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Chen L, Cheng Y, Zhang G, Zhou Y, Zhang Z, Chen Q, Feng Y. WGBS of embryonic gonads revealed that long non-coding RNAs in the MHM region might be involved in cell autonomous sex identity and female gonadal development in chickens. Epigenetics 2024; 19:2283657. [PMID: 38037805 PMCID: PMC10761181 DOI: 10.1080/15592294.2023.2283657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/01/2023] [Indexed: 12/02/2023] Open
Abstract
DNA methylation plays a key role in sex determination and differentiation in vertebrates. However, there are few studies on DNA methylation involved in chicken gonad development, and most focused on male hypermethylated regions (MHM). It is unclear whether there are specific differentially methylated regions (DMRs) in chicken embryonic gonads regulating sex determination and differentiation. Here, the DNA methylation maps showed that the difference of DNA methylation level between sexes was much higher at embryonic day 10 (E10) than that at embryonic day 6 (E6), and the significant differentially methylated regions at both stages were mainly distributed on the Z chromosome, including MHM1 and MHM2. The results of bisulphite sequencing PCR (BSP) and qRT-PCR showed hypomethylation of female MHM and upregulation of long non-coding RNAs (lncRNAs) whose promoter in the MHM region was consistent with the sequencing results, and similar results were in brain and muscle. In female sex-reversed gonads, the methylation pattern of MHM remained unchanged, and the expression levels of the three candidate lncRNAs were significantly decreased compared with those in females, but were significantly increased compared to males. The fluorescence in situ hybridization (FISH) results also showed that these lncRNAs were highly expressed in female embryonic gonads. The results of methyltransferase inhibitor and dual-luciferase reporter assay suggest that lncRNA expression may be regulated by DNA methylation within their promoters. Therefore, we speculated that MHM may be involved in cell-autonomous sex identity in chickens, and that lncRNAs regulated by MHM may be involved in female sexual differentiation.
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Affiliation(s)
- Ligen Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yu Cheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Guixin Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zhen Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qianhong Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
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Górska A, Urbanowicz M, Grochowalski Ł, Seweryn M, Sobalska-Kwapis M, Wojdacz T, Lange M, Gruchała-Niedoszytko M, Jarczak J, Strapagiel D, Górska-Ponikowska M, Pelikant-Małecka I, Kalinowski L, Nedoszytko B, Gutowska-Owsiak D, Niedoszytko M. Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis. Int J Mol Sci 2023; 24:13910. [PMID: 37762215 PMCID: PMC10530743 DOI: 10.3390/ijms241813910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Mastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that are relevant to the pathology. Epigenetic alterations are responsible for regulating the expression of genes that do not modify the DNA sequence. In general, it is accepted that DNA methylation inhibits the binding of transcription factors, thereby down-regulating gene expression. However, so far, little is known about the epigenetic factors leading to the clinical onset of mastocytosis. Therefore, it is essential to identify possible epigenetic predictors, indicators of disease progression, and their link to the clinical picture to establish appropriate management and a therapeutic strategy. The aim of this study was to analyze genome-wide methylation profiles to identify differentially methylated regions (DMRs) in patients with mastocytosis compared to healthy individuals, as well as the genes located in those regulatory regions. Genome-wide DNA methylation profiling was performed in peripheral blood collected from 80 adult patients with indolent systemic mastocytosis (ISM), the most prevalent subvariant of mastocytosis, and 40 healthy adult volunteers. A total of 117 DNA samples met the criteria for the bisulfide conversion step and microarray analysis. Genome-wide DNA methylation analysis was performed using a MethylationEPIC BeadChip kit. Further analysis was focused on the genomic regions rather than individual CpG sites. Co-methylated regions (CMRs) were assigned via the CoMeBack method. To identify DMRs between the groups, a linear regression model with age as the covariate on CMRs was performed using Limma. Using the available data for cases only, an association analysis was performed between methylation status and tryptase levels, as well as the context of allergy, and anaphylaxis. KEGG pathway mapping was used to identify genes differentially expressed in anaphylaxis. Based on the DNA methylation results, the expression of 18 genes was then analyzed via real-time PCR in 20 patients with mastocytosis and 20 healthy adults. A comparison of the genome-wide DNA methylation profile between the mastocytosis patients and healthy controls revealed significant differences in the methylation levels of 85 selected CMRs. Among those, the most intriguing CMRs are 31 genes located within the regulatory regions. In addition, among the 10 CMRs located in the promoter regions, 4 and 6 regions were found to be either hypo- or hypermethylated, respectively. Importantly, three oncogenes-FOXQ1, TWIST1, and ERG-were identified as differentially methylated in mastocytosis patients, for the first time. Functional annotation revealed the most important biological processes in which the differentially methylated genes were involved as transcription, multicellular development, and signal transduction. The biological process related to histone H2A monoubiquitination (GO:0035518) was found to be enriched in association with higher tryptase levels, which may be associated with more aberrant mast cells and, therefore, more atypical mast cell disease. The signal in the BAIAP2 gene was detected in the context of anaphylaxis, but no significant differential methylation was found in the context of allergy. Furthermore, increased expression of genes encoding integral membrane components (GRM2 and KRTCAP3) was found in mastocytosis patients. This study confirms that patients with mastocytosis differ significantly in terms of methylation levels in selected CMRs of genes involved in specific molecular processes. The results of gene expression profiling indicate the increased expression of genes belonging to the integral component of the membrane in mastocytosis patients (GRM2 and KRTCAP3). Further work is warranted, especially in relation to the disease subvariants, to identify links between the methylation status and the symptoms and novel therapeutic targets.
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Affiliation(s)
- Aleksandra Górska
- Department of Allergology, Medical University of Gdansk, 7 Dębinki Street, 80-210 Gdansk, Poland;
| | - Maria Urbanowicz
- Biobank Lab, Department of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland (M.S.); (M.S.-K.); (D.S.)
| | - Łukasz Grochowalski
- Biobank Lab, Department of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland (M.S.); (M.S.-K.); (D.S.)
| | - Michał Seweryn
- Biobank Lab, Department of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland (M.S.); (M.S.-K.); (D.S.)
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland (M.S.); (M.S.-K.); (D.S.)
| | - Tomasz Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, 71-281 Szczecin, Poland;
| | - Magdalena Lange
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland; (M.L.); (B.N.)
| | | | - Justyna Jarczak
- Biobank Lab, Department of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland (M.S.); (M.S.-K.); (D.S.)
| | - Dominik Strapagiel
- Biobank Lab, Department of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland (M.S.); (M.S.-K.); (D.S.)
| | | | - Iwona Pelikant-Małecka
- Department of Medical Laboratory Diagnostics–Biobank Fahrenheit, Medical University of Gdansk, 80-210 Gdansk, Poland; (I.P.-M.); (L.K.)
| | - Leszek Kalinowski
- Department of Medical Laboratory Diagnostics–Biobank Fahrenheit, Medical University of Gdansk, 80-210 Gdansk, Poland; (I.P.-M.); (L.K.)
- BioTechMed Centre, Department of Mechanics of Materials and Structures, Gdansk University of Technology, 80-233 Gdansk, Poland
| | - Bogusław Nedoszytko
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland; (M.L.); (B.N.)
- Invicta Fertility and Reproductive Center, Molecular Laboratory, 81-740 Sopot, Poland
| | - Danuta Gutowska-Owsiak
- Laboratory of Experimental and Translational Immunology, University of Gdansk, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland;
| | - Marek Niedoszytko
- Department of Allergology, Medical University of Gdansk, 7 Dębinki Street, 80-210 Gdansk, Poland;
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Ren C, Yan R, Yuan Z, Yin L, Li H, Ding J, Wu T, Chen R. Maternal exposure to sunlight-irradiated graphene oxide induces neurodegeneration-like symptoms in zebrafish offspring through intergenerational translocation and genomic DNA methylation alterations. Environ Int 2023; 179:108188. [PMID: 37690221 DOI: 10.1016/j.envint.2023.108188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/20/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
The physiochemical properties of graphene oxide may be affected by sunlight irradiation. However, the underlying mechanisms that alter the properties and subsequent intergenerational effects are not sufficiently investigate. Epigenetics is an early sensitive marker for the intergenerational effects of nanomaterial exposure due to the epigenetic memory. In this study, we investigate changes in the physicochemical properties and the intergenerational effects of maternal exposure to simulated sunlight-irradiated polyethyleneimine-functionalized graphene oxide (SL-PEI-GO). Results show that the physicochemical properties of polyethyleneimine-functionalized graphene oxide (PEI-GO) can be altered significantly by the oxidation of carbon atoms with unpaired electrons present in the defects and on the edges of PEI-GO by sunlight. First, the positive charges, sharp edges, defects and disordered structures of SL-PEI-GO make it translocate from maternal zebrafish to offspring, thus catalyzing the production of reactive oxygen species and damaging mitochondria directly. In addition, changes in DNA methylation reduce the expression of protocadherin1a, protocadherin19 and cadherin4, thus destroying cell membrane integrity, cell adhesion and Ca2+ binding. The alteration of DNA methylation induced by maternal exposure activates the Ca2+-CaMKK-brsk2a pathway, which catalyzes the phosphorylation of Tau and eventually results in the appearance of neurodegeneration-like symptoms, including the loss of neurons and neurobehavioral disorders. This study demonstrates that maternal exposure to SL-PEI-GO induces clear neurodegeneration-like symptoms in offspring through both the intergenerational translocation of nanomaterials and differential DNA methylation. These findings may provide new insights into the health risks of nanomaterials altered by nature conditions.
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Affiliation(s)
- Chaoxiu Ren
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary chemistry, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Ruyu Yan
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary chemistry, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Ziyi Yuan
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary chemistry, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Lijia Yin
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary chemistry, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Hongji Li
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary chemistry, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Jing Ding
- Tianjin Environmental Meteorological Center, Tianjin 300074, China
| | - Tao Wu
- Beijing Key Laboratory of Enze Biomass Fine Chemicals, College of New Materials and Chemical Engineering, Beijing institute of Petrochemical Technology, Beijing 102617, China.
| | - Rui Chen
- Beijing Key Laboratory of Environmental Toxicology, Department of Toxicology and Sanitary chemistry, School of Public Health, Capital Medical University, Beijing 100069, China.
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Xie Y, Zhao H, Luo H, Zuo X, Li Q, Liu S. Genome-wide DNA methylation and transcriptome expression profiles of peripheral blood mononuclear cells in patients with systemic sclerosis with interstitial lung disease. Zhong Nan Da Xue Xue Bao Yi Xue Ban 2023; 48:829-836. [PMID: 37587067 PMCID: PMC10930437 DOI: 10.11817/j.issn.1672-7347.2023.220538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 08/18/2023]
Abstract
OBJECTIVES This study aims to investigate the genome-wide DNA methylation and transcriptome expression profiles of peripheral blood mononuclear cells (PBMCs) in patients with systemic sclerosis (SSc) with interstitial lung disease (ILD), and to analyze the effects of DNA methylation on Wnt/β-catenin and chemokine signaling pathways. METHODS PBMCs were collected from 19 patients with SSc (SSc group) and 18 healthy persons (control group). Among SSc patients, there were 10 patients with ILD (SSc with ILD subgroup) and 9 patients without ILD (SSc without ILD subgroup). The genome-wide DNA methylation and gene expression level were analyzed by using Illumina 450K methylation chip and Illumina HT-12 v4.0 gene expression profiling chip. The effect of DNA methylation on Wnt/β-catenin and chemokine signal pathways was investigated. RESULTS Genome-wide DNA methylation analysis identified 71 hypermethylated CpG sites and 98 hypomethylated CpG sites in the SSc with ILD subgroup compared with the SSc without ILD subgroup. Transcriptome analysis distinguished 164 upregulated genes and 191 downregulated genes in the SSc with ILD subgroup as compared with the SSc without ILD subgroup. In PBMCs of the SSc group, 35 genes in Wnt/β-catenin signaling pathway were hypomethylated, while frizzled-1 (FZD1), mitogen-activated protein kinase 9 (MAPK9), mothers against DPP homolog 2 (SMAD2), transcription factor 7-like 2 (TCF7L2), and wingless-type MMTV integration site family, member 5B (WNT5B) mRNA expressions were upregulated as compared with the control group (all P<0.05). Compared with the SSc without ILD subgroup, the mRNA expressions of dickkopf homolog 2 (DKK2), FZD1, MAPK9 were upregulated in the SSc with ILD subgroup, but the differences were not statistically significant (all P>0.05). In PBMCs of the SSc group, 38 genes in chemokine signaling pathway were hypomethylated, while β-arrestin 1 (ARRB1), C-X-C motif chemokine ligand 10 (CXCL10), C-X-C motif chemokine ligand 16 (CXCL16), FGR, and neutrophil cytosolic factor 1C (NCF1C) mRNA expressions were upregulated as compared with the control group (all P<0.05). Compared with the SSc without ILD subgroup, the mRNA expressions of ARRB1, CXCL10, CXCL16 were upregulated in the SSc with ILD subgroup, but the differences were not statistically significant (all P>0.05). CONCLUSIONS There are differences in DNA methylation and transcriptome profiles between SSc with ILD and SSc without ILD. The expression levels of multiple genes in Wnt/β- catenin and chemokine signaling pathways are upregulated, which might be associatea with the pathogenesis of SSc.
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Affiliation(s)
- Yanli Xie
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hui Luo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaoxia Zuo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Quanzhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sijia Liu
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha 410008, China.
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Makino K, Otani Y, Fujii K, Ishida J, Hirano S, Suruga Y, Washio K, Nishida K, Yanai H, Tomida S, Ennishi D, Date I. Utility of Comprehensive Genomic Profiling for Precise Diagnosis of Pediatric-Type Diffuse High-Grade Glioma. Acta Med Okayama 2023; 77:323-330. [PMID: 37357634 DOI: 10.18926/amo/65502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
In the current World Health Organization classification of central nervous system tumors, comprehensive genetic and epigenetic analyses are considered essential for precise diagnosis. A 14-year-old male patient who presented with a cerebellar tumor was initially diagnosed with glioblastoma and treated with radiation and concomitant temozolomide chemotherapy after resection. During maintenance temozolomide therapy, a new contrast-enhanced lesion developed in the bottom of the cavity formed by the resection. A second surgery was performed, but the histological findings in specimens from the second surgery were different from those of the first surgery. Although genome-wide DNA methylation profiling was conducted using frozen tissue for a precise diagnosis, the proportion of tumor cells was insufficient and only normal cerebellum was observed. We then performed comprehensive genetic analysis using formalin-fixed paraffin-embedded sections, which revealed MYCN amplification without alteration of IDH1, IDH2, or Histone H3. Finally, the patient was diagnosed with pediatric-type diffuse high-grade glioma, H3-wildtype and IDH-wildtype. In conclusion, comprehensive genetic and epigenetic analysis should be considered in pediatric brain tumor cases.
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Affiliation(s)
- Keigo Makino
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Yoshihiro Otani
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Kentaro Fujii
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Joji Ishida
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Shuichiro Hirano
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Yasuki Suruga
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Kana Washio
- Departments of Pediatrics, Okayama University Hospital
| | - Kenji Nishida
- Departments of Pathology, Okayama University Hospital
| | | | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Daisuke Ennishi
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Isao Date
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
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Lin R, Qian Y, Zhang J, Xia D, Guo D, Hong L, Qing B, Xu M, Huang Y, Lin W, Chen G, Liu S. Genome-wide DNA methylation profiling of gastric cardia cancer. J Gastroenterol Hepatol 2023; 38:290-300. [PMID: 36342849 DOI: 10.1111/jgh.16054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND AND AIM Aberrant DNA methylation has been found in various cancer types including gastric cancer, yet the genome-wide DNA methylation profile of gastric cardia cancer (GCC) remains unclear. Therefore, we aimed to profile the DNA methylation pattern of GCC and identify promising diagnostic epigenetic biomarkers. METHODS We investigated the genome-wide DNA methylation pattern in eight pairs of GCC and adjacent normal tissues using Illumina 850K microarrays. Subsequently, bisulfite-pyrosequencing and quantitative real-time PCR were performed on eight pairs of GCC-adjacent normal tissues for validation. Finally, we performed immunohistochemistry to examine ADHFE1 expression on 126 pairs of GCC-adjacent normal samples. RESULTS DNA methylome analysis showed global hypomethylation and local hypermethylation of promoter cytosine-phosphate-guanine (CpG) islands (CGIs) in GCC tissues compared with gastric cardia normal mucosa (P < 2.2 × 10-16 ). Differential methylation analysis identified a total of 91 723 differentially-methylated probes (DMPs), and the candidate gene with the largest average DNA methylation difference mapped to ADHFE1 (mean Δβ = 0.53). Subsequently, three DMPs in the ADHFE1 promoter were validated by pyrosequencing. Notably, the mean methylation level of the three candidate DMPs (ADHFE1_cg08090772, ADHFE1_cg19283840, and ADHFE1_cg20295442) was negatively associated with ADHFE1 mRNA expression level (Spearman rho = -0.64, P = 0.01). Moreover, both mRNA (P = 0.0213) and protein (P < 0.0001) expression of ADHFE1 were significantly decreased in GCCs compared with the adjacent normal tissues. CONCLUSIONS Our results reveal DNA methylation aberrations in GCC and that ADHFE1 gene DNA methylation contributes to the risk of GCC, thus providing novel mechanistic insights into gastric cardia cancer carcinogenesis.
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Affiliation(s)
- Runhua Lin
- Department of Pathology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Yanli Qian
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Jinhai Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Di Xia
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Dongming Guo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Liangli Hong
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Bojuan Qing
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Muming Xu
- Department of Abdominal Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Yiteng Huang
- Health Care Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Wenting Lin
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Guangcan Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Shuhui Liu
- Department of Pathology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
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Hergalant S, Saurel C, Divoux M, Rech F, Pouget C, Godfraind C, Rouyer P, Lacomme S, Battaglia-Hsu SF, Gauchotte G. Correlation between DNA Methylation and Cell Proliferation Identifies New Candidate Predictive Markers in Meningioma. Cancers (Basel) 2022; 14. [PMID: 36551712 DOI: 10.3390/cancers14246227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/05/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Meningiomas are the most common primary tumors of the central nervous system. Based on the 2021 WHO classification, they are classified into three grades reflecting recurrence risk and aggressiveness. However, the WHO's histopathological criteria defining these grades are somewhat subjective. Together with reliable immunohistochemical proliferation indices, other molecular markers such as those studied with genome-wide epigenetics promise to revamp the current prognostic classification. In this study, 48 meningiomas of various grades were randomly included and explored for DNA methylation with the Infinium MethylationEPIC microarray over 850k CpG sites. We conducted differential and correlative analyses on grade and several proliferation indices and markers, such as mitotic index and Ki-67 or MCM6 immunohistochemistry. We also set up Cox proportional hazard models for extensive associations between CpG methylation and survival. We identified loci highly correlated with cell growth and a targeted methylation signature of regulatory regions persistently associated with proliferation, grade, and survival. Candidate genes under the control of these regions include SMC4, ESRRG, PAX6, DOK7, VAV2, OTX1, and PCDHA-PCDHB-PCDHG, i.e., the protocadherin gene clusters. This study highlights the crucial role played by epigenetic mechanisms in shaping dysregulated cellular proliferation and provides potential biomarkers bearing prognostic and therapeutic value for the clinical management of meningioma.
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Pan X, Wu Y, Peng H, Cai X, Hu Z, Lin X, Peng XE. Genome-wide DNA methylation profiling in nonalcoholic fatty liver reveals predictive aberrant methylation in PRKCE and SEC14L3 promoters. Dig Liver Dis 2022; 54:521-528. [PMID: 34108094 DOI: 10.1016/j.dld.2021.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Optimal non-invasive biomarkers for diagnosis and treatment of nonalcoholic fatty liver disease (NAFLD) remain to be identified. AIMS To identify potential DNA methylation biomarkers for NAFLD. METHODS Genome-wide DNA methylation profiling was performed to identify differentially methylated CpG sites in peripheral blood leukocytes. Differentially methylated regions were validated using the MassCLEAVE assay. The expression levels of candidate genes were explored by Gene Expression Omnibus database. RESULTS The hypomethylation of PRKCE CpG 4.5 and CpG 18.19 was associated with nonalcoholic fatty liver (NAFL), the odds ratio (OR) and 95% confidence interval (CI) were 0.129 (0.026-0.639) and 0.231 (0.069-0.768). The methylation level of CpG 1.2 and average methylation level of SEC14L3 were correlated with NAFL, with OR (95% CI) being 0.283 (0.093-0.865) and 0.264 (0.087-0.799). PRKCE CpG 4.5 and cg17802464 of SEC14L3 were correlated with body mass index, waist circumference, total triglyceride, high-density lipoprotein cholesterol, alanine aminotransferase and aspartate aminotransferase. All selected datasets showed high expression levels of PRKCE and SEC14L3 in patients with NAFLD. CONCLUSIONS Our findings suggest that the hypomethylation of PRKCE and SEC14L3 promoters represent attractive biomarkers for NAFLD. Further studies are warranted to validate these biomarkers as molecular tools for diagnosis of NAFLD and therapeutic targets.
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Affiliation(s)
- Xinting Pan
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, PR China
| | - Yunli Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, PR China
| | - Hewei Peng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China
| | - Xiaoling Cai
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China
| | - Zhijian Hu
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China
| | - Xu Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, PR China
| | - Xian-E Peng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, PR China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, PR China.
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9
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Lin X, Zhou M, Yao J, Li QQ, Zhang YY. Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions. Front Plant Sci 2022; 13:841154. [PMID: 35310665 PMCID: PMC8931716 DOI: 10.3389/fpls.2022.841154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ming Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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10
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Abstract
Tweetable abstract The diagnostic application of genome-wide methylation signatures is increasing in various syndromic forms of autism, but further studies are warranted to clarify whether epigenetic biomarkers can be of diagnostic utility in idiopathic ASD.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, Pisa, 56126, Italy
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11
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Wang M, Liang Y, Ibeagha-Awemu EM, Li M, Zhang H, Chen Z, Sun Y, Karrow NA, Yang Z, Mao Y. Genome-Wide DNA Methylation Analysis of Mammary Gland Tissues From Chinese Holstein Cows With Staphylococcus aureus Induced Mastitis. Front Genet 2020; 11:550515. [PMID: 33193625 PMCID: PMC7604493 DOI: 10.3389/fgene.2020.550515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus intramammary infection is one of the most common causes of chronic mastitis in dairy cows, whose development may be associated with epigenetic changes in the expression of important host defense genes. This study aimed to construct a genome-wide DNA methylation profile of the mammary gland of Chinese Holstein cows (n = 3) following experimentally induced S. aureus mastitis, and to explore the potential gene regulatory mechanisms affected by DNA methylation during S. aureus mastitis. DNA was extracted from S. aureus-positive (n = 3) and S. aureus-negative (n = 3) mammary gland quarters and subjected to methylation-dependent restriction-site associated DNA sequencing (Methyl-RAD Seq). Results showed that CmCGG/CmCWGG DNA methylation sites were unevenly distributed and concentrated on chromosomes 5, 11, and 19, and within intergenic regions and intron regions of genes. Compared with healthy control quarters, 9,181 significantly differentially methylated (DM) CmCGG sites and 1,790 DM CmCWGG sites were found in the S. aureus-positive quarters (P < 0.05, |log2FC| > 1). Furthermore, 363 CmCGG differently methylated genes (DMGs) and 301 CmCWGG DMGs (adjusted P < 0.05, |log2FC| > 1) were identified. Gene ontology and KEGG enrichment analysis indicated that CmCGG DMGs are involved in immune response pathways, while the CmCWGG DMGs were mainly enriched in gene ontology terms related to metabolism. The mRNAs of 526 differentially methylated CmCGG genes and 124 differentially methylated CmCWGG genes were also significantly differentially expressed (RNA-Seq data) in the same samples, herein denoted differentially methylated and expressed genes (DMEGs) (P < 0.05). Functional enrichment analysis of DMEGs revealed roles related to biological processes, especially the regulation of immune response to diseases. CmCGG DMEGs like IL6R, TNF, BTK, IL1R2, and TNFSF8 enriched in several immune-related GO terms and pathways indicated their important roles in host immune response and their potential as candidate genes for S. aureus mastitis. These results suggest potential regulatory roles for DNA methylation in bovine mammary gland processes during S. aureus mastitis and serves as a reference for future epigenetic regulation and mechanistic studies.
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Affiliation(s)
- Mengqi Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Yan Liang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Mingxun Li
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Huimin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Zhi Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Niel A. Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Zhangping Yang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yongjiang Mao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
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12
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Tilburg J, Slieker RC, Suchiman HED, Heath A, Heemst DV, Slagboom PE, de Gruijl FR, Gunn DA, Heijmans BT. Repeat UVA exposure of human skin fibroblasts induces both a transitionary and recovery DNA methylation response. Epigenomics 2020; 12:563-573. [PMID: 32516006 DOI: 10.2217/epi-2019-0251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Aim: UVA radiation drives skin photoaging in the dermis, plausibly via persistent changes to DNA methylation in dermal fibroblasts. Methods: Genome-wide DNA methylation changes after five repeated daily UVA doses were determined at 48 h (transitionary) and 1 week (recovery) post final irradiation. Results: Differential methylation was found at the transitionary time point in active chromatin states near genes that are highly expressed in fibroblasts and are involved in cellular defensive mechanisms; the majority of these methylation differences were restored to control levels after 7 day recovery. At the recovery time point, new differential methylation occurred at repressed regions near developmental genes, normally weakly expressed in fibroblasts. Conclusion: UVA irradiation induces transitionary and recovery-associated DNA methylation responses in fibroblasts with contrasting functional characteristics.
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Affiliation(s)
- Julia Tilburg
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Division of Thrombosis & Hemostasis, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Roderick C Slieker
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - H Eka D Suchiman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Alan Heath
- Unilever Research & Development, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Diana van Heemst
- Gerontology & Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank R de Gruijl
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - David A Gunn
- Unilever Research & Development, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
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13
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Carnero-Montoro E, Barturen G, Povedano E, Kerick M, Martinez-Bueno M, Ballestar E, Martin J, Teruel M, Alarcón-Riquelme ME. Epigenome-Wide Comparative Study Reveals Key Differences Between Mixed Connective Tissue Disease and Related Systemic Autoimmune Diseases. Front Immunol 2019; 10:1880. [PMID: 31440254 PMCID: PMC6693476 DOI: 10.3389/fimmu.2019.01880] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/24/2019] [Indexed: 11/26/2022] Open
Abstract
Mixed Connective Tissue Disease (MCTD) is a rare complex systemic autoimmune disease (SAD) characterized by the presence of increased levels of anti-U1 ribonucleoprotein autoantibodies and signs and symptoms that resemble other SADs such as systemic sclerosis (SSc), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). Due to its low prevalence, this disease has been very poorly studied at the molecular level. We performed for the first time an epigenome-wide association study interrogating DNA methylation data obtained with the Infinium MethylationEPIC array from whole blood samples in 31 patients diagnosed with MCTD and 255 healthy subjects. We observed a pervasive hypomethylation involving 170 genes enriched for immune-related function such as those involved in type I interferon signaling pathways or in negative regulation of viral genome replication. We mostly identified epigenetic signals at genes previously implicated in other SADs, for example MX1, PARP9, DDX60, or IFI44L, for which we also observed that MCTD patients exhibit higher DNA methylation variability compared with controls, suggesting that these sites might be involved in plastic immune responses that are relevant to the disease. Through methylation quantitative trait locus (meQTL) analysis we identified widespread local genetic effects influencing DNA methylation variability at MCTD-associated sites. Interestingly, for IRF7, IFI44 genes, and the HLA region we have evidence that they could be exerting a genetic risk on MCTD mediated through DNA methylation changes. Comparison of MCTD-associated epigenome with patients diagnosed with SLE, or Sjögren's Syndrome, reveals a common interferon-related epigenetic signature, however we find substantial epigenetic differences when compared with patients diagnosed with rheumatoid arthritis and systemic sclerosis. Furthermore, we show that MCTD-associated CpGs are potential epigenetic biomarkers with high diagnostic value. Our study serves to reveal new genes and pathways involved in MCTD, to illustrate the important role of epigenetic modifications in MCTD pathology, in mediating the interaction between different genetic and environmental MCTD risk factors, and as potential biomarkers of SADs.
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Affiliation(s)
- Elena Carnero-Montoro
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Guillermo Barturen
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Elena Povedano
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Martin Kerick
- CSIC-IBPLN, Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López-Neyra, Granada, Spain
| | - Manuel Martinez-Bueno
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | | | - Esteban Ballestar
- IDIBELL, Bellvitge Biomedical Research Institute L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Martin
- CSIC-IBPLN, Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López-Neyra, Granada, Spain
| | - María Teruel
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain.,Institute for Environmental Medicine, Karolinska Institutet, Solna, Sweden
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14
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Yuan X, Zhou X, Chen Z, He Y, Kong Y, Ye S, Gao N, Zhang Z, Zhang H, Li J. Genome-Wide DNA Methylation Analysis of Hypothalamus During the Onset of Puberty in Gilts. Front Genet 2019; 10:228. [PMID: 30941164 PMCID: PMC6433709 DOI: 10.3389/fgene.2019.00228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/28/2019] [Indexed: 12/30/2022] Open
Abstract
Although selection of the early age at puberty in gilts will make for a favorable effect on the reproductivity of sow, a large proportion of phenotypic variation in age at puberty of gilts cannot be explained by genetics. Previous studies have implicated hypothalamic DNA methylation in the onset of puberty in mammals. However, the underlying molecular mechanism regarding the regulation of the onset of puberty has remained largely unexplored in gilts. Herein, the genome-scale DNA methylation of hypothalamus was acquired, using the reduced representation bisulfite sequencing, to compare and describe the changes of DNA methylation across Pre-, In- and Post-pubertal gilts. In this study, the average methylation levels of CpGs and CpHs (where H = C, T, or A) in CpG islands- and gene-related regions were gradually decreased in hypothalamic methylomes during the pubertal transition. Comparisons of Pre- vs. In-, In- vs. Post-, and Pre- vs. Post-pubertal stage revealed that there were 85726, 92914, and 100421 differentially methylated CpGs and 5940, 14804, and 16893 differentially methylated CpHs (where H = C, T, or A) in the hypothalamic methylomes. The methylation changes of CpHs were more dynamic than that of CpGs, and methylation changes of CpGs and CpHs were likely to be, respectively, involved in the developmental processes of reproduction and the molecular processes of cellular communications in the hypothalamus. Moreover, methylation changes of CpHs were observed to overrepresent in the quantitative trait loci of age at puberty, and the biological function of these CpH methylation changes was enriched in the pancreas development in gilts. Furthermore, the mRNA levels of several differentially CpG or CpH methylated genes related to the transcription of RNA II polymerase, GnRH signaling pathway, Estrogen signaling pathway, PI3K-AKt signaling pathway, and Insulin signaling pathway, including MAX, MMP2, FGF11, IGF1R, FGF21, and GSK3B, were significantly changed across these pubertal stages in the hypothalamus. These results will help our understanding of how DNA methylation contributes to phenotypic variation of age at puberty.
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Affiliation(s)
- Xiaolong Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiaofeng Zhou
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zitao Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yingting He
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yaru Kong
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shaopan Ye
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ning Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Guangzhou Higher Education Mega Center, Sun Yat-sen University, Guangzhou, China
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiaqi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
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15
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Willmer T, Johnson R, Louw J, Pheiffer C. Corrigendum: Blood-Based DNA Methylation Biomarkers for Type 2 Diabetes: Potential for Clinical Applications. Front Endocrinol (Lausanne) 2019; 10:1. [PMID: 30723457 PMCID: PMC6349824 DOI: 10.3389/fendo.2019.00001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fendo.2018.00744.].
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Affiliation(s)
- Tarryn Willmer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- *Correspondence: Tarryn Willmer
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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16
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Willmer T, Johnson R, Louw J, Pheiffer C. Blood-Based DNA Methylation Biomarkers for Type 2 Diabetes: Potential for Clinical Applications. Front Endocrinol (Lausanne) 2018; 9:744. [PMID: 30564199 PMCID: PMC6288427 DOI: 10.3389/fendo.2018.00744] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes (T2D) is a leading cause of death and disability worldwide. It is a chronic metabolic disorder that develops due to an interplay of genetic, lifestyle, and environmental factors. The biological onset of the disease occurs long before clinical symptoms develop, thus the search for early diagnostic and prognostic biomarkers, which could facilitate intervention strategies to prevent or delay disease progression, has increased considerably in recent years. Epigenetic modifications represent important links between genetic, environmental and lifestyle cues and increasing evidence implicate altered epigenetic marks such as DNA methylation, the most characterized and widely studied epigenetic mechanism, in the pathogenesis of T2D. This review provides an update of the current status of DNA methylation as a biomarker for T2D. Four databases, Scopus, Pubmed, Cochrane Central, and Google Scholar were searched for studies investigating DNA methylation in blood. Thirty-seven studies were identified, and are summarized with respect to population characteristics, biological source, and method of DNA methylation quantification (global, candidate gene or genome-wide). We highlight that differential methylation of the TCF7L2, KCNQ1, ABCG1, TXNIP, PHOSPHO1, SREBF1, SLC30A8, and FTO genes in blood are reproducibly associated with T2D in different population groups. These genes should be prioritized and replicated in longitudinal studies across more populations in future studies. Finally, we discuss the limitations faced by DNA methylation studies, which include including interpatient variability, cellular heterogeneity, and lack of accounting for study confounders. These limitations and challenges must be overcome before the implementation of blood-based DNA methylation biomarkers into a clinical setting. We emphasize the need for longitudinal prospective studies to support the robustness of the current findings of this review.
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Affiliation(s)
- Tarryn Willmer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- *Correspondence: Tarryn Willmer
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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17
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Song MA, Brasky TM, Weng DY, McElroy JP, Marian C, Higgins MJ, Ambrosone C, Spear SL, Llanos AA, Kallakury BVS, Freudenheim JL, Shields PG. Landscape of genome-wide age-related DNA methylation in breast tissue. Oncotarget 2017; 8:114648-114662. [PMID: 29383109 PMCID: PMC5777721 DOI: 10.18632/oncotarget.22754] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 11/06/2017] [Indexed: 12/15/2022] Open
Abstract
Despite known age-related DNA methylation (aDNAm) changes in breast tumors, little is known about aDNAm in normal breast tissues. Breast tissues from a cross-sectional study of 121 cancer-free women, were assayed for genome-wide DNA methylation. mRNA expression was assayed by microarray technology. Analysis of covariance was used to identify aDNAm’s. Altered methylation was correlated with expression of the corresponding gene and with DNA methyltransferase protein DNMT3A, assayed by immunohistochemistry. Publically-available TCGA-BRCA data were used for replication. 1,214 aDNAm’s were identified; 97% with increased methylation, and all on autosomes. Sites with increased methylation were predominantly in CpG lslands and non-enhancers. aDNAm’s with decreased methylation were generally located in intergenic regions, non-CpG Islands, and enhancers. Of the aDNAm’s identified, 650 are known to be involved in cancer, including ESR1 and beta-estradiol responsive genes. Expression of DNMT3A was positively associated with age. Two aDNAm’s showed borderline significant associations with DNMT3A expression; KRR1 (OR 6.57, 95% CI: 2.51–17.23) and DHRS12 (OR 6.08, 95% CI: 2.33–15.86). A subset of aDNAm’s co-localized within vulnerable regions for somatic mutations in cancers including breast cancer. Expression of C19orf48 was inversely and significantly correlated with its methylation level. In the TCGA dataset, 84% and 64% of the previously identified aDNAm’s were correlated with age in both normal-adjacent and tumor breast tissues, with differential associations by histological subtype. Given the similarity of findings in the breast tissues of healthy women and breast tumors, aDNAm’s may be one pathway for increased breast cancer risk with age.
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Affiliation(s)
- Min-Ae Song
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.,College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Theodore M Brasky
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Joseph P McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.,Center for Biostatistics and Department of Bioinformatics, The Ohio State University, Columbus, OH, USA
| | - Catalin Marian
- Biochemistry and Pharmacology Department, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Scott L Spear
- Department of Plastic Surgery, Georgetown University, Washington, DC, USA
| | - Adana A Llanos
- Department of Epidemiology, Rutgers School of Public Health and Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
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18
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Segal NL, Montoya YS, Loke YJ, Craig JM. Identical twins doubly exchanged at birth: a case report of genetic and environmental influences on the adult epigenome. Epigenomics 2016; 9:5-12. [PMID: 27936916 DOI: 10.2217/epi-2016-0104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AIM Epigenetic comparisons within monozygotic twin pairs have enhanced our understanding of nongenetic mechanisms underlying disease etiology. We present epigenetic findings for a unique case of doubly exchanged Colombian male monozygotic twins raised in extremely different environments. RESULTS Using genome-wide DNA methylation data from cheek swabs from which blood-specific differentially methylated probes had been removed, the individuals grouped by shared genetics rather than shared environment, except for one twin who presented as an outlier. Closer inspection of DNA methylation differences within both reared-apart twin pairs revealed several genes and genetic pathways likely to be influenced by the rearing environment. CONCLUSION Together with our previous findings, we suggest that genetics, pre- and postnatal environments contribute to the epigenetic profile, although additional studies are needed to quantify these effects.
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Affiliation(s)
- Nancy L Segal
- Department of Psychology, California State University, Fullerton, CA, USA
| | - Yesika S Montoya
- School of Social Work, Columbia University, New York City, NY, USA
| | - Yuk J Loke
- Early Life Epigenetics, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Jeffrey M Craig
- Early Life Epigenetics, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Song MA, Brasky TM, Marian C, Weng DY, Taslim C, Dumitrescu RG, Llanos AA, Freudenheim JL, Shields PG. Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women. Epigenetics 2016; 10:1177-87. [PMID: 26680018 DOI: 10.1080/15592294.2015.1121362] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Breast cancer is more common in European Americans (EAs) than in African Americans (AAs) but mortality from breast cancer is higher among AAs. While there are racial differences in DNA methylation and gene expression in breast tumors, little is known whether such racial differences exist in breast tissues of healthy women. Genome-wide DNA methylation and gene expression profiling was performed in histologically normal breast tissues of healthy women. Linear regression models were used to identify differentially-methylated CpG sites (CpGs) between EAs (n = 61) and AAs (n = 22). Correlations for methylation and expression were assessed. Biological functions of the differentially-methylated genes were assigned using the Ingenuity Pathway Analysis. Among 485 differentially-methylated CpGs by race, 203 were hypermethylated in EAs, and 282 were hypermethylated in AAs. Promoter-related differentially-methylated CpGs were more frequently hypermethylated in EAs (52%) than AAs (27%) while gene body and intergenic CpGs were more frequently hypermethylated in AAs. The differentially-methylated CpGs were enriched for cancer-associated genes with roles in cell death and survival, cellular development, and cell-to-cell signaling. In a separate analysis for correlation in EAs and AAs, different patterns of correlation were found between EAs and AAs. The correlated genes showed different biological networks between EAs and AAs; networks were connected by Ubiquitin C. To our knowledge, this is the first comprehensive genome-wide study to identify differences in methylation and gene expression between EAs and AAs in breast tissues from healthy women. These findings may provide further insights regarding the contribution of epigenetic differences to racial disparities in breast cancer.
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Affiliation(s)
- Min-Ae Song
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | - Theodore M Brasky
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | - Catalin Marian
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA.,b Biochemistry and Pharmacology Department ; Victor Babes University of Medicine and Pharmacy ; 300041 Timisoara , Romania
| | - Daniel Y Weng
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | - Cenny Taslim
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | | | - Adana A Llanos
- d Department of Epidemiology ; Rutgers School of Public Health and Rutgers Cancer Institute of New Jersey ; New Brunswick , NJ 08903 , USA
| | - Jo L Freudenheim
- e Department of Epidemiology and Environmental Health; School of Public Health and Health Professions ; University at Buffalo ; Buffalo , NY 14214 , USA
| | - Peter G Shields
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
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20
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Hing B, Gardner C, Potash JB. Effects of negative stressors on DNA methylation in the brain: implications for mood and anxiety disorders. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:541-54. [PMID: 25139739 PMCID: PMC5096645 DOI: 10.1002/ajmg.b.32265] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 07/18/2014] [Indexed: 01/31/2023]
Abstract
Stress is a major contributor to anxiety and mood disorders. The recent discovery of epigenetic changes in the brain resulting from stress has enhanced our understanding of the mechanism by which stress is able to promote these disorders. Although epigenetics encompasses chemical modifications that occur at both DNA and histones, much attention has been focused on stress-induced DNA methylation changes on behavior. Here, we review the effect of stress-induced DNA methylation changes on physiological mechanisms that govern behavior and cognition, dysregulation of which can be harmful to mental health. A literature review was performed in the areas of DNA methylation, stress, and their impact on the brain and psychiatric illness. Key findings center on genes involved in the hypothalamic-pituitary-adrenal axis, neurotransmission and neuroplasticity. Using animal models of different stress paradigms and clinical studies, we detail how DNA methylation changes to these genes can alter physiological mechanisms that influence behavior. Appropriate levels of gene expression in the brain play an important role in mental health. This dynamic control can be disrupted by stress-induced changes to DNA methylation patterns. Advancement in other areas of epigenetics, such as histone modifications and the discovery of the novel DNA epigenetic mark, 5-hydroxymethylcytosine, could provide additional avenues to consider when determining the epigenetic effects of stress on the brain.
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Affiliation(s)
- Benjamin Hing
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa,Correspondence to: Dr Benjamin Hing, 25 South Grand Ave, Medical Laboratories, B002, Iowa City, Iowa, USA 52242.
| | - Caleb Gardner
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James B. Potash
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa
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21
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Marzese DM, Scolyer RA, Roqué M, Vargas-Roig LM, Huynh JL, Wilmott JS, Murali R, Buckland ME, Barkhoudarian G, Thompson JF, Morton DL, Kelly DF, Hoon DSB. DNA methylation and gene deletion analysis of brain metastases in melanoma patients identifies mutually exclusive molecular alterations. Neuro Oncol 2014; 16:1499-509. [PMID: 24968695 DOI: 10.1093/neuonc/nou107] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The brain is a common target of metastases for melanoma patients. Little is known about the genetic and epigenetic alterations in melanoma brain metastases (MBMs). Unraveling these molecular alterations is a key step in understanding their aggressive nature and identifying novel therapeutic targets. METHODS Genome-wide DNA methylation analyses of MBMs (n = 15) and normal brain tissues (n = 91) and simultaneous multigene DNA methylation and gene deletion analyses of metastatic melanoma tissues (99 MBMs and 43 extracranial metastases) were performed. BRAF and NRAS mutations were evaluated in MBMs by targeted sequencing. RESULTS MBMs showed significant epigenetic heterogeneity. RARB, RASSF1, ESR1, APC, PTEN, and CDH13 genes were frequently hypermethylated. Deletions were frequently detected in the CDKN2A/B locus. Of MBMs, 46.1% and 28.8% had BRAF and NRAS missense mutations, respectively. Compared with lung and liver metastases, MBMs exhibited higher frequency of CDH13 hypermethylation and CDKN2A/B locus deletion. Mutual exclusivity between hypermethylated genes and CDKN2A/B locus deletion identified 2 clinically relevant molecular subtypes of MBMs. CDKN2A/B deletions were associated with multiple MBMs and frequently hypermethylated genes with shorter time to brain metastasis. CONCLUSIONS Melanoma cells that colonize the brain harbor numerous genetically and epigenetically altered genes. This study presents an integrated genomic and epigenomic analysis that reveals MBM-specific molecular alterations and mutually exclusive molecular subtypes.
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Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Richard A Scolyer
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Maria Roqué
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Laura M Vargas-Roig
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Jamie L Huynh
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - James S Wilmott
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Rajmohan Murali
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Michael E Buckland
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Garni Barkhoudarian
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - John F Thompson
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Donald L Morton
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Daniel F Kelly
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
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Bediaga NG, Marichalar-Mendia X, Aguirre-Urizar JM, Calvo B, Echebarria-Goicouria MA, de Pancorbo MM, Acha-Sagredo A. Global DNA methylation: uncommon event in oral lichenoid disease. Oral Dis 2014; 20:821-6. [PMID: 24724918 DOI: 10.1111/odi.12243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/04/2014] [Accepted: 03/24/2014] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Accumulating evidence indicates that aberrant DNA methylation is closely related to oral carcinogenesis, and it has been shown that methylation changes might be used as prognostic biomarker in oral squamous cell carcinoma. Oral lichenoid disease (OLD) is the most common oral potentially malignant disorder in our region. The aim of this study was to perform the first wide DNA methylation study in OLD in order to investigate the relevance of DNA methylation changes in this premalignant disorder. MATERIALS AND METHODS Two different Illumina microarray platforms, namely the GoldenGate Cancer Panel I and the HumanMethylation27 DNA Analysis BeadChip, were utilized in the discovery phase to interrogate the methylation profile of 59 OLD cases and 9 healthy individuals. Top-ranked genes were further validated by pyrosequencing in a second sample set consisting of 160 OLD and 65 controls. RESULTS Our results show that the frequency of aberrant DNA methylation is rare in OLD, and this finding was further corroborated by pyrosequencing in the biological validation. CONCLUSIONS These findings reinforce the notion that molecular alterations associated with oral carcinogenesis do not seem to be common events in OLD, which in turn might explain the low rate of malignization of this disorder.
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Affiliation(s)
- N G Bediaga
- Oral Medicine & Pathology, Department of Stomatology II, UFI 11/25, University of the Basque Country (UPV/EHU), Leioa, Spain; BIOMICs Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
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