe and compare the genome-wide patterns of DNA methylation in fetal and adult human erythroblasts. Methods We used the Illumina HumanMethylation 450 k BeadChip to measure DNA methylation at 402,819 CpGs in ex vivo-differentiated erythroblasts from 12 fetal liver and 12 bone marrow CD34+ donors. Results We identified 5,937 differentially methylated CpGs that overlap with erythroid enhancers and binding sites for erythropoiesis-related transcription factors. Combining this information with genome-wide association study results, we show that erythroid enhancers define particularly promising genomic regions to identify new genetic variants associated with fetal hemoglobin (HbF) levels in humans. Many differentially methylated CpGs are located near genes with unanticipated roles in red blood cell differentiation and proliferation. For some of these new candidate genes, we confirm the correlation between DNA methylation and gene expression levels in red blood cell progenitors. We also provide evidence that DNA methylation and genetic variation at the β-globin locus independently control globin gene expression in adult erythroblasts. Conclusions Our DNA methylome maps confirm the widespread dynamic changes in DNA methylation that occur during human erythropoiesis. These changes tend to happen near erythroid enhancers, further highlighting their importance in erythroid regulation and HbF production. Finally, DNA methylation may act independently of the transcription factor BCL11A to repress fetal hemoglobin production. This provides cues on strategies to more efficiently re-activate HbF production in sickle cell disease and β-thalassemia patients. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0122-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel Lessard
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada ; Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, Québec H3T 1J4 Canada
| | - Mélissa Beaudoin
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada
| | - Karim Benkirane
- Hôpital Maisonneuve-Rosemont, 5415 Boul. de l'Assomption, Montréal, Québec H1T 2M4 Canada
| | - Guillaume Lettre
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada ; Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, Québec H3T 1J4 Canada
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Rao MK, Matsumoto Y, Richardson ME, Panneerdoss S, Bhardwaj A, Ward JM, Shanker S, Bettegowda A, Wilkinson MF. Hormone-induced and DNA demethylation-induced relief of a tissue-specific and developmentally regulated block in transcriptional elongation. J Biol Chem 2014; 289:35087-101. [PMID: 25331959 DOI: 10.1074/jbc.m114.615435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genome-wide studies have revealed that genes commonly have a high density of RNA polymerase II just downstream of the transcription start site. This has raised the possibility that genes are commonly regulated by transcriptional elongation, but this remains largely untested in vivo, particularly in vertebrates. Here, we show that the proximal promoter from the Rhox5 homeobox gene recruits polymerase II and begins elongating in all tissues and cell lines that we tested, but it only completes elongation in a tissue-specific and developmentally regulated manner. Relief of the elongation block is associated with recruitment of the elongation factor P-TEFb, the co-activator GRIP1, the chromatin remodeling factor BRG1, and specific histone modifications. We provide evidence that two mechanisms relieve the elongation block at the proximal promoter: demethylation and recruitment of androgen receptor. Together, our findings support a model in which promoter proximal pausing helps confer tissue-specific and developmental gene expression through a mechanism regulated by DNA demethylation-dependent nuclear hormone receptor recruitment.
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Affiliation(s)
- Manjeet K Rao
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Yuiko Matsumoto
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Marcy E Richardson
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Subbarayalu Panneerdoss
- the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Anjana Bhardwaj
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Jacqueline M Ward
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Sreenath Shanker
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Anilkumar Bettegowda
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Miles F Wilkinson
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
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Diminished humoral responses against and reduced gene expression levels of human endogenous retrovirus-K (HERV-K) in psoriasis. J Transl Med 2014; 12:256. [PMID: 25224121 PMCID: PMC4174287 DOI: 10.1186/s12967-014-0256-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/05/2014] [Indexed: 11/15/2022] Open
Abstract
Background Psoriasis is a multifactorial, chronic disease of skin affecting 2-3% of the world’s population. Genetic studies of psoriasis have identified a number of susceptibility genes that are involved in anti-viral immunity. Furthermore, physiological studies have also found an increase in anti-viral proteins in psoriatic skin. These findings suggest the presence of an anti-viral state in psoriatic skin. However, the triggers for this anti-viral cascade and its consequences for host immunity are not known. Endogenous retroviruses have previously been described in many autoimmune diseases including psoriasis. Methods In the present study we examined the humoral immune response against human endogenous retrovirus-K (HERV-K) proteins and the cutaneous expression levels of multiple HERV-K genes in psoriasis patients and healthy controls. Results In psoriatic sera we observed a significant decrease in IgM response against three HERV-K proteins: Env surface unit (SU), Env transmembrane protein (TM), and Gag capsid (CA) in comparison to sera obtained from blood bank healthy controls. A decrease in IgG response was also observed against CA. Furthermore, using quantitative RT-PCR we observed a decrease in the expression of HERV-K Env, Gag, Pol and Rec as well as ERV-9 genes in lesional psoriatic skin as compared to healthy skin. Conclusions Together, our results suggest that the pro-inflammatory, anti-viral state in psoriasis is associated with diminished expression of HERV-K gene transcripts and a concomitant decrease in humoral responses to HERV-K. Our results indicate that a simple model where continuous, minimally changing HERV-K expression serves as an antigenic trigger in psoriasis might not be correct and further studies are needed to decipher the possible relationship between psoriasis and HERVs. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0256-4) contains supplementary material, which is available to authorized users.
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21
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Epigenetic control of the genome-lessons from genomic imprinting. Genes (Basel) 2014; 5:635-55. [PMID: 25257202 PMCID: PMC4198922 DOI: 10.3390/genes5030635] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms modulate genome function by writing, reading and erasing chromatin structural features. These have an impact on gene expression, contributing to the establishment, maintenance and dynamic changes in cellular properties in normal and abnormal situations. Great effort has recently been undertaken to catalogue the genome-wide patterns of epigenetic marks—creating reference epigenomes—which will deepen our understanding of their contributions to genome regulation and function with the promise of revealing further insights into disease etiology. The foundation for these global studies is the smaller scale experimentally-derived observations and questions that have arisen through the study of epigenetic mechanisms in model systems. One such system is genomic imprinting, a process causing the mono-allelic expression of genes in a parental-origin specific manner controlled by a hierarchy of epigenetic events that have taught us much about the dynamic interplay between key regulators of epigenetic control. Here, we summarize some of the most noteworthy lessons that studies on imprinting have revealed about epigenetic control on a wider scale. Specifically, we will consider what these studies have revealed about: the variety of relationships between DNA methylation and transcriptional control; the regulation of important protein-DNA interactions by DNA methylation; the interplay between DNA methylation and histone modifications; and the regulation and functions of long non-coding RNAs.
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22
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Sacco MA, Nair VK. Prototype endogenous avian retroviruses of the genus Gallus. J Gen Virol 2014; 95:2060-2070. [PMID: 24903328 DOI: 10.1099/vir.0.066852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ancient endogenous retroviruses (ERVs), designated endogenous avian retrovirus (EAVs), are present in all Gallus spp. including the chicken, and resemble the modern avian sarcoma and leukosis viruses (ASLVs). The EAVs comprise several distinct retroviruses, including EAV-0, EAV-E51 and EAV-HP, as well as a putative member previously named the avian retrotransposon of chickens (ART-CH). Thus far, only the EAV-HP elements have been well characterized. Here, we determined sequences of representative EAV-0 and EAV-E51 proviruses by cloning and data mining of the 2011 assembly of the Gallus gallus genome. Although the EAV-0 elements are primarily deleted in the env region, we identified two complete EAV-0 env genes within the G. gallus genome and prototype elements sharing identity with an EAV-E51-related clone previously designated EAV-E33. Prototype EAV-0, EAV-E51 and EAV-E33 gag, pol and env gene sequences used for phylogenetic analysis of deduced proteins showed that the EAVs formed three distinct clades, with EAV-0 sharing the last common ancestor with the ASLVs. The EAV-E51 clade showed the greatest level of divergence compared with other EAVs or ASLVs, suggesting that these ERVs represented exogenous retroviruses that evolved and integrated into the germline over a long period of time. Moreover, the degree of divergence between the chicken and red jungle fowl EAV-E51 sequences suggested that they were more ancient than the other EAVs and may have diverged through mutations that accumulated post-integration. Finally, we showed that the ART-CH elements were chimeric defective ERVs comprising portions of EAV-E51 and EAV-HP rather than authentic retrotransposons.
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Affiliation(s)
- Melanie Ann Sacco
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA
| | - Venugopal K Nair
- Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, UK
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Southerland KW, Frazier SB, Bowles DE, Milano CA, Kontos CD. Gene therapy for the prevention of vein graft disease. Transl Res 2013; 161:321-38. [PMID: 23274305 PMCID: PMC3602161 DOI: 10.1016/j.trsl.2012.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/04/2012] [Accepted: 12/04/2012] [Indexed: 11/20/2022]
Abstract
Ischemic cardiovascular disease remains the leading cause of death worldwide. Despite advances in the medical management of atherosclerosis over the past several decades, many patients require arterial revascularization to reduce mortality and alleviate ischemic symptoms. Technological advancements have led to dramatic increases in the use of percutaneous and endovascular approaches, yet surgical revascularization (bypass surgery) with autologous vein grafts remains a mainstay of therapy for both coronary and peripheral artery disease. Although bypass surgery is highly efficacious in the short term, long-term outcomes are limited by relatively high failure rates as a result of intimal hyperplasia, which is a common feature of vein graft disease. The supply of native veins is limited, and many individuals require multiple grafts and repeat procedures. The need to prevent vein graft failure has led to great interest in gene therapy approaches to this problem. Bypass grafting presents an ideal opportunity for gene therapy, as surgically harvested vein grafts can be treated with gene delivery vectors ex vivo, thereby maximizing gene delivery while minimizing the potential for systemic toxicity and targeting the pathogenesis of vein graft disease at its onset. Here we will review the pathogenesis of vein graft disease and discuss vector delivery strategies and potential molecular targets for its prevention. We will summarize the preclinical and clinical literature on gene therapy in vein grafting and discuss additional considerations for future therapies to prevent vein graft disease.
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Affiliation(s)
- Kevin W Southerland
- Department of Surgery, Division of Surgical Sciences, Duke University Medical Center, Durham, North Carolina, USA
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Clinical experience with fetal hemoglobin induction therapy in patients with β-thalassemia. Blood 2013; 121:2199-212; quiz 2372. [PMID: 23315167 DOI: 10.1182/blood-2012-10-408021] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent molecular studies of fetal hemoglobin (HbF) regulation have reinvigorated the field and shown promise for the development of clinical HbF inducers to be used in patients with β-thalassemia and sickle cell disease. However, while numerous promising inducers of HbF have been studied in the past in β-thalassemia patient populations, with limited success in some cases, no universally effective agents have been found. Here we examine the clinical studies of such inducers in an attempt to systematically review the field. We examine trials of agents, including 5-azacytidine, hydroxyurea, and short-chain fatty acids. This review highlights the heterogeneity of clinical studies done on these agents, including both the patient populations examined and the study end points. By examining the published studies of these agents, we hope to provide a resource that will be valuable for the design of future studies of HbF inducers in β-thalassemia patient populations.
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Abstract
The fetal-to-adult hemoglobin switch and silencing of fetal hemoglobin (HbF) have been areas of long-standing interest among hematologists, given the fact that clinical induction of HbF production holds tremendous promise to ameliorate the clinical symptoms of sickle cell disease (SCD) and β-thalassemia. In this article, we discuss historic attempts to induce HbF that have resulted in some therapeutic approaches to manage SCD and β-thalassemia. We then go on to discuss how more recent molecular studies that have identified regulators, including BCL11A, MYB, and KLF1, hold great promise to develop targeted and more effective approaches for HbF induction. We go on to discuss strategies by which such approaches may be developed. Older studies in this field can provide important lessons for future studies aimed at developing more effective strategies for HbF induction, and we therefore chronologically cover the work accomplished as this field has evolved over the course of the past four decades.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA.
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26
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Abstract
Cellular reprogramming involves the artificial dedifferentiation of somatic cells to a pluripotent state. When affected by overexpressing specific transcription factors, the process is highly inefficient, as only 0.1-1% of cells typically undergo the transformation. This low efficiency has been attributed to high kinetic barriers that affect all cells equally and can only be overcome by rare stochastic events. The barriers to reprogramming are likely to involve transformations of chromatin state because (i) inhibitors of chromatin-modifying enzymes can enhance the efficiency of reprogramming and (ii) knockdown or knock-out of chromatin-modifying enzymes can lower the efficiency of reprogramming. Here, we review the relationship between chromatin state transformations (chromatin reprogramming) and cellular reprogramming, with an emphasis on transcription factors, chromatin remodeling factors, histone modifications and DNA methylation.
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Abstract
Retroviral replication involves the formation of a DNA provirus integrated into the host genome. Through this process, retroviruses can colonize the germ line to form endogenous retroviruses (ERVs). ERV inheritance can have multiple adverse consequences for the host, some resembling those resulting from exogenous retrovirus infection but others arising by mechanisms unique to ERVs. Inherited retroviruses can also confer benefits on the host. To meet the different threats posed by endogenous and exogenous retroviruses, various host defences have arisen during evolution, acting at various stages on the retrovirus life cycle. In this Review, I describe our current understanding of the distribution and architecture of ERVs, the consequences of their acquisition for the host and the emerging details of the intimate evolutionary relationship between virus and vertebrate host.
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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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Bacon LD, Fulton JE, Kulkarni GB. Methods for evaluating and developing commercial chicken strains free of endogenous subgroup E avian leukosis virus. Avian Pathol 2010; 33:233-43. [PMID: 15276994 DOI: 10.1080/0307943042000195731] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The genome of nearly all chickens contains various DNA proviral insertions of retroviruses of subgroup E avian leukosis virus (ALVE). However, the elimination or control of ALVE gene expression is desirable to improve productivity, to improve resistance to avian leukosis virus (ALV)-induced tumours, and to develop safer live virus vaccines in chick embryos and cultured chick cells. Restriction fragment length polymorphism and polymerase chain reaction methods are used to define the presence of ALVE genes; and the expression of ALVE in chicken plasma or on cells, and the susceptibility of cells to ALVE is determined by flow cytometry using a specific (R2) antibody. ADOL line 0 chickens have been selected to be free of ALVE genes, while being resistant (i.e. lack receptors to ALVE), but susceptible to exogenous ALV (i.e. ALVA, ALVB, ALVC and ALVJ). To develop improved line 0-type chickens, ADOL line 0 was outcrossed to a commercial line that had one ALVE gene and evidence for ALVE resistance. Rous sarcoma virus (RSV) challenge was used to confirm resistance of F1 chickens to ALVE, and susceptibility of F2 breeders to ALVA and ALVB using test chicks produced by matings to line 7(2). Selected F2 breeders were resistant to ALVE, but susceptible to exogenous ALVA, ALVB, ALVC and ALVJ, based on challenge tests of progeny chick cells using an enzyme-linked immunosorbent assay. The new line, 0(1), has evidence for improved egg size, productivity, fertility and hatchability. Similar procedures may be used for development of productive ALVE free chicken lines with preferred ALV susceptibility traits.
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Affiliation(s)
- L D Bacon
- US Department of Agriculture Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA.
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Baudino L, Yoshinobu K, Dunand-Sauthier I, Evans LH, Izui S. TLR-mediated up-regulation of serum retroviral gp70 is controlled by the Sgp loci of lupus-prone mice. J Autoimmun 2010; 35:153-9. [PMID: 20619604 DOI: 10.1016/j.jaut.2010.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 06/08/2010] [Accepted: 06/13/2010] [Indexed: 12/29/2022]
Abstract
The endogenous retroviral envelope glycoprotein, gp70, implicated in murine systemic lupus erythematosus (SLE), has been considered to be a product of xenotropic, polytropic (PT) and modified PT (mPT) endogenous retroviruses. It is secreted by hepatocytes like an acute phase protein, but its response is under a genetic control. Given critical roles of TLR7 and TLR9 in the pathogenesis of SLE, we assessed their contribution to the acute phase expression of serum gp70, and defined a pivotal role of the Sgp3 (serum gp70 production 3) and Sgp4 loci in this response. Our results demonstrated that serum levels of gp70 were up-regulated in lupus-prone NZB mice injected with TLR7 or TLR9 agonist at levels comparable to those induced by injection of IL-1, IL-6 or TNF. In addition, studies of C57BL/6 Sgp3 and/or Sgp4 congenic mice defined the major roles of these two loci in up-regulated production of serum gp70 during acute phase responses. Finally, the analysis of Sgp3 congenic mice strongly suggests the presence of at least two distinct genetic factors in the Sgp3 interval, one of which controlled the basal-level expression of xenotropic, PT and mPT gp70 and the other which controlled the up-regulated production of xenotropic and mPT gp70 during acute phase responses. Our results uncovered an additional pathogenic role of TLR7 and TLR9 in murine lupus nephritis by promoting the expression of nephritogenic gp70 autoantigen. Furthermore, they revealed the involvement of multiple regulatory genes for the expression of gp70 autoantigen under steady-state and inflammatory conditions in lupus-prone mice.
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Affiliation(s)
- Lucie Baudino
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
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31
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Fluhr R, Kuhlemeier C, Nagy F, Chua NH. Organ-specific and light-induced expression of plant genes. Science 2010; 232:1106-12. [PMID: 17754498 DOI: 10.1126/science.232.4754.1106] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Light plays a pivotal role in the development of plants. The photoregulation of plant genes involves recognition of light quality and quantity by phytochrome and other light receptors. Two gene families, rbcS and Cab, which code for abundant proteins active in photosynthesis, the small subunit of ribulose bisphosphate carboxylase and the chlorophyll a/b binding protein, show a 20-to 50-fold increase in transcript abundance in the light. Analyses in calli and transgenic plants of deletions of the rbcS gene and of chimeric constructions has allowed localization of two regions involved in light-induced transcription. One element is confined to a 33-base pair region surrounding the TATA box. In addition, an enhancer-like element contained within a 240-base pair fragment can confer phytochrome-induced transcription and organ specificity on nonregulated promoters.
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Chari R, Thu KL, Wilson IM, Lockwood WW, Lonergan KM, Coe BP, Malloff CA, Gazdar AF, Lam S, Garnis C, MacAulay CE, Alvarez CE, Lam WL. Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. Cancer Metastasis Rev 2010; 29:73-93. [PMID: 20108112 DOI: 10.1007/s10555-010-9199-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Advances in high-throughput, genome-wide profiling technologies have allowed for an unprecedented view of the cancer genome landscape. Specifically, high-density microarrays and sequencing-based strategies have been widely utilized to identify genetic (such as gene dosage, allelic status, and mutations in gene sequence) and epigenetic (such as DNA methylation, histone modification, and microRNA) aberrations in cancer. Although the application of these profiling technologies in unidimensional analyses has been instrumental in cancer gene discovery, genes affected by low-frequency events are often overlooked. The integrative approach of analyzing parallel dimensions has enabled the identification of (a) genes that are often disrupted by multiple mechanisms but at low frequencies by any one mechanism and (b) pathways that are often disrupted at multiple components but at low frequencies at individual components. These benefits of using an integrative approach illustrate the concept that the whole is greater than the sum of its parts. As efforts have now turned toward parallel and integrative multidimensional approaches for studying the cancer genome landscape in hopes of obtaining a more insightful understanding of the key genes and pathways driving cancer cells, this review describes key findings disseminating from such high-throughput, integrative analyses, including contributions to our understanding of causative genetic events in cancer cell biology.
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Affiliation(s)
- Raj Chari
- Genetics Unit - Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
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33
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The LTR of endogenous retrovirus ev21 retains promoter activity and exhibits tissue specific transcription in chicken. Sci Bull (Beijing) 2010. [DOI: 10.1007/s11434-009-0547-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Perron H, Bernard C, Bertrand JB, Lang AB, Popa I, Sanhadji K, Portoukalian J. Endogenous retroviral genes, Herpesviruses and gender in Multiple Sclerosis. J Neurol Sci 2009; 286:65-72. [DOI: 10.1016/j.jns.2009.04.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 04/02/2009] [Accepted: 04/14/2009] [Indexed: 01/13/2023]
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Abstract
Genetic, environmental, and hormonal factors contribute to disease susceptibility in systemic lupus erythematosus. Among environmental factors, infectious agents play a major role. When considering the complex relationship between genetic predisposition and infections in the pathogenesis of systemic lupus erythematosus, we have to consider that infectious agents can interact with the immune system in several ways. For example, molecular mimicry, altered apoptosis of the host cells, exposure of as yet masked antigens to the immune system by a given microorganism, and direct viral invasion of immunocompetent cells are all mechanisms that may give rise to dysfunction of the immune system; in addition, some genetically determined deficit of the immune system, such as complement deficiency or deficit of mannose binding lectine, may cause insufficient clearance of infectious agents, whose persistence in the host may determine autoimmunity. Finally, evidence has been emerging suggesting that the production of autoantibodies, by infected B-lymphocytes, may be drawn by altered expression of particular microRNA in these cells. In this paper, we review some of the distinct scenarios that can account for the role of infectious agents, acting on a genetically prone host, in determining systemic lupus erythematosus.
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Yoshinobu K, Baudino L, Santiago-Raber ML, Morito N, Dunand-Sauthier I, Morley BJ, Evans LH, Izui S. Selective up-regulation of intact, but not defective env RNAs of endogenous modified polytropic retrovirus by the Sgp3 locus of lupus-prone mice. THE JOURNAL OF IMMUNOLOGY 2009; 182:8094-103. [PMID: 19494335 DOI: 10.4049/jimmunol.0900263] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Endogenous retroviruses are implicated in the pathogenesis of systemic lupus erythematosus (SLE). Because four different classes of endogenous retroviruses, i.e., ecotropic, xenotropic, polytropic, or modified polytropic (mPT), are expressed in mice, we investigated the possibility that a particular class of endogenous retroviruses is associated with the development of murine SLE. We observed >15-fold increased expression of mPT env (envelope) RNA in livers of all four lupus-prone mice, as compared with those of nine nonautoimmune strains of mice. This was not the case for the three other classes of retroviruses. Furthermore, we found that in addition to intact mPT transcripts, many strains of mice expressed two defective mPT env transcripts which carry a deletion in the env sequence of the 3' portion of the gp70 surface protein and the 5' portion of the p15E transmembrane protein, respectively. Remarkably, in contrast to nonautoimmune strains of mice, all four lupus-prone mice expressed abundant levels of intact mPT env transcripts, but only low or nondetectable levels of the mutant env transcripts. The Sgp3 (serum gp70 production 3) locus derived from lupus-prone mice was responsible for the selective up-regulation of the intact mPT env RNA. Finally, we observed that single-stranded RNA-specific TLR7 played a critical role in the production of anti-gp70 autoantibodies. These data suggest that lupus-prone mice may possess a unique genetic mechanism responsible for the expression of mPT retroviruses, which could act as a triggering factor through activating TLR7 for the development of autoimmune responses in mice predisposed to SLE.
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Affiliation(s)
- Kumiko Yoshinobu
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
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37
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Li Y, Sawalha AH, Lu Q. Aberrant DNA methylation in skin diseases. J Dermatol Sci 2009; 54:143-9. [PMID: 19395242 DOI: 10.1016/j.jdermsci.2009.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 01/16/2009] [Accepted: 01/29/2009] [Indexed: 12/21/2022]
Abstract
Epigenetic mechanisms are involved in regulating cell growth and differentiation without inducing changes in the gene sequence. The main epigenetic mechanisms include DNA methylation, histone modification, and microRNA. Recent studies indicate that aberrant DNA methylation is a common feature of many human disorders, including cancer, autoimmune diseases, heart diseases, skin diseases, and others. Skin diseases comprise various diseases that have a complex etiology and pathogenesis, including genetics and acquired factors such as environment and diet. These acquired factors often have pathogenic effects through modification of DNA and histones, of which DNA methylation is the most common mechanism. Aberrant DNA methylation has been demonstrated in skin diseases, including skin tumors and autoimmune-related skin disorders. Herein, we review the role of DNA methylation in the pathogenesis of skin diseases.
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Affiliation(s)
- Yaping Li
- Department of Dermatology and Epigenetic Research Center, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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38
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Labet V, Morell C, Cadet J, Eriksson LA, Grand A. Hydrolytic Deamination of 5-Methylcytosine in Protic Medium—A Theoretical Study. J Phys Chem A 2009; 113:2524-33. [DOI: 10.1021/jp808902j] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vanessa Labet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Christophe Morell
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Jean Cadet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - André Grand
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
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39
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Horseman ND, Will CL. Orcadian regulation of RNA polymerases and nuclease sensitivity in rat liver nuclei. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/09291018409359848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Perl A, Nagy G, Koncz A, Gergely P, Fernandez D, Doherty E, Telarico T, Bonilla E, Phillips PE. Molecular mimicry and immunomodulation by the HRES-1 endogenous retrovirus in SLE. Autoimmunity 2008; 41:287-97. [PMID: 18432409 PMCID: PMC5294745 DOI: 10.1080/08916930802024764] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Genetic and environmental factors are believed to influence development of systemic lupus erythematosus (SLE). Endogenous retroviruses (ERV) correspond to the integrated proviral form of infectious retroviruses, which are trapped within the genome due to mutations. ERV represent a key molecular link between the host genome and infectious viral particles. ERV-encoded proteins are recognized by antiviral immune responses and become targets of autoreactivity. Alternatively, ERV protein may influence cellular processes and the life cycle of infectious viruses. As examples, the HRES-1 human ERV encodes a 28-kDa nuclear autoantigen and a 24-kDa small GTP-ase, termed HRES-1/Rab4. HRES-1/p28 is a nuclear autoantigen recognized by cross-reactive antiviral antibodies, while HRES-1/Rab4 regulates surface expression of CD4 and the transferrin receptor (TFR) through endosome recycling. Expression of HRES-1/Rab4 is induced by the tat gene of HIV-1, which in turn down-regulates expression of CD4 and susceptibility to re-infection by HIV-1. CD4 and the TFR play essential roles in formation of the immunological synapse (IS) during normal T-cell activation by a cognate MHC class II peptide complex. The key intracellular transducer of T-cell activation, Lck, is brought to the IS via binding to CD4. T-cell receptorzeta (TCRzeta) chain binds to the TFR. Abnormal T-cell responses in SLE have been associated with reduced lck and TCRzeta chain levels. HRES-1 is centrally located on chromosome 1 at q42 relative to lupus-linked microsatellite markers and polymorphic HRES-1 alleles have been linked to the development of SLE. 1q42 is one of the three most common fragile sites in the human genome, and is inducible by DNA demethylation, a known mechanism of retroviral gene activation. Molecular mimicry and immunomodulation by a ERV, such as HRES-1, may contribute to self-reactivity and abnormal T and B-cell functions in SLE.
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Affiliation(s)
- Andras Perl
- Division of Rheumatology, Department of Medicine, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.
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41
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Abstract
We show that macroH2A1 histone variants are important for repressing the expression of endogenous murine leukemia viruses (MLVs) in mouse liver. Intact MLV proviruses and proviruses with deletions in env were nearly silent in normal mouse liver and showed substantial derepression in macroH2A1 knockout liver. In contrast, MLV proviruses with a deletion in the 5' end of pro-pol were expressed in normal liver and showed relatively low levels of derepression in knockout liver. macroH2A1 nucleosomes were enriched on endogenous MLVs, with the highest enrichment occurring on the 5' end of pro-pol. The absence of macroH2A1 also led to a localized loss of DNA methylation on the 5' ends of MLV proviruses. These results demonstrate that macroH2A1 histones have a significant role in silencing endogenous MLVs in vivo and suggest that specific internal MLV sequences are targeted by a macroH2A1-dependent silencing mechanism.
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42
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Pullmann R, Bonilla E, Phillips PE, Middleton FA, Perl A. Haplotypes of the HRES-1 endogenous retrovirus are associated with development and disease manifestations of systemic lupus erythematosus. ACTA ACUST UNITED AC 2008; 58:532-40. [DOI: 10.1002/art.23161] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Forde GK, Forde AE, Hill G, Ford A, Nazario A, Leszczynski J. Comprehensive study of the effects of methylation on tautomeric equilibria of nucleic acid bases. J Phys Chem B 2007; 110:15564-71. [PMID: 16884280 DOI: 10.1021/jp056574d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minor tautomers of nucleic acid bases can result by intramolecular proton transfer. These rare tautomers could be stabilized through the addition of methyl groups to DNA bases. A comprehensive theoretical study of tautomers of methylated derivatives of guanine, adenine, cytosine, thymine, and uracil was performed. Molecular geometries of all tautomers were obtained at the density functional theory and MP2 levels with the 6-31G(d,p) basis set, and single-point calculations were performed at the CCSD(T)/6-311G(d,p) level. Tautomers obtained by protonation at the preferred protonation site for methylated isolated bases were compared to their nonmethylated counterparts. The effects of methylation on the relative stabilities of nucleic acid base tautomers are also studied and discussed in this work. The results suggest that some sites on the bases may not be mutagenic and may even stabilize the canonical Watson-Crick form. The results also indicate that a number of methylation sites can stabilize the tautomers, suggesting possible mechanisms for mutagenic changes.
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Affiliation(s)
- Gareth K Forde
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, USA
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44
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Mogal AP, van der Meer R, Crooke PS, Abdulkadir SA. Haploinsufficient prostate tumor suppression by Nkx3.1: a role for chromatin accessibility in dosage-sensitive gene regulation. J Biol Chem 2007; 282:25790-800. [PMID: 17602165 DOI: 10.1074/jbc.m702438200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transcription factor haploinsufficiency plays a role in the pathogenesis of many diseases, including cancer. In a mouse model of prostate tumor initiation, loss of a single allele of the tumor suppressor Nkx3.1 stochastically inactivates the expression of a class of dosage-sensitive target genes. Here we show that dosage sensitivity is associated with the differential histone H3/H4 acetylation states of Nkx3.1 target genes. When histone acetylation is induced in Nkx3.1+/- mouse prostates with the histone deacetylase inhibitor Trichostatin A, Nkx3.1 can bind to and reactivate the expression of dosage-sensitive target genes. We incorporated our findings into a mathematical model that entails the association of Nkx3.1 with histone acetyltransferase activity. Subsequent experiments indicate that Nkx3.1 associates with and recruits the histone acetyltransferase p300/CREB-binding protein-associated factor to chromatin. Finally, we demonstrate a role for the dosage-sensitive target gene intelectin/omentin in suppressing prostate tumorigenicity. Our results reveal how the interplay between transcription factor dosage and chromatin affects target gene expression in tumor initiation.
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Affiliation(s)
- Ashish P Mogal
- Department of Pathology, Vanderbilt University Medical Center, Nashville 37232, USA
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45
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Hofmann A, Kessler B, Ewerling S, Kabermann A, Brem G, Wolf E, Pfeifer A. Epigenetic Regulation of Lentiviral Transgene Vectors in a Large Animal Model. Mol Ther 2006; 13:59-66. [PMID: 16140581 DOI: 10.1016/j.ymthe.2005.07.685] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Revised: 07/17/2005] [Accepted: 07/18/2005] [Indexed: 11/21/2022] Open
Abstract
Transgenic animals are of outstanding relevance for genetic studies and the development of novel therapies for human diseases. A recent development is the generation of transgenic animals by lentiviral gene transfer. So far, studies on lentiviral transgenesis focused on first-generation (founder or F0) animals-most of which carry multiple integrants. Here, we analyze transgene expression and epigenetic regulation of individual integrants in lentiviral transgenic pigs after segregation to the F1 generation. Unexpectedly, one-third of lentiviral integrants exhibited low expression levels and were hypermethylated, as demonstrated by methylation-sensitive Southern blotting and bisulfite sequencing. Proviral methylation density correlated inversely with expression levels. In addition, treatment of isolated transgenic fibroblasts with the DNA methylase inhibitor 5-azacytidine induced a threefold increase in mean fluorescence intensity (MFI) from 8 to 26.1. Treatment with the histone deacetylase inhibitor trichostatin A enhanced MFI to only 11.1. Taken together, expression of lentiviral integrants in higher mammals is regulated by epigenetic modifications. In contrast to previous expectations, DNA methylation plays an important role in lentiviral expression.
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Affiliation(s)
- Andreas Hofmann
- Department of Pharmacy, Molecular Pharmacology, Center for Drug Research, Butenandtstrasse 5 (C), 81377 Munich, Germany
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46
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Wang G, Liu T, Wei LN, Law PY, Loh HH. DNA Methylation-Related Chromatin Modification in the Regulation of Mouse δ-Opioid Receptor Gene. Mol Pharmacol 2005; 67:2032-9. [PMID: 15769948 DOI: 10.1124/mol.105.011056] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA methylation plays critical roles in gene-silencing through chromatin modification. We reported previously that promoter-region CpG methylation repressed mouse delta-opioid receptor (mDOR) gene expression. In the current study, we demonstrated that the methylation of mDOR gene promoter is correlated with a repressive chromatin structure that has less HaeIII and MspI nuclear accessibility and more deacetylated histone H3 and H4 than that of unmethylated mDOR promoter. Chromatin immunoprecipitation analysis showed the association of a methyl-CpG-binding domain protein 2 (MBD2) with methylated mDOR promoter. Transient expression of MBD2 enhanced the repression of partially methylated mDOR promoter activity, and this repression was partially reversed by treatment of trichostatin A, a specific histone deacetylase inhibitor, indicating that MBD2 may mediate DNA methylation-related chromatin modification through recruiting histone deacetylases to mDOR promoter region. In addition, trichostatin A treatment increased both methylated mDOR promoter activity in a transient transfection assay and endogenous mDOR mRNA level in Neuro2A cells. Taken together, these results demonstrate that the mDOR gene expression is regulated by DNA methylation-related chromatin modification, especially histone acetylation and deacetylation.
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Affiliation(s)
- Guilin Wang
- Department of Pharmacology, University of Minnesota, 6-120 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA.
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47
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Lorincz MC, Dickerson DR, Schmitt M, Groudine M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 2004; 11:1068-75. [PMID: 15467727 DOI: 10.1038/nsmb840] [Citation(s) in RCA: 348] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Accepted: 08/30/2004] [Indexed: 11/09/2022]
Abstract
Transcriptional silencing in mammals is often associated with promoter methylation. However, a considerable number of genomic methylated CpGs exist in transposable elements, which are frequently found in intronic regions. To determine whether intragenic methylation influences transcription efficiency, we used the Cre/loxP-based system, RMCE, to introduce a transgene, methylated exclusively in a region downstream of the promoter, into a specific genomic site. This methylation pattern was maintained in vivo, and yielded a clear decrease in transgene expression relative to an unmethylated control. Notably, RNA polymerase II (Pol II) was depleted exclusively in the methylated region, as was histone H3 di- and trimethylated on Lys4 and acetylated on Lys9 and Lys14. As the methylated region adopts a closed chromatin structure in vivo, we propose that dense intragenic DNA methylation in mammalian cells initiates formation of a chromatin structure that reduces the efficiency of Pol II elongation.
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Affiliation(s)
- Matthew C Lorincz
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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Sekigawa I, Naito T, Hira K, Mitsuishi K, Ogasawara H, Hashimoto H, Ogawa H. Possible mechanisms of gender bias in SLE: a new hypothesis involving a comparison of SLE with atopy. Lupus 2004; 13:217-22. [PMID: 15176655 DOI: 10.1191/0961203304lu1012ed] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The prevalence of systemic lupus erythematosus (SLE) is far higher in females than in males, and numerous investigations of this gender bias have been performed from several perspectives. Sex hormones, particularly estrogens, may be significant in causing the gender discrepancy. This article discusses the possible importance of estrogens in regulating the expression of and responsivity to autoantigens in SLE and in atopic disorders, which are associated with hyperreactivity to exogenous antigens. Estrogens seem to play an important role in the overexpression of endogenous autoantigens, such as human endogenous retroviruses (HERV), and this may be related to the existence of a gender bias in the incidence of SLE but not atopy.
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Affiliation(s)
- I Sekigawa
- Department of Medicine, Juntendo University Izu-Nagaoka Hospital, Tagata-gun, Shizuoka, Japan.
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49
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Shen CH, Steiner LA. Genome structure and thymic expression of an endogenous retrovirus in zebrafish. J Virol 2004; 78:899-911. [PMID: 14694121 PMCID: PMC368747 DOI: 10.1128/jvi.78.2.899-911.2004] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2003] [Accepted: 10/03/2003] [Indexed: 11/20/2022] Open
Abstract
In a search for previously unknown genes that are required for lymphocyte development in zebrafish, a retroviral sequence was identified in a subtracted thymus cDNA library and in genomic DNA libraries. The provirus is 11.2 kb and contains intact open reading frames for the gag, pol, and env genes, as well as nearly identical flanking long terminal repeat sequences. As determined by in situ hybridization, the thymus appears to be a major tissue for retroviral expression in both larval and adult fish. Several viral transcripts were found by Northern blotting in the adult thymus. The provirus was found at the same genomic locus in sperm from four fish, suggesting that it is an endogenous retrovirus. Phylogenetic analysis indicates that it is closest to, yet distinct from, the cluster of murine leukemia virus-related retroviruses, suggesting that this virus represents a new group of retroviruses.
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Affiliation(s)
- Ching-Hung Shen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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50
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Conklin KF, Coffin JM, Robinson HL, Groudine M, Eisenman R. Role of methylation in the induced and spontaneous expression of the avian endogenous virus ev-1: DNA structure and gene products. Mol Cell Biol 2003; 2:638-52. [PMID: 14582159 PMCID: PMC369840 DOI: 10.1128/mcb.2.6.638-652.1982] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The endogenous avian provirus ev-1 is widespread in white leghorn chickens. Although it has no major structural defects, ev-1 has not been associated with any phenotype and is ordinarily expressed at a very low level. In this report, we describe a chicken embryo (Number 1836) cell culture containing both ev-1 and ev-6 which spontaneously expressed the ev-1 provirus. This culture released a high level of noninfectious virions containing a full complement of virion structural (gag) proteins but devoid of reverse transcriptase activity or antigen. These virions contained 70S RNA closely related to the genome of Rous-associated virus type 0, but identifiable as the ev-1 genome by oligonucleotide mapping. A fraction of the RNA molecules in the 70S complex were unusual in that they were polyadenylated 100 to 200 nucleotides downstream of the usual polyadenylation site. Eight sibling embryo cultures did not share this unusual phenotype with 1836, indicating that it was not inherited. However, an identical phenotype was inducible in the sibling cultures by treatment with 5-azacytidine, an inhibitor of DNA methylation, and the induced expression was stable for more than 10 generations. Analysis of chromatin structure and DNA methylation of the ev-1 provirus in 1836 cells revealed the presence (in a fraction of the proviruses) of both DNase I hypersensitive sites in the long terminal repeats and in gag and a pattern of cleavage sites for methyl-sensitive restriction endonuclease not found in a nonexpressing sibling. These results lend strong support to the role of DNA methylation in the control of gene expression. Additionally, they explain the lack of phenotype associated with ev-1 as due to a combination of its low expression and defectiveness in pol and env.
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Affiliation(s)
- K F Conklin
- Department of Molecular Biology and Microbiology and Cancer Research Center, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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