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Kiełbus M, Czapiński J, Odrzywolski A, Stasiak G, Szymańska K, Kałafut J, Kos M, Giannopoulos K, Stepulak A, Rivero-Müller A. Optogenetics in cancer drug discovery. Expert Opin Drug Discov 2018; 13:459-472. [DOI: 10.1080/17460441.2018.1437138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Michał Kiełbus
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Adrian Odrzywolski
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Grażyna Stasiak
- Department of Experimental Haematooncology, Medical University of Lublin, Lublin, Poland
| | - Kamila Szymańska
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Michał Kos
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Krzysztof Giannopoulos
- Department of Experimental Haematooncology, Medical University of Lublin, Lublin, Poland
- Department of Hematology, St. John’s Cancer Center, Lublin, Poland
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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Burassakarn A, Pientong C, Sunthamala N, Chuerduangphui J, Vatanasapt P, Patarapadungkit N, Kongyingyoes B, Ekalaksananan T. Aberrant gene promoter methylation of E-cadherin, p16 INK4a , p14 ARF , and MGMT in Epstein–Barr virus-associated oral squamous cell carcinomas. Med Oncol 2017; 34:128. [DOI: 10.1007/s12032-017-0983-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 05/24/2017] [Indexed: 12/23/2022]
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Henrich KO, Bender S, Saadati M, Dreidax D, Gartlgruber M, Shao C, Herrmann C, Wiesenfarth M, Parzonka M, Wehrmann L, Fischer M, Duffy DJ, Bell E, Torkov A, Schmezer P, Plass C, Höfer T, Benner A, Pfister SM, Westermann F. Integrative Genome-Scale Analysis Identifies Epigenetic Mechanisms of Transcriptional Deregulation in Unfavorable Neuroblastomas. Cancer Res 2016; 76:5523-37. [PMID: 27635046 DOI: 10.1158/0008-5472.can-15-2507] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 05/29/2016] [Indexed: 11/16/2022]
Abstract
The broad clinical spectrum of neuroblastoma ranges from spontaneous regression to rapid progression despite intensive multimodal therapy. This diversity is not fully explained by known genetic aberrations, suggesting the possibility of epigenetic involvement in pathogenesis. In pursuit of this hypothesis, we took an integrative approach to analyze the methylomes, transcriptomes, and copy number variations in 105 cases of neuroblastoma, complemented by primary tumor- and cell line-derived global histone modification analyses and epigenetic drug treatment in vitro We found that DNA methylation patterns identify divergent patient subgroups with respect to survival and clinicobiologic variables, including amplified MYCN Transcriptome integration and histone modification-based definition of enhancer elements revealed intragenic enhancer methylation as a mechanism for high-risk-associated transcriptional deregulation. Furthermore, in high-risk neuroblastomas, we obtained evidence for cooperation between PRC2 activity and DNA methylation in blocking tumor-suppressive differentiation programs. Notably, these programs could be re-activated by combination treatments, which targeted both PRC2 and DNA methylation. Overall, our results illuminate how epigenetic deregulation contributes to neuroblastoma pathogenesis, with novel implications for its diagnosis and therapy. Cancer Res; 76(18); 5523-37. ©2016 AACR.
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Affiliation(s)
- Kai-Oliver Henrich
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany. k.henrich@dkfz
| | - Sebastian Bender
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany & Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Germany
| | - Maral Saadati
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Daniel Dreidax
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Moritz Gartlgruber
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Chunxuan Shao
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Carl Herrmann
- Division of Theoretical Bioinformatics, German Cancer Research Center, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Germany
| | - Manuel Wiesenfarth
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Martha Parzonka
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Lea Wehrmann
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Emma Bell
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Alica Torkov
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany & Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Germany
| | - Frank Westermann
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany. k.henrich@dkfz
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Decock A, Ongenaert M, Van Criekinge W, Speleman F, Vandesompele J. DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing. Sci Data 2016; 3:160004. [PMID: 26836295 PMCID: PMC4736656 DOI: 10.1038/sdata.2016.4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/04/2016] [Indexed: 02/07/2023] Open
Abstract
Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors by methyl-CpG-binding domain (MBD) sequencing, in order to identify prognostic biomarker candidates. In this data descriptor, we give details on how this data set was generated and which bioinformatics analyses were applied during data processing. Through a series of technical validations, we illustrate that the data are of high quality and that the sequenced fragments represent methylated genomic regions. Furthermore, genes previously described to be methylated in NB are confirmed. As such, these MBD sequencing data are a valuable resource to further study the association of NB risk factors with the NB methylome, and offer the opportunity to integrate methylome data with other -omic data sets on the same tumor samples such as gene copy number and gene expression, also publically available.
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Affiliation(s)
- Anneleen Decock
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan 185, Ghent 9000, Belgium
| | - Maté Ongenaert
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Ghent 9000, Belgium.,MDxHealth, 15279 Alton Parkway, Suite 100, Irvine, California 92618, USA.,NXTGNT, Ghent University, Ottergemsesteenweg 460, Ghent 9000, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan 185, Ghent 9000, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium.,Cancer Research Institute Ghent (CRIG), De Pintelaan 185, Ghent 9000, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan 185, Ghent 9000, Belgium
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DNA methylation patterns in EBV-positive and EBV-negative Hodgkin lymphomas. Cell Oncol (Dordr) 2015; 38:453-62. [PMID: 26350502 DOI: 10.1007/s13402-015-0242-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2015] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Hodgkin lymphoma (HL) is characterized by the presence of Hodgkin and Reed-Sternberg cells. Epstein-Barr virus (EBV) infection is thought to play an important role in the development of HL. Although epigenetic alterations, such as aberrant DNA methylation, are known to contribute to the pathogenesis of various malignancies, little is known about such alterations in HL and their putative relationships with EBV infection. METHODS We investigated promoter methylation patterns of seven tumor-associated genes in 53 primary HL cases using methylation-specific PCR (MS-PCR). Concomitantly, the EBV infection status was assessed using PCR, in situ hybridization and immunohistochemistry. RESULTS The gene promoter hypermethylation frequencies observed were 77.3 % for P16, 58.5 % for RASSF1A, 50.9 % for CDH1, 45.3 % for DAPK, 43.4 % for GSTP1, 37.7 % for SHP1 and 24.3 % for MGMT. SHP1 gene promoter hypermethylation was more frequently observed in patients at extreme ages (i.e., ≤ 15 and >54 years) than in adult patients (p = 0.006) and in patients with B symptoms (p = 0.03). Interestingly, most of the analyzed gene promoters were more frequently hypermethylated in EBV-negative than in EBV-positive cases, in particular the DAPK gene promoter (58 % versus 27 %, p = 0.04). Furthermore, hypermethylation of multiple gene promoters (≥ 3) was encountered more frequently in females than in males (86 % versus 57 %, p = 0.04), whereas EBV-positive cases were more common among males than females (55 % versus 30 %, p = 0.02). CONCLUSIONS Our results indicate that epigenetic changes frequently occur in both EBV-positive and EBV-negative HL. The rates of these changes were found to vary according to clinico-pathological parameters. These observations probably reflect the multitude of factors involved in HL development and the complexity of their interactions with genetic and/or hormonal factors.
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Cortés C, Kozma SC, Tauler A, Ambrosio S. MYCN concurrence with SAHA-induced cell death in human neuroblastoma cells. Cell Oncol (Dordr) 2015; 38:341-52. [PMID: 26306783 DOI: 10.1007/s13402-015-0233-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND In the past, the HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) has been shown to induce apoptosis in several human tumor types, including neuroblastomas. Amplification and over-expression of the MYCN oncogene is a diagnostic hallmark and a poor prognostic indicator in high-risk neuroblastomas. Here, we studied the relationship between MYCN amplification and over-expression and the anti-tumor effect of SAHA to assess whether this drug may serve as a treatment option for high-risk neuroblastomas. METHODS Different human neuroblastoma cell lines, over-expressing or not over-expressing MYCN, were used in this study. Targeted knockdown and exogenous over-expression of MYCN were employed to examine correlations between MYCN expression levels and SAHA responses. After various time periods and concentration exposures to the drug, cell viability was measured by MTS assay, and variations in MYCN mRNA and protein levels were assessed by qPCR and Western blotting, respectively. RESULTS We found that SAHA decreased cell viability in all cell lines tested through apoptosis induction, and that SAHA had a stronger effect on cell lines carrying an amplified MYCN gene. A decrease in MYCN mRNA and protein levels was observed in the SAHA treated cell lines. Subsequent silencing and exogenous over-expression of MYCN changed the proliferation rate of the cells, but did not have any significant impact on the effect of SAHA on the viability of the cells. We also found that SAHA blocked the expression of MYCN and, by doing so, reduced the effects mediated by this protein. CONCLUSIONS Our results suggest that SAHA may be used as a single-drug treatment option for neuroblastomas with an amplified MYCN gene, and as an adjuvant treatment option for all neuroblastomas.
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Affiliation(s)
- Constanza Cortés
- Departament de Bioquímica i Biologia Molecular, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Catalunya, Spain.,Laboratory of Cancer Metabolism, IDIBELL, Hospital Duran i Reynals, L'Hospitalet de Llobregat, Catalunya, 08907, Spain
| | - Sara C Kozma
- Laboratory of Cancer Metabolism, IDIBELL, Hospital Duran i Reynals, L'Hospitalet de Llobregat, Catalunya, 08907, Spain
| | - Albert Tauler
- Departament de Bioquímica i Biologia Molecular, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Catalunya, Spain.,Laboratory of Cancer Metabolism, IDIBELL, Hospital Duran i Reynals, L'Hospitalet de Llobregat, Catalunya, 08907, Spain
| | - Santiago Ambrosio
- Unitat de Bioquímica, Dep. Ciències Fisiològiques II, Facultat de Medicina, Campus Universitari de Bellvitge - IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Catalunya, 08907, Spain.
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Falahi F, Sgro A, Blancafort P. Epigenome engineering in cancer: fairytale or a realistic path to the clinic? Front Oncol 2015; 5:22. [PMID: 25705610 PMCID: PMC4319383 DOI: 10.3389/fonc.2015.00022] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/19/2015] [Indexed: 01/15/2023] Open
Abstract
Epigenetic modifications such as histone post-transcriptional modifications, DNA methylation, and non-protein-coding RNAs organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. These epigenetic modifications are reversible and precisely regulated by epigenetic enzymes. In addition to genetic mutations, epigenetic modifications are highly disrupted in cancer relative to normal tissues. Many epigenetic alterations (epi-mutations) are associated with aberrations in the expression and/or activity of epigenetic enzymes. Thus, epigenetic regulators have emerged as prime targets for cancer therapy. Currently, several inhibitors of epigenetic enzymes (epi-drugs) have been approved for use in the clinic to treat cancer patients with hematological malignancies. However, one potential disadvantage of epi-drugs is their lack of locus-selective specificity, which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome-wide “off-target” effects of the treatment. In the current review, we will first describe the language of epigenetic modifications and their involvement in cancer. Next, we will overview the current strategies for engineering of artificial DNA-binding domains in order to manipulate and ultimately normalize the aberrant landscape of the cancer epigenome (epigenome engineering). Lastly, the potential clinical applications of these emerging genome-engineering approaches will be discussed.
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Affiliation(s)
- Fahimeh Falahi
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Agustin Sgro
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
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Green BB, McKay SD, Kerr DE. Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome. BMC Genomics 2015; 16:30. [PMID: 25623529 PMCID: PMC4312471 DOI: 10.1186/s12864-015-1223-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 11/15/2022] Open
Abstract
Background By comparing fibroblasts collected from animals at 5-months or 16-months of age we have previously found that the cultures from older animals produce much more IL-8 in response to lipopolysaccharide (LPS) stimulation. We now expand this finding by examining whole transcriptome differences in the LPS response between cultures from the same animals at different ages, and also investigate the contribution of DNA methylation to the epigenetic basis for the age-dependent increases in responsiveness. Results Age-dependent differences in IL-8 production by fibroblasts in response to LPS exposure for 24 h were abolished by pretreatment of cultures with a DNA demethylation agent, 5-aza-2′deoxycytidine (AZA). RNA-Seq analysis of fibroblasts collected from the same individuals at either 5 or 16 months of age and exposed in parallel to LPS for 0, 2, and 8 h revealed a robust response to LPS that was much greater in the cultures from older animals. Pro-inflammatory genes including IL-8, IL-6, TNF-α, and CCL20 (among many other immune associated genes), were more highly expressed (FDR < 0.05) in the 16-month old cultures following LPS exposure. Methylated CpG island recovery assay sequencing (MIRA-Seq) revealed numerous methylation peaks spread across the genome, combined with an overall hypomethylation of gene promoter regions, and a remarkable similarity, except for 20 regions along the genome, between the fibroblasts collected at the two ages from the same animals. Conclusions The fibroblast pro-inflammatory response to LPS increases dramatically from 5 to 16 months of age within individual animals. A better understanding of the mechanisms underlying this process could illuminate the physiological processes by which the innate immune response develops and possibly individual variation in innate immune response arises. In addition, although relatively unchanged by age, our data presents a general overview of the bovine fibroblast methylome as a guide for future studies in cattle epigenetics utilizing this cell type. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1223-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin B Green
- Department of Animal Science, University of Vermont, Terrill Hall, 570 Main Street, Burlington, VT, 05405, USA.
| | - Stephanie D McKay
- Department of Animal Science, University of Vermont, Terrill Hall, 570 Main Street, Burlington, VT, 05405, USA.
| | - David E Kerr
- Department of Animal Science, University of Vermont, Terrill Hall, 570 Main Street, Burlington, VT, 05405, USA.
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Oh HR, An CH, Yoo NJ, Lee SH. Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity--a short report. Cell Oncol (Dordr) 2014; 37:455-61. [PMID: 25450519 DOI: 10.1007/s13402-014-0209-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Metabolic reprogramming is an emerging topic in cancer research. However, genetic alterations in genes encoding enzymes involved in amino acid metabolism are largely unknown. The aim of this study was to explore whether genes known to be involved in amino acid metabolism are mutated in gastric cancer (GC) and/or colorectal cancer (CRC). METHODS Through a public database search, we found that a number of genes known to be involved in amino acid metabolism, i.e., AGXT, ALDH2, APIP, MTR, DNMT1, ASH1L, ASPA, CAD, DDC, GCDH, DLD, LAP3, MCEE and MUT, harbor mononucleotide repeats that may serve as mutation targets in cancers exhibiting microsatellite instability (MSI). We assessed these genes for the presence of the mutations in 79 GCs and 124 CRCs using single-strand conformation polymorphism (SSCP) and direct sequencing analyses. RESULTS Using SSCP in conjunction with DNA sequencing we detected frameshift mutations in AGXT (17 cases), ALDH2 (3 cases), APIP (4 cases), MTR (5 cases), DNMT1 (1 case), ASH1L (1 case), ASPA (2 cases), CAD (2 cases), DDC (1 case), GCDH (3 cases), DLD (1 case), LAP3 (1 case), MCEE (5 cases) and MUT (1 case). These mutations were exclusively detected in MSI-high (MSI-H), and not in MSI-low or MSI-stable (MSI-L/MSS) cases. In addition, we analyzed 16 CRCs for the presence of intra-tumor heterogeneity (ITH) and found that two CRCs harbored regional ITH for GCDH frameshift mutations. CONCLUSIONS Our data indicate that genes known to be involved in amino acid metabolism recurrently acquire somatic mutations in MSH-H GCs and MSH-H CRCs and that, in addition, mutation ITH does occur in at least some of these tumors. Together, these data suggest that metabolic reprogramming may play a role in the etiology of MSI-H GCs and CRCs. Our data also suggest that ultra-regional mutation analysis is required for a more comprehensive evaluation of the mutation status in these tumors.
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Affiliation(s)
- Hye Rim Oh
- Departments of Pathology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Socho-gu, Seoul, 137-701, South Korea
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Yiannakopoulou E. Targeting epigenetic mechanisms and microRNAs by aspirin and other non steroidal anti-inflammatory agents - implications for cancer treatment and chemoprevention. Cell Oncol (Dordr) 2014; 37:167-78. [DOI: 10.1007/s13402-014-0175-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2014] [Indexed: 12/21/2022] Open
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Green BB, Kerr DE. Epigenetic contribution to individual variation in response to lipopolysaccharide in bovine dermal fibroblasts. Vet Immunol Immunopathol 2013; 157:49-58. [PMID: 24268632 DOI: 10.1016/j.vetimm.2013.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 10/22/2013] [Accepted: 10/24/2013] [Indexed: 12/17/2022]
Abstract
The innate immune signaling pathway plays a crucial role in the recognition and early response to pathogens associated with disease. Genetic analysis has been unable to completely account for individual variability in the strength of the innate immune response. The aim of this study was to determine the role of the epigenetic markers (DNA methylation or histone acetylation) in controlling bovine gene expression in relation to the response to lipopolysaccharide (LPS). To determine the impact epigenetics may have in controlling innate immunity, dermal fibroblasts from fifteen dairy heifers having previously displayed a differential response to LPS were exposed to 5-aza-2'-deoxycytidine (AZA) and trichostatin A (TSA); de-methylating and hyper-acetylating agents, respectively. The AZA-TSA exposure resulted in a loss of variability between individuals' response to LPS as measured by fibroblast IL-8 protein production. Transcriptomic analysis by microarray was used to elucidate the role of epigenetics in innate immune signaling at 2, 4, and 8h post-LPS exposure. A subset of genes displayed altered expression due to AZA-TSA alone, suggesting an epigenetic regulatory element modifying expression under normal conditions. Treatment with AZA-TSA also led to increased expression of IL-8 (7.0-fold), IL-6 (2.5-fold), TNF-α (1.6-fold), and serum amyloid A 3 (SAA3) (11.3-fold) among other genes compared to control cultures for at least one of the measured times following LPS exposure. These data support the conclusion that epigenetic regulation significantly alters LPS-induced responses and constitutive cytokine gene expression.
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Affiliation(s)
- Benjamin B Green
- Terrill Hall, University of Vermont, 570 Main Street, Burlington 05405, United States
| | - David E Kerr
- Terrill Hall, University of Vermont, 570 Main Street, Burlington 05405, United States.
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