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Cadena C, Kornfeld OS, Lee BL, Kayagaki N. Epigenetic and transcriptional control of gasdermins. Semin Immunol 2023; 70:101841. [PMID: 37703611 DOI: 10.1016/j.smim.2023.101841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
Cells undergo an inflammatory programmed lytic cell death called 'pyroptosis' (with the Greek roots 'fiery'), often featuring morphological hallmarks such as large ballooning protrusions and subsequent bursting. Originally described as a caspase-1-dependent cell death in response to bacterial infection, pyroptosis has since been re-defined in 2018 as a cell death dependent on plasma membrane pores by a gasdermin (GSDM) family member [1,2]. GSDMs form pores in the plasma membrane as well as organelle membranes, thereby initiating membrane destruction and the rapid and lytic demise of a cell. The gasdermin family plays a profound role in the execution of pyroptosis in the context of infection, inflammation, tumor pathogenesis, and anti-tumor therapy. More recently, cell-death-independent functions for some of the GSDMs have been proposed. Therefore, a comprehensive understanding of gasdermin gene regulation, including mechanisms in both homeostatic conditions and during inflammation, is essential. In this review, we will summarize the role of gasdermins in pyroptosis and focus our discussion on the transcriptional and epigenetic mechanisms controlling the expression of GSDMs.
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Affiliation(s)
- Cristhian Cadena
- Physiological Chemistry Department, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Opher S Kornfeld
- Physiological Chemistry Department, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Bettina L Lee
- Physiological Chemistry Department, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nobuhiko Kayagaki
- Physiological Chemistry Department, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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2
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Distinct GSDMB protein isoforms and protease cleavage processes differentially control pyroptotic cell death and mitochondrial damage in cancer cells. Cell Death Differ 2023; 30:1366-1381. [PMID: 36899106 PMCID: PMC10154425 DOI: 10.1038/s41418-023-01143-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
Gasdermin (GSDM)-mediated pyroptosis is functionally involved in multiple diseases, but Gasdermin-B (GSDMB) exhibit cell death-dependent and independent activities in several pathologies including cancer. When the GSDMB pore-forming N-terminal domain is released by Granzyme-A cleavage, it provokes cancer cell death, but uncleaved GSDMB promotes multiple pro-tumoral effects (invasion, metastasis, and drug resistance). To uncover the mechanisms of GSDMB pyroptosis, here we determined the GSDMB regions essential for cell death and described for the first time a differential role of the four translated GSDMB isoforms (GSDMB1-4, that differ in the alternative usage of exons 6-7) in this process. Accordingly, we here prove that exon 6 translation is essential for GSDMB mediated pyroptosis, and therefore, GSDMB isoforms lacking this exon (GSDMB1-2) cannot provoke cancer cell death. Consistently, in breast carcinomas the expression of GSDMB2, and not exon 6-containing variants (GSDMB3-4), associates with unfavourable clinical-pathological parameters. Mechanistically, we show that GSDMB N-terminal constructs containing exon-6 provoke cell membrane lysis and a concomitant mitochondrial damage. Moreover, we have identified specific residues within exon 6 and other regions of the N-terminal domain that are important for GSDMB-triggered cell death as well as for mitochondrial impairment. Additionally, we demonstrated that GSDMB cleavage by specific proteases (Granzyme-A, Neutrophil Elastase and caspases) have different effects on pyroptosis regulation. Thus, immunocyte-derived Granzyme-A can cleave all GSDMB isoforms, but in only those containing exon 6, this processing results in pyroptosis induction. By contrast, the cleavage of GSDMB isoforms by Neutrophil Elastase or caspases produces short N-terminal fragments with no cytotoxic activity, thus suggesting that these proteases act as inhibitory mechanisms of pyroptosis. Summarizing, our results have important implications for understanding the complex roles of GSDMB isoforms in cancer or other pathologies and for the future design of GSDMB-targeted therapies.
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3
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Lee DH, Bae WH, Ha H, Park EG, Lee YJ, Kim WR, Kim HS. Z-DNA-Containing Long Terminal Repeats of Human Endogenous Retrovirus Families Provide Alternative Promoters for Human Functional Genes. Mol Cells 2022; 45:522-530. [PMID: 35950452 PMCID: PMC9385571 DOI: 10.14348/molcells.2022.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/16/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022] Open
Abstract
Transposable elements (TEs) account for approximately 45% of the human genome. TEs have proliferated randomly and integrated into functional genes during hominoid radiation. They appear as right-handed B-DNA double helices and slightly elongated left-handed Z-DNAs. Human endogenous retrovirus (HERV) families are widely distributed in human chromosomes at a ratio of 8%. They contain a 5'-long terminal repeat (LTR)-gag-pol-env-3'-LTR structure. LTRs contain the U3 enhancer and promoter region, transcribed R region, and U5 region. LTRs can influence host gene expression by acting as regulatory elements. In this review, we describe the alternative promoters derived from LTR elements that overlap Z-DNA by comparing Z-hunt and DeepZ data for human functional genes. We also present evidence showing the regulatory activity of LTR elements containing Z-DNA in GSDML. Taken together, the regulatory activity of LTR elements with Z-DNA allows us to understand gene function in relation to various human diseases.
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Affiliation(s)
- Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Hongseok Ha
- Division of Life Sciences, Korea University, Seoul 02841, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46231, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
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Sarrió D, Martínez-Val J, Molina-Crespo Á, Sánchez L, Moreno-Bueno G. The multifaceted roles of gasdermins in cancer biology and oncologic therapies. Biochim Biophys Acta Rev Cancer 2021; 1876:188635. [PMID: 34656686 DOI: 10.1016/j.bbcan.2021.188635] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/28/2021] [Accepted: 10/10/2021] [Indexed: 12/18/2022]
Abstract
The involvement of the Gasdermin (GSDM) protein family in cancer and other pathologies is one of the hottest topics in biomedical research. There are six GSDMs in humans (GSDMA, B, C, D, GSDME/DFNA5 and PJVK/DFNB59) and, except PJVK, they can trigger cell death mostly by pyroptosis (a form of lytic and pro-inflammatory cell death) but also other mechanisms. The exact role of GSDMs in cancer is intricate, since depending on the biological context, these proteins have diverse cell-death dependent and independent functions, exhibit either pro-tumor or anti-tumor functions, and promote either sensitization or resistance to oncologic treatments. In this review we provide a comprehensive overview on the multifaceted roles of the GSDMs in cancer, and we critically discuss the possibilities of exploiting GSDM functions as determinants of anti-cancer treatment and as novel therapeutic targets, with special emphasis on innovative GSDM-directed nano-therapies. Finally, we discuss the issues to be resolved before GSDM-mediated oncologic therapies became a reality at the clinical level.
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Affiliation(s)
- David Sarrió
- Biochemistry Department, UAM, & IIBm "Alberto Sols" CSIC-UAM, c/ Arzobispo Morcillo 4, 28029 Madrid, Spain.; Centro de Investigación Biomédica en Red, área de Cáncer (CIBERONC), c/ Melchor Fernández Almagro 3, 28029 Madrid, Spain..
| | - Jeannette Martínez-Val
- Zoology, Genetics and Physical Anthropology Department, Santiago de Compostela University, Avda/ Alfonso X O Sabio s/n, 27002 Lugo, Spain
| | - Ángela Molina-Crespo
- Biochemistry Department, UAM, & IIBm "Alberto Sols" CSIC-UAM, c/ Arzobispo Morcillo 4, 28029 Madrid, Spain.; Centro de Investigación Biomédica en Red, área de Cáncer (CIBERONC), c/ Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Laura Sánchez
- Zoology, Genetics and Physical Anthropology Department, Santiago de Compostela University, Avda/ Alfonso X O Sabio s/n, 27002 Lugo, Spain
| | - Gema Moreno-Bueno
- Biochemistry Department, UAM, & IIBm "Alberto Sols" CSIC-UAM, c/ Arzobispo Morcillo 4, 28029 Madrid, Spain.; Centro de Investigación Biomédica en Red, área de Cáncer (CIBERONC), c/ Melchor Fernández Almagro 3, 28029 Madrid, Spain.; MD Anderson Cancer Center Foundation, c/ Arturo Soria 270, 28033 Madrid, Spain..
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5
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Bourdonnay E, Henry T. Transcriptional and Epigenetic Regulation of Gasdermins. J Mol Biol 2021; 434:167253. [PMID: 34537234 DOI: 10.1016/j.jmb.2021.167253] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/26/2021] [Accepted: 09/09/2021] [Indexed: 12/29/2022]
Abstract
Gasdermins (GSDM) are a family of six homologous proteins (GSDMA to E and Pejvakin) in humans. GSDMA-E are pore-forming proteins targeting the plasma membrane to trigger a rapid cell death termed pyroptosis or bacterial membranes to promote antibacterial immune defenses. Activation of GSDM relies on a proteolytic cleavage but is highly dependent on GSDM expression levels. The different GSDM genes have tissue-specific expression pattern although metabolic, environmental signals, cell stress and numerous cytokines modulate their expression levels in tissues. Furthermore, expression of GSDM genes can be modulated by polymorphisms and have been associated with susceptibility to asthma, inflammatory bowel diseases and rhinovirus wheezing illness. Finally, the expression level of GSDMs controls the balance between apoptosis and pyroptosis affecting both the response and the toxicity to chemotactic drugs and antitumoral treatments. Numerous cancer demonstrate positive or negative modulation of GSDM expression levels correlating with distinct tumor-specific prognosis. In this review, we present the transcriptional and epigenetic mechanisms controlling GSDM levels and their functional consequences in asthma, infection, cancers and inflammatory bowel disease to highlight how this first layer of regulations has key consequences on disease susceptibility and response to treatment.
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Affiliation(s)
- Emilie Bourdonnay
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007 Lyon, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007 Lyon, France.
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Li L, Li Y, Bai Y. Role of GSDMB in Pyroptosis and Cancer. Cancer Manag Res 2020; 12:3033-3043. [PMID: 32431546 PMCID: PMC7201009 DOI: 10.2147/cmar.s246948] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/04/2020] [Indexed: 12/14/2022] Open
Abstract
Gasdermin B (GSDMB) belongs to the gasdermin (GSDM) family which may adopt different mechanisms of intramolecular domain interactions to modulate their lipid-binding and pore-forming activities. The GSDM family has regulatory functions in cell proliferation and differentiation, especially in pyroptosis process. Pyroptosis is a pro-inflammatory form of regulated cell death and is designed to attract a nonspecific innate response to the site of infection. For cancer cells, the activation of pyroptosis may promote cell death and exert anticancer properties. Also, recent studies have observed the pyroptosis-like features in GSDMB and some researches have shown that GSDMB overexpression occurred in several kinds of cancers; these findings bring a contradiction with the participation of GSDMB in pyroptosis. Although people pay less attention to GSDMB, it still has some essential research value. It is a paradox that GSDMB might participate in programmed cell death, which might put forward a research direction of therapeutic targets for cancer. Here, we review the possible progress of how GSDMB participated in this inflammatory regulation mechanistically and the potential functions of GSDMB in cancer.
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Affiliation(s)
- Lisha Li
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, People's Republic of China
| | - Yanjing Li
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, People's Republic of China
| | - Yuxian Bai
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, People's Republic of China
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Garcia-Montojo M, Doucet-O'Hare T, Henderson L, Nath A. Human endogenous retrovirus-K (HML-2): a comprehensive review. Crit Rev Microbiol 2018; 44:715-738. [PMID: 30318978 DOI: 10.1080/1040841x.2018.1501345] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The human genome contains a large number of retroviral elements acquired over the process of evolution, some of which are specific to primates. However, as many of these are defective or silenced through epigenetic changes, they were historically considered "junk DNA" and their potential role in human physiology or pathological circumstances have been poorly studied. The most recently acquired, human endogenous retrovirus-K (HERV-K), has multiple copies in the human genome and some of them have complete open reading frames that are transcribed and translated, especially in early embryogenesis. Phylogenetically, HERV-K is considered a supergroup of viruses. One of the subtypes, termed HML-2, seems to be the most active and hence, it is the best studied. Aberrant expression of HML-2 in adult tissues has been associated with certain types of cancer and with neurodegenerative diseases. This review discusses the discovery of these viruses, their classification, structure, regulation and potential for replication, physiological roles, and their involvement in disease pathogenesis. Finally, it presents different therapeutic approaches being considered to target these viruses.
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Affiliation(s)
- Marta Garcia-Montojo
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Tara Doucet-O'Hare
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Lisa Henderson
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Avindra Nath
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
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Lutkowska A, Roszak A, Lianeri M, Sowińska A, Sotiri E, Jagodziński PP. Analysis of rs8067378 Polymorphism in the Risk of Uterine Cervical Cancer from a Polish Population and its Impact on Gasdermin B Expression. Mol Diagn Ther 2017; 21:199-207. [PMID: 28120299 PMCID: PMC5355524 DOI: 10.1007/s40291-017-0256-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE We studied the role of the NC_000017.10:g.38051348A>G (rs8067378) single nucleotide polymorphism (SNP) located 9.5 kb downstream of gasdermin B (GSDMB), in the development and progression of cervical squamous cell carcinomas (SCC). METHODS Using high-resolution melting curve analysis, we genotyped this SNP in patients with cervical SCC (n = 486) and controls (n = 511) from the Polish Caucasian population. Logistic regression analysis was used to adjust for the effect of confounders such as age, parity, oral contraceptive use, tobacco smoking, and menopausal status. The effect of this SNP on the expression of GSDMB was studied by reverse transcription and quantitative real-time polymerase chain reaction analysis of GSDMB transcript levels in SCC tissues. RESULTS For all patients with SCC, the p trend value calculated for rs8067378 was statistically significant (p trend = 0.0019). The adjusted odds ratio for the G/G vs. A/A genotype was 1.304 (95% confidence interval 1.080-1.574, p = 0.0057) and the adjusted odds ratio for the G/A + G/G vs. A/A genotype was 1.444 (95% confidence interval 1.064-1.959, p = 0.0181). We also found a significant association of the rs8067378 SNP with tumor stages III, IV, and grade of differentiation G3, and with parity, oral contraceptive use, smoking, and women of postmenopausal age. We found increased GSDMB1 isoform transcripts in the cancerous and non-cancerous tissues from carriers of the G allele vs. carriers of the A/A genotype. CONCLUSIONS The rs8067378 SNP variants may increase the expression of GSDMB and the risk of the development and progression of cervical SCC.
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Affiliation(s)
- Anna Lutkowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland
| | - Andrzej Roszak
- Department of Radiotherapy and Gynecological Oncology, Greater Poland Cancer Center, Poznań, Poland.,Department of Electroradiology, Poznań University of Medical Sciences, Poznań, Poland
| | - Margarita Lianeri
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland
| | - Anna Sowińska
- Department of Computer Science and Statistics, Poznań University of Medical Sciences, Poznań, Poland
| | - Emianka Sotiri
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland
| | - Pawel P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland.
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Das S, Miller M, Broide DH. Chromosome 17q21 Genes ORMDL3 and GSDMB in Asthma and Immune Diseases. Adv Immunol 2017; 135:1-52. [PMID: 28826527 DOI: 10.1016/bs.ai.2017.06.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chromosome 17q21 contains a cluster of genes including ORMDL3 and GSDMB, which have been highly linked to asthma in genome-wide association studies. ORMDL3 is localized to the endoplasmic reticulum and regulates downstream pathways including sphingolipids, metalloproteases, remodeling genes, and chemokines. ORMDL3 inhibits serine palmitoyl-CoA transferase, the rate-limiting enzyme for sphingolipid biosynthesis. In addition, ORMDL3 activates the ATF6α branch of the unfolded protein response which regulates SERCA2b and IL-6, pathways of potential importance to asthma. The SNP-linking chromosome 17q21 to asthma is associated with increased ORMDL3 and GSDMB expression. Mice expressing either increased levels of human ORMDL3, or human GSDMB, have an asthma phenotype characterized by increased airway responsiveness and increased airway remodeling (increased smooth muscle and fibrosis) in the absence of airway inflammation. GSDMB regulates expression of 5-LO and TGF-β1 which are known pathways involved in the pathogenesis of asthma. GSDMB is one of four members of the GSDM family (GSDMA, GSDMB, GSDMC, and GSDMD). GSDMD (located on chromosome 8q24 and not linked to asthma) has emerged as a key mediator of pyroptosis. GSDMD is a key component of the NLPR3 inflammasome and is required for its activation. GSDMD undergoes proteolytic cleavage by caspase-1 to release its N-terminal fragment, which in turn mediates pyroptosis and IL-1β secretion. Chromosome 17q21 has not only been linked to asthma but also to type 1 diabetes, inflammatory bowel disease, and primary biliary cirrhosis suggesting that future insights into the biology of genes located in this region will increase our understanding of these diseases.
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Affiliation(s)
- Sudipta Das
- University of California, San Diego, CA, United States
| | - Marina Miller
- University of California, San Diego, CA, United States
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Broecker F, Horton R, Heinrich J, Franz A, Schweiger MR, Lehrach H, Moelling K. The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. Mob DNA 2016; 7:25. [PMID: 27980690 PMCID: PMC5142424 DOI: 10.1186/s13100-016-0081-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/19/2016] [Indexed: 02/06/2023] Open
Abstract
Background Human endogenous retroviruses (HERVs) constitute 8% of the human genome and contribute substantially to the transcriptome. HERVs have been shown to generate RNAs that modulate host gene expression. However, experimental evidence for an impact of these regulatory transcripts on the cellular phenotype has been lacking. Results We characterized the previously little described HERV-K(HML-10) endogenous retrovirus family on a genome-wide scale. HML-10 invaded the ancestral genome of Old World monkeys about 35 Million years ago and is enriched within introns of human genes when compared to other HERV families. We show that long terminal repeats (LTRs) of HML-10 exhibit variable promoter activity in human cancer cell lines. One identified HML-10 LTR-primed RNA was in opposite orientation to the pro-apoptotic Death-associated protein 3 (DAP3). In HeLa cells, experimental inactivation of HML-10 LTR-primed transcripts induced DAP3 expression levels, which led to apoptosis. Conclusions Its enrichment within introns suggests that HML-10 may have been evolutionary co-opted for gene regulation more than other HERV families. We demonstrated such a regulatory activity for an HML-10 RNA that suppressed DAP3-mediated apoptosis in HeLa cells. Since HML-10 RNA appears to be upregulated in various tumor cell lines and primary tumor samples, it may contribute to evasion of apoptosis in malignant cells. However, the overall weak expression of HML-10 transcripts described here raises the question whether our result described for HeLa represent a rare event in cancer. A possible function in other cells or tissues requires further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0081-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Felix Broecker
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland ; Current affiliation: Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Roger Horton
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jochen Heinrich
- Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland
| | - Alexandra Franz
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Current affiliation: University of Zurich, Institute of Molecular Life Sciences, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Michal-Ruth Schweiger
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Current affiliation: Functional Epigenomics, CCG, Cologne University Hospital, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Hans Lehrach
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Dahlem Centre for Genome Research and Medical Systems Biology, Fabeckstr. 60-62, 14195 Berlin, Germany
| | - Karin Moelling
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland
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Sokol M, Jessen KM, Pedersen FS. Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses. APMIS 2016; 124:127-39. [PMID: 26818267 DOI: 10.1111/apm.12477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/12/2015] [Indexed: 12/13/2022]
Abstract
Several studies have shown that human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively HERVs) impose direct regulation on human genes through enhancer and promoter motifs present in their long terminal repeats (LTRs). Although chimeric transcription in which novel gene isoforms containing retroviral and human sequence are transcribed from viral promoters are commonly associated with disease, regulation by HERVs is beneficial in other settings; for example, in human testis chimeric isoforms of TP63 induced by an ERV9 LTR protect the male germ line upon DNA damage by inducing apoptosis, whereas in the human globin locus the γ- and β-globin switch during normal hematopoiesis is mediated by complex interactions of an ERV9 LTR and surrounding human sequence. The advent of deep sequencing or next-generation sequencing (NGS) has revolutionized the way researchers solve important scientific questions and develop novel hypotheses in relation to human genome regulation. We recently applied next-generation paired-end RNA-sequencing (RNA-seq) together with chromatin immunoprecipitation with sequencing (ChIP-seq) to examine ERV9 chimeric transcription in human reference cell lines from Encyclopedia of DNA Elements (ENCODE). This led to the discovery of advanced regulation mechanisms by ERV9s and other HERVs across numerous human loci including transcription of large gene-unannotated genomic regions, as well as cooperative regulation by multiple HERVs and non-LTR repeats such as Alu elements. In this article, well-established examples of human gene regulation by HERVs are reviewed followed by a description of paired-end RNA-seq, and its application in identifying chimeric transcription genome-widely. Based on integrative analyses of RNA-seq and ChIP-seq, data we then present novel examples of regulation by ERV9s of tumor suppressor genes CADM2 and SEMA3A, as well as transcription of an unannotated region. Taken together, this article highlights the high suitability of contemporary sequencing methods in future analyses of human biology in relation to evolutionary acquired retroviruses in the human genome.
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Affiliation(s)
- Martin Sokol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Finn Skou Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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Nam GH, Gim JA, Lee HE, Kim WJ, Jung H, Kim W, Kim HS. Expression and promoter activity of endogenous retroviruses in the Olive flounder (Paralichthys olivaceus). Genes Genomics 2016. [DOI: 10.1007/s13258-016-0404-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Saeki N, Komatsuzaki R, Chiwaki F, Yanagihara K, Sasaki H. A GSDMB enhancer-driven HSV thymidine kinase-expressing vector for controlling occult peritoneal dissemination of gastric cancer cells. BMC Cancer 2015; 15:439. [PMID: 26016667 PMCID: PMC4446855 DOI: 10.1186/s12885-015-1436-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 05/13/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Gastric cancer (GC) is one of the major malignant diseases worldwide, especially in Asia, and Japan and Korea have the highest incidence in the world. Because most of the cases that are refractory to therapies die due to peritoneal dissemination (PD) of the cancer cells, controlling PD is important for patient survival. GSDMB is a member of the gasdermin gene family. Because GSDMB is expressed in many types of cancer, including GC, it is likely that the gene contains a regulatory region that is utilized for therapy of occult PD through cancer cell-specific expression of cytotoxic genes. METHODS We performed reporter assays to identify the regulatory region for the cancer cell-specific expression. We also constructed a lentiviral therapeutic vector that expresses herpes simplex virus thymidine kinase (HSVtk) in a GC cell-specific manner, and tested it in a mouse model of PD. RESULTS We identified the regulatory region at +496 to +989 from the GSDMB transcription start site and designated it as a GSDMB enhancer. The lentiviral therapeutic vector suppressed proliferation of a GC cell line, 60As6, in vitro in the presence of ganciclovir, and intraperitoneal administration of the vector prolonged the survival term of mice that were intraperitoneally inoculated with 60As6 one week prior to the administration. CONCLUSIONS The GSDMB-driven HSVtk expression vector had a therapeutic effect on the occult PD model mice. This strategy can potentially be used to treat GC patients with PD.
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Affiliation(s)
- Norihisa Saeki
- Division of Genetics, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Rie Komatsuzaki
- Department of Translational Oncology, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Fumiko Chiwaki
- Department of Translational Oncology, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Kazuyoshi Yanagihara
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center Hospital East, Kashiwanoha 6-5-1, Kashiwa, Chiba, 277-8577, Japan.
| | - Hiroki Sasaki
- Department of Translational Oncology, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo, 104-0045, Japan.
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14
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Ayarpadikannan S, Lee HE, Han K, Kim HS. Transposable element-driven transcript diversification and its relevance to genetic disorders. Gene 2015; 558:187-94. [PMID: 25617522 DOI: 10.1016/j.gene.2015.01.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 01/13/2015] [Accepted: 01/20/2015] [Indexed: 12/14/2022]
Abstract
The human genome project and subsequent gene annotation projects have shown that the human genome contains 22,000-25,000 functional genes. Therefore, it is believed that the diversity of protein repertoire is achieved by the alternative splicing (AS) mechanism. Transposable elements (TEs) are mobile in nature and can therefore alter their position in the genome. The insertion of TEs into a new gene region can result in AS of a particular transcript through various mechanisms, including intron retention, and alternative donor or acceptor splice sites. TE-derived AS is thought to have played a part in primate evolution and in hominid radiation. However, TE-derived AS or genetic instability may sometimes result in genetic disorders. For the past two decades, numerous studies have been performed on TEs and their role in genomes. Accumulating evidence shows that the term 'junk DNA', previously used for TEs is a misnomer. Recent research has indicated that TEs may have clinical potential. However, to explore the feasibility of using TEs in clinical practice, additional studies are required. This review summarizes the available literature on TE-derived AS, alternative promoter, and alternative polyadenylation. The review covers the effects of TEs on coding genes and their clinical implications, and provides our perspectives and directions for future research.
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Affiliation(s)
- Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea.
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15
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Lee HE, Ayarpadikannan S, Kim HS. Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates. Genes Genet Syst 2015; 90:245-57. [DOI: 10.1266/ggs.15-00016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
- Genetic Engineering Institute, Pusan National University
| | - Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
- Genetic Engineering Institute, Pusan National University
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16
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Bae JH, Eo J, Kim TO, Yi JM. Biological changes of transposable elements by radiation: recent progress. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0256-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Lim SL, Kortschak RD, Adelson DL. Discovery of a novel long terminal repeat (LTR2i_SS) in Sus Scrofa. Anim Genet 2014; 45:367-72. [DOI: 10.1111/age.12138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Sim L. Lim
- School of Molecular and Biomedical Science; The University of Adelaide; North Terrace, Adelaide 5005 SA Australia
| | - R. Daniel Kortschak
- School of Molecular and Biomedical Science; The University of Adelaide; North Terrace, Adelaide 5005 SA Australia
| | - David L. Adelson
- School of Molecular and Biomedical Science; The University of Adelaide; North Terrace, Adelaide 5005 SA Australia
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18
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Hergueta-Redondo M, Sarrió D, Molina-Crespo Á, Megias D, Mota A, Rojo-Sebastian A, García-Sanz P, Morales S, Abril S, Cano A, Peinado H, Moreno-Bueno G. Gasdermin-B promotes invasion and metastasis in breast cancer cells. PLoS One 2014; 9:e90099. [PMID: 24675552 PMCID: PMC3967990 DOI: 10.1371/journal.pone.0090099] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/29/2014] [Indexed: 12/21/2022] Open
Abstract
Gasdermin B (GSDMB) belongs to the Gasdermin protein family that comprises four members (GSDMA-D). Gasdermin B expression has been detected in some tumor types such as hepatocarcinomas, gastric and cervix cancers; and its over-expression has been related to tumor progression. At least four splicing isoforms of GSDMB have been identified, which may play differential roles in cancer. However, the implication of GSDMB in carcinogenesis and tumor progression is not well understood. Here, we uncover for the first time the functional implication of GSDMB in breast cancer. Our data shows that high levels of GSDMB expression is correlated with reduced survival and increased metastasis in breast cancer patients included in an expression dataset (>1,000 cases). We demonstrate that GSDMB is upregulated in breast carcinomas compared to normal breast tissue, being the isoform 2 (GSDMB-2) the most differentially expressed. In order to evaluate the functional role of GSDMB in breast cancer two GSDMB isoforms were studied (GSDMB-1 and GSDMB-2). The overexpression of both isoforms in the MCF7 breast carcinoma cell line promotes cell motility and invasion, while its silencing in HCC1954 breast carcinoma cells decreases the migratory and invasive phenotype. Importantly, we demonstrate that both isoforms have a differential role on the activation of Rac-1 and Cdc-42 Rho-GTPases. Moreover, our data support that GSMDB-2 induces a pro-tumorigenic and pro-metastatic behavior in mouse xenograft models as compared to GSDMB-1. Finally, we observed that although both GSDMB isoforms interact in vitro with the chaperone Hsp90, only the GSDMB-2 isoform relies on this chaperone for its stability. Taken together, our results provide for the first time evidences that GSDMB-2 induces invasion, tumor progression and metastasis in MCF7 cells and that GSDMB can be considered as a new potential prognostic marker in breast cancer.
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MESH Headings
- Aged
- Aged, 80 and over
- Animals
- Breast Neoplasms/genetics
- Breast Neoplasms/mortality
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/mortality
- Carcinoma, Ductal, Breast/pathology
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Datasets as Topic
- Disease Models, Animal
- Female
- Gelatin/metabolism
- Gene Expression
- Genes, Reporter
- HSP90 Heat-Shock Proteins/metabolism
- Heterografts
- Humans
- Mice
- Middle Aged
- Molecular Imaging
- Neoplasm Grading
- Neoplasm Invasiveness
- Neoplasm Metastasis
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Phenotype
- Prognosis
- Protein Binding
- Proteolysis
- rho GTP-Binding Proteins/metabolism
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Affiliation(s)
- Marta Hergueta-Redondo
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - David Sarrió
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Ángela Molina-Crespo
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Diego Megias
- Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid, Spain
| | - Alba Mota
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | | | | | - Saleta Morales
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Sandra Abril
- Hospital MD Anderson Cancer Centre, Madrid, Spain
| | - Amparo Cano
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Héctor Peinado
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Gema Moreno-Bueno
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
- Fundación MD Anderson Internacional, Madrid, Spain
- * E-mail:
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19
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Yu HL, Zhao ZK, Zhu F. The role of human endogenous retroviral long terminal repeat sequences in human cancer (Review). Int J Mol Med 2013; 32:755-62. [PMID: 23900638 DOI: 10.3892/ijmm.2013.1460] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 05/30/2013] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retrovirus (HERV) and solitary long terminal repeats (LTRs) constitute 8% of the human genome. Although most HERV genes are partially deleted and not intact, HERV LTRs comprise features including promoters, enhancers, selective splicer sites and polyadenylation sites in order to regulate the expression of neighboring genes. Owing to the genetic instability of LTRs, their wide distributions along human chromosomes are not only non-random, but are also correlated with gene density. Considerable evidence indicates that HERV LTRs regulate the expression of their adjacent viral and cellular genes in placental development and tumorigenesis. However, the regulatory mechanism of HERV LTRs on the expression of its neighboring cancer-associated genes in human cancers remains to be elucidated. Insertional mutagenesis, recombination and polymorphism are three principal factors of LTR that contribute to its genetic instability. Moreover, genetic instability, hypomethylation, transactivation and the antisense transcript of LTRs enhance the activity of LTRs and regulate the expression of their adjacent genes in human cancers. Therefore, in the present review, we examined the mechanism of HERV LTRs in tumorigenesis in combination with the structure and function of LTRs.
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Affiliation(s)
- Hong-Lian Yu
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, Hubei 430071, PR China
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20
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Jung YD, Ahn K, Kim YJ, Bae JH, Lee JR, Kim HS. Retroelements: molecular features and implications for disease. Genes Genet Syst 2013; 88:31-43. [PMID: 23676708 DOI: 10.1266/ggs.88.31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic genomes comprise numerous retroelements that have a major impact on the structure and regulation of gene function. Retroelements are regulated by epigenetic controls, and they generate multiple miRNAs that are involved in the induction and progression of genomic instability. Elucidation of the biological roles of retroelements deserves continuous investigation to better understand their evolutionary features and implications for disease.
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Affiliation(s)
- Yi-Deun Jung
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
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21
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Sequence periodic pattern of HERV LTRs: A matrix simulation algorithm. J Biosci 2012; 37:19-24. [DOI: 10.1007/s12038-012-9182-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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22
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Abrarova ND, Stoukacheva EA, Pleshkan VV, Vinogradova TV, Sverdlov ED. Functional analysis of the HERV-K LTR residing in the KIAA1245/NBPF subfamily genes. Mol Biol 2010. [DOI: 10.1134/s0026893310040084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Komiyama H, Aoki A, Tanaka S, Maekawa H, Kato Y, Wada R, Maekawa T, Tamura M, Shiroishi T. Alu-derived cis-element regulates tumorigenesis-dependent gastric expression of GASDERMIN B (GSDMB). Genes Genet Syst 2010; 85:75-83. [PMID: 20410667 DOI: 10.1266/ggs.85.75] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
GASDERMIN B (GSDMB) belongs to the novel gene family GASDERMIN (GSDM). All GSDM family members are located in amplicons, genomic regions often amplified during cancer development. Given that GSDMB is highly expressed in cancerous cells and the locus resides in an amplicon, GSDMB may be involved in cancer development and/or progression. However, only limited information is available on GSDMB expression in tissues, normal and cancerous, from cancer patients. Furthermore, the molecular mechanisms that regulate GSDMB expression in gastric tissues are poorly understood. We investigated the spatiotemporal expression patterns of GSDMB in gastric cancer patients and the 5' regulatory sequences upstream of GSDMB. GSDMB was not expressed in the majority of normal gastric-tissue samples, and the expression level was very low in the few normal samples with GSDMB expression. Most pre-cancer samples showed moderate GSDMB expression, and most cancerous samples showed augmented GSDMB expression. Analysis of genome sequences revealed that an Alu element resides in the 5' region upstream of GSDMB. Reporter assays using intact, deleted, and mutated Alu elements clearly showed that this Alu element positively regulates GSDMB expression and that a putative IKZF binding motif in this element is crucial to upregulate GSDMB expression.
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Affiliation(s)
- Hiromitsu Komiyama
- Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 111 Yata, Mishima, Shizuoka 411-8540, Japan
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24
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Li M, Wang L, Peng Y, Wang JC, Zhou LH. Knockdown of the neuronal nitric oxide synthase gene retard the development of the cerebellar granule neurons in vitro. Dev Dyn 2010; 239:474-81. [PMID: 20014403 DOI: 10.1002/dvdy.22189] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The role of endogenous neuronal nitric oxide synthase (nNOS) gene in the development of cerebellar granule neurons (CGNs) is conflicting. Here, we tested the effect of antisense oligos (AS-ODN) on the endogenous nNOS gene and the development of the CGNs in vitro. The expression of nNOS increased in a development-dependent pattern both in terms of mRNA and protein. AS-ODN down-regulated nNOS gene, but in a posttranscriptional manner. Knockdown of nNOS protein decreased the viability of the CGNs from 7 to 13 days in culture (DIC). This activity of AS-ODN was mimicked by nNOS inhibitor I. The antagonist (nNOSi, MK-801, or ODQ) -induced decrease of cell viability was normalized by the provision of the sodium nitroprusside, an NO donor. This study provides direct evidence that endogenous nNOS, mainly by means of its principal product NO, plays an active role in sustaining the survival of developing CGNs at transition from differentiation to maturation.
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Affiliation(s)
- Mei Li
- Department of Neurology, The Second Affiliated Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
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25
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Jintaridth P, Mutirangura A. Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences. Physiol Genomics 2010; 41:194-200. [PMID: 20145203 DOI: 10.1152/physiolgenomics.00146.2009] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Interspersed repetitive sequences (IRSs) are a major contributor to genome size and may contribute to cellular functions. IRSs are subdivided according to size and functionally related structures into short interspersed elements, long interspersed elements (LINEs), DNA transposons, and LTR-retrotransposons. Many IRSs may produce RNA and regulate genes by a variety of mechanisms. The majority of DNA methylation occurs in IRSs and is believed to suppress IRS activities. Global hypomethylation, or the loss of genome-wide methylation, is a common epigenetic event not only in senescent cells but also in cancer cells. Loss of LINE-1 methylation has been characterized in many cancers. Here, we evaluated the methylation levels of peripheral blood mononuclear cells of LINE-1, Alu, and human endogenous retrovirus K (HERV-K) in 177 samples obtained from volunteers between 20 and 88 yr of age. Age was negatively associated with methylation levels of Alu (r = -0.452, P < 10(-3)) and HERV-K (r = -0.326, P < 10(-3)) but not LINE-1 (r = 0.145, P = 0.055). Loss of methylation of Alu occurred during ages 34-68 yr, and loss of methylation of HERV-K occurred during ages 40-63 yr and again during ages 64-83 yr. Interestingly, methylation of Alu and LINE-1 are directly associated, particularly at ages 49 yr and older (r = 0.49, P < 10(-3)). Therefore, only some types of IRSs lose methylation at certain ages. Moreover, Alu and HERV-K become hypomethylated differently. Finally, there may be several mechanisms of global methylation. However, not all of these mechanisms are age-dependent. This finding may lead to a better understanding of not only the biological causes and consequences of genome-wide hypomethylation but also the role of IRSs in the aging process.
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Affiliation(s)
- Pornrutsami Jintaridth
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University
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26
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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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27
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Unique functions of repetitive transcriptomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 285:115-88. [PMID: 21035099 DOI: 10.1016/b978-0-12-381047-2.00003-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Repetitive sequences occupy a huge fraction of essentially every eukaryotic genome. Repetitive sequences cover more than 50% of mammalian genomic DNAs, whereas gene exons and protein-coding sequences occupy only ~3% and 1%, respectively. Numerous genomic repeats include genes themselves. They generally encode "selfish" proteins necessary for the proliferation of transposable elements (TEs) in the host genome. The major part of evolutionary "older" TEs accumulated mutations over time and fails to encode functional proteins. However, repeats have important functions also on the RNA level. Repetitive transcripts may serve as multifunctional RNAs by participating in the antisense regulation of gene activity and by competing with the host-encoded transcripts for cellular factors. In addition, genomic repeats include regulatory sequences like promoters, enhancers, splice sites, polyadenylation signals, and insulators, which actively reshape cellular transcriptomes. TE expression is tightly controlled by the host cells, and some mechanisms of this regulation were recently decoded. Finally, capacity of TEs to proliferate in the host genome led to the development of multiple biotechnological applications.
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28
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Gogvadze E, Buzdin A. Retroelements and their impact on genome evolution and functioning. Cell Mol Life Sci 2009; 66:3727-42. [PMID: 19649766 PMCID: PMC11115525 DOI: 10.1007/s00018-009-0107-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/11/2009] [Accepted: 07/14/2009] [Indexed: 12/31/2022]
Abstract
Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.
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Affiliation(s)
- Elena Gogvadze
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya st, 117997 Moscow, Russia.
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29
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Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 2009; 448:105-14. [PMID: 19577618 DOI: 10.1016/j.gene.2009.06.020] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 06/10/2009] [Accepted: 06/22/2009] [Indexed: 12/24/2022]
Abstract
Gene regulatory changes are thought to be major factors driving species evolution, with creation of new regulatory regions likely being instrumental in contributing to diversity among vertebrates. There is growing appreciation for the role of transposable elements (TEs) in gene regulation and, indeed, laboratory investigations have confirmed many specific examples of mammalian genes regulated by promoters donated by endogenous retroviruses (ERVs) or other TEs. Bioinformatics studies have revealed hundreds of additional instances where this is likely to be the case. Since the long terminal repeats (LTRs) of retroviruses naturally contain abundant transcriptional regulatory signals, roles for ERV LTRs in regulating mammalian genes are eminently plausible. Moreover, it seems reasonable that exaptation of an LTR regulatory module provides opportunities for evolution of new gene regulatory patterns. In this Review we summarize known examples of LTRs that function as human gene alternative promoters, as well as the evidence that LTR exaptation has resulted in a pattern of novel gene expression significantly different from the pattern before LTR insertion or from that of gene orthologs lacking the LTR. Available data suggest that, while new expression patterns can arise as a result of LTR usage, this situation is relatively rare and is largely restricted to the placenta. In many cases, the LTR appears to be a minor, alternative promoter with an expression pattern similar to that of the native promoter(s) and hence likely exerts a subtle overall effect on gene expression. We discuss these findings and offer evolutionary models to explain these trends.
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30
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Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions. J Virol 2009; 83:6098-105. [PMID: 19339349 DOI: 10.1128/jvi.00123-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many phenotypic differences exist between Homo sapiens and its closest relatives, chimpanzees, and these differences can arise as a result of variations in the regulation of certain genes common to these closely related species. Human-specific endogenous retroviruses (HERVs) and their solitary long terminal repeats (LTRs) are probable candidates for such a role due to the presence of regulatory elements, such as enhancers, promoters, splice sites, and polyadenylation signals. In this study we show for the first time that HERVs can participate in the specific antisense regulation of human gene expression owing to their LTR promoter activity. We found that two HERV LTRs situated in the introns of genes SLC4A8 (for sodium bicarbonate cotransporter) and IFT172 (for intraflagellar transport protein 172) in the antisense orientation serve in vivo as promoters for generating RNAs complementary to the exons of enclosing genes. The antisense transcripts formed from LTR promoter were shown to decrease the mRNA level of the corresponding genes. The human-specific regulation of these genes suggests their involvement in the evolutionary process.
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