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Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features. EMBO Rep 2024; 25:2306-2322. [PMID: 38528170 PMCID: PMC11093987 DOI: 10.1038/s44319-024-00122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low-variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen-recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.
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Affiliation(s)
- Chandler A Sutherland
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
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2
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Marra PS, Seki T, Nishizawa Y, Chang G, Yamanishi K, Nishiguchi T, Shibata K, Braun P, Shinozaki G. Genome-wide DNA methylation analysis in female veterans with military sexual trauma and comorbid PTSD/MDD. J Affect Disord 2024; 351:624-630. [PMID: 38309478 PMCID: PMC11107447 DOI: 10.1016/j.jad.2024.01.241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND Military sexual trauma (MST) is a prevalent issue within the U.S. military. Victims are more likely to develop comorbid diseases such as posttraumatic stress disorder (PTSD) and major depressive disorder (MDD). Nonetheless, not everyone who suffers from MST develops PTSD and/or MDD. DNA methylation, which can regulate gene expression, might give us insight into the molecular mechanisms behind this discrepancy. Therefore, we sought to identify genomic loci and enriched biological pathways that differ between patients with and without MST, PTSD, and MDD. METHODS Saliva samples were collected from 113 female veterans. Following DNA extraction and processing, DNA methylation levels were measured through the Infinium HumanMethylationEPIC BeadChip array. We used limma and bump hunting methods to generate the differentially methylated positions and differentially methylated regions (DMRs), respectively. Concurrently, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome to find enriched pathways. RESULTS A DMR close to the transcription start site of ZFP57 was differentially methylated between subjects with and without PTSD, replicating previous findings and emphasizing the potential role of ZFP57 in PTSD susceptibility. In the pathway analyses, none survived multiple correction, although top GO terms included some potentially relevant to MST, PTSD, and MDD etiology. CONCLUSION We conducted one of the first DNA methylation analyses investigating MST along with PTSD and MDD. In addition, we found one DMR near ZFP57 to be associated with PTSD. The replication of this finding indicates further investigation of ZFP57 in PTSD may be warranted.
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Affiliation(s)
- Pedro S Marra
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA; University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Tomoteru Seki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, Tokyo Medical University, Shinjuku, Tokyo, Japan
| | - Yoshitaka Nishizawa
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Gloria Chang
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA; Developmental Psychology Graduate Program, Department of Psychological Sciences, University of Missouri, Columbia, MO, USA
| | - Kyosuke Yamanishi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Hyogo Medical University, Nishinomiya, Hyogo, Japan
| | - Tsuyoshi Nishiguchi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago, Tottori, Japan
| | - Kazuki Shibata
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Sumitomo Pharma Co. Ltd, Osaka, Osaka, Japan
| | - Patricia Braun
- Department of Biology, Clarke University, Dubuque, IA, USA
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
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Shastri GG, Sudre G, Ahn K, Jung B, Kolachana B, Auluck PK, Elnitski L, Marenco S, Shaw P. Cortico-striatal differences in the epigenome in attention-deficit/ hyperactivity disorder. Transl Psychiatry 2024; 14:189. [PMID: 38605038 PMCID: PMC11009227 DOI: 10.1038/s41398-024-02896-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
While epigenetic modifications have been implicated in ADHD through studies of peripheral tissue, to date there has been no examination of the epigenome of the brain in the disorder. To address this gap, we mapped the methylome of the caudate nucleus and anterior cingulate cortex in post-mortem tissue from fifty-eight individuals with or without ADHD. While no single probe showed adjusted significance in differential methylation, several differentially methylated regions emerged. These regions implicated genes involved in developmental processes including neurogenesis and the differentiation of oligodendrocytes and glial cells. We demonstrate a significant association between differentially methylated genes in the caudate and genes implicated by GWAS not only in ADHD but also in autistic spectrum, obsessive compulsive and bipolar affective disorders through GWAS. Using transcriptomic data available on the same subjects, we found modest correlations between the methylation and expression of genes. In conclusion, this study of the cortico-striatal methylome points to gene and gene pathways involved in neurodevelopment, consistent with studies of common and rare genetic variation, as well as the post-mortem transcriptome in ADHD.
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Affiliation(s)
- Gauri G Shastri
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Gustavo Sudre
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Kwangmi Ahn
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Benjamin Jung
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Bhaskar Kolachana
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Pavan K Auluck
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Philip Shaw
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA.
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Li JL, Jain N, Tamayo LI, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL. The association of cigarette smoking with DNA methylation and gene expression in human tissue samples. Am J Hum Genet 2024; 111:636-653. [PMID: 38490207 PMCID: PMC11023923 DOI: 10.1016/j.ajhg.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Cigarette smoking adversely affects many aspects of human health, and epigenetic responses to smoking may reflect mechanisms that mediate or defend against these effects. Prior studies of smoking and DNA methylation (DNAm), typically measured in leukocytes, have identified numerous smoking-associated regions (e.g., AHRR). To identify smoking-associated DNAm features in typically inaccessible tissues, we generated array-based DNAm data for 916 tissue samples from the GTEx (Genotype-Tissue Expression) project representing 9 tissue types (lung, colon, ovary, prostate, blood, breast, testis, kidney, and muscle). We identified 6,350 smoking-associated CpGs in lung tissue (n = 212) and 2,735 in colon tissue (n = 210), most not reported previously. For all 7 other tissue types (sample sizes 38-153), no clear associations were observed (false discovery rate 0.05), but some tissues showed enrichment for smoking-associated CpGs reported previously. For 1,646 loci (in lung) and 22 (in colon), smoking was associated with both DNAm and local gene expression. For loci detected in both lung and colon (e.g., AHRR, CYP1B1, CYP1A1), top CpGs often differed between tissues, but similar clusters of hyper- or hypomethylated CpGs were observed, with hypomethylation at regulatory elements corresponding to increased expression. For lung tissue, 17 hallmark gene sets were enriched for smoking-associated CpGs, including xenobiotic- and cancer-related gene sets. At least four smoking-associated regions in lung were impacted by lung methylation quantitative trait loci (QTLs) that co-localize with genome-wide association study (GWAS) signals for lung function (FEV1/FVC), suggesting epigenetic alterations can mediate the effects of smoking on lung health. Our multi-tissue approach has identified smoking-associated regions in disease-relevant tissues, including effects that are shared across tissue types.
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Affiliation(s)
- James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Niyati Jain
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lizeth I Tamayo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, University of Chicago, Chicago, IL 60637, USA.
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Shapiro BD, Battle A. Bayesian Multi-View Clustering given complex inter-view structure. F1000Res 2024; 11:1460. [PMID: 38495778 PMCID: PMC10940850 DOI: 10.12688/f1000research.126215.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 03/19/2024] Open
Abstract
Multi-view datasets are becoming increasingly prevalent. These datasets consist of different modalities that provide complementary characterizations of the same underlying system. They can include heterogeneous types of information with complex relationships, varying degrees of missingness, and assorted sample sizes, as is often the case in multi-omic biological studies. Clustering multi-view data allows us to leverage different modalities to infer underlying systematic structure, but most existing approaches are limited to contexts in which entities are the same across views or have clear one-to-one relationships across data types with a common sample size. Many methods also make strong assumptions about the similarities of clusterings across views. We propose a Bayesian multi-view clustering approach (BMVC) which can handle the realities of multi-view datasets that often have complex relationships and diverse structure. BMVC incorporates known and complex many-to-many relationships between entities via a probabilistic graphical model that enables the joint inference of clusterings specific to each view, but where each view informs the others. Additionally, BMVC estimates the strength of the relationships between each pair of views, thus moderating the degree to which it imposes dependence constraints. We benchmarked BMVC on simulated data to show that it accurately estimates varying degrees of inter-view dependence when inter-view relationships are not limited to one-to-one correspondence. Next, we demonstrated its ability to capture visually interpretable inter-view structure in a public health survey of individuals and households in Puerto Rico following Hurricane Maria. Finally, we showed that BMVC clusters integrate the complex relationships between multi-omic profiles of breast cancer patient data, improving the biological homogeneity of clusters and elucidating hypotheses for functional biological mechanisms. We found that BMVC leverages complex inter-view structure to produce higher quality clusters than those generated by standard approaches. We also showed that BMVC is a valuable tool for real-world discovery and hypothesis generation.
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Affiliation(s)
- Benjamin D. Shapiro
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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Collender P, Bozack AK, Veazie S, Nwanaji-Enwerem JC, Van Der Laan L, Kogut K, Riddell C, Eskenazi B, Holland N, Deardorff J, Cardenas A. Maternal adverse childhood experiences (ACEs) and DNA methylation of newborns in cord blood. Clin Epigenetics 2023; 15:162. [PMID: 37845746 PMCID: PMC10577922 DOI: 10.1186/s13148-023-01581-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/07/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Adverse childhood experiences (ACEs) increase the risk of poor health outcomes later in life. Psychosocial stressors may also have intergenerational health effects by which parental ACEs are associated with mental and physical health of children. Epigenetic programming may be one mechanism linking parental ACEs to child health. This study aimed to investigate epigenome-wide associations of maternal preconception ACEs with DNA methylation patterns of children. In the Center for the Health Assessment of Mothers and Children of Salinas study, cord blood DNA methylation was measured using the Illumina HumanMethylation450 BeadChip. Preconception ACEs, which occurred during the mothers' childhoods, were collected using a standard ACE questionnaire including 10 ACE indicators. Maternal ACE exposures were defined in this study as (1) the total number of ACEs; (2) the total number of ACEs categorized as 0, 1-3, and > 4; and (3) individual ACEs. Associations of ACE exposures with differential methylated positions, regions, and CpG modules determined using weighted gene co-expression network analysis were evaluated adjusting for covariates. RESULTS Data on maternal ACEs and cord blood DNA methylation were available for 196 mother/newborn pairs. One differential methylated position was associated with maternal experience of emotional abuse (cg05486260/FAM135B gene; q value < 0.05). Five differential methylated regions were significantly associated with the total number of ACEs, and 36 unique differential methylated regions were associated with individual ACEs (Šidák p value < 0.05). Fifteen CpG modules were significantly correlated with the total number of ACEs or individual ACEs, of which 8 remained significant in fully adjusted models (p value < 0.05). Significant modules were enriched for pathways related to neurological and immune development and function. CONCLUSIONS Maternal ACEs prior to conception were associated with cord blood DNA methylation of offspring at birth. Although there was limited overlap between differential methylated regions and CpGs in modules associated with ACE exposures, statistically significant regions and networks were related to genes involved in neurological and immune function. Findings may provide insights to pathways linking psychosocial stressors to health. Further research is needed to understand the relationship between changes in DNA methylation and child health.
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Affiliation(s)
- Phillip Collender
- Division of Environmental Health Sciences, University of California, Berkeley, CA, USA
| | - Anne K Bozack
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Research Park, 1701 Page Mill Road, Stanford, CA, 94304, USA
| | - Stephanie Veazie
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Jamaji C Nwanaji-Enwerem
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Department of Emergency Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Lars Van Der Laan
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Katherine Kogut
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
| | - Corinne Riddell
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
- Division of Community Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Nina Holland
- Division of Environmental Health Sciences, University of California, Berkeley, CA, USA
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
| | - Julianna Deardorff
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
- Division of Community Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Research Park, 1701 Page Mill Road, Stanford, CA, 94304, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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7
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.11.23296741. [PMID: 37873138 PMCID: PMC10592992 DOI: 10.1101/2023.10.11.23296741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
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Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with distinct genomic and epigenomic features. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523861. [PMID: 36711945 PMCID: PMC9882162 DOI: 10.1101/2023.01.12.523861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.
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Affiliation(s)
- Chandler A Sutherland
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA 94720
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 94720
| | - J Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA 94720
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9
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Perini S, Filosi M, Domenici E. Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs. Transl Psychiatry 2023; 13:109. [PMID: 37012247 PMCID: PMC10070641 DOI: 10.1038/s41398-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
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Affiliation(s)
- Samuel Perini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
- EURAC Research, Bolzano, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy.
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.
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10
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Cheng X, Wei Y, Zhang Z, Wang F, He J, Wang R, Xu Y, Keerman M, Zhang S, Zhang Y, Bi J, Yao J, He M. Plasma PFOA and PFOS Levels, DNA Methylation, and Blood Lipid Levels: A Pilot Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17039-17051. [PMID: 36374530 DOI: 10.1021/acs.est.2c04107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Exposure to perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) is associated with blood lipids in adults, but the underlying mechanisms remain unclear. This pilot study aimed to investigate the associations between PFOA or PFOS and epigenome-wide DNA methylation and assess the mediating effect of DNA methylation on the PFOA/PFOS-blood lipid association. We measured plasma PFOA/PFOS and leukocyte DNA methylation in 98 patients enrolled from the hospital between October 2018 and August 2019. The median plasma PFOA/PFOS levels were 0.85 and 2.29 ng/mL. Plasma PFOA and PFOS levels were significantly associated with elevated total cholesterol (TC) and low-density lipoprotein cholesterol (LDL) levels. There were 63/87 CpG positions and 8/11 differentially methylated regions (DMRs) associated with plasma PFOA/PFOS levels, respectively. In addition, 5 CpG positions (annotated to AFF3, CREB5, NRG2, USF2, and intergenic region) and one DMR annotated to IRF6 may mediate the association between plasma PFOA/PFOS and LDL levels (mediated proportion from 7.29 to 46.77%); two CpG positions may mediate the association between plasma PFOA/PFOS and TC levels (annotated to CREB5 and USF2, mediated proportion is around 30%). The data suggest that PFOA/PFOS exposure alters DNA methylation. More importantly, the association of PFOA/PFOS with lipid indicators was partly mediated by DNA methylation changes in lipid metabolism-related genes.
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Affiliation(s)
- Xu Cheng
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yue Wei
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Zefang Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Fei Wang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Jia He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Ruixin Wang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yali Xu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Mulatibieke Keerman
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Shiyang Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Ying Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Jiao Bi
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Jinqiu Yao
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
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11
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Phillips RV, Wei L, Cardenas A, Hubbard AE, McHale CM, Vermeulen R, Wei H, Smith MT, Zhang L, Lan Q, Rothman N. Epigenome-wide association studies of occupational exposure to benzene and formaldehyde. Epigenetics 2022; 17:2259-2277. [PMID: 36017556 PMCID: PMC9665125 DOI: 10.1080/15592294.2022.2115604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022] Open
Abstract
Sufficient evidence supports a relationship between certain myeloid neoplasms and exposure to benzene or formaldehyde. DNA methylation could underlie benzene- and formaldehyde-induced health outcomes, but data in exposed human populations are limited. We conducted two cross-sectional epigenome-wide association studies (EWAS), one in workers exposed to benzene and another in workers exposed to formaldehyde. Using HumanMethylation450 BeadChips, we investigated differences in blood cell DNA methylation among 50 benzene-exposed subjects and 48 controls, and among 31 formaldehyde-exposed subjects and 40 controls. We performed CpG-level and regional-level analyses. In the benzene EWAS, we found genome-wide significant alterations, i.e., FWER-controlled P-values <0.05, in the mean and variance of methylation at 22 and 318 CpG sites, respectively, and in mean methylation of a large genomic region. Pathway analysis of genes corresponding to benzene-associated differential methylation sites revealed an impact on the AMPK signalling pathway. In formaldehyde-exposed subjects compared to controls, 9 CpGs in the DUSP22 gene promoter had genome-wide significant decreased methylation variability and a large region of the HOXA5 promoter with 44 CpGs was hypomethylated. Our findings suggest that DNA methylation may contribute to the pathogenesis of diseases related to benzene and formaldehyde exposure. Aberrant expression and methylation of HOXA5 previously has been shown to be clinically significant in myeloid leukaemias. The tumour suppressor gene DUSP22 is a potential biomarker of exposure to formaldehyde, and irregularities have been associated with multiple exposures and diseases.
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Affiliation(s)
- Rachael V. Phillips
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Linqing Wei
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Andres Cardenas
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Alan E. Hubbard
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Cliona M. McHale
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Roel Vermeulen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteit Utrecht (UU), Utrecht, The Netherlands
| | - Hu Wei
- Division of Cancer Epidemiology and Genetics, Occupational and Environmental Epidemiology Branch, NCI, NIH, DHHS, Bethesda, MD, USA
| | - Martyn T. Smith
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Luoping Zhang
- School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, Occupational and Environmental Epidemiology Branch, NCI, NIH, DHHS, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, Occupational and Environmental Epidemiology Branch, NCI, NIH, DHHS, Bethesda, MD, USA
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12
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Armignacco R, Reel PS, Reel S, Jouinot A, Septier A, Gaspar C, Perlemoine K, Larsen CK, Bouys L, Braun L, Riester A, Kroiss M, Bonnet-Serrano F, Amar L, Blanchard A, Gimenez-Roqueplo AP, Prejbisz A, Januszewicz A, Dobrowolski P, Davies E, MacKenzie SM, Rossi GP, Lenzini L, Ceccato F, Scaroni C, Mulatero P, Williams TA, Pecori A, Monticone S, Beuschlein F, Reincke M, Zennaro MC, Bertherat J, Jefferson E, Assié G. Whole blood methylome-derived features to discriminate endocrine hypertension. Clin Epigenetics 2022; 14:142. [PMCID: PMC9635165 DOI: 10.1186/s13148-022-01347-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Arterial hypertension represents a worldwide health burden and a major risk factor for cardiovascular morbidity and mortality. Hypertension can be primary (primary hypertension, PHT), or secondary to endocrine disorders (endocrine hypertension, EHT), such as Cushing's syndrome (CS), primary aldosteronism (PA), and pheochromocytoma/paraganglioma (PPGL). Diagnosis of EHT is currently based on hormone assays. Efficient detection remains challenging, but is crucial to properly orientate patients for diagnostic confirmation and specific treatment. More accurate biomarkers would help in the diagnostic pathway. We hypothesized that each type of endocrine hypertension could be associated with a specific blood DNA methylation signature, which could be used for disease discrimination. To identify such markers, we aimed at exploring the methylome profiles in a cohort of 255 patients with hypertension, either PHT (n = 42) or EHT (n = 213), and at identifying specific discriminating signatures using machine learning approaches. Results Unsupervised classification of samples showed discrimination of PHT from EHT. CS patients clustered separately from all other patients, whereas PA and PPGL showed an overall overlap. Global methylation was decreased in the CS group compared to PHT. Supervised comparison with PHT identified differentially methylated CpG sites for each type of endocrine hypertension, showing a diffuse genomic location. Among the most differentially methylated genes, FKBP5 was identified in the CS group. Using four different machine learning methods—Lasso (Least Absolute Shrinkage and Selection Operator), Logistic Regression, Random Forest, and Support Vector Machine—predictive models for each type of endocrine hypertension were built on training cohorts (80% of samples for each hypertension type) and estimated on validation cohorts (20% of samples for each hypertension type). Balanced accuracies ranged from 0.55 to 0.74 for predicting EHT, 0.85 to 0.95 for predicting CS, 0.66 to 0.88 for predicting PA, and 0.70 to 0.83 for predicting PPGL. Conclusions The blood DNA methylome can discriminate endocrine hypertension, with methylation signatures for each type of endocrine disorder. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01347-y.
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Affiliation(s)
- Roberta Armignacco
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Parminder S. Reel
- grid.8241.f0000 0004 0397 2876Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF UK
| | - Smarti Reel
- grid.8241.f0000 0004 0397 2876Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF UK
| | - Anne Jouinot
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.440907.e0000 0004 1784 3645Institut Curie, INSERM U900, MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Amandine Septier
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Cassandra Gaspar
- Sorbonne Université, INSERM, UMS Production et Analyse de données en Sciences de la vie et en Santé, PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, 75013 Paris, France
| | - Karine Perlemoine
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Casper K. Larsen
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France
| | - Lucas Bouys
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France
| | - Leah Braun
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna Riester
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Matthias Kroiss
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fidéline Bonnet-Serrano
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.411784.f0000 0001 0274 3893Service d’Hormonologie, AP-HP, Hôpital Cochin, F-75014 Paris, France
| | - Laurence Amar
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France ,grid.414093.b0000 0001 2183 5849Unité Hypertension Artérielle, AP-HP, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Anne Blanchard
- grid.414093.b0000 0001 2183 5849Centre d’Investigations Cliniques 9201, AP-HP, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Anne-Paule Gimenez-Roqueplo
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France ,grid.414093.b0000 0001 2183 5849Département de Médecine Génomique des Tumeurs et des Cancers, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Aleksander Prejbisz
- grid.418887.aDepartment of Hypertension, Institute of Cardiology, Warsaw, Poland
| | - Andrzej Januszewicz
- grid.418887.aDepartment of Hypertension, Institute of Cardiology, Warsaw, Poland
| | - Piotr Dobrowolski
- grid.418887.aDepartment of Hypertension, Institute of Cardiology, Warsaw, Poland
| | - Eleanor Davies
- grid.8756.c0000 0001 2193 314XBHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA UK
| | - Scott M. MacKenzie
- grid.8756.c0000 0001 2193 314XBHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA UK
| | - Gian Paolo Rossi
- Department of Medicine-DIMED, Emergency and Hypertension Unit, University of Padova, University Hospital, Padua, Italy
| | - Livia Lenzini
- Department of Medicine-DIMED, Emergency and Hypertension Unit, University of Padova, University Hospital, Padua, Italy
| | - Filippo Ceccato
- grid.411474.30000 0004 1760 2630UOC Endocrinologia, Dipartimento di Medicina DIMED, Azienda Ospedaliera-Università di Padova, Padua, Italy
| | - Carla Scaroni
- grid.411474.30000 0004 1760 2630UOC Endocrinologia, Dipartimento di Medicina DIMED, Azienda Ospedaliera-Università di Padova, Padua, Italy
| | - Paolo Mulatero
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Tracy A. Williams
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Alessio Pecori
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Silvia Monticone
- grid.7605.40000 0001 2336 6580Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, Turin, Italy
| | - Felix Beuschlein
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany ,grid.412004.30000 0004 0478 9977Klinikfür Endokrinologie, Diabetologie Und Klinische Ernährung, UniversitätsSpital Zürich (USZ) and Universität Zürich (UZH), Raemistrasse 100, 8091 Zurich, Switzerland
| | - Martin Reincke
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maria-Christina Zennaro
- grid.462416.30000 0004 0495 1460Université Paris Cité, Inserm, PARCC, F-75015 Paris, France ,grid.414093.b0000 0001 2183 5849Service de Génétique, AP-HP, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Jérôme Bertherat
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.411784.f0000 0001 0274 3893Service d’Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, F-75014 Paris, France
| | - Emily Jefferson
- grid.8241.f0000 0004 0397 2876Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD2 4BF UK ,grid.8756.c0000 0001 2193 314XInstitute of Health and Wellbeing, University of Glasgow, Glasgow, G12 8RZ UK
| | - Guillaume Assié
- grid.462098.10000 0004 0643 431XUniversité Paris Cité, CNRS, INSERM, Institut Cochin, F-75014 Paris, France ,grid.411784.f0000 0001 0274 3893Service d’Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, F-75014 Paris, France
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13
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Zachou K, Arvaniti P, Lyberopoulou A, Sevdali E, Speletas M, Ioannou M, Koukoulis GK, Renaudineau Y, Dalekos GN. Altered DNA methylation pattern characterizes the peripheral immune cells of patients with autoimmune hepatitis. Liver Int 2022; 42:1355-1368. [PMID: 35108441 DOI: 10.1111/liv.15176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/18/2021] [Accepted: 01/12/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Little is known about the impact of DNA methylation modifications on autoimmune hepatitis (AIH) pathogenesis and therapeutic response. We investigated the potential alterations of DNA methylation in AIH peripheral lymphocytes at diagnosis and remission. METHODS Ten AIH patients at diagnosis (time-point 1; AIH-tp1), 8/10 following biochemical response (time-point 2; AIH-tp2), 9 primary biliary cholangitis (PBC) and 10 healthy controls (HC) were investigated. Peripheral CD19(+) and CD4(+) cells were isolated. Global DNA methylation (5m C)/hydroxymethylation (5hm C) was studied by ELISAs. mRNA of DNA methylation (DNMT1/3A/3B) and their counteracting hydroxymethylation enzymes (TET1/2/3) was determined by quantitative RT-PCR. Epigenome wide association study (EWAS) was performed in CD4(+) cells (Illumina HumanMethylation 850 K array) in AIH and HC. Total 5m C/5hm C was also assessed by immunohistochemistry (IHC) on paraffin-embedded liver sections. RESULTS Reduced TET1 and increased DNMT3A mRNA levels characterized CD19(+) and CD4(+)-lymphocytes from AIH-tp1 compared to HC and PBC, respectively, without affecting global DNA 5m C/5hm C. In AIH-tp1, CD4(+) DNMT3A expression was negatively correlated with serum IgG (P = .03). In remission, DNMT3A decreased in both CD19(+) and CD4(+) cells compared to AIH-tp1 (P = .02, P = .03 respectively). EWAS in CD4(+) cells from AIH patients confirmed important modifications in genes implicated in immune responses (HLA-DP, TNF, lnRNAs and CD86). IHC showed increased 5hm C staining of periportal infiltrating lymphocytes in AIH-tp1 compared to HC and PBC. CONCLUSION Altered TET1 and DNMT3A expressions, characterize peripheral lymphocytes in AIH. DNMT3A was associated with disease activity and decreased following remission. Gene DNA methylation modifications affect immunological pathways that may play an important role in AIH pathogenesis.
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Affiliation(s)
- Kalliopi Zachou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Pinelopi Arvaniti
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Aggeliki Lyberopoulou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Eirini Sevdali
- Faculty of Medicine, Department of Immunology and Histocompatibility, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Matthaios Speletas
- Faculty of Medicine, Department of Immunology and Histocompatibility, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Maria Ioannou
- Faculty of Medicine, Department of Pathology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - George K Koukoulis
- Faculty of Medicine, Department of Pathology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Yves Renaudineau
- INSERN U1291, CNR U5051, University Toulouse III, Toulouse Institute for infectious and inflammatory diseases, Toulouse, France.,Department of Immunology, Purpan University Hospital Toulouse, Toulouse, France
| | - George N Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
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14
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Epigenome-wide association analyses of active injection drug use. Drug Alcohol Depend 2022; 235:109431. [PMID: 35395503 DOI: 10.1016/j.drugalcdep.2022.109431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Injection drug use (IDU) is prevalent in the US and is associated with substantial risk of blood-borne infections, morbidity, and mortality. However, the spectrum of its biologic effects on DNA methylation in blood is not well characterized. METHODS 401 participants (Mage = 47.9; 68% male; 90% African American) over several timepoints (1054 visits) were drawn from a longitudinal cohort of people who inject drugs. DNA methylation was measured among buffy coat samples from the 1054 visits. Compared to samples collected after ≥ 6 months of abstinence, separate EWAS were conducted for active injecting of any drug, quantitative injection frequency, injecting of heroin and injecting of cocaine. Linear mixed effect models were used and analyses were adjusted for repeated measurements and key technical, biological, and sociodemographic characteristics. RESULTS We found epigenome-wide significant CpG sites associated with active injection (cg10636246, AIM2, p = 2.33 × 10-8) and injection intensity (cg13117953, p = 4.30 × 10-8). We found converging evidence that cg10636246 (AIM2), cg23110600 (PRKCH), cg03546163 (FKBP5), cg04590956 (GMCL1), and cg16317961 (MAPRE2) were among the top 0.1% significantly differentially methylated CpG sites shared across the five EWAS. Top ranked CpGs among the five EWAS were enriched (p < 0.0001) in AIM2 inflammasome complex, T cell migration, insulin regulation and epinephrine synthesis pathways. During periods of active injection, samples had 0.46 years of epigenetic age acceleration relative to the abstinence period, within the same subject (p = 0.03). CONCLUSIONS Findings from this study demonstrate modest, common, and specific effects on DNA methylation during a relatively short time between periods of active drug injection and abstinence.
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15
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Han B, Fang T, Wang Y, Zhang Y, Xue Y. TGFβ2 is a Prognostic Biomarker for Gastric Cancer and is Associated With Methylation and Immunotherapy Responses. Front Genet 2022; 13:808041. [PMID: 35620459 PMCID: PMC9127534 DOI: 10.3389/fgene.2022.808041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/25/2022] [Indexed: 12/24/2022] Open
Abstract
TGFβ signaling plays a key role in cancer progression and by shaping tumor architecture and inhibiting the anti-tumor activity of immune cells. It was reported that high expression of TGFβ can promote the invasion and metastasis of cancer cells in a variety of tumors. However, there are few studies on TGFβ2 and its methylation in gastric cancer. We analyzed the Harbin Medical University Cancer Hospital (HMUCH) sequencing data and used public data to explore the potential function and prognostic value of TGFβ2 and its methylation in gastric cancer. In this study, we used the ssGSEA algorithm to quantify 23 methylation sites related to TGFβ2. Survival analysis showed that high expression of TGFβ2 and hypomethylation levels of TGFβ2 were negative factors in the prognosis of gastric cancer. Functional enrichment analysis of methylation revealed that methylation of different TGFβ2 methylation scores was mainly involved in energy metabolism, extracellular matrix formation and cell cycle regulation. In the gastric cancer microenvironment TGFβ2 was associated with high levels of multiple immune cell infiltration and cytokine expression, and high TGFβ2 expression was significantly and positively correlated with stemness markers, stromalscore and EMT. Gene set enrichment analysis also revealed an important role of TGFβ2 in promoting EMT. In addition, we discussed the relationship between TGFβ2 and immunotherapy. The expression of PD-1, PD-L1 and CTLA-4 was elevated in the TGFβ2 high expression group. Also when TGFβ2 was highly expressed, the responsiveness of immune checkpoint blockade (ICB) was significantly enhanced. This indicates that TGFβ2 may become an indicator for predicting the efficacy of immunosuppressive agents and a potential target for immunotherapy.
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Affiliation(s)
- Bangling Han
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tianyi Fang
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yimin Wang
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yongle Zhang
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yingwei Xue
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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16
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Functional Enrichment Analysis of Regulatory Elements. Biomedicines 2022; 10:biomedicines10030590. [PMID: 35327392 PMCID: PMC8945021 DOI: 10.3390/biomedicines10030590] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 01/27/2023] Open
Abstract
Statistical methods for enrichment analysis are important tools to extract biological information from omics experiments. Although these methods have been widely used for the analysis of gene and protein lists, the development of high-throughput technologies for regulatory elements demands dedicated statistical and bioinformatics tools. Here, we present a set of enrichment analysis methods for regulatory elements, including CpG sites, miRNAs, and transcription factors. Statistical significance is determined via a power weighting function for target genes and tested by the Wallenius noncentral hypergeometric distribution model to avoid selection bias. These new methodologies have been applied to the analysis of a set of miRNAs associated with arrhythmia, showing the potential of this tool to extract biological information from a list of regulatory elements. These new methods are available in GeneCodis 4, a web tool able to perform singular and modular enrichment analysis that allows the integration of heterogeneous information.
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17
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Domingo-Relloso A, Bozack A, Kiihl S, Rodriguez-Hernandez Z, Rentero-Garrido P, Casasnovas JA, Leon-Latre M, Garcia-Barrera T, Gomez-Ariza JL, Moreno B, Cenarro A, de Marco G, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Navas-Acien A, Gamble M, Tellez-Plaza M. Arsenic exposure and human blood DNA methylation and hydroxymethylation profiles in two diverse populations from Bangladesh and Spain. ENVIRONMENTAL RESEARCH 2022; 204:112021. [PMID: 34516978 PMCID: PMC8734953 DOI: 10.1016/j.envres.2021.112021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Associations of arsenic (As) with the sum of 5-mC and 5-hmC levels have been reported; however, As exposure-related differences of the separated 5-mC and 5-hmC markers have rarely been studied. METHODS In this study, we evaluated the association of arsenic exposure biomarkers and 5-mC and 5-hmC in 30 healthy men (43-55 years) from the Aragon Workers Health Study (AWHS) (Spain) and 31 healthy men (31-50 years) from the Folic Acid and Creatinine Trial (FACT) (Bangladesh). We conducted 5-mC and 5-hmC profiling using Infinium MethylationEPIC arrays, on paired standard and modified (ox-BS in AWHS and TAB in FACT) bisulfite converted blood DNA samples. RESULTS The median for the sum of urine inorganic and methylated As species (ΣAs) (μg/L) was 12.5 for AWHS and 89.6 for FACT. The median of blood As (μg/L) was 8.8 for AWHS and 10.2 for FACT. At a statistical significance p-value cut-off of 0.01, the differentially methylated (DMP) and hydroxymethylated (DHP) positions were mostly located in different genomic sites. Several DMPs and DHPs were consistently found in AWHS and FACT both for urine ΣAs and blood models, being of special interest those attributed to the DIP2C gene. Three DMPs (annotated to CLEC12A) for AWHS and one DHP (annotated to NPLOC4) for FACT remained statistically significant after false discovery rate (FDR) correction. Pathways related to chronic diseases including cardiovascular, cancer and neurological were enriched. CONCLUSIONS While we identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, differences in As-related epigenetic sites across the study populations may additionally reflect low and high As-specific associations. This work contributes a deeper understanding of potential epigenetic dysregulations of As. However, further research is needed to confirm biological consequences associated with DIP2C epigenetic regulation and to investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.
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Affiliation(s)
- Arce Domingo-Relloso
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain; Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA; Department of Statistics and Operations Research, University of Valencia, Spain
| | - Anne Bozack
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA; Department of Environmental Health Sciences, School of Public Health, University of California, Berkeley, USA
| | - Samara Kiihl
- Department of Statistics, State University of Campinas, Brazil
| | - Zulema Rodriguez-Hernandez
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Pilar Rentero-Garrido
- Precision Medicine Unit, Biomedical Research Institute Hospital Clinic de Valencia INCLIVA, Valencia, Spain
| | - J Antonio Casasnovas
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Montserrat Leon-Latre
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Tamara Garcia-Barrera
- Research Center on Natural Resources, Health and the Environment, Department of Chemistry, University of Huelva, Huelva, Spain
| | - J Luis Gomez-Ariza
- Research Center on Natural Resources, Health and the Environment, Department of Chemistry, University of Huelva, Huelva, Spain
| | - Belen Moreno
- Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Ana Cenarro
- CIBERCV, And Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain; Aragon Health Research Institute Foundation (IIS Aragon), University of Zaragoza, Zaragoza, Spain
| | - Griselda de Marco
- Genomics Area, Foundation for the Promotion of Health and Biomedical Research of the Valencian Region (FISABIO), Valencia, Spain
| | - Faruque Parvez
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Abu B Siddique
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Hasan Shahriar
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Mohammad N Uddin
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Tariqul Islam
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Mary Gamble
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Maria Tellez-Plaza
- Integrative Epidemiology Group, Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Instituto de Salud Carlos III, Madrid, Spain.
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18
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Rathod A, Zhang H, Arshad SH, Ewart S, Relton CL, Karmaus W, Holloway JW. DNA Methylation and Asthma Acquisition during Adolescence and Post-Adolescence, an Epigenome-Wide Longitudinal Study. J Pers Med 2022; 12:202. [PMID: 35207690 PMCID: PMC8877984 DOI: 10.3390/jpm12020202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/19/2022] [Indexed: 02/01/2023] Open
Abstract
The role of epigenetics in the pathogenesis of asthma acquisition in adolescence and post-adolescence has been unknown. We carried out a longitudinal epigenome-wide association study, using data from the Isle of Wight Birth Cohort (IOWBC). To improve statistical power, we first screened CpGs based on associations of DNA methylation (DNAm) at an age of 10 years (pre-adolescence) with asthma acquisition at 10-18 years (during adolescence). A logistic regression with repeated measures was applied to CpGs that passed screening to examine the associations of pre-adolescence DNAm with asthma acquisition from 10-18 years and 18-26 years, with an interaction term to evaluate transition period specificity. Findings were further tested in an independent birth cohort, ALSPAC. In total, 205 CpGs (with 150 being females) showed associations with asthma acquisition (main or interaction effects) at FDR = 0.05 in IOWBC, of which 112 (90 being females) showed consistent associations in the ALSPAC. Genes that the identified CpGs were mapped to, e.g., AKAP1 and ENO1, have been shown to be associated with the risk of asthma. Our findings indicated that DNAm at specific CpGs was associated with asthma acquisition. CpGs showing such associations were likely to be different between males and females and, at certain CpGs, were unique to a specific transition period.
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Affiliation(s)
- Aniruddha Rathod
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight PO30 5TG, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA;
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1QU, UK;
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
- National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust, University of Bristol, Bristol BS8 2BN, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - John W. Holloway
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
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19
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Ghamrawi R, Velickovic I, Milicevic O, White WM, Thistlethwaite LR, Cunningham JM, Milosavljevic A, Milic NM, Garovic VD. Buffy Coat DNA Methylation Profile Is Representative of Methylation Patterns in White Blood Cell Types in Normal Pregnancy. Front Bioeng Biotechnol 2022; 9:782843. [PMID: 35071203 PMCID: PMC8766967 DOI: 10.3389/fbioe.2021.782843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background: We aimed to assess the extent to which the buffy coat DNA methylome is representative of methylation patterns in constitutive white blood cell (WBC) types in normal pregnancy. Methods: A comparison of differential methylation of buffy coat DNA vs DNA isolated from polymorphonuclear (PMN) and lymphocytic fractions was performed for each blood sample obtained within 24 h prior to delivery from 29 normotensive pregnant women. Methylation profiles were obtained using an Illumina Human Methylation 450 BeadChip and CHaMP bioinformatics pipeline. A subset of differentially methylated probes (DMPs) showing discordant methylation were further investigated using statistical modeling and enrichment analysis. Results: The smallest number of DMPs was found between the buffy coat and the PMN fraction (2.96%). Pathway enrichment analysis of the DMPs identified biological pathways involved in the particular leukocyte lineage, consistent with perturbations during isolation. The comparisons between the buffy coat and the isolated fractions as a group using linear modeling yielded a small number of probes (∼29,000) with discordant methylation. Demethylation of probes in the buffy coat compared to derived cell lines was more common and was prevalent in shelf and open sea regions. Conclusion: Buffy coat is representative of methylation patterns in WBC types in normal pregnancy. The differential methylations are consistent with perturbations during isolation of constituent cells and likely originate in vitro due to the physical stress during cell separation and are of no physiological relevance. These findings help the interpretation of DNA methylation profiling in pregnancy and numerous other conditions.
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Affiliation(s)
- Ranine Ghamrawi
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN, United States
| | - Igor Velickovic
- Department of Medical Statistics and Informatics, Medical Faculty University of Belgrade, Belgrade, Serbia
| | - Ognjen Milicevic
- Department of Medical Statistics and Informatics, Medical Faculty University of Belgrade, Belgrade, Serbia
| | - Wendy M White
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States.,Department of Perinatology, Olmsted Medical Center, Rochester, MN, United States
| | | | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Aleksandar Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Natasa M Milic
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Medical Statistics and Informatics, Medical Faculty University of Belgrade, Belgrade, Serbia
| | - Vesna D Garovic
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States
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20
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Armignacco R, Jouinot A, Bouys L, Septier A, Lartigue T, Neou M, Gaspar C, Perlemoine K, Braun L, Riester A, Bonnet-Serrano F, Blanchard A, Amar L, Scaroni C, Ceccato F, Rossi GP, Williams TA, Larsen CK, Allassonnière S, Zennaro MC, Beuschlein F, Reincke M, Bertherat J, Assié G. Identification of glucocorticoid-related molecular signature by whole blood methylome analysis. Eur J Endocrinol 2022; 186:297-308. [PMID: 34914631 PMCID: PMC8789024 DOI: 10.1530/eje-21-0907] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/16/2021] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Cushing's syndrome represents a state of excessive glucocorticoids related to glucocorticoid treatments or to endogenous hypercortisolism. Cushing's syndrome is associated with high morbidity, with significant inter-individual variability. Likewise, adrenal insufficiency is a life-threatening condition of cortisol deprivation. Currently, hormone assays contribute to identify Cushing's syndrome or adrenal insufficiency. However, no biomarker directly quantifies the biological glucocorticoid action. The aim of this study was to identify such markers. DESIGN We evaluated whole blood DNA methylome in 94 samples obtained from patients with different glucocorticoid states (Cushing's syndrome, eucortisolism, adrenal insufficiency). We used an independent cohort of 91 samples for validation. METHODS Leukocyte DNA was obtained from whole blood samples. Methylome was determined using the Illumina methylation chip array (~850 000 CpG sites). Both unsupervised (principal component analysis) and supervised (Limma) methods were used to explore methylome profiles. A Lasso-penalized regression was used to select optimal discriminating features. RESULTS Whole blood methylation profile was able to discriminate samples by their glucocorticoid status: glucocorticoid excess was associated with DNA hypomethylation, recovering within months after Cushing's syndrome correction. In Cushing's syndrome, an enrichment in hypomethylated CpG sites was observed in the region of FKBP5 gene locus. A methylation predictor of glucocorticoid excess was built on a training cohort and validated on two independent cohorts. Potential CpG sites associated with the risk for specific complications, such as glucocorticoid-related hypertension or osteoporosis, were identified, needing now to be confirmed on independent cohorts. CONCLUSIONS Whole blood DNA methylome is dynamically impacted by glucocorticoids. This biomarker could contribute to better assessment of glucocorticoid action beyond hormone assays.
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Affiliation(s)
- Roberta Armignacco
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
- Correspondence should be addressed to R Armignacco or G Assié; or
| | - Anne Jouinot
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Lucas Bouys
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Amandine Septier
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Thomas Lartigue
- ARAMIS Project-Team, Inria Paris, France
- CMAP, UMR 7641, CNRS, École polytechnique, I.P. Paris, France
| | - Mario Neou
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Cassandra Gaspar
- Sorbonne Université, Inserm, UMS Pass, Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, Paris, France
| | - Karine Perlemoine
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Leah Braun
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna Riester
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fidéline Bonnet-Serrano
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service d’Hormonologie, Paris, France
| | - Anne Blanchard
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Centre d’Investigations Cliniques 9201, Paris, France
| | - Laurence Amar
- Université de Paris, PARCC, INSERM, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Unité Hypertension Artérielle, Paris, France
| | - Carla Scaroni
- UOC Endocrinologia, Dipartimento di Medicina DIMED, Azienda Ospedaliera-Università di Padova, Padua, Italy
| | - Filippo Ceccato
- UOC Endocrinologia, Dipartimento di Medicina DIMED, Azienda Ospedaliera-Università di Padova, Padua, Italy
| | - Gian Paolo Rossi
- Clinica dell’Ipertensione Arteriosa, Department of Medicine-DIMED, University of Padua, Padua, Italy
| | - Tracy Ann Williams
- Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Maria-Christina Zennaro
- Université de Paris, PARCC, INSERM, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Génétique, Paris, France
| | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, UniversitätsSpital Zürich, Zürich, Switzerland
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jérôme Bertherat
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service d’Endocrinologie, Center for Rare Adrenal Diseases, Paris, France
| | - Guillaume Assié
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service d’Endocrinologie, Center for Rare Adrenal Diseases, Paris, France
- Correspondence should be addressed to R Armignacco or G Assié; or
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21
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Brorson I, Eriksson A, Høgestøl E, Leikfoss I, Harbo H, Berge T, Vitelli V, Bos S. Global DNA methylation changes in treated and untreated MS patients measured over time. J Neuroimmunol 2022; 364:577808. [DOI: 10.1016/j.jneuroim.2022.577808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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22
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Epigenetic Age Acceleration Is Not Associated with Age-Related Macular Degeneration. Int J Mol Sci 2021; 22:ijms222413457. [PMID: 34948253 PMCID: PMC8705580 DOI: 10.3390/ijms222413457] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
DNA methylation age (DNAm age) estimation is a powerful biomarker of human ageing. To date, epigenetic clocks have not been evaluated in age-related macular degeneration (AMD). Here, we perform genome-wide DNA methylation analyses in blood of AMD patients with a documented smoking history (14 AMD, 16 Normal), identifying loci of differential methylation (DML) with a relaxed p-value criterion (p ≤ 10−4). We conduct DNAm age analyses using the Horvath-multi tissue, Hannum and Skin & Blood epigenetic clocks in both blood and retinal pigment epithelium (RPE). We perform Ingenuity Pathway Analysis Causal Network Analysis (IPA CNA) on the topmost significantly differentially methylated CpG probes in blood and RPE. Results show poor performance of epigenetic clocks in RPE. Epigenetic age acceleration (EAA) was not observed in AMD. However, we observe positive EAA in blood of smokers, and in smokers with AMD. DML analysis revealed hypomethylation at cg04953735 within RPTOR (p = 6.51 × 10−5; Δβ = −11.95%). IPA CNA in the RPE also identified RPTOR as the putative master regulator, predicted to be inhibited in AMD. In conclusion, this is the first study evaluating an association of epigenetic ageing in AMD. We posit a role for RPTOR as a common master regulator of methylation changes in the RPE in AMD.
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23
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Bozack AK, Rifas-Shiman SL, Coull BA, Baccarelli AA, Wright RO, Amarasiriwardena C, Gold DR, Oken E, Hivert MF, Cardenas A. Prenatal metal exposure, cord blood DNA methylation and persistence in childhood: an epigenome-wide association study of 12 metals. Clin Epigenetics 2021; 13:208. [PMID: 34798907 PMCID: PMC8605513 DOI: 10.1186/s13148-021-01198-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022] Open
Abstract
Background Prenatal exposure to essential and non-essential metals impacts birth and child health, including fetal growth and neurodevelopment. DNA methylation (DNAm) may be involved in pathways linking prenatal metal exposure and health. In the Project Viva cohort, we analyzed the extent to which metals (As, Ba, Cd, Cr, Cs, Cu, Hg, Mg, Mn, Pb, Se, and Zn) measured in maternal erythrocytes were associated with differentially methylated positions (DMPs) and regions (DMRs) in cord blood and tested if associations persisted in blood collected in mid-childhood. We measured metal concentrations in first-trimester maternal erythrocytes, and DNAm in cord blood (N = 361) and mid-childhood blood (N = 333, 6–10 years) with the Illumina HumanMethylation450 BeadChip. For each metal individually, we tested for DMPs using linear models (considered significant at FDR < 0.05), and for DMRs using comb-p (Sidak p < 0.05). Covariates included biologically relevant variables and estimated cell-type composition. We also performed sex-stratified analyses. Results Pb was associated with decreased methylation of cg20608990 (CASP8) (FDR = 0.04), and Mn was associated with increased methylation of cg02042823 (A2BP1) in cord blood (FDR = 9.73 × 10–6). Both associations remained significant but attenuated in blood DNAm collected at mid-childhood (p < 0.01). Two and nine Mn-associated DMPs were identified in male and female infants, respectively (FDR < 0.05), with two and six persisting in mid-childhood (p < 0.05). All metals except Ba and Pb were associated with ≥ 1 DMR among all infants (Sidak p < 0.05). Overlapping DMRs annotated to genes in the human leukocyte antigen (HLA) region were identified for Cr, Cs, Cu, Hg, Mg, and Mn. Conclusions Prenatal metal exposure is associated with DNAm, including DMRs annotated to genes involved in neurodevelopment. Future research is needed to determine if DNAm partially explains the relationship between prenatal metal exposures and health outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01198-z.
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Affiliation(s)
- Anne K Bozack
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, 2121 Berkeley Way, Room 5302, Berkeley, CA, 94720, USA
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Brent A Coull
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health and Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, NY, New York City, USA
| | - Chitra Amarasiriwardena
- Department of Environmental Medicine and Public Health and Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, NY, New York City, USA
| | - Diane R Gold
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, 2121 Berkeley Way, Room 5302, Berkeley, CA, 94720, USA. .,Center for Computational Biology, University of California, Berkeley, CA, USA.
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24
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Bozack AK, Colicino E, Just AC, Wright RO, Baccarelli AA, Wright RJ, Lee AG. Associations between infant sex and DNA methylation across umbilical cord blood, artery, and placenta samples. Epigenetics 2021; 17:1080-1097. [PMID: 34569420 PMCID: PMC9542631 DOI: 10.1080/15592294.2021.1985300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA methylation (DNAm) is vulnerable to dysregulation by environmental exposures during epigenetic reprogramming that occurs in embryogenesis. Sexual dimorphism in environmentally induced DNAm dysregulation has been identified and therefore it is important to understand sex-specific DNAm patterns. DNAm at several autosomal sites has been consistently associated with sex in cord blood and placental foetal tissues. However, there is limited research comparing sex-specific DNAm across tissues, particularly differentially methylated regions (DMRs). This study leverages DNAm data measured using the Illumina HumanMethylation450 BeadChip in cord blood (N = 179), placenta (N = 229), and umbilical artery samples (N = 229) in the PRogramming of Intergenerational Stress Mechanisms (PRISM) cohort to identify autosomal DMRs and differentially methylated positions (DMPs). A replication analyses was conducted in an independent cohort (GEO Accession GSE129841). We identified 183, 257, and 419 DMRs and 2119, 2281, and 3405 DMPs (pBonferroni < 0.05) in cord blood, placenta, and artery samples, respectively. Thirty-nine DMRs overlapped in all three tissues, overlapping with genes involved in spermatogenesis (NKAPL, PIWIL2 and AURKC) and X-inactivation (LRIF1). In replication analysis, 85% of DMRs overlapped with those identified in PRISM. Overall, DMRs and DMPs had higher methylation levels among females in cord blood and artery samples, but higher methylation levels among males in placenta samples. Further research is necessary to understand biological mechanisms that contribute to differences in sex-specific DNAm signatures across tissues, as well as to determine if sexual dimorphism in the epigenome impacts response to environmental stressors.
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Affiliation(s)
- Anne K Bozack
- Division of Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea A Baccarelli
- Departments of Environmental Health Sciences and Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rosalind J Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison G Lee
- Division of Pulmonary Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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25
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Jin X, Zheng Y, Chen Z, Wang F, Bi G, Li M, Liang J, Sui Q, Bian Y, Hu Z, Qiao Y, Xu S. Integrated analysis of patients with KEAP1/NFE2L2/CUL3 mutations in lung adenocarcinomas. Cancer Med 2021; 10:8673-8692. [PMID: 34617407 PMCID: PMC8633244 DOI: 10.1002/cam4.4338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Objectives To explore the clinical features, molecular characteristics, and immune landscape of lung adenocarcinoma patients with KEAP1/NFE2L2/CUL3 mutations. Methods The multi‐omics data from the GDC‐TCGA LUAD project of The Cancer Genome Atlas (TCGA) database were downloaded from the Xena browser. The estimate of the immune infiltration was implemented by using the GSVA analysis and CIBERSORT. The status of KEAP1/NFE2L2/CUL3 mutation in 50 LUAD samples of our department was detected by using Sanger sequencing, following the relative expression level of differentially expressed genes (DEGs), miRNAs (DEmiRNAs), and lncRNAs (DElncRNAs) was validated by IHC and real‐time quantitative polymerase chain reaction (RT‐qPCR). Results The Kaplan–Meier and multivariable Cox regression analyses demonstrated that KEAP1/NFE2L2/CUL3 mutations had independent prognostic value for OS and PFS in LUAD patients. The differential analysis detected 207 upregulated genes (like GSR/UGT1A6) and 447 downregulated genes (such as PIGR). GO, KEGG, and GSEA analyses demonstrated that DEGs were enriched in glutamate metabolism and the immune response. The constructed ceRNA network shows the linkage of differential lncRNAs and mRNAs. Three hundred and nine somatic mutations were detected, alterations in immune infiltration DNA methylations and stemness scores were also founded between the two groups. Eight mutated LUAD patients were detected by Sanger DNA sequencing in 50 surgical patients. GSR and UGT1A6 were validated to express higher in the Mut group, whereas the expression of PIGR was restrained. Furthermore, the IHC staining conducted on paraffin‐embedded tissue emphasizes the consistency of our result. Conclusion This research implemented the comprehensive analysis of KEAP1/NFE2L2/CUL3 somatic mutations in the LUAD patients. Compared with the wild type of LUAD patients, the Mut group shows a large difference in clinical features, RNA sequence, DNA methylation, and immune infiltrations, indicating complex mechanism oncogenesis and also reveals potential therapeutic targets.
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Affiliation(s)
- Xing Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuansheng Zheng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Wang
- Taizhou People's Hospital, Taizhou, Jiangsu, China
| | - Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ming Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qihai Sui
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunyi Bian
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhengyang Hu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yulei Qiao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Songtao Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Thoracic Surgery, Zhongshan Hospital, Fudan University (Xiamen Branch), Xiamen, Fujian, China
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26
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Silva R, Moran B, Baird AM, O'Rourke CJ, Finn SP, McDermott R, Watson W, Gallagher WM, Brennan DJ, Perry AS. Longitudinal analysis of individual cfDNA methylome patterns in metastatic prostate cancer. Clin Epigenetics 2021; 13:168. [PMID: 34454584 PMCID: PMC8403420 DOI: 10.1186/s13148-021-01155-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/17/2021] [Indexed: 01/27/2023] Open
Abstract
Background Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled with the use of liquid biopsies, offer a potentially new and minimally invasive platform to study the dynamics of tumour progression. Our aim was to investigate the dynamics of personal DNA methylomic profiles of metastatic PCa (mPCa) patients, during disease progression and therapy administration. Results Forty-eight plasma samples from 9 mPCa patients were collected, longitudinally, over 13–21 months. After circulating cell-free DNA (cfDNA) isolation, DNA methylation was profiled using the Infinium MethylationEPIC BeadChip. The top 5% most variable probes across time, within each individual, were utilised to study dynamic methylation patterns during disease progression and therapeutic response. Statistical testing was carried out to identify differentially methylated genes (DMGs) in cfDNA, which were subsequently validated in two independent mPCa (cfDNA and FFPE tissue) cohorts. Individual cfDNA global methylation patterns were temporally stable throughout the disease course. However, a proportion of CpG sites presented a dynamic temporal pattern that was consistent with clinical events, including different therapies, and were prominently associated with genes linked to immune response pathways. Additionally, study of the tumour fraction of cfDNA identified > 2000 DMGs with dynamic methylation patterns. Conclusions Longitudinal assessment of cfDNA methylation in mPCa patients unveiled dynamic patterns associated with disease progression and therapy administration, thus highlighting the potential of using liquid biopsies to study PCa evolution at a methylomic level. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01155-w.
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Affiliation(s)
- Romina Silva
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,School of Biology and Environmental Science, Science West, O'Brien Science Centre, University College Dublin, Dublin, Ireland
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Dublin, Ireland
| | - Anne-Marie Baird
- Department of Clinical Medicine, Trinity College, Dublin, Ireland
| | - Colm J O'Rourke
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephen P Finn
- Department of Clinical Medicine, Trinity College, Dublin, Ireland.,Department of Histopathology, St James's Hospital, Dublin, Ireland
| | - Ray McDermott
- Cancer Trials Ireland, Dublin, Ireland.,Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| | - William Watson
- School of Medicine, University College Dublin, Dublin, Ireland
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Donal J Brennan
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland
| | - Antoinette S Perry
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland. .,School of Biology and Environmental Science, Science West, O'Brien Science Centre, University College Dublin, Dublin, Ireland.
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27
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Caramaschi D, Jungius J, Page CM, Novakovic B, Saffery R, Halliday J, Lewis S, Magnus MC, London SJ, Håberg SE, Relton CL, Lawlor DA, Elliott HR. Association of medically assisted reproduction with offspring cord blood DNA methylation across cohorts. Hum Reprod 2021; 36:2403-2413. [PMID: 34136910 PMCID: PMC8289315 DOI: 10.1093/humrep/deab137] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
STUDY QUESTION Is cord blood DNA methylation associated with having been conceived by medically assisted reproduction? SUMMARY ANSWER This study does not provide strong evidence of an association of conception by medically assisted reproduction with variation in infant blood cell DNA methylation. WHAT IS KNOWN ALREADY Medically assisted reproduction consists of procedures used to help infertile/subfertile couples conceive, including ART. Due to its importance in gene regulation during early development programming, DNA methylation and its perturbations associated with medically assisted reproduction could reveal new insights into the biological effects of assisted reproductive technologies and potential adverse offspring outcomes. STUDY DESIGN, SIZE, DURATION We investigated the association of DNA methylation and medically assisted reproduction using a case–control study design (N = 205 medically assisted reproduction cases and N = 2439 naturally conceived controls in discovery cohorts; N = 149 ART cases and N = 58 non-ART controls in replication cohort). PARTICIPANTS/MATERIALS, SETTINGS, METHODS We assessed the association between medically assisted reproduction and DNA methylation at birth in cord blood (205 medically assisted conceptions and 2439 naturally conceived controls) at >450 000 CpG sites across the genome in two sub-samples of the UK Avon Longitudinal Study of Parents and Children (ALSPAC) and two sub-samples of the Norwegian Mother, Father and Child Cohort Study (MoBa) by meta-analysis. We explored replication of findings in the Australian Clinical review of the Health of adults conceived following Assisted Reproductive Technologies (CHART) study (N = 149 ART conceptions and N = 58 controls). MAIN RESULTS AND THE ROLE OF CHANCE The ALSPAC and MoBa meta-analysis revealed evidence of association between conception by medically assisted reproduction and DNA methylation (false-discovery-rate-corrected P-value < 0.05) at five CpG sites which are annotated to two genes (percentage difference in methylation per CpG, cg24051276: Beta = 0.23 (95% CI 0.15,0.31); cg00012522: Beta = 0.47 (95% CI 0.31, 0.63); cg17855264: Beta = 0.31 (95% CI 0.20, 0.43); cg17132421: Beta = 0.30 (95% CI 0.18, 0.42); cg18529845: Beta = 0.41 (95% CI 0.25, 0.57)). Methylation at three of these sites has been previously linked to cancer, aging, HIV infection and neurological diseases. None of these associations replicated in the CHART cohort. There was evidence of a functional role of medically assisted reproduction-induced hypermethylation at CpG sites located within regulatory regions as shown by putative transcription factor binding and chromatin remodelling. LIMITATIONS, REASONS FOR CAUTIONS While insufficient power is likely, heterogeneity in types of medically assisted reproduction procedures and between populations may also contribute. Larger studies might identify replicable variation in DNA methylation at birth due to medically assisted reproduction. WIDER IMPLICATIONS OF THE FINDINGS Newborns conceived with medically assisted procedures present with divergent DNA methylation in cord blood white cells. If these associations are true and causal, they might have long-term consequences for offspring health. STUDY FUNDING/COMPETING INTERESTS(S) This study has been supported by the US National Institute of Health (R01 DK10324), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement no. 669545, European Union’s Horizon 2020 research and innovation programme under Grant agreement no. 733206 (LifeCycle) and the NIHR Biomedical Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol. The UK Medical Research Council and Wellcome (Grant ref: 102215/2/13/2) and the University of Bristol provide core support for ALSPAC. Methylation data in the ALSPAC cohort were generated as part of the UK BBSRC funded (BB/I025751/1 and BB/I025263/1) Accessible Resource for Integrated Epigenomic Studies (ARIES, http://www.ariesepigenomics.org.uk). D.C., J.J., C.L.R. D.A.L and H.R.E. work in a Unit that is supported by the University of Bristol and the UK Medical Research Council (Grant nos. MC_UU_00011/1, MC_UU_00011/5 and MC_UU_00011/6). B.N. is supported by an NHMRC (Australia) Investigator Grant (1173314). ALSPAC GWAS data were generated by Sample Logistics and Genotyping Facilities at Wellcome Sanger Institute and LabCorp (Laboratory Corporation of America) using support from 23andMe. The Norwegian Mother, Father and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research, NIH/NIEHS (Contract no. N01-ES-75558), NIH/NINDS (Grant nos. (i) UO1 NS 047537-01 and (ii) UO1 NS 047537-06A1). For this work, MoBa 1 and 2 were supported by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences (Z01-ES-49019) and the Norwegian Research Council/BIOBANK (Grant no. 221097). This work was partly supported by the Research Council of Norway through its Centres of Excellence funding scheme, Project no. 262700. D.A.L. has received support from national and international government and charity funders, as well as from Roche Diagnostics and Medtronic for research unrelated to this study. The other authors declare no conflicts of interest. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Doretta Caramaschi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - James Jungius
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian M Page
- Division for Research Support, Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Health, Oslo, Norway
| | - Boris Novakovic
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Jane Halliday
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Sharon Lewis
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK.,Centre for Fertility and Health, Norwegian Institute of Health, Oslo, Norway
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Health, Oslo, Norway
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK.,Bristol NIHR Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust, University of Bristol, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
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Bozack AK, Boileau P, Wei L, Hubbard AE, Sillé FCM, Ferreccio C, Acevedo J, Hou L, Ilievski V, Steinmaus CM, Smith MT, Navas-Acien A, Gamble MV, Cardenas A. Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes. Environ Health 2021; 20:79. [PMID: 34243768 PMCID: PMC8272372 DOI: 10.1186/s12940-021-00754-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Arsenic (As) exposure through drinking water is a global public health concern. Epigenetic dysregulation including changes in DNA methylation (DNAm), may be involved in arsenic toxicity. Epigenome-wide association studies (EWAS) of arsenic exposure have been restricted to single populations and comparison across EWAS has been limited by methodological differences. Leveraging data from epidemiological studies conducted in Chile and Bangladesh, we use a harmonized data processing and analysis pipeline and meta-analysis to combine results from four EWAS. METHODS DNAm was measured among adults in Chile with and without prenatal and early-life As exposure in PBMCs and buccal cells (N = 40, 850K array) and among men in Bangladesh with high and low As exposure in PBMCs (N = 32, 850K array; N = 48, 450K array). Linear models were used to identify differentially methylated positions (DMPs) and differentially variable positions (DVPs) adjusting for age, smoking, cell type, and sex in the Chile cohort. Probes common across EWAS were meta-analyzed using METAL, and differentially methylated and variable regions (DMRs and DVRs, respectively) were identified using comb-p. KEGG pathway analysis was used to understand biological functions of DMPs and DVPs. RESULTS In a meta-analysis restricted to PBMCs, we identified one DMP and 23 DVPs associated with arsenic exposure; including buccal cells, we identified 3 DMPs and 19 DVPs (FDR < 0.05). Using meta-analyzed results, we identified 11 DMRs and 11 DVRs in PBMC samples, and 16 DMRs and 19 DVRs in PBMC and buccal cell samples. One region annotated to LRRC27 was identified as a DMR and DVR. Arsenic-associated KEGG pathways included lysosome, autophagy, and mTOR signaling, AMPK signaling, and one carbon pool by folate. CONCLUSIONS Using a two-step process of (1) harmonized data processing and analysis and (2) meta-analysis, we leverage four DNAm datasets from two continents of individuals exposed to high levels of As prenatally and during adulthood to identify DMPs and DVPs associated with arsenic exposure. Our approach suggests that standardizing analytical pipelines can aid in identifying biological meaningful signals.
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Affiliation(s)
- Anne K Bozack
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA.
| | - Philippe Boileau
- Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Linqing Wei
- Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Alan E Hubbard
- Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Fenna C M Sillé
- Department of Environmental Health and Engineering, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Catterina Ferreccio
- Advanced Center for Chronic Diseases (ACCDiS), School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Johanna Acevedo
- Department of Public Health, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Health Planning Division in the Ministry of Health, Santiago, Chile
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Vesna Ilievski
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Craig M Steinmaus
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA
| | - Ana Navas-Acien
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Mary V Gamble
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA
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29
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Minegishi R, Gotoh O, Tanaka N, Maruyama R, Chang JT, Mori S. A method of sample-wise region-set enrichment analysis for DNA methylomics. Epigenomics 2021; 13:1081-1093. [PMID: 34241544 DOI: 10.2217/epi-2021-0065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Gene set analysis has commonly been used to interpret DNA methylome data. However, summarizing the DNA methylation level of a gene is challenging due to variability in the number, density and methylation levels of CpG sites, and the numerous intergenic CpGs. Instead, we propose to use region sets to annotate the DNA methylome. Methods: We developed single sample region-set enrichment analysis for DNA methylome (methyl-ssRSEA) to conduct sample-wise, region-set enrichment analysis. Results: Methyl-ssRSEA can handle both microarray- and sequencing-based platforms and reproducibly recover the known biology from the methylation profiles of peripheral blood cells and breast cancers. The performance was superior to existing tools for region-set analysis in discriminating blood cell types. Conclusion: Methyl-ssRSEA offers a novel way to functionally interpret the DNA methylome in the cell.
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Affiliation(s)
- Ryu Minegishi
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Osamu Gotoh
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Norio Tanaka
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Jeffrey T Chang
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Seiichi Mori
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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30
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Koo HK, Morrow J, Kachroo P, Tantisira K, Weiss ST, Hersh CP, Silverman EK, DeMeo DL. Sex-specific associations with DNA methylation in lung tissue demonstrate smoking interactions. Epigenetics 2021; 16:692-703. [PMID: 32962511 PMCID: PMC8143227 DOI: 10.1080/15592294.2020.1819662] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/08/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cigarette smoking impacts DNA methylation, but the investigation of sex-specific features of lung tissue DNA methylation in smokers has been limited. Women appear more susceptible to cigarette smoke, and often develop more severe lung disease at an earlier age with less smoke exposure. We aimed to analyse whether there are sex differences in DNA methylation in lung tissue and whether these DNA methylation marks interact with smoking. We collected lung tissue samples from former smokers who underwent lung tissue resection. One hundred thirty samples from white subjects were included for this analysis. Regression models for sex as a predictor of methylation were adjusted for age, presence of COPD, smoking variables and technical batch variables revealed 710 associated sites. 294 sites demonstrated robust sex-specific methylation associations in foetal lung tissue. Pathway analysis identified 6 nominally significant pathways including the mitophagy pathway. Three CpG sites demonstrated a suggested interaction between sex and pack-years of smoking: GPR132, ANKRD44 and C19orf60. All of them were nominally significant in both male- and female-specific models, and the effect estimates were in opposite directions for male and female; GPR132 demonstrated significant association between DNA methylation and gene expression in lung tissue (P < 0.05). Sex-specific associations with DNA methylation in lung tissue are wide-spread and may reveal genes and pathways relevant to sex differences for lung damaging effects of cigarette smoking.
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Affiliation(s)
- Hyeon-Kyoung Koo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Ilsan Paik Hospital, Inje University College of Medicine, Ilsan, Republic of Korea
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
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31
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Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor J, Xu Z, Lie RT, Gjessing HK, Jugessur A. Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. NAR Genom Bioinform 2021; 3:lqab035. [PMID: 33987535 PMCID: PMC8092375 DOI: 10.1093/nargab/lqab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/04/2022] Open
Abstract
DNA methylation is the most widely studied epigenetic mark in humans and plays an essential role in normal biological processes as well as in disease development. More focus has recently been placed on understanding functional aspects of methylation, prompting the development of methods to investigate the relationship between heterogeneity in methylation patterns and disease risk. However, most of these methods are limited in that they use simplified models that may rely on arbitrarily chosen parameters, they can only detect differentially methylated regions (DMRs) one at a time, or they are computationally intensive. To address these shortcomings, we present a wavelet-based method called 'Wavelet Screening' (WS) that can perform an epigenome-wide association study (EWAS) of thousands of individuals on a single CPU in only a matter of hours. By detecting multiple DMRs located near each other, WS identifies more complex patterns that can differentiate between different methylation profiles. We performed an extensive set of simulations to demonstrate the robustness and high power of WS, before applying it to a previously published EWAS dataset of orofacial clefts (OFCs). WS identified 82 associated regions containing several known genes and loci for OFCs, while other findings are novel and warrant replication in other OFCs cohorts.
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Affiliation(s)
- William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, 0450, Oslo, Norway
| | - Jack A Taylor
- Epidemiology Branch and Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
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32
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Lee YS, Zhang H, Jiang Y, Kadalayil L, Karmaus W, Ewart SL, H Arshad S, Holloway JW. Epigenome-scale comparison of DNA methylation between blood leukocytes and bronchial epithelial cells. Epigenomics 2021; 13:485-498. [PMID: 33736458 DOI: 10.2217/epi-2020-0384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: Agreement in DNA methylation (DNAm) at the genome scale between blood leukocytes (BL) and bronchial epithelial cells (BEC) is unknown. We examine as to what extent DNAm in BL is comparable with that in BEC and serves as a surrogate for BEC. Materials & methods: Overall agreement (paired t-tests with false discovery rate adjusted p > 0.05) and consistency (Pearson's correlation coefficients >0.5) between two tissues, at each of the 767,412 CpGs, were evaluated. Results: We identified 247,721 CpGs showing overall agreement and 47,371 CpGs showing consistency in DNAm. Identified CpGs are involved in certain immune pathways, indicating the potential of using blood as a biomarker for BEC at those CpGs in lower airway-related diseases. Conclusion: CpGs showing overall agreement and those without overall agreement are distributed differently on the genome.
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Affiliation(s)
- Yu-Sheng Lee
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Latha Kadalayil
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Susan L Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Syed H Arshad
- David Hide Asthma & Allergy Research Centre, St Mary's Hospital, Newport, Isle of Wight, UK.,Clinical & Experimental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
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33
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Silva CP, Kamens HM. Cigarette smoke-induced alterations in blood: A review of research on DNA methylation and gene expression. Exp Clin Psychopharmacol 2021; 29:116-135. [PMID: 32658533 PMCID: PMC7854868 DOI: 10.1037/pha0000382] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Worldwide, smoking remains a threat to public health, causing preventable diseases and premature mortality. Cigarette smoke is a powerful inducer of DNA methylation and gene expression alterations, which have been associated with negative health consequences. Here, we review the current knowledge on smoking-related changes in DNA methylation and gene expression in human blood samples. We identified 30 studies focused on the association between active smoking, DNA methylation modifications, and gene expression alterations. Overall, we identified 1,758 genes with differentially methylated sites (DMS) and differentially expressed genes (DEG) between smokers and nonsmokers, of which 261 were detected in multiple studies (≥4). The most frequently (≥10 studies) reported genes were AHRR, GPR15, GFI1, and RARA. Functional enrichment analysis of the 261 genes identified the aryl hydrocarbon receptor repressor and T cell pathways (T helpers 1 and 2) as influenced by smoking status. These results highlight specific genes for future mechanistic and translational research that may be associated with cigarette smoke exposure and smoking-related diseases. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
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Affiliation(s)
- Constanza P. Silva
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States of America
| | - Helen M. Kamens
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States of America.,Correspondence concerning this article should be addressed to Helen M. Kamens, 228 Biobehavioral Health Building, The Pennsylvania State University, University Park, PA 16802; ; Phone number: 814-865-1269; Fax number: 814-863-7525
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34
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Kandaswamy R, Hannon E, Arseneault L, Mansell G, Sugden K, Williams B, Burrage J, Staley JR, Pishva E, Dahir A, Roberts S, Danese A, Mill J, Fisher HL, Wong CCY. DNA methylation signatures of adolescent victimization: analysis of a longitudinal monozygotic twin sample. Epigenetics 2020; 16:1169-1186. [PMID: 33371772 PMCID: PMC8813077 DOI: 10.1080/15592294.2020.1853317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence suggests that individuals exposed to victimization at key developmental stages may have different epigenetic fingerprints compared to those exposed to no/minimal stressful events, however results are inconclusive. This study aimed to strengthen causal inference regarding the impact of adolescent victimization on the epigenome by controlling for genetic variation, age, gender, and shared environmental exposures. We conducted longitudinal epigenome-wide association analyses (EWAS) on DNA methylation (DNAm) profiles of 118 monozygotic (MZ) twin pairs from the Environmental Risk study with and without severe adolescent victimization generated using buccal DNA collected at ages 5, 10 and 18, and the Illumina EPIC array. Additionally, we performed cross-sectional EWAS on age-18 blood and buccal DNA from the same individuals to elucidate tissue-specific signatures of severe adolescent victimization. Our analyses identified 20 suggestive differentially methylated positions (DMPs) (P < 5e-05), with altered DNAm trajectories between ages 10–18 associated with severe adolescent victimization (∆Beta range = −5.5%−5.3%). Age-18 cross-sectional analyses revealed 72 blood (∆Beta range = −2.2%−3.4%) and 42 buccal (∆Beta range = −3.6%−4.6%) suggestive severe adolescent victimization-associated DMPs, with some evidence of convergent signals between these two tissue types. Downstream regional analysis identified significant differentially methylated regions (DMRs) in LGR6 and ANK3 (Šidák P = 5e-09 and 4.07e-06), and one upstream of CCL27 (Šidák P = 2.80e-06) in age-18 blood and buccal EWAS, respectively. Our study represents the first longitudinal MZ twin analysis of DNAm and severe adolescent victimization, providing initial evidence for altered DNA methylomic signatures in individuals exposed to adolescent victimization.
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Affiliation(s)
- Radhika Kandaswamy
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Louise Arseneault
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK.,ESRC Centre for Society & Mental Health, King's College London, London, UK
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Benjamin Williams
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - James R Staley
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ehsan Pishva
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Aisha Dahir
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Susanna Roberts
- King's College London, Department of Psychology, Institute of Psychiatry, Psychology & Neuroscience, London UK
| | - Andrea Danese
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK.,King's College London, Department of Child & Adolescent Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, London UK.,National & Specialist CAMHS Clinic for Trauma, Anxiety and Depression, South London & Maudsley NHS Foundation Trust, London, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Helen L Fisher
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK.,ESRC Centre for Society & Mental Health, King's College London, London, UK
| | - Chloe C Y Wong
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
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35
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LaBarre JL, McCabe CF, Jones TR, Song PX, Domino SE, Treadwell MC, Dolinoy DC, Padmanabhan V, Burant CF, Goodrich JM. Maternal lipodome across pregnancy is associated with the neonatal DNA methylome. Epigenomics 2020; 12:2077-2092. [PMID: 33290095 DOI: 10.2217/epi-2020-0234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aim: To classify the association between the maternal lipidome and DNA methylation in cord blood leukocytes. Materials & methods: Untargeted lipidomics was performed on first trimester maternal plasma (M1) and delivery maternal plasma (M3) in 100 mothers from the Michigan Mother-Infant Pairs cohort. Cord blood leukocyte DNA methylation was profiled using the Infinium EPIC bead array and empirical Bayes modeling identified differential DNA methylation related to maternal lipid groups. Results: M3-saturated lysophosphatidylcholine was associated with 45 differentially methylated loci and M3-saturated lysophosphatidylethanolamine was associated with 18 differentially methylated loci. Biological pathways enriched among differentially methylated loci by M3 saturated lysophosphatidylcholines were related to cell proliferation and growth. Conclusion: The maternal lipidome may be influential in establishing the infant epigenome.
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Affiliation(s)
- Jennifer L LaBarre
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Carolyn F McCabe
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Peter Xk Song
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Steven E Domino
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marjorie C Treadwell
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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36
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Shu C, Jaffe AE, Sabunciyan S, Ji H, Astemborski J, Sun J, Bakulski KM, Mehta SH, Kirk GD, Maher BS. Epigenome-wide association scan identifies methylation sites associated with HIV infection. Epigenomics 2020; 12:1917-1927. [PMID: 33232214 DOI: 10.2217/epi-2020-0123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: To investigate the role of epigenetics in HIV pathophysiology. Materials & methods: We conducted an epigenome-wide association scan on HIV infection status among people who inject drugs in the AIDS Linked to the IntraVenous Experience study with primary (n = 397) and validation samples (n = 390). DNA methylation from blood was measured by the Illumina EPIC BeadChip. We controlled for cell type heterogeneity by HIV status. Results: HIV infection status was associated (p < 10-8) with DNA methylation at 49 CpG sites. Sites were enriched in response to virus, interferon signaling pathway, etc. Among these sites, discovery and validation t-statistics were highly correlated (r = 0.96). Conclusion: In a cohort of people who inject drugs, HIV status was associated with differential DNA methylation at biologically meaningful sites.
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Affiliation(s)
- Chang Shu
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrew E Jaffe
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.,Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jacquie Astemborski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jing Sun
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shruti H Mehta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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37
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Neumann A, Walton E, Alemany S, Cecil C, González JR, Jima DD, Lahti J, Tuominen ST, Barker ED, Binder E, Caramaschi D, Carracedo Á, Czamara D, Evandt J, Felix JF, Fuemmeler BF, Gutzkow KB, Hoyo C, Julvez J, Kajantie E, Laivuori H, Maguire R, Maitre L, Murphy SK, Murcia M, Villa PM, Sharp G, Sunyer J, Raikkönen K, Bakermans-Kranenburg M, IJzendoorn MV, Guxens M, Relton CL, Tiemeier H. Association between DNA methylation and ADHD symptoms from birth to school age: a prospective meta-analysis. Transl Psychiatry 2020; 10:398. [PMID: 33184255 PMCID: PMC7665047 DOI: 10.1038/s41398-020-01058-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/29/2020] [Accepted: 07/22/2020] [Indexed: 01/06/2023] Open
Abstract
Attention-deficit and hyperactivity disorder (ADHD) is a common childhood disorder with a substantial genetic component. However, the extent to which epigenetic mechanisms play a role in the etiology of the disorder is unknown. We performed epigenome-wide association studies (EWAS) within the Pregnancy And Childhood Epigenetics (PACE) Consortium to identify DNA methylation sites associated with ADHD symptoms at two methylation assessment periods: birth and school age. We examined associations of both DNA methylation in cord blood with repeatedly assessed ADHD symptoms (age 4-15 years) in 2477 children from 5 cohorts and of DNA methylation at school age with concurrent ADHD symptoms (age 7-11 years) in 2374 children from 9 cohorts, with 3 cohorts participating at both timepoints. CpGs identified with nominal significance (p < 0.05) in either of the EWAS were correlated between timepoints (ρ = 0.30), suggesting overlap in associations; however, top signals were very different. At birth, we identified nine CpGs that predicted later ADHD symptoms (p < 1 × 10-7), including ERC2 and CREB5. Peripheral blood DNA methylation at one of these CpGs (cg01271805 in the promoter region of ERC2, which regulates neurotransmitter release) was previously associated with brain methylation. Another (cg25520701) lies within the gene body of CREB5, which previously was associated with neurite outgrowth and an ADHD diagnosis. In contrast, at school age, no CpGs were associated with ADHD with p < 1 × 10-7. In conclusion, we found evidence in this study that DNA methylation at birth is associated with ADHD. Future studies are needed to confirm the utility of methylation variation as biomarker and its involvement in causal pathways.
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Affiliation(s)
- Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Esther Walton
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.,Department of Psychology, University of Bath, Bath, UK
| | - Silvia Alemany
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Charlotte Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands.,The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Juan Ramon González
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Dereje D Jima
- Center for Human Health and the Environment, NCSU, Raleigh, NC, USA.,Bioinformatics Research Center, NCSU, Raleigh, NC, USA
| | - Jari Lahti
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland.,Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Samuli T Tuominen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Edward D Barker
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.,Centre for Population Neuroscience and Stratified Medicine (PONS), MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Elisabeth Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Fundación Pública Galega de Merdicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), SERGAS, Santiago de Compostela, Spain.,Centro de Investigación en Red de Enfermedades Raras (CIBERER) y Centro Nacional de Genotipado (CEGEN-PRB3), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Jorunn Evandt
- Department of Air Pollution and Noise, Norwegian Institute of Public Health, Oslo, Norway
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Bernard F Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, USA.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Kristine B Gutzkow
- Department of Molecular Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - Cathrine Hoyo
- Center for Human Health and the Environment, NCSU, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jordi Julvez
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Eero Kajantie
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.,Hospital for Children and Adolescents, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Hannele Laivuori
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Rachel Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Léa Maitre
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Mario Murcia
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,Joint Research Unit of Epidemiology and Environmental Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
| | - Pia M Villa
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Gemma Sharp
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Katri Raikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | - Mònica Guxens
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands.,ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands. .,Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, MA, USA.
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38
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Dodgshun AJ, Fukuoka K, Edwards M, Bianchi VJ, Das A, Sexton-Oates A, Larouche V, Vanan MI, Lindhorst S, Yalon M, Mason G, Crooks B, Constantini S, Massimino M, Chiaravalli S, Ramdas J, Mason W, Ashraf S, Farah R, Van Damme A, Opocher E, Hamid SA, Ziegler DS, Samuel D, Cole KA, Tomboc P, Stearns D, Thomas GA, Lossos A, Sullivan M, Hansford JR, Mackay A, Jones C, Jones DTW, Ramaswamy V, Hawkins C, Bouffet E, Tabori U. Germline-driven replication repair-deficient high-grade gliomas exhibit unique hypomethylation patterns. Acta Neuropathol 2020; 140:765-776. [PMID: 32895736 DOI: 10.1007/s00401-020-02209-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 08/03/2020] [Indexed: 01/02/2023]
Abstract
Replication repair deficiency (RRD) leading to hypermutation is an important driving mechanism of high-grade glioma (HGG) occurring predominantly in the context of germline mutations in RRD-associated genes. Although HGG presents specific patterns of DNA methylation corresponding to oncogenic mutations, this has not been well studied in replication repair-deficient tumors. We analyzed 51 HGG arising in the background of gene mutations in RRD utilizing either 450 k or 850 k methylation arrays. These were compared with HGG not known to be from patients with RRD. RRD HGG harboring secondary mutations in glioma genes such as IDH1 and H3F3A displayed a methylation pattern corresponding to these methylation subgroups. Strikingly, RRD HGG lacking these known secondary mutations clustered together with an incompletely described group of HGG previously labeled "Wild type-C" or "Paediatric RTK 1". Independent analysis of two comparator HGG cohorts showed that other RRD/hypermutant tumors clustered within these subgroups, suggesting that undiagnosed RRD may be driving some HGG clustering in this location. RRD HGG displayed a unique CpG Island Demethylator Phenotype in contrast to the CpG Island Methylator Phenotype described in other cancers. Hypomethylation was enriched at gene promoters with prominent demethylation in genes and pathways critical to cellular survival including cell cycle, gene expression, cellular metabolism, and organization. These data suggest that methylation arrays may provide diagnostic information for the detection of RRD HGG. Furthermore, our findings highlight the unique natural selection pressures in these highly dysregulated, hypermutant cancers and provide the novel impact of hypermutation and RRD on the cancer epigenome.
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Affiliation(s)
- Andrew J Dodgshun
- Children's Haematology/Oncology Centre, Christchurch Hospital and University of Otago Christchurch, 2 Riccarton Ave, Christchurch, 8041, New Zealand.
| | - Kohei Fukuoka
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Melissa Edwards
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Vanessa J Bianchi
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Anirban Das
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Alexandra Sexton-Oates
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Valérie Larouche
- Université Laval, 2325 Rue de l'Université, Québec, QC, G1V 0A6, Canada
| | - Magimairajan I Vanan
- Cancer Care Manitoba and University of Manitoba, 675 McDermot Ave, Winnipeg, MB, R3E 0V9, Canada
| | - Scott Lindhorst
- Medical University of South Carolina, 171 Ashley Ave Suite 419, MSC 403, Charleston, SC, 29425, USA
| | - Michal Yalon
- Sheba Medical CenterSheba Medical Center, Derech Sheba 2, Tel Hashomer, Ramat Gan, Israel
| | - Gary Mason
- Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Bruce Crooks
- IWK Health Centre, 5850-5980 University Avenue, Halifax, NS, Canada
| | | | - Maura Massimino
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133, Milano, MI, Italy
| | - Stefano Chiaravalli
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133, Milano, MI, Italy
| | - Jagadeesh Ramdas
- Geisinger Medical Center, 100 N. Academy Ave, Danville, PA, 17822, USA
| | - Warren Mason
- Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON, M5G 2C1, Canada
| | | | - Roula Farah
- LAU Medical Center Rizk Hospital, Zahra Street, Achrafieh, Beirut, Lebanon
| | - An Van Damme
- St Luc University Hospital Université Catholique de Louvain, 10 Avenue Hippocrate, 1200, Brussels, Belgium
| | - Enrico Opocher
- Azienda Ospedaliera di Padova, via Giustiniani n.2, 35121, Padova, PD, Italy
| | | | - David S Ziegler
- Sydney Children's Hospital, High St, Randwick, NSW, 2031, Australia
| | - David Samuel
- Valley Children's Hospital, 9300 Valley Children's Pl, Madera, CA, 93636, USA
| | - Kristina A Cole
- Children's Hospital of Philadelphia and University of Pennsylvania, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Patrick Tomboc
- WVU Medicine Children's Hospital, 1 Medical Center Dr, Morgantown, WV, 26505, USA
| | - Duncan Stearns
- University Hospitals Cleveland, 2101 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Gregory A Thomas
- Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, USA
| | - Alexander Lossos
- Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Michael Sullivan
- The Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Jordan R Hansford
- The Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Alan Mackay
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Chris Jones
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Cynthia Hawkins
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Eric Bouffet
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Uri Tabori
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada.
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Kachroo P, Morrow JD, Kho AT, Vyhlidal CA, Silverman EK, Weiss ST, Tantisira KG, DeMeo DL. Co-methylation analysis in lung tissue identifies pathways for fetal origins of COPD. Eur Respir J 2020; 56:13993003.02347-2019. [PMID: 32482784 DOI: 10.1183/13993003.02347-2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
COPD likely has developmental origins; however, the underlying molecular mechanisms are not fully identified. Investigation of lung tissue-specific epigenetic modifications such as DNA methylation using network approaches might facilitate insights linking in utero smoke (IUS) exposure and risk for COPD in adulthood.We performed genome-wide methylation profiling for adult lung DNA from 160 surgical samples and 78 fetal lung DNA samples isolated from discarded tissue at 8-18 weeks of gestation. Co-methylation networks were constructed to identify preserved modules that shared methylation patterns in fetal and adult lung tissues and associations with fetal IUS exposure, gestational age and COPD.Weighted correlation networks highlighted preserved and co-methylated modules for both fetal and adult lung data associated with fetal IUS exposure, COPD and lower adult lung function. These modules were significantly enriched for genes involved in embryonic organ development and specific inflammation-related pathways, including Hippo, phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT), Wnt, mitogen-activated protein kinase and transforming growth factor-β signalling. Gestational age-associated modules were remarkably preserved for COPD and lung function, and were also annotated to genes enriched for the Wnt and PI3K/AKT pathways.Epigenetic network perturbations in fetal lung tissue exposed to IUS and of early lung development recapitulated in adult lung tissue from ex-smokers with COPD. Overlapping fetal and adult lung tissue network modules highlighted putative disease pathways supportive of exposure-related and age-associated developmental origins of COPD.
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Affiliation(s)
- Priyadarshini Kachroo
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alvin T Kho
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Edwin K Silverman
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA .,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population. Epigenetics 2020; 16:741-753. [PMID: 33092459 PMCID: PMC8216205 DOI: 10.1080/15592294.2020.1824097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. Methods: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. Results: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. Conclusions: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Vincent C Marconi
- Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
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Xiao C, Fedirko V, Beitler J, Bai J, Peng G, Zhou C, Gu J, Zhao H, Lin IH, Chico CE, Jeon S, Knobf TM, Conneely KN, Higgins K, Shin DM, Saba N, Miller A, Bruner D. The role of the gut microbiome in cancer-related fatigue: pilot study on epigenetic mechanisms. Support Care Cancer 2020; 29:3173-3182. [PMID: 33078326 DOI: 10.1007/s00520-020-05820-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE Recent evidence supports a key role of gut microbiome in brain health. We conducted a pilot study to assess associations of gut microbiome with cancer-related fatigue and explore the associations with DNA methylation changes. METHODS Self-reported Multidimensional Fatigue Inventory and stool samples were collected at pre-radiotherapy and one-month post-radiotherapy in patients with head and neck cancer. Gut microbiome data were obtained by sequencing the 16S ribosomal ribonucleic acid gene. DNA methylation changes in the blood were assessed using Illumina Methylation EPIC BeadChip. RESULTS We observed significantly different gut microbiota patterns among patients with high vs. low fatigue across time. This pattern was characterized by low relative abundance in short-chain fatty acid-producing taxa (family Ruminococcaceae, genera Subdoligranulum and Faecalibacterium; all p < 0.05), with high abundance in taxa associated with inflammation (genera Family XIII AD3011 and Erysipelatoclostridium; all p < 0.05) for high-fatigue group. We identified nine KEGG Orthology pathways significantly different between high- vs. low-fatigue groups over time (all p < 0.001), including pathways related to fatty acid synthesis and oxidation, inflammation, and brain function. Gene set enrichment analysis (GSEA) was performed on the top differentially methylated CpG sites that were associated with the taxa and fatigue. All biological processes from the GSEA were related to immune responses and inflammation (FDR < 0.05). CONCLUSIONS Our results suggest different patterns of the gut microbiota in cancer patients with high vs. low fatigue. Results from functional pathways and DNA methylation analyses indicate that inflammation is likely to be the major driver in the gut-brain axis for cancer-related fatigue.
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Affiliation(s)
- Canhua Xiao
- School of Nursing, Yale University, 400 West Campus Drive, Room 20102, Orange, CT, 06477, USA.
| | - Veronika Fedirko
- School of Public Health, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
| | - Jonathan Beitler
- Department of Radiation, School of Medicine, Emory University, 1365-C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Jinbing Bai
- School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, 30322, USA
| | - Gang Peng
- Department of Epidemiology and Public Health, School of Medicine, Yale University, 300 George Street, New Haven, CT, 06510, USA
| | - Chao Zhou
- Department of Epidemiology and Public Health, School of Medicine, Yale University, 300 George Street, New Haven, CT, 06510, USA
| | - Jianlei Gu
- Department of Epidemiology and Public Health, School of Medicine, Yale University, 300 George Street, New Haven, CT, 06510, USA
| | - Hongyu Zhao
- Department of Epidemiology and Public Health, School of Medicine, Yale University, 300 George Street, New Haven, CT, 06510, USA
| | - I-Hsin Lin
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, 485 Lexington Ave, New York, NY, 10017, USA
| | - Cynthia E Chico
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, 1365-B Clifton Road, Atlanta, GA, 30322, USA
| | - Sangchoon Jeon
- School of Nursing, Yale University, 400 West Campus Drive, Room 20102, Orange, CT, 06477, USA
| | - Tish M Knobf
- School of Nursing, Yale University, 400 West Campus Drive, Room 20102, Orange, CT, 06477, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
| | - Kristin Higgins
- Department of Radiation, School of Medicine, Emory University, 1365-C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Dong M Shin
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, 1365-C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Nabil Saba
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, 1365-C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Andrew Miller
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, 1365-B Clifton Road, Atlanta, GA, 30322, USA
| | - Deborah Bruner
- School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, 30322, USA
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Castellani CA, Longchamps RJ, Sumpter JA, Newcomb CE, Lane JA, Grove ML, Bressler J, Brody JA, Floyd JS, Bartz TM, Taylor KD, Wang P, Tin A, Coresh J, Pankow JS, Fornage M, Guallar E, O'Rourke B, Pankratz N, Liu C, Levy D, Sotoodehnia N, Boerwinkle E, Arking DE. Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs. Genome Med 2020; 12:84. [PMID: 32988399 PMCID: PMC7523322 DOI: 10.1186/s13073-020-00778-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation. METHODS To investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2507 African American (AA) and European American (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study. To validate our findings, we assayed an additional 2528 participants from the Cardiovascular Health Study (CHS) (N = 533) and Framingham Heart Study (FHS) (N = 1995). We further assessed the effect of experimental modification of mtDNA-CN through knockout of TFAM, a regulator of mtDNA replication, via CRISPR-Cas9. RESULTS Thirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P < 5 × 10- 8). Meta-analysis across all cohorts identified six mtDNA-CN-associated CpGs at genome-wide significance (P < 5 × 10- 8). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including coronary heart disease, cardiovascular disease, and mortality. Experimental modification of mtDNA-CN demonstrated that modulation of mtDNA-CN results in changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the "neuroactive ligand receptor interaction" KEGG pathway was found to be highly overrepresented in the ARIC cohort (P = 5.24 × 10- 12), as well as the TFAM knockout methylation (P = 4.41 × 10- 4) and expression (P = 4.30 × 10- 4) studies. CONCLUSIONS These results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential expression of specific genes that may impact human health and disease via altered cell signaling.
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Affiliation(s)
- Christina A Castellani
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan J Longchamps
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jason A Sumpter
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles E Newcomb
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John A Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Megan L Grove
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Penglong Wang
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrienne Tin
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Josef Coresh
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James S Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eliseo Guallar
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Brian O'Rourke
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dan E Arking
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Wang Y, Franks JM, Whitfield ML, Cheng C. BioMethyl: an R package for biological interpretation of DNA methylation data. Bioinformatics 2020; 35:3635-3641. [PMID: 30799505 PMCID: PMC6761945 DOI: 10.1093/bioinformatics/btz137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/25/2019] [Accepted: 02/22/2019] [Indexed: 12/16/2022] Open
Abstract
Motivation The accumulation of publicly available DNA methylation datasets has resulted in the need for tools to interpret the specific cellular phenotypes in bulk tissue data. Current approaches use either single differentially methylated CpG sites or differentially methylated regions that map to genes. However, these approaches may introduce biases in downstream analyses of biological interpretation, because of the variability in gene length. There is a lack of approaches to interpret DNA methylation effectively. Therefore, we have developed computational models to provide biological interpretation of relevant gene sets using DNA methylation data in the context of The Cancer Genome Atlas. Results We illustrate that Biological interpretation of DNA Methylation (BioMethyl) utilizes the complete DNA methylation data for a given cancer type to reflect corresponding gene expression profiles and performs pathway enrichment analyses, providing unique biological insight. Using breast cancer as an example, BioMethyl shows high consistency in the identification of enriched biological pathways from DNA methylation data compared to the results calculated from RNA sequencing data. We find that 12 out of 14 pathways identified by BioMethyl are shared with those by using RNA-seq data, with a Jaccard score 0.8 for estrogen receptor (ER) positive samples. For ER negative samples, three pathways are shared in the two enrichments with a slight lower similarity (Jaccard score = 0.6). Using BioMethyl, we can successfully identify those hidden biological pathways in DNA methylation data when gene expression profile is lacking. Availability and implementation BioMethyl R package is freely available in the GitHub repository (https://github.com/yuewangpanda/BioMethyl). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yue Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jennifer M Franks
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Chao Cheng
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Norris Cotton Cancer Center, Lebanon, NH, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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44
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Dong D, Tian Y, Zheng SC, Teschendorff AE. ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies. Bioinformatics 2020; 35:3514-3516. [PMID: 30715212 PMCID: PMC6748733 DOI: 10.1093/bioinformatics/btz073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/20/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023] Open
Abstract
Motivation The biological interpretation of differentially methylated sites derived from Epigenome-Wide-Association Studies (EWAS) remains a significant challenge. Gene Set Enrichment Analysis (GSEA) is a general tool to aid biological interpretation, yet its correct and unbiased implementation in the EWAS context is difficult due to the differential probe representation of Illumina Infinium DNA methylation beadchips. Results We present a novel GSEA method, called ebGSEA, which ranks genes, not CpGs, according to the overall level of differential methylation, as assessed using all the probes mapping to the given gene. Applied on simulated and real EWAS data, we show how ebGSEA may exhibit higher sensitivity and specificity than the current state-of-the-art, whilst also avoiding differential probe representation bias. Thus, ebGSEA will be a useful additional tool to aid the interpretation of EWAS data. Availability and implementation ebGSEA is available from https://github.com/aet21/ebGSEA, and has been incorporated into the ChAMP Bioconductor package (https://www.bioconductor.org). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Danyue Dong
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuan Tian
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
| | - Shijie C Zheng
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
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45
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Ren X, Kuan PF. methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics 2020; 35:1958-1959. [PMID: 30346483 DOI: 10.1093/bioinformatics/bty892] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/31/2018] [Accepted: 10/19/2018] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION An important downstream analysis following differential expression from RNA sequencing (RNA-Seq) or DNA methylation analysis is the gene set testing to relate significant genes or CpGs to known biological properties. However, the traditional gene set testing approaches result in biased P-values due to the difference in gene length. Existing methods accounting for length bias were primarily developed for RNA-Seq data. For DNA methylation data profiled using the Illumina arrays, separate methods adjusting for the number of CpGs instead of gene length are necessary. RESULTS We developed methylGSA, a Bioconductor package for gene set testing in DNA methylation data. Our accompanying Shiny app provides an interactive way of accessing functions and visualizing the results in methylGSA package. AVAILABILITY AND IMPLEMENTATION methylGSA is available at Bioconductor repository: https://bioconductor.org/packages/methylGSA and Shiny app is available at: http://www.ams.sunysb.edu/%7epfkuan/softwares.html#methylGSA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xu Ren
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Pei Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
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46
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Bozack AK, Domingo-Relloso A, Haack K, Gamble MV, Tellez-Plaza M, Umans JG, Best LG, Yracheta J, Gribble MO, Cardenas A, Francesconi KA, Goessler W, Tang WY, Fallin MD, Cole SA, Navas-Acien A. Locus-Specific Differential DNA Methylation and Urinary Arsenic: An Epigenome-Wide Association Study in Blood among Adults with Low-to-Moderate Arsenic Exposure. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:67015. [PMID: 32603190 PMCID: PMC7534587 DOI: 10.1289/ehp6263] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 03/18/2020] [Accepted: 05/29/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Chronic exposure to arsenic (As), a human toxicant and carcinogen, remains a global public health problem. Health risks persist after As exposure has ended, suggesting epigenetic dysregulation as a mechanistic link between exposure and health outcomes. OBJECTIVES We investigated the association between total urinary As and locus-specific DNA methylation in the Strong Heart Study, a cohort of American Indian adults with low-to-moderate As exposure [total urinary As, mean ( ± SD ) μ g / g creatinine: 11.7 (10.6)]. METHODS DNA methylation was measured in 2,325 participants using the Illumina MethylationEPIC array. We implemented linear models to test differentially methylated positions (DMPs) and the DMRcate method to identify regions (DMRs) and conducted gene ontology enrichment analysis. Models were adjusted for estimated cell type proportions, age, sex, body mass index, smoking, education, estimated glomerular filtration rate, and study center. Arsenic was measured in urine as the sum of inorganic and methylated species. RESULTS In adjusted models, methylation at 20 CpGs was associated with urinary As after false discovery rate (FDR) correction (FDR < 0.05 ). After Bonferroni correction, 5 CpGs remained associated with total urinary As (p Bonferroni < 0.05 ), located in SLC7A11, ANKS3, LINGO3, CSNK1D, ADAMTSL4. We identified one DMR on chromosome 11 (chr11:2,322,050-2,323,247), annotated to C11orf2; TSPAN32 genes. DISCUSSION This is one of the first epigenome-wide association studies to investigate As exposure and locus-specific DNA methylation using the Illumina MethylationEPIC array and the largest epigenome-wide study of As exposure. The top DMP was located in SLC7A11A, a gene involved in cystine/glutamate transport and the biosynthesis of glutathione, an antioxidant that may protect against As-induced oxidative stress. Additional DMPs were located in genes associated with tumor development and glucose metabolism. Further research is needed, including research in more diverse populations, to investigate whether As-related DNA methylation signatures are associated with gene expression or may serve as biomarkers of disease development. https://doi.org/10.1289/EHP6263.
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Affiliation(s)
- Anne K Bozack
- Department of Environmental Health Science, Columbia University, New York, New York, USA
| | - Arce Domingo-Relloso
- Department of Environmental Health Science, Columbia University, New York, New York, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institutes, Madrid, Spain
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Mary V Gamble
- Department of Environmental Health Science, Columbia University, New York, New York, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institutes, Madrid, Spain
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jason G Umans
- MedStar Health Research Institute, Washington, District of Columbia, USA
- Center for Clinical and Translational Sciences, Georgetown/Howard Universities, Washington, DC, USA
| | - Lyle G Best
- Missouri Breaks Industries Research, Eagle Butte, South Dakota, USA
| | - Joseph Yracheta
- Missouri Breaks Industries Research, Eagle Butte, South Dakota, USA
| | - Matthew O Gribble
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkley, California, USA
| | | | | | - Wan-Yee Tang
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ana Navas-Acien
- Department of Environmental Health Science, Columbia University, New York, New York, USA
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Natri HM, Bobowik KS, Kusuma P, Crenna Darusallam C, Jacobs GS, Hudjashov G, Lansing JS, Sudoyo H, Banovich NE, Cox MP, Gallego Romero I. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PLoS Genet 2020; 16:e1008749. [PMID: 32453742 PMCID: PMC7274483 DOI: 10.1371/journal.pgen.1008749] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 06/05/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Indonesia is the world's fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.
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Affiliation(s)
- Heini M. Natri
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Katalina S. Bobowik
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of BioSciences, University of Melbourne, Parkville, Australia
- Centre for Stem Cell Systems, University of Melbourne, Parkville, Australia
| | - Pradiptajati Kusuma
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Complexity Institute, Nanyang Technological University, Singapore, Singapore
| | - Chelzie Crenna Darusallam
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Guy S. Jacobs
- Complexity Institute, Nanyang Technological University, Singapore, Singapore
| | - Georgi Hudjashov
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - J. Stephen Lansing
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Vienna Complexity Science Hub, Vienna, Austria
- Stockholm Resilience Center, Kräftriket, Stockholm, Sweden
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Nicholas E. Banovich
- The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Murray P. Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of BioSciences, University of Melbourne, Parkville, Australia
- Centre for Stem Cell Systems, University of Melbourne, Parkville, Australia
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48
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Levy JJ, Titus AJ, Petersen CL, Chen Y, Salas LA, Christensen BC. MethylNet: an automated and modular deep learning approach for DNA methylation analysis. BMC Bioinformatics 2020; 21:108. [PMID: 32183722 PMCID: PMC7076991 DOI: 10.1186/s12859-020-3443-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/04/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations with phenotypes suffer from multiple hypothesis testing and multi-collinearity due to the high-dimensional, continuous, interacting and non-linear nature of the data. Deep learning analyses have shown much promise to study disease heterogeneity. DNAm deep learning approaches have not yet been formalized into user-friendly frameworks for execution, training, and interpreting models. Here, we describe MethylNet, a DNAm deep learning method that can construct embeddings, make predictions, generate new data, and uncover unknown heterogeneity with minimal user supervision. RESULTS The results of our experiments indicate that MethylNet can study cellular differences, grasp higher order information of cancer sub-types, estimate age and capture factors associated with smoking in concordance with known differences. CONCLUSION The ability of MethylNet to capture nonlinear interactions presents an opportunity for further study of unknown disease, cellular heterogeneity and aging processes.
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Affiliation(s)
- Joshua J Levy
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
| | - Alexander J Titus
- Department of Defense, Office of the Under Secretary of Defense for Research & Engineering, Washington, DC, USA
| | - Curtis L Petersen
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, 03766, USA
| | - Youdinghuan Chen
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
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49
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Housman G, Quillen EE, Stone AC. Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:34-49. [PMID: 32170728 DOI: 10.1002/ajpa.24041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Epigenetic mechanisms influence the development and maintenance of complex phenotypes and may also contribute to the evolution of species-specific phenotypes. With respect to skeletal traits, little is known about the gene regulation underlying these hard tissues or how tissue-specific patterns are associated with bone morphology or vary among species. To begin exploring these topics, this study evaluates one epigenetic mechanism, DNA methylation, in skeletal tissues from five nonhuman primate species which display anatomical and locomotor differences representative of their phylogenetic groups. MATERIALS AND METHODS First, we test whether intraspecific variation in skeletal DNA methylation is associated with intraspecific variation in femur morphology. Second, we identify interspecific differences in DNA methylation and assess whether these lineage-specific patterns may have contributed to species-specific morphologies. Specifically, we use the Illumina Infinium MethylationEPIC BeadChip to identify DNA methylation patterns in femur trabecular bone from baboons (n = 28), macaques (n = 10), vervets (n = 10), chimpanzees (n = 4), and marmosets (n = 6). RESULTS Significant differentially methylated positions (DMPs) were associated with a subset of morphological variants, but these likely have small biological effects and may be confounded by other variables associated with morphological variation. Conversely, several species-specific DMPs were identified, and these are found in genes enriched for functions associated with complex skeletal traits. DISCUSSION Overall, these findings reveal that while intraspecific epigenetic variation is not readily associated with skeletal morphology differences, some interspecific epigenetic differences in skeletal tissues exist and may contribute to evolutionarily distinct phenotypes. This work forms a foundation for future explorations of gene regulation and skeletal trait evolution in primates.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
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50
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Wang Z, Du M, Yuan Q, Guo Y, Hutchinson JN, Su L, Zheng Y, Wang J, Mucci LA, Lin X, Hou L, Christiani DC. Epigenomic analysis of 5-hydroxymethylcytosine (5hmC) reveals novel DNA methylation markers for lung cancers. Neoplasia 2020; 22:154-161. [PMID: 32062069 PMCID: PMC7021546 DOI: 10.1016/j.neo.2020.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND DNA methylation at the fifth position of cytosine (5mC) is a common epigenetic alteration affecting a range of cellular processes. In recent years, 5-hydroxymethylcytosine (5hmC), an oxidized form of 5mC, has risen broad interests as a potential biomarker for lung cancer diagnosis and survival. METHODS We analyzed the epigenome-wide 5hmC profiles of paired lung tumor and adjacent normal tissues, using the TET-Assisted Bisulfite (TAB) array - Infinium MethylationEPIC BeadChip (EPIC) approach. The differentially methylated CpG sites were identified, and the biological relevance of 5hmC was assessed by differential methylation regions (DMR) analysis and gene set analysis (GSA). RESULTS We observed global hypomethylation of 5hmC comparing tumor to normal tissues, and hypermethylated 5hmC were enriched in CpG islands and gene upstream. Comparison of 5hmC and 5modC (total methylation: 5mC + 5hmC) profiling showed low correlation, and only a small proportion of the significant 5hmC loci overlapped with the significant total methylation loci. GSA analysis suggested that 5hmC was mainly involved in biological processes such as cellular process, biological regulation, and metabolic process. CONCLUSION This is the first study to analyze the epigenome-wide 5hmC profiles among paired lung tumor and normal tissues. We observed global hypomethylation of 5hmC in lung cancers, and hypermethylated 5hmC enriched in CpG islands and gene upstream. We found that the genome-wide 5hmC levels do not correlate with the total methylation, and the GSA suggested different biological functions of 5hmC compared to 5modC. Overall, our results demonstrate the potential of 5hmC as a novel biomarker for lung cancer.
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Affiliation(s)
- Zhihui Wang
- Harvard Graduate School of Arts and Sciences, Harvard University, Boston, MA, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Mulong Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qianyu Yuan
- Harvard Graduate School of Arts and Sciences, Harvard University, Boston, MA, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Yichen Guo
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - John N Hutchinson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Li Su
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jun Wang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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