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Seddon AR, Damiano OM, Hampton MB, Stevens AJ. Widespread genomic de novo DNA methylation occurs following CD8 + T cell activation and proliferation. Epigenetics 2024; 19:2367385. [PMID: 38899429 PMCID: PMC11195465 DOI: 10.1080/15592294.2024.2367385] [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: 03/21/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
This research investigates the intricate dynamics of DNA methylation in the hours following CD8+ T cell activation, during a critical yet understudied temporal window. DNA methylation is an epigenetic modification central to regulation of gene expression and directing immune responses. Our investigation spanned 96-h post-activation and unveils a nuanced tapestry of global and site-specific methylation changes. We identified 15,626 significant differentially methylated CpGs spread across the genome, with the most significant changes occurring within the genes ADAM10, ICA1, and LAPTM5. While many changes had modest effect sizes, approximately 120 CpGs exhibited a log2FC above 1.5, with cell activation and proliferation pathways the most affected. Relatively few of the differentially methylated CpGs occurred along adjacent gene regions. The exceptions were seven differentially methylated gene regions, with the Human T cell Receptor Alpha Joining Genes demonstrating consistent methylation change over a 3kb window. We also investigated whether an inflammatory environment could alter DNA methylation during activation, with proliferating cells exposed to the oxidant glycine chloramine. No substantial differential methylation was observed in this context. The temporal perspective of early activation adds depth to the evolving field of epigenetic immunology, offering insights with implications for therapeutic innovation and expanding our understanding of epigenetic modulation in immune function.
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Affiliation(s)
- Annika R. Seddon
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago, Christchurch, New Zealand
| | - Olivia M. Damiano
- Department of Pathology and Molecular Medicine, Genetics and Epigenetics Research Group, University of Otago, Wellington, New Zealand
| | - Mark B. Hampton
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago, Christchurch, New Zealand
| | - Aaron J. Stevens
- Department of Pathology and Molecular Medicine, Genetics and Epigenetics Research Group, University of Otago, Wellington, New Zealand
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Mortillo M, Kennedy EG, Hermetz KM, Burt AA, Marsit CJ. Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta. Epigenetics 2024; 19:2326869. [PMID: 38507502 PMCID: PMC10956631 DOI: 10.1080/15592294.2024.2326869] [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: 09/28/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in 'open sea' regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.
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Affiliation(s)
- Michael Mortillo
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth G. Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karen M. Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Amber A. Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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3
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Du Y, Benny PA, Shao Y, Schlueter RJ, Gurary A, Lum-Jones A, Lassiter CB, AlAkwaa FM, Tiirikainen M, Towner D, Ward WS, Garmire LX. Multi-omics Analysis of Umbilical Cord Hematopoietic Stem Cells from a Multi-ethnic Cohort of Hawaii Reveals the Transgenerational Effect of Maternal Pre-Pregnancy Obesity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.27.24310936. [PMID: 39108521 PMCID: PMC11302719 DOI: 10.1101/2024.07.27.24310936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
Background Maternal obesity is a health concern that may predispose newborns to a high risk of medical problems later in life. To understand the transgenerational effect of maternal obesity, we conducted a multi-omics study, using DNA methylation and gene expression in the CD34+/CD38-/Lin-umbilical cord blood hematopoietic stem cells (uHSCs) and metabolomics of the cord blood, all from a multi-ethnic cohort (n=72) from Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (collected between 2016 and 2018). Results Differential methylation (DM) analysis unveiled a global hypermethylation pattern in the maternal pre-pregnancy obese group (BH adjusted p<0.05), after adjusting for major clinical confounders. Comprehensive functional analysis showed hypermethylation in promoters of genes involved in cell cycle, protein synthesis, immune signaling, and lipid metabolism. Utilizing Shannon entropy on uHSCs methylation, we discerned notably higher quiescence of uHSCs impacted by maternal obesity. Additionally, the integration of multi-omics data-including methylation, gene expression, and metabolomics-provided further evidence of dysfunctions in adipogenesis, erythropoietin production, cell differentiation, and DNA repair, aligning with the findings at the epigenetic level. Furthermore, the CpG sites associated with maternal obesity from these pathways also predicted highly accurately (average AUC = 0.8687) between cancer vs. normal tissues in 14 cancer types in The Cancer Genome Atlas (TCGA). Conclusions This study revealed the significant correlation between pre-pregnancy maternal obesity and multi-omics level molecular changes in the uHSCs of offspring, particularly in DNA methylation. Moreover, these maternal obesity epigenetic markers in uHSCs may predispose offspring to higher cancer risks.
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Hervoso JL, Amoah K, Dodson J, Choudhury M, Bhattacharya A, Quinones-Valdez G, Pasaniuc B, Xiao X. Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia. Am J Hum Genet 2024; 111:1573-1587. [PMID: 38925119 PMCID: PMC11339621 DOI: 10.1016/j.ajhg.2024.06.001] [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: 10/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with genome-wide association studies to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-sequencing datasets, BrainGVEX and CommonMind, revealing 137 and 88 trait-associated exons (in 84 and 67 genes), respectively. Enriched biological functions in the associated gene sets converged on neuronal function and development, immune cell activation, and cellular transport, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein binding sites, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level, identifying 36 genes and 48 exons as putatively causal for SCZ. We highlight VPS45 and APOPT1, where splicing of specific exons was associated with disease risk, eluding detection by conventional gene expression analysis. Collectively, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ, providing a valuable approach for future investigations in this area.
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Affiliation(s)
- Jonatan L Hervoso
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kofi Amoah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jack Dodson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Lukyanchuk A, Muraki N, Kawai T, Sato T, Hata K, Ito T, Tajima A. Long-term exposure to diesel exhaust particles induces concordant changes in DNA methylation and transcriptome in human adenocarcinoma alveolar basal epithelial cells. Epigenetics Chromatin 2024; 17:24. [PMID: 39103936 DOI: 10.1186/s13072-024-00549-3] [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: 03/08/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Diesel exhaust particles (DEP), which contain hazardous compounds, are emitted during the combustion of diesel. As approximately one-third of the vehicles worldwide use diesel, there are growing concerns about the risks posed by DEP to human health. Long-term exposure to DEP is associated with airway hyperresponsiveness, pulmonary fibrosis, and inflammation; however, the molecular mechanisms behind the effects of DEP on the respiratory tract are poorly understood. Such mechanisms can be addressed by examining transcriptional and DNA methylation changes. Although several studies have focused on the effects of short-term DEP exposure on gene expression, research on the transcriptional effects and genome-wide DNA methylation changes caused by long-term DEP exposure is lacking. Hence, in this study, we investigated transcriptional and DNA methylation changes in human adenocarcinoma alveolar basal epithelial A549 cells caused by prolonged exposure to DEP and determined whether these changes are concordant. RESULTS DNA methylation analysis using the Illumina Infinium MethylationEPIC BeadChips showed that the methylation levels of DEP-affected CpG sites in A549 cells changed in a dose-dependent manner; the extent of change increased with increasing dose reaching the statistical significance only in samples exposed to 30 µg/ml DEP. Four-week exposure to 30 µg/ml of DEP significantly induced DNA hypomethylation at 24,464 CpG sites, which were significantly enriched for DNase hypersensitive sites, genomic regions marked by H3K4me1 and H3K27ac, and several transcription factor binding sites. In contrast, 9,436 CpG sites with increased DNA methylation levels were significantly overrepresented in genomic regions marked by H3K27me3 as well as H3K4me1 and H3K27ac. In parallel, gene expression profiling by RNA sequencing demonstrated that long-term exposure to DEP altered the expression levels of 2,410 genes, enriching 16 gene sets including Xenobiotic metabolism, Inflammatory response, and Senescence. In silico analysis revealed that the expression levels of 854 genes correlated with the methylation levels of the DEP-affected cis-CpG sites. CONCLUSIONS To our knowledge, this is the first report of genome-wide transcriptional and DNA methylation changes and their associations in A549 cells following long-term exposure to DEP.
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Affiliation(s)
- Alexandra Lukyanchuk
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan
- Krasnoyarsk State Medical University Named After Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
| | - Naomi Muraki
- Health Effects Research Group, Environment Research Division, Japan Automobile Research Institute, Tsukuba, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tsuyoshi Ito
- Health Effects Research Group, Environment Research Division, Japan Automobile Research Institute, Tsukuba, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan.
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Hodge KM, Burt AA, Camerota M, Carter BS, Check J, Conneely KN, Helderman J, Hofheimer JA, Hüls A, McGowan EC, Neal CR, Pastyrnak SL, Smith LM, DellaGrotta SA, Dansereau LM, O'Shea TM, Marsit CJ, Lester BM, Everson TM. Epigenetic associations with neonatal age in infants born very preterm, particularly among genes involved in neurodevelopment. Sci Rep 2024; 14:18147. [PMID: 39103365 PMCID: PMC11300786 DOI: 10.1038/s41598-024-68071-w] [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: 03/08/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024] Open
Abstract
The time from conception through the first year of life is the most dynamic period in human development. This time period is particularly important for infants born very preterm (< 30 weeks gestation; VPT), as they experience a significant disruption in the normal developmental trajectories and are at heightened risk of experiencing developmental impairments and delays. Variations in the epigenetic landscape during this period may reflect this disruption and shed light on the interrelationships between aging, maturation, and the epigenome. We evaluated how gestational age (GA) and age since conception in neonates [post-menstrual age (PMA)], were related to DNA methylation in buccal cells collected at NICU discharge from VPT infants (n = 538). After adjusting for confounders and applying Bonferroni correction, we identified 2,366 individual CpGs associated with GA and 14,979 individual CpGs associated with PMA, as well as multiple differentially methylated regions. Pathway enrichment analysis identified pathways involved in axonogenesis and regulation of neuron projection development, among many other growth and developmental pathways (FDR q < 0.001). Our findings align with prior work, and also identify numerous novel associations, suggesting that genes important in growth and development, particularly neurodevelopment, are subject to substantial epigenetic changes during early development among children born VPT.
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Affiliation(s)
- Kenyaita M Hodge
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Amber A Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Marie Camerota
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
| | - Brian S Carter
- Department of Pediatrics-Neonatology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Jennifer Check
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jennifer Helderman
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Julie A Hofheimer
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Anke Hüls
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elisabeth C McGowan
- Department of Pediatrics, Warren Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
| | - Charles R Neal
- Department of Pediatrics, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Steven L Pastyrnak
- Department of Pediatrics, Spectrum Health-Helen Devos Hospital, Grand Rapids, MI, USA
| | - Lynne M Smith
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sheri A DellaGrotta
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
| | - Lynne M Dansereau
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Barry M Lester
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
- Brown Center for the Study of Children at Risk, Women and Infants Hospital, Providence, RI, USA
- Department of Pediatrics, Warren Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
| | - Todd M Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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Mojica E, Kültz D. A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms. J Proteome Res 2024; 23:2780-2794. [PMID: 37624673 PMCID: PMC11301685 DOI: 10.1021/acs.jproteome.3c00246] [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: 04/25/2023] [Indexed: 08/27/2023]
Abstract
Histone post-translational modifications (PTMs) are epigenetic marks that play a critical role in the expression and maintenance of DNA, but they remain largely uninvestigated in nonmodel organisms due to technical challenges. To begin alleviating this issue, we developed a workflow for histone PTM analysis in Mozambique tilapia (Oreochromis mossambicus), being a widespread and environmentally hardy fish, using mass spectrometry methods. By incorporating multiple protein digestion methods into the preparation of each sample, we reliably quantified 214 biologically relevant histone PTMs. All of these histone PTMs, collectively referred to as the global histone PTM landscape, were characterized in the gills, kidney, and testes of this fish. By comparing the global histone PTM landscape between the three tissues, we found that 91.59% of histone PTMs were tissue-dependent. The workflow and tools for histone PTM analysis described in this study are now publicly available and enable comprehensive investigation into the influence of environmental stress on histone PTMs in nonmodel organisms. Given the functionality and flexibility of histone PTMs, we anticipate that the study of histone PTMs in ecologically relevant contexts will provide ground-breaking insights into comparative physiology and evolution.
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Affiliation(s)
- Elizabeth
A. Mojica
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
| | - Dietmar Kültz
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
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Rintala TJ, Fortino V. COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms. PLoS Comput Biol 2024; 20:e1012275. [PMID: 39102448 PMCID: PMC11326705 DOI: 10.1371/journal.pcbi.1012275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 08/15/2024] [Accepted: 06/25/2024] [Indexed: 08/07/2024] Open
Abstract
Recent research on multi-view clustering algorithms for complex disease subtyping often overlooks aspects like clustering stability and critical assessment of prognostic relevance. Furthermore, current frameworks do not allow for a comparison between data-driven and pathway-driven clustering, highlighting a significant gap in the methodology. We present the COPS R-package, tailored for robust evaluation of single and multi-omics clustering results. COPS features advanced methods, including similarity networks, kernel-based approaches, dimensionality reduction, and pathway knowledge integration. Some of these methods are not accessible through R, and some correspond to new approaches proposed with COPS. Our framework was rigorously applied to multi-omics data across seven cancer types, including breast, prostate, and lung, utilizing mRNA, CNV, miRNA, and DNA methylation data. Unlike previous studies, our approach contrasts data- and knowledge-driven multi-view clustering methods and incorporates cross-fold validation for robustness. Clustering outcomes were assessed using the ARI score, survival analysis via Cox regression models including relevant covariates, and the stability of the results. While survival analysis and gold-standard agreement are standard metrics, they vary considerably across methods and datasets. Therefore, it is essential to assess multi-view clustering methods using multiple criteria, from cluster stability to prognostic relevance, and to provide ways of comparing these metrics simultaneously to select the optimal approach for disease subtype discovery in novel datasets. Emphasizing multi-objective evaluation, we applied the Pareto efficiency concept to gauge the equilibrium of evaluation metrics in each cancer case-study. Affinity Network Fusion, Integrative Non-negative Matrix Factorization, and Multiple Kernel K-Means with linear or Pathway Induced Kernels were the most stable and effective in discerning groups with significantly different survival outcomes in several case studies.
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Affiliation(s)
- Teemu J. Rintala
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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9
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Konigsberg IR, Lin NW, Liao SY, Liu C, MacPhail K, Mroz MM, Davidson E, Restrepo CI, Sharma S, Li L, Maier LA, Yang IV. Multi-omic signatures of sarcoidosis and progression in bronchoalveolar lavage cells. Respir Res 2024; 25:289. [PMID: 39080656 PMCID: PMC11290275 DOI: 10.1186/s12931-024-02919-7] [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: 04/16/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Sarcoidosis is a heterogeneous granulomatous disease with no accurate biomarkers of disease progression. Therefore, we profiled and integrated the DNA methylome, mRNAs, and microRNAs to identify molecular changes associated with sarcoidosis and disease progression that might illuminate underlying mechanisms of disease and potential biomarkers. METHODS Bronchoalveolar lavage cells from 64 sarcoidosis subjects and 16 healthy controls were used. DNA methylation was profiled on Illumina HumanMethylationEPIC arrays, mRNA by RNA-sequencing, and miRNAs by small RNA-sequencing. Linear models were fit to test for effect of sarcoidosis diagnosis and progression phenotype, adjusting for age, sex, smoking, and principal components of the data. We built a supervised multi-omics model using a subset of features from each dataset. RESULTS We identified 1,459 CpGs, 64 mRNAs, and five miRNAs associated with sarcoidosis versus controls and four mRNAs associated with disease progression. Our integrated model emphasized the prominence of the PI3K/AKT1 pathway, which is important in T cell and mTOR function. Novel immune related genes and miRNAs including LYST, RGS14, SLFN12L, and hsa-miR-199b-5p, distinguished sarcoidosis from controls. Our integrated model also demonstrated differential expression/methylation of IL20RB, ABCC11, SFSWAP, AGBL4, miR-146a-3p, and miR-378b between non-progressive and progressive sarcoidosis. CONCLUSIONS Leveraging the DNA methylome, transcriptome, and miRNA-sequencing in sarcoidosis BAL cells, we detected widespread molecular changes associated with disease, many which are involved in immune response. These molecules may serve as diagnostic/prognostic biomarkers and/or drug targets, although future testing is required for confirmation.
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Affiliation(s)
- Iain R Konigsberg
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA.
| | - Nancy W Lin
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA.
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Shu-Yi Liao
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Cuining Liu
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Kristyn MacPhail
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Margaret M Mroz
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Elizabeth Davidson
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Clara I Restrepo
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Sunita Sharma
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Li Li
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana V Yang
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
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10
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Eckhardt CM, Balte P, Morris JE, Bhatt SP, Couper D, Fetterman J, Freedman N, Jacobs DR, Hou L, Kalhan R, Liu Y, Loehr L, Lutsey PL, Schwartz JE, White W, Yende S, London SJ, Sanchez TR, Oelsner EC. Non-cigarette tobacco products, aryl-hydrocarbon receptor repressor gene methylation and smoking-related health outcomes. Thorax 2024:thorax-2023-220731. [PMID: 39033027 DOI: 10.1136/thorax-2023-220731] [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: 07/18/2023] [Accepted: 07/01/2024] [Indexed: 07/23/2024]
Abstract
INTRODUCTION Cigarette smoking leads to altered DNA methylation at the aryl-hydrocarbon receptor repressor (AHRR) gene. However, it remains unknown whether pipe or cigar smoking is associated with AHRR methylation. We evaluated associations of non-cigarette tobacco use with AHRR methylation and determined if AHRR methylation was associated with smoking-related health outcomes. METHODS Data were pooled across four population-based cohorts that enrolled participants from 1985 to 2002. Tobacco exposures were evaluated using smoking questionnaires. AHRR cg05575921 methylation was measured in peripheral blood leucocyte DNA. Spirometry and respiratory symptoms were evaluated at the time of methylation measurements and in subsequent visits. Vital status was monitored using the National Death Index. RESULTS Among 8252 adults (mean age 56.7±10.3 years, 58.1% women, 40.6% black), 4857 (58.9%) participants used cigarettes and 634 (7.7%) used non-cigarette tobacco products. Exclusive use of non-cigarette tobacco products was independently associated with lower AHRR methylation (-2.44 units, 95% CI -4.42 to -0.45), though to a lesser extent than exclusive use of cigarettes (-6.01 units, 95% CI -6.01 to -4.10). Among participants who exclusively used non-cigarette tobacco products, reduced AHRR methylation was associated with increased respiratory symptom burden (OR 1.60, 95% CI 1.03 to 2.68) and higher all-cause mortality (log-rank p=0.02). CONCLUSION Pipe and cigar smoking were independently associated with lower AHRR methylation in a multiethnic cohort of US adults. Among users of non-cigarette tobacco products, lower AHRR methylation was associated with poor respiratory health outcomes and increased mortality. AHRR methylation may identify non-cigarette tobacco users with an increased risk of adverse smoking-related health outcomes.
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Affiliation(s)
- Christina M Eckhardt
- Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Pallavi Balte
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Jack E Morris
- Columbia University Mailman School of Public Health, New York, New York, USA
| | - Surya P Bhatt
- Pulmonary, Allergy and Critical Care Medicine, University of Alabama School of Natural Sciences and Mathematics, Birmingham, Alabama, USA
| | - David Couper
- Biostatistics, The University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Neal Freedman
- Nutritional Epidemiology, National Institutes of Health, Bethesda, Maryland, USA
| | - David R Jacobs
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, Minnesota, USA
| | - Lifang Hou
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ravi Kalhan
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yongmei Liu
- Duke University, Durham, North Carolina, USA
| | - Laura Loehr
- The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Pamela L Lutsey
- University of Minnesota School of Public Health, Minneapolis, Minnesota, USA
| | - Joseph E Schwartz
- Center for Behavioral Cardiovascular Health, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Wendy White
- Tougaloo College, Tougaloo, Mississippi, USA
| | - Sachin Yende
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Tiffany R Sanchez
- Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Elizabeth C Oelsner
- Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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11
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Chen YC, Liaw YC, Nfor ON, Hsiao CH, Zhong JH, Wu SL, Liaw YP. Epigenetic associations of GPNMB rs199347 variant with alcohol consumption in Parkinson's disease. Front Psychiatry 2024; 15:1377403. [PMID: 39091454 PMCID: PMC11293056 DOI: 10.3389/fpsyt.2024.1377403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/27/2024] [Indexed: 08/04/2024] Open
Abstract
Introduction Alcohol consumption can induce a neuroinflammatory response and contribute to the progression of neurodegeneration. However, its association with Parkinson's disease (PD), the second most common neurodegenerative disorder, remains undetermined. Recent studies suggest that the glycoprotein non-metastatic melanoma protein B (GPNMB) is a potential biomarker for PD. We evaluated the association of rs199347, a variant of the GPNMB gene, with alcohol consumption and methylation upstream of GPNMB. Methods We retrieved genetic and DNA methylation data obtained from participants enrolled in the Taiwan Biobank (TWB) between 2008 and 2016. After excluding individuals with incomplete or missing information about potential PD risk factors, we included 1,357 participants in our final analyses. We used multiple linear regression to assess the association of GPNMB rs199347 and chronic alcohol consumption (and other potential risk factors) with GPNMB cg17274742 methylation. Results There was no difference between the distribution of GPNMB rs199347 genotypes between chronic alcohol consumers and the other study participants. A significant interaction was observed between the GPNMB rs199347 variant and alcohol consumption (p = 0.0102) concerning cg17274742 methylation. Compared to non-chronic alcohol consumers with the AA genotype, alcohol drinkers with the rs199347 GG genotype had significantly lower levels (hypomethylation) of cg17274742 (p = 0.0187). Conclusion Alcohol consumption among individuals with the rs199347 GG genotype was associated with lower levels of cg17274742 methylation, which could increase expression of the GPNMB gene, an important neuroinflammatory-related risk gene for PD.
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Affiliation(s)
- Yen-Chung Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Chia Liaw
- Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Shey-Lin Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Electrical Engineering, National Changhua University of Education, Changhua, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
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12
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Carvalho Silva R, Martini P, Hohoff C, Mattevi S, Bortolomasi M, Abate M, Menesello V, Gennarelli M, Baune BT, Minelli A. Unraveling epigenomic signatures and effectiveness of electroconvulsive therapy in treatment-resistant depression patients: a prospective longitudinal study. Clin Epigenetics 2024; 16:93. [PMID: 39020437 PMCID: PMC11256624 DOI: 10.1186/s13148-024-01704-z] [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: 02/14/2024] [Accepted: 07/05/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Electroconvulsive therapy (ECT) benefits patients with treatment-resistant depression (TRD), but the underlying biological processes are unclear. We conducted an epigenome-wide association study in 32 TRD patients undergoing ECT to depict ECT-associated methylation changes. Illness severity and ECT outcomes were assessed with the Montgomery-Åsberg Depression Rating Scale at baseline (T0) and 1 month after its end (T1). Methylation was profiled at T0 and T1 with the Illumina Infinium Methylation EPIC BeadChip array. RESULTS Longitudinal T0-T1 analyses showed 3 differentially methylated probes (DMPs) with nominal p values ≤ 10-5, with 2 annotated in the genes CYB5B and PVRL4. Including covariates, we found 4 DMPs for symptoms variation, annotated in FAM20C, EPB41, OTUB1 and ADARB1, and 3 DMPs for response status, with 2 annotated in IQCE and FAM20C. Regional analysis revealed 54 differentially methylated regions (DMRs) with nominal p value area ≤ 0.05, with 9 presenting adjusted p-value area ≤ 0.10, annotated in MCF2L, SLC25A24, RUNX3, MIR637, FOXK2, FAM180B, POU6F1, ALS2CL and CCRL2. Considering covariates, we found 21 DMRs for symptoms variation and 26 DMRs for response (nominal p value area ≤ 0.05), with 4 presenting adjusted p-value area ≤ 0.10 for response, annotated in SNORD34, NLRP6, GALNT2 and SFT2D3. None remained significant after false discovery rate correction. Notably, ADARB1 variants are associated with suicide attempt in patients with psychiatric disorders, and SLC25A24 relates to conduct disorder. Several DMPs and DMRs are annotated in genes associated with inflammatory/immune processes. Longitudinal analyses on females (n = 22) revealed statistically significant DMRs (adjusted p value area ≤ 0.05) and trend-significant DMRs (adjusted p value area ≤ 0.07) for symptoms variation and response status, annotated in genes related to psychiatric disorders (ZFP57, POLD4, TRIM10, GAS7, ADORA2A, TOLLIP), trauma exposure (RIPOR2) and inflammatory/immune responses (LAT, DLX4, POLD4, FAM30A, H19). Pathway analysis on females revealed enrichment for transcriptional activity, growth factors, DNA maintenance, and immune pathways including IRF7 and IRF2. CONCLUSION Although no significant results were found for the whole cohort, the study provides insights into ECT-associated methylation changes, highlighting DMPs and DMRs related to ECT outcomes. Analyses on females revealed significant DMRs and pathways related to psychiatric disorders and inflammatory/immune processes.
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Affiliation(s)
- Rosana Carvalho Silva
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | - Christa Hohoff
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Stefania Mattevi
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
| | | | - Maria Abate
- Psychiatric Hospital "Villa Santa Chiara", Verona, Italy
| | - Valentina Menesello
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, Biology and Genetic Division, University of Brescia, Viale Europa, 11, 25123, Brescia, Italy.
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.
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13
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Mortillo M, Kennedy E, Hermetz K, Burt A, Marsit C. Associations between placental hydroxymethylation and birthweight. EPIGENETICS REPORTS 2024; 2:1-7. [PMID: 39091447 PMCID: PMC11290493 DOI: 10.1080/28361512.2024.2376954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024]
Abstract
5-hydroxymethylcytosine (5hmC), formed through the ten-eleven translocation (TET) methylcytosine dioxygenase mediated oxidation of 5-methylcytosine (5mC) at cytosine-phosphate-guanine (CpG) dinucleotides, is believed to mainly serve as an intermediate in the DNA demethylation pathway, though recent evidence suggests that 5hmC may also play a functionally relevant role. We have conducted an epigenome-wide association study (EWAS) to assess the association between placenta 5hmC, obtained through parallel bisulfite and oxidative bisulfite modification of DNA and array-based assessment, and newborn birthweight in the Rhode Island Child Health Study (RICHS). We also assessed whether the removal of 5hmC signal impacts the observed results from traditional epigenome-wide studies that rely on BS modification-based (combined 5mC and 5hmC) assessment alone. We identified 5hmC at one CpG in the CUBN gene to be significantly associated with birthweight (FDR < 0.05) and demonstrate that expression of that gene was also associated with birthweight. Comparison of 5hmC+5mC and 5mC EWAS effect estimates reveal a strong correlation (r = 0.77, p < 0.0001). Our study suggests that traditional assessment of 5mC through bisulfite modification alone provides an accurate assessment of CpG-specific DNA methylation for EWAS studies but was unable to provide evidence of widespread associations between placental 5hmC and birthweight.
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Affiliation(s)
- Michael Mortillo
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Elizabeth Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Karen Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Amber Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Carmen Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
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14
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Tomasova K, Seborova K, Kroupa M, Horak J, Kavec M, Vodickova L, Rob L, Hruda M, Mrhalova M, Bartakova A, Bouda J, Fleischer T, Kristensen VN, Vodicka P, Vaclavikova R. Telomere length as a predictor of therapy response and survival in patients diagnosed with ovarian carcinoma. Heliyon 2024; 10:e33525. [PMID: 39050459 PMCID: PMC11268197 DOI: 10.1016/j.heliyon.2024.e33525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 06/14/2024] [Accepted: 06/23/2024] [Indexed: 07/27/2024] Open
Abstract
Impaired telomere length (TL) maintenance in ovarian tissue may play a pivotal role in the onset of epithelial ovarian cancer (OvC). TL in either target or surrogate tissue (blood) is currently being investigated for use as a predictor in anti-OvC therapy or as a biomarker of the disease progression, respectively. There is currently an urgent need for an appropriate approach to chemotherapy response prediction. We performed a monochrome multiplex qPCR measurement of TL in peripheral blood leukocytes (PBL) and tumor tissues of 209 OvC patients. The methylation status and gene expression of the shelterin complex and telomerase catalytic subunit (hTERT) were determined within tumor tissues by High-Throughput DNA methylation profiling and RNA sequencing (RNA-Seq) analysis, respectively. The patients sensitive to cancer treatment (n = 46) had shorter telomeres in PBL compared to treatment-resistant patients (n = 93; P = 0.037). In the patients with a different therapy response, transcriptomic analysis showed alterations in the peroxisome proliferator-activated receptor (PPAR) signaling pathway (q = 0.001). Moreover, tumor TL shorter than the median corresponded to better overall survival (OS) (P = 0.006). TPP1 gene expression was positively associated with TL in tumor tissue (P = 0.026). TL measured in PBL could serve as a marker of platinum therapy response in OvC patients. Additionally, TL determined in tumor tissue provides information on OvC patients' OS.
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Affiliation(s)
- Kristyna Tomasova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/77, 32300, Pilsen, Czech Republic
| | - Karolina Seborova
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 100 42, Prague, Czech Republic
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00, Pilsen, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/77, 32300, Pilsen, Czech Republic
| | - Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Third Faculty of Medicine, Charles University, Ruska 87, 100 00, Prague, Czech Republic
| | - Miriam Kavec
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/77, 32300, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Lukas Rob
- Department of Gynecology and Obstetrics, Third Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Martin Hruda
- Department of Gynecology and Obstetrics, Third Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Marcela Mrhalova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine and Motol University Hospital, Charles University, Prague, Czech Republic
| | - Alena Bartakova
- Department of Gynecology and Obstetrics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jiri Bouda
- Department of Gynecology and Obstetrics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Vessela N. Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/77, 32300, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Radka Vaclavikova
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 100 42, Prague, Czech Republic
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00, Pilsen, Czech Republic
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15
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Murthy M, Fodder K, Miki Y, Rambarack N, De Pablo Fernandez E, Pihlstrøm L, Mill J, Warner TT, Lashley T, Bettencourt C. DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson's disease, and progressive supranuclear palsy: a cross-comparative investigation. Acta Neuropathol 2024; 148:4. [PMID: 38995454 PMCID: PMC11245434 DOI: 10.1007/s00401-024-02764-4] [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: 04/22/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, with oligodendroglial cytoplasmic inclusions (GCIs) containing α-synuclein being the primary pathological hallmark. Clinical presentations of MSA overlap with other parkinsonian disorders, such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP), posing challenges in early diagnosis. Numerous studies have reported alterations in DNA methylation in neurodegenerative diseases, with candidate loci being identified in various parkinsonian disorders including MSA, PD, and PSP. Although MSA and PSP present with substantial white matter pathology, alterations in white matter have also been reported in PD. However, studies comparing the DNA methylation architectures of white matter in these diseases are lacking. We therefore aimed to investigate genome-wide DNA methylation patterns in the frontal lobe white matter of individuals with MSA (n = 17), PD (n = 17), and PSP (n = 16) along with controls (n = 15) using the Illumina EPIC array, to identify shared and disease-specific DNA methylation alterations. Genome-wide DNA methylation profiling of frontal lobe white matter in the three parkinsonian disorders revealed substantial commonalities in DNA methylation alterations in MSA, PD, and PSP. We further used weighted gene correlation network analysis to identify disease-associated co-methylation signatures and identified dysregulation in processes relating to Wnt signaling, signal transduction, endoplasmic reticulum stress, mitochondrial processes, RNA interference, and endosomal transport to be shared between these parkinsonian disorders. Our overall analysis points toward more similarities in DNA methylation patterns between MSA and PD, both synucleinopathies, compared to that between MSA and PD with PSP, which is a tauopathy. Our results also highlight several shared DNA methylation changes and pathways indicative of converging molecular mechanisms in the white matter contributing toward neurodegeneration in all three parkinsonian disorders.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Katherine Fodder
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Yasuo Miki
- Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Naiomi Rambarack
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Eduardo De Pablo Fernandez
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Thomas T Warner
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
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16
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Hannon ER, Marsit CJ, Dent AE, Embury P, Ogolla S, Midem D, Williams SM, Kazura JW. Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation. BioData Min 2024; 17:21. [PMID: 38992677 PMCID: PMC11241886 DOI: 10.1186/s13040-024-00374-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs). METHODS Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively. RESULTS Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils. CONCLUSION Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.
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Affiliation(s)
- Emily R Hannon
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA.
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Arlene E Dent
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
- Division of Pediatric Infectious Diseases, Rainbow Babies and Children's Hospital, Cleveland, OH, 44106, USA
| | - Paula Embury
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
| | | | - David Midem
- Chulaimbo Sub-county Hospital, Kisumu County, Kenya
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
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Xiao C, Peng G, Conneely KN, Zhao H, Felger JC, Wommack EC, Higgins KA, Shin DM, Saba NF, Bruner DW, Miller AH. DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism. Mol Psychiatry 2024:10.1038/s41380-024-02652-z. [PMID: 38977918 DOI: 10.1038/s41380-024-02652-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 06/19/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Cancer patients are commonly affected by fatigue. Herein, we sought to examine epigenetic modifications (i.e., DNA methylation) related to fatigue in peripheral blood among patients during and after treatment for head and neck cancer (HNC). Further, we determined whether these modifications were associated with gene expression and inflammatory protein markers, which we have previously linked to fatigue in HNC. This prospective, longitudinal study enrolled eligible patients with data collected at pre-radiotherapy, end of radiotherapy, and six months and one-year post-radiotherapy. Fatigue data were reported by patients using the Multidimensional Fatigue Inventory (MFI)-20. DNA methylation (Illumina MethylationEPIC) and gene expression (Applied Biosystems Clariom S) arrays and assays for seven inflammatory markers (R&D Systems multiplex) were performed. Mixed models and enrichment analyses were applied to establish the associations. A total of 386 methylation loci were associated with fatigue among 145 patients (False Discovery Rate [FDR] < 0.05). Enrichment analyses showed the involvement of genes related to immune and inflammatory responses, insulin and lipid metabolism, neuropsychological disorders, and tumors. We further identified 16 methylation-gene expression pairs (FDR < 0.05), which were linked to immune and inflammatory responses and lipid metabolism. Ninety-one percent (351) of the 386 methylation loci were also significantly associated with inflammatory markers (e.g., interleukin 6, c-reactive protein; FDR < 0.05), which further mediated the association between methylation and fatigue (FDR < 0.05). These data suggest that epigenetic modifications associated with inflammation and immunometabolism, in conjunction with relevant gene expression and protein markers, are potential targets for treating fatigue in HNC patients. The findings also merit future prospective studies in other cancer populations as well as interventional investigations.
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Affiliation(s)
- Canhua Xiao
- Emory University School of Nursing, Atlanta, GA, USA.
| | - Gang Peng
- Indianan University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN, USA
| | - Karen N Conneely
- Emory University School of Medicine, Department of Human Genetics, Atlanta, GA, USA
| | - Hongyu Zhao
- Yale University School of Medicine, Department of Genetics, New Haven, CT, USA
| | - Jennifer C Felger
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Evanthia C Wommack
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Kristin A Higgins
- Emory University School of Medicine, Department of Radiation Oncology, Atlanta, GA, USA
| | - Dong M Shin
- Emory University School of Medicine, Department of Hematology and Medical Oncology, Atlanta, GA, USA
| | - Nabil F Saba
- Emory University School of Medicine, Department of Hematology and Medical Oncology, Atlanta, GA, USA
| | | | - Andrew H Miller
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
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18
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Wei Y, Zhou YF, Xiao L, Qin J, Cheng H, Cai H, Chen X, Zou Y, Yang L, Zhang H, Zhang Z, Yang X. Associations of Heavy Metals with Cognitive Function: An Epigenome-Wide View of DNA Methylation and Mediation Analysis. Ann Neurol 2024; 96:87-98. [PMID: 38661228 DOI: 10.1002/ana.26942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
OBJECTIVE Exposure to heavy metals has been reported to be associated with impaired cognitive function, but the underlying mechanisms remain unclear. This pilot study aimed to identify key heavy metal elements associated with cognitive function and further explore the potential mediating role of metal-related DNA methylation. METHODS Blood levels of arsenic, cadmium, lead, copper, manganese, and zinc and genome-wide DNA methylations were separately detected in peripheral blood in 155 older adults. Cognitive function was evaluated using the Mini-Mental State Examination (MMSE). Least absolute shrinkage and selection operator penalized regression and Bayesian kernel machine regression were used to identify metals associated with cognitive function. An epigenome-wide association study examined the DNA methylation profile of the identified metal, and mediation analysis investigated its mediating role. RESULTS The MMSE scores showed a significant decrease of 1.61 (95% confidence interval [CI]: -2.64, -0.59) with each 1 standard deviation increase in ln-transformed arsenic level; this association was significant in multiple-metal models and dominated the overall negative effect of 6 heavy metal mixture on cognitive function. Seventy-three differentially methylated positions were associated with blood arsenic (p < 1.0 × 10-5). The methylation levels at cg05226051 (annotated to TDRD3) and cg18886932 (annotated to GAL3ST3) mediated 24.8% and 25.5% of the association between blood arsenic and cognitive function, respectively (all p < 0.05). INTERPRETATION Blood arsenic levels displayed a negative association with the cognitive function of older adults. This finding shows that arsenic-related DNA methylation alterations are critical partial mediators that may serve as potential biomarkers for further mechanism-related studies. ANN NEUROL 2024;96:87-98.
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Affiliation(s)
- Yue Wei
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yan-Feng Zhou
- Department of Social Medicine, School of Public Health, Guangxi Medical University, Nanning, China
| | - Lili Xiao
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jian Qin
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Hong Cheng
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Haiqing Cai
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Xing Chen
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yunfeng Zou
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Li Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Haiying Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Zhiyong Zhang
- Department of Environmental Health and Occupational Medicine, Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath Research, Guilin Medical University, Guilin, China
| | - Xiaobo Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
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19
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Puvvula J, Braun JM, DeFranco EA, Ho SM, Leung YK, Huang S, Zhang X, Vuong AM, Kim SS, Percy Z, Calafat AM, Botelho JC, Chen A. Gestational exposure to environmental chemicals and epigenetic alterations in the placenta and cord blood mononuclear cells. EPIGENETICS COMMUNICATIONS 2024; 4:4. [PMID: 38962689 PMCID: PMC11217138 DOI: 10.1186/s43682-024-00027-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
Background Exposure to environmental chemicals such as phthalates, phenols, and polycyclic aromatic hydrocarbons (PAHs) during pregnancy can increase the risk of adverse newborn outcomes. We explored the associations between maternal exposure to select environmental chemicals and DNA methylation in cord blood mononuclear cells (CBMC) and placental tissue (maternal and fetal sides) to identify potential mechanisms underlying these associations. Method This study included 75 pregnant individuals who planned to give birth at the University of Cincinnati Hospital between 2014 and 2017. Maternal urine samples during the delivery visit were collected and analyzed for 37 biomarkers of phenols (12), phthalates (13), phthalate replacements (4), and PAHs (8). Cord blood and placenta tissue (maternal and fetal sides) were also collected to measure the DNA methylation intensities using the Infinium HumanMethylation450K BeadChip. We used linear regression, adjusting for potential confounders, to assess CpG-specific methylation changes in CBMC (n = 54) and placenta [fetal (n = 67) and maternal (n = 68) sides] associated with gestational chemical exposures (29 of 37 biomarkers measured in this study). To account for multiple testing, we used a false discovery rate q-values < 0.05 and presented results by limiting results with a genomic inflation factor of 1±0.5. Additionally, gene set enrichment analysis was conducted using the Kyoto Encyclopedia of Genes and Genomics pathways. Results Among the 29 chemical biomarkers assessed for differential methylation, maternal concentrations of PAH metabolites (1-hydroxynaphthalene, 2-hydroxyfluorene, 4-hydroxyphenanthrene, 1-hydroxypyrene), monocarboxyisononyl phthalate, mono-3-carboxypropyl phthalate, and bisphenol A were associated with altered methylation in placenta (maternal or fetal side). Among exposure biomarkers associated with epigenetic changes, 1-hydroxynaphthalene, and mono-3-carboxypropyl phthalate were consistently associated with differential CpG methylation in the placenta. Gene enrichment analysis indicated that maternal 1-hydroxynaphthalene was associated with lipid metabolism and cellular processes of the placenta. Additionally, mono-3-carboxypropyl phthalate was associated with organismal systems and genetic information processing of the placenta. Conclusion Among the 29 chemical biomarkers assessed during delivery, 1-hydroxynaphthalene and mono-3-carboxypropyl phthalate were associated with DNA methylation in the placenta. Supplementary Information The online version contains supplementary material available at 10.1186/s43682-024-00027-7.
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Affiliation(s)
- Jagadeesh Puvvula
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Joseph M. Braun
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Emily A. DeFranco
- Department of Obstetrics and Gynecology, College of Medicine, University of Kentucky, Lexington, KY USA
| | - Shuk-Mei Ho
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Yuet-Kin Leung
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Shouxiong Huang
- Pathogen-Host Interaction Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Xiang Zhang
- Department of Environmental & Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH USA
| | - Ann M. Vuong
- Department of Epidemiology and Biostatistics, School of Public Health, University of Nevada Las Vegas, Las Vegas, NV USA
| | - Stephani S. Kim
- Health Research, Battelle Memorial Institute, Columbus, OH USA
| | - Zana Percy
- Department of Environmental & Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH USA
| | - Antonia M. Calafat
- National Center for Environmental Health, U.S. Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Julianne C. Botelho
- National Center for Environmental Health, U.S. Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Aimin Chen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
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20
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Alhassan D, Olbricht GR, Adekpedjou A. Differential methylation region detection via an array-adaptive normalized kernel-weighted model. PLoS One 2024; 19:e0306036. [PMID: 38941289 PMCID: PMC11213316 DOI: 10.1371/journal.pone.0306036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 06/09/2024] [Indexed: 06/30/2024] Open
Abstract
A differentially methylated region (DMR) is a genomic region that has significantly different methylation patterns between biological conditions. Identifying DMRs between different biological conditions is critical for developing disease biomarkers. Although methods for detecting DMRs in microarray data have been introduced, developing methods with high precision, recall, and accuracy in determining the true length of DMRs remains a challenge. In this study, we propose a normalized kernel-weighted model to account for similar methylation profiles using the relative probe distance from "nearby" CpG sites. We also extend this model by proposing an array-adaptive version in attempt to account for the differences in probe spacing between Illumina's Infinium 450K and EPIC bead array respectively. We also study the asymptotic results of our proposed statistic. We compare our approach with a popular DMR detection method via simulation studies under large and small treatment effect settings. We also discuss the susceptibility of our method in detecting the true length of the DMRs under these two settings. Lastly, we demonstrate the biological usefulness of our method when combined with pathway analysis methods on oral cancer data. We have created an R package called idDMR, downloadable from GitHub repository with link: https://github.com/DanielAlhassan/idDMR, that allows for the convenient implementation of our array-adaptive DMR method.
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Affiliation(s)
- Daniel Alhassan
- Department of Mathematics and Statistics, Missouri University of Science and Technology, Rolla, MO, United States of America
| | - Gayla R. Olbricht
- Department of Mathematics and Statistics, Missouri University of Science and Technology, Rolla, MO, United States of America
| | - Akim Adekpedjou
- Department of Mathematics and Statistics, Missouri University of Science and Technology, Rolla, MO, United States of America
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21
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Elliott HR, Bennett CL, Caramaschi D, English S. Negative association between higher maternal pre-pregnancy body mass index and breastfeeding outcomes is not mediated by DNA methylation. Sci Rep 2024; 14:14675. [PMID: 38918574 PMCID: PMC11199553 DOI: 10.1038/s41598-024-65605-0] [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: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
The benefits of breastfeeding for the health and wellbeing of both infants and mothers are well documented, yet global breastfeeding rates are low. One factor associated with low breast feeding is maternal body mass index (BMI), which is used as a measure of obesity. The negative relationship between maternal obesity and breastfeeding is likely caused by a variety of social, psychological, and physiological factors. Maternal obesity may also have a direct biological association with breastfeeding through changes in maternal DNA methylation. Here, we investigate this potential biological association using data from a UK-based cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC). We find that pre-pregnancy body mass index (BMI) is associated with lower initiation to breastfeed and shorter breastfeeding duration. We conduct epigenome-wide association studies (EWAS) of pre-pregnancy BMI and breastfeeding outcomes, and run candidate-gene analysis of methylation sites associated with BMI identified via previous meta-EWAS. We find that DNA methylation at cg11453712, annotated to PHTP1, is associated with pre-pregnancy BMI. From our results, neither this association nor those at candidate-gene sites are likely to mediate the link between pre-pregnancy BMI and breastfeeding.
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Affiliation(s)
- Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Chloe L Bennett
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Doretta Caramaschi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Faculty of Health and Life Sciences, Department of Psychology, University of Exeter, Exeter, UK
| | - Sinead English
- School of Biological Sciences, University of Bristol, Bristol, UK.
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22
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Rönn T, Perfilyev A, Oskolkov N, Ling C. Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets. Sci Rep 2024; 14:14637. [PMID: 38918439 PMCID: PMC11199577 DOI: 10.1038/s41598-024-64846-3] [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: 12/14/2023] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Type 2 diabetes (T2D) is the fastest growing non-infectious disease worldwide. Impaired insulin secretion from pancreatic beta-cells is a hallmark of T2D, but the mechanisms behind this defect are insufficiently characterized. Integrating multiple layers of biomedical information, such as different Omics, may allow more accurate understanding of complex diseases such as T2D. Our aim was to explore and use Machine Learning to integrate multiple sources of biological/molecular information (multiOmics), in our case RNA-sequening, DNA methylation, SNP and phenotypic data from islet donors with T2D and non-diabetic controls. We exploited Machine Learning to perform multiOmics integration of DNA methylation, expression, SNPs, and phenotypes from pancreatic islets of 110 individuals, with ~ 30% being T2D cases. DNA methylation was analyzed using Infinium MethylationEPIC array, expression was analyzed using RNA-sequencing, and SNPs were analyzed using HumanOmniExpress arrays. Supervised linear multiOmics integration via DIABLO based on Partial Least Squares (PLS) achieved an accuracy of 91 ± 15% of T2D prediction with an area under the curve of 0.96 ± 0.08 on the test dataset after cross-validation. Biomarkers identified by this multiOmics integration, including SACS and TXNIP DNA methylation, OPRD1 and RHOT1 expression and a SNP annotated to ANO1, provide novel insights into the interplay between different biological mechanisms contributing to T2D. This Machine Learning approach of multiOmics cross-sectional data from human pancreatic islets achieved a promising accuracy of T2D prediction, which may potentially find broad applications in clinical diagnostics. In addition, it delivered novel candidate biomarkers for T2D and links between them across the different Omics.
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Affiliation(s)
- Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Lund University, 205 02, Malmö, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Lund University, 205 02, Malmö, Sweden
| | - Nikolay Oskolkov
- Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Sölvegatan 35, 223 62, Lund, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Lund University, 205 02, Malmö, Sweden.
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23
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Patel D, McElroy JP, Weng DY, Sahar K, Reisinger SA, Freudenheim JL, Wewers MD, Shields PG, Song MA. Sex-related DNA methylation is associated with inflammation and gene expression in the lungs of healthy individuals. Sci Rep 2024; 14:14280. [PMID: 38902313 PMCID: PMC11190195 DOI: 10.1038/s41598-024-65027-y] [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: 03/07/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024] Open
Abstract
Lung cancer exhibits sex-biased molecular characteristics and epidemiological trends, suggesting a need for sex-specific approaches to understanding its etiology and treatment. DNA methylation alterations play critical roles in lung carcinogenesis and may serve as valuable biomarkers for precision medicine strategies. We employed the Infinium MethylationEPIC array to identify autosomal sex-related differentially methylated CpG sites (DM-CpGs) in lung epithelium of healthy individuals (32 females and 37 males) while controlling for age, BMI, and tobacco use. We correlated DM-CpGs with gene expression in lung epithelium and immune responses in bronchoalveolar lavage. We validated these DM-CpGs in lung tumors and adjacent normal tissue from The Cancer Genome Atlas (TCGA). Among 522 identified DM-CpGs, 61% were hypermethylated in females, predominantly located in promoter regions. These DM genes were implicated in cell-to-cell signaling, cellular function, transport, and lipid metabolism. Correlation analysis revealed sex-specific patterns between DM-CpGs and gene expression. Additionally, several DM-CpGs were correlated significantly with cytokines (IL-1β, IL-4, IL-12p70, and IFN-γ), macrophage, and lymphocyte counts. Also, some DM-CpGs were observed in TCGA lung adenocarcinoma, squamous cell carcinoma, and adjacent normal tissues. Our findings highlight sex-specific DNA methylation patterns in healthy lung epithelium and their associations with lung gene expression and lung immune biomarkers. These findings underscore the potential role of lung sex-related CpGs as epigenetic predispositions influencing sex disparities in lung cancer risk and outcomes, warranting further investigation for personalized lung cancer management strategies.
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Affiliation(s)
- Devki Patel
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Joseph P McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Kamel Sahar
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Sarah A Reisinger
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Mark D Wewers
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.
- Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
| | - Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA.
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24
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Newsham I, Sendera M, Jammula SG, Samarajiwa SA. Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns. Biol Methods Protoc 2024; 9:bpae028. [PMID: 38903861 PMCID: PMC11186673 DOI: 10.1093/biomethods/bpae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 06/22/2024] Open
Abstract
Cancer, a collection of more than two hundred different diseases, remains a leading cause of morbidity and mortality worldwide. Usually detected at the advanced stages of disease, metastatic cancer accounts for 90% of cancer-associated deaths. Therefore, the early detection of cancer, combined with current therapies, would have a significant impact on survival and treatment of various cancer types. Epigenetic changes such as DNA methylation are some of the early events underlying carcinogenesis. Here, we report on an interpretable machine learning model that can classify 13 cancer types as well as non-cancer tissue samples using only DNA methylome data, with 98.2% accuracy. We utilize the features identified by this model to develop EMethylNET, a robust model consisting of an XGBoost model that provides information to a deep neural network that can generalize to independent data sets. We also demonstrate that the methylation-associated genomic loci detected by the classifier are associated with genes, pathways and networks involved in cancer, providing insights into the epigenomic regulation of carcinogenesis.
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Affiliation(s)
- Izzy Newsham
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, United Kingdom
| | - Marcin Sendera
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- Jagiellonian University, Faculty of Mathematics and Computer Science, 30-348 Kraków, Poland
| | - Sri Ganesh Jammula
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, United Kingdom
- MedGenome labs, Bengaluru, 560099, India
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- Imperial College London, Hammersmith Campus, London, W12 0NN, United Kingdom
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25
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Hicks J, Robinson K, Lee S, Marsh A, Akins R. Novel Machine Learning Analysis Algorithm of DNA Methylation Patterns Identifies Cerebral Palsy with Concurrent Epilepsy. RESEARCH SQUARE 2024:rs.3.rs-4560364. [PMID: 38946953 PMCID: PMC11213172 DOI: 10.21203/rs.3.rs-4560364/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Spastic cerebral palsy, the most common pediatric-onset disabling condition with an estimated prevalence of 0.2% in children, is a complex condition characterized by stiff movement, muscle contractures, and abnormal gait that can diminish quality of life. Spastic CP accounts for approximately 83% of all CP cases and frequently co-occurs with other complex conditions, like epilepsy. An estimated 42% of spastic CP cases have co-occurring epilepsy. Unfortunately, CP is often difficult to diagnose. Although most children with CP are born with it or acquire it immediately after birth, many are not identified until after 19 months of age with CP diagnosis often not confirmed until 5 years of age. New bioinformatic approaches to identify CP earlier are needed. Recent studies indicate that altered DNA methylation patterns associated with CP may have diagnostic value. The potential confounding effects of co-occurrent epilepsy on these patterns are not known. We evaluated machine learning classification of CP patients with or without co-occurring epilepsy. Results Whole blood samples were collected from 30 study participants diagnosed with epilepsy (n=4), spastic CP (n=10), both (n=8), or neither (n=8). A novel Support-Vector-Machine learning algorithm was developed to identify methylation loci that have ability to classify CP from controls in the presence or absence of epilepsy. This algorithm was also employed to measure classification ability of identified methylation loci. After preprocessing of data, isolation of important methylation loci was performed in a binary comparison between CP and controls, as well as in a 4-way scheme, encapsulating epilepsy diagnoses. The classification ability was similarly assessed. CP Classification performance was evaluated with and without inclusion of epilepsy as a feature. Median F1 scores were 0.67 in 4-class comparison, and 1.0 in the binary classification, outperforming Linear-Discriminant-Analysis (0.57 and 0.86, respectively). Conclusion This novel algorithm was able to classify study participants with spastic CP and/or epilepsy from controls with significant performance. The algorithm shows promise for rapid identification in methylation data of diagnostic methylation loci. In this model, Support Vector Machines outperformed Linear Discriminant Analysis in classification. In the evaluation of epigenetics-based diagnostics for CP, epilepsy may not be a significant confounding factor.
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Affiliation(s)
- Jonathan Hicks
- Bioinformatics and Computational Biology, University of Delaware
- Nemours Children's Health, Wilmington DE, USA
| | | | | | - Adam Marsh
- Bioinformatics and Computational Biology, University of Delaware
| | - Robert Akins
- Bioinformatics and Computational Biology, University of Delaware
- Nemours Children's Health, Wilmington DE, USA
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26
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Burgermeister S, Stoykova S, Krebs FS, Zoete V, Mbefo M, Egervari K, Reinhard A, Bisig B, Hewer E. Methylation-Based Characterization of a New IDH2 Mutation in Sinonasal Undifferentiated Carcinoma. Int J Mol Sci 2024; 25:6518. [PMID: 38928223 PMCID: PMC11204065 DOI: 10.3390/ijms25126518] [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: 04/22/2024] [Revised: 06/01/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations affecting codon 172 of the isocitrate dehydrogenase 2 (IDH2) gene define a subgroup of sinonasal undifferentiated carcinomas (SNUCs) with a relatively favorable prognosis and a globally hypermethylated phenotype. They are also recurrent (along with IDH1 mutations) in gliomas, acute myeloid leukemia, and intrahepatic cholangiocarcinoma. Commonly reported mutations, all associated with aberrant IDH2 enzymatic activity, include R172K, R172S, R172T, R172G, and R172M. We present a case of SNUC with a never-before-described IDH2 mutation, R172A. Our report compares the methylation pattern of our sample to other cases from the Gene Expression Omnibus database. Hierarchical clustering suggests a strong association between our sample and other IDH-mutant SNUCs and a clear distinction between sinonasal normal tissues and tumors. Principal component analysis (PCA), using 100 principal components explaining 94.5% of the variance, showed the position of our sample to be within 1.02 standard deviation of the other IDH-mutant SNUCs. A molecular modeling analysis of the IDH2 R172A versus other R172 variants provides a structural explanation to how they affect the protein active site. Our findings thus suggest that the R172A mutation in IDH2 confers a gain of function similar to other R172 mutations in IDH2, resulting in a similar hypermethylated profile.
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Affiliation(s)
- Simon Burgermeister
- Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (S.S.); (M.M.); (B.B.)
| | - Simona Stoykova
- Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (S.S.); (M.M.); (B.B.)
| | - Fanny S. Krebs
- Computer-Aided Molecular Engineering, Department of Oncology UNIL-CHUV, University of Lausanne, 1066 Epalinges, Switzerland; (F.S.K.); (V.Z.)
- Ludwig Institute for Cancer Research, 1066 Epalinges, Switzerland
| | - Vincent Zoete
- Computer-Aided Molecular Engineering, Department of Oncology UNIL-CHUV, University of Lausanne, 1066 Epalinges, Switzerland; (F.S.K.); (V.Z.)
- Ludwig Institute for Cancer Research, 1066 Epalinges, Switzerland
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martial Mbefo
- Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (S.S.); (M.M.); (B.B.)
| | - Kristof Egervari
- Service of Clinical Pathology, Department of Diagnostics, Geneva University Hospitals, 1206 Geneva, Switzerland;
| | - Antoine Reinhard
- Department of Otorhinolaryngology-Head and Neck Surgery, Lausanne University Hospital, 1011 Lausanne, Switzerland;
| | - Bettina Bisig
- Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (S.S.); (M.M.); (B.B.)
| | - Ekkehard Hewer
- Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (S.S.); (M.M.); (B.B.)
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Wang Y, Li H, Huang J, Jiang M, Tian S, Liu S, Zhang L, Wu S, Kan H, Gao X. Short-Term PM 2.5 Exposure and DNA Methylation Changes of Circadian Rhythm Genes: Evidence from Two Experimental Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9991-10000. [PMID: 38814053 DOI: 10.1021/acs.est.4c00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The circadian rhythm regulates many crucial physiological processes, impacting human aging and aging-related outcomes. Observational evidence links circadian rhythm disturbance to PM2.5 exposure, yet the underlying DNA methylation mechanisms remain unclear due to limited PM2.5-dominated experimental settings. Therefore, we investigated the associations between short-term PM2.5 exposure and DNA methylation changes of 1188 CpG candidates across circadian genes among 32 young adults in the FDU study, with the validation in 26 individuals from the PKU study. Further mediation analyses tested whether DNA methylation of circadian genes could mediate the influence of PM2.5 on aging measured by three epigenetic ages: DNAmGrimAge, DunedinPoAm, and the mortality risk score. We identified three CpG sites associated with personal PM2.5 exposure: cg01248361 (CSNK2A2), cg17728065 (RORA), and cg22513396 (PRKAG2). Acute effects of PM2.5 on the three loci could be mediated by several circulating biomarkers, including MDA and EGF, with up to ∼30% of mediated proportions. Three loci further showed varying potentials in mediating the aging acceleration effect of PM2.5. Locus cg17728065 is the key site exhibiting a robust mediating effect (7.54-12.52%) on PM2.5-induced aging acceleration. Our findings demonstrated that PM2.5, even short-term peaks, could leave imprints on human aging via inducing aberrant temporal fluctuation in circadian homeostasis captured by DNA methylation profiles.
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Affiliation(s)
- Yuting Wang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Huichu Li
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai 200032, China
| | - Jing Huang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Meijie Jiang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Sifan Tian
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Shuzhen Liu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Ling Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Shaowei Wu
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710049, China
- Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi 710049, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi 710049, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai 200032, China
- IRDR ICoE on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Fudan University, Shanghai 200438, China
- National Center for Children's Health, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xu Gao
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing 100871, China
- Peking University Institute of Environmental Medicine, Beijing 100191, China
- Center for Healthy Aging, Peking University Health Science Center, Beijing 100083, China
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Sánchez-Ortí JV, Correa-Ghisays P, Balanzá-Martínez V, Macías Saint-Gerons D, Berenguer-Pascual E, Romá-Mateo C, Victor VM, Forés-Martos J, San-Martin C, Selva-Vera G, Tabarés-Seisdedos R. Systemic inflammation, oxidative damage and neurocognition predict telomere length in a transdiagnostic sample stratified by global DNA methylation levels. Sci Rep 2024; 14:13159. [PMID: 38849401 PMCID: PMC11161596 DOI: 10.1038/s41598-024-62980-6] [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: 12/05/2023] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Epigenetic mechanisms contribute to the maintenance of both type 2 diabetes mellitus (T2DM) and psychiatric disorders. Emerging evidence suggests that molecular pathways and neurocognitive performance regulate epigenetic dynamics in these disorders. The current combined and transdiagnostic study investigated whether inflammatory, oxidative stress, adhesion molecule, neurocognitive and functional performance are significant predictors of telomere dynamics in a sample stratified by global DNA methylation levels. Peripheral blood inflammation, oxidative stress and adhesion molecule biomarkers and neurocognitive function were assessed twice over a 1-year period in 80 individuals, including 16 with schizophrenia (SZ), 16 with bipolar disorder (BD), 16 with major depressive disorder (MDD), 15 with T2DM, and 17 healthy controls (HCs). Leukocyte telomere length (LTL) was measured by qRT-PCR using deoxyribonucleic acid (DNA) extracted from peripheral blood samples. A posteriori, individuals were classified based on their global methylation score (GMS) at baseline into two groups: the below-average methylation (BM) and above-average methylation (AM) groups. Hierarchical and k-means clustering methods, mixed one-way analysis of variance and linear regression analyses were performed. Overall, the BM group showed a significantly higher leukocyte telomere length (LTL) than the AM group at both time points (p = 0.02; η2p = 0.06). Moreover, the BM group had significantly lower levels of tumor necrosis factor alpha (TNF-α) (p = 0.03; η2p = 0.06) and C-reactive protein (CRP) (p = 0.03; η2p = 0.06) than the AM group at the 1-year follow-up. Across all participants, the regression models showed that oxidative stress (reactive oxygen species [ROS]) (p = 0.04) and global cognitive score [GCS] (p = 0.02) were significantly negatively associated with LTL, whereas inflammatory (TNF-α) (p = 0.04), adhesion molecule biomarkers (inter cellular adhesion molecule [ICAM]) (p = 0.009), and intelligence quotient [IQ] (p = 0.03) were significantly positively associated with LTL. Moreover, the model predictive power was increased when tested in both groups separately, explaining 15.8% and 28.1% of the LTL variance at the 1-year follow-up for the AM and BM groups, respectively. Heterogeneous DNA methylation in individuals with T2DM and severe mental disorders seems to support the hypothesis that epigenetic dysregulation occurs in a transdiagnostic manner. Our results may help to elucidate the interplay between epigenetics, molecular processes and neurocognitive function in these disorders. DNA methylation and LTL are potential therapeutic targets for transdiagnostic interventions to decrease the risk of comorbidities.
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Affiliation(s)
- Joan Vicent Sánchez-Ortí
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Faculty of Psychology, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | - Patricia Correa-Ghisays
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Faculty of Psychology, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | - Vicent Balanzá-Martínez
- INCLIVA - Health Research Institute, Valencia, Spain.
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain.
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain.
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Valencia, Spain.
- VALSME (VALencia Salut Mental i Estigma), University of Valencia, Valencia, Spain.
| | - Diego Macías Saint-Gerons
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | | | - Carlos Romá-Mateo
- INCLIVA - Health Research Institute, Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER), Health Institute, Carlos III, Madrid, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Víctor M Victor
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Service of Endocrinology and Nutrition, University Hospital Dr. Peset, Valencia, Spain
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
| | - Jaume Forés-Martos
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
| | - Constanza San-Martin
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
- Department of Physiotherapy, University of Valencia, Valencia, Spain
| | - Gabriel Selva-Vera
- INCLIVA - Health Research Institute, Valencia, Spain
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Valencia, Spain
| | - Rafael Tabarés-Seisdedos
- INCLIVA - Health Research Institute, Valencia, Spain.
- TMAP - Evaluation Unit in Personal Autonomy, Dependency and Serious Mental Disorders, University of Valencia, Valencia, Spain.
- Center for Biomedical Research in Mental Health Network (CIBERSAM), Health Institute, Carlos III, Madrid, Spain.
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Valencia, Spain.
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Laven-Law G, Kichenadasse G, Young GP, Symonds EL, Winter JM. BCAT1, IKZF1 and SEPT9: methylated DNA biomarkers for detection of pan-gastrointestinal adenocarcinomas. Biomarkers 2024; 29:194-204. [PMID: 38644767 DOI: 10.1080/1354750x.2024.2340663] [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: 01/23/2024] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
INTRODUCTION Methylated circulating tumour DNA (ctDNA) blood tests for BCAT1/IKZF1 (COLVERA) and SEPT9 (Epi proColon) are used to detect colorectal cancer (CRC). However, there are no ctDNA assays approved for other gastrointestinal adenocarcinomas. We aimed to characterize BCAT1, IKZF1 and SEPT9 methylation in different gastrointestinal adenocarcinoma and non-gastrointestinal tumours to determine if these validated CRC biomarkers might be useful for pan-gastrointestinal adenocarcinoma detection. METHODS Tissue DNA methylation data from colorectal (COAD, READ), gastroesophageal (ESCA, STAD), pancreatic (PAAD) and cholangiocarcinoma (CHOL) adenocarcinoma cohorts within The Cancer Genome Atlas were used for differential methylation analyses. Clinicodemographic predictors of BCAT1, IKZF1 and SEPT9 methylation, and the selectivity of hypermethylated BCAT1, IKZF1 and SEPT9 for colorectal adenocarcinomas in comparison to other cancers were each explored with beta regression. RESULTS Hypermethylated BCAT1, IKZF1 and SEPT9 were each differentially methylated in colorectal and gastroesophageal adenocarcinomas. IKZF1 was differentially methylated in pancreatic adenocarcinoma. Hypermethylated DNA biomarkers BCAT1, IKZF1 and SEPT9 were largely stable across different stages of disease and were highly selective for gastrointestinal adenocarcinomas relative to other cancer types. DISCUSSION Existing CRC methylated ctDNA blood tests for BCAT1/IKZF1 and SEPT9 might be usefully repurposed for use in other gastrointestinal adenocarcinomas and warrant further prospective ctDNA studies.
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Affiliation(s)
- Geraldine Laven-Law
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
| | - Ganessan Kichenadasse
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
- Department of Medical Oncology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia
| | - Graeme P Young
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
| | - Erin L Symonds
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
- Department of Gastroenterology and Hepatology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia
| | - Jean M Winter
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
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30
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Oganezovi N, Lagani V, Kikvidze M, Gamkrelidze G, Tsverava L, Lepsveridze E, Kelly KM, Solomonia R. Long-term effects of myo-inositol on traumatic brain injury: Epigenomic and transcriptomic studies. IBRO Neurosci Rep 2024; 16:291-299. [PMID: 38374956 PMCID: PMC10875114 DOI: 10.1016/j.ibneur.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/27/2024] [Indexed: 02/21/2024] Open
Abstract
Background and purpose Traumatic brain injury (TBI) and its consequences remain great challenges for neurology. Consequences of TBI are associated with various alterations in the brain but little is known about long-term changes of epigenetic DNA methylation patterns. Moreover, nothing is known about potential treatments that can alter these epigenetic changes in beneficial ways. Therefore, we have examined myo-inositol (MI), which has positive effects on several pathological conditions. Methods TBI was induced in mice by controlled cortical impact (CCI). One group of CCI animals received saline injections for two months (TBI+SAL), another CCI group received MI treatment (TBI+MI) for the same period and one group served as a sham-operated control. Mice were sacrificed 4 months after CCI and changes in DNA methylome and transcriptomes were examined. Results For the first time we: (i) provide comprehensive map of long-term DNA methylation changes after CCI in the hippocampus; (ii) identify differences by methylation sites between the groups; (iii) characterize transcriptome changes; (iv) provide association between DNA methylation sites and gene expression. MI treatment is linked with upregulation of genes covering 33 biological processes, involved in immune response and inflammation. In support of these findings, we have shown that expression of BATF2, a transcription factor involved in immune-regulatory networks, is upregulated in the hippocampus of the TBI+MI group where the BATF2 gene is demethylated. Conclusion TBI is followed by long-term epigenetic and transcriptomic changes in hippocampus. MI treatment has a significant effect on these processes by modulation of immune response and biological pathways of inflammation.
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Affiliation(s)
- Nino Oganezovi
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Vincenzo Lagani
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Marine Kikvidze
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Georgi Gamkrelidze
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Lia Tsverava
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
- Iv. Beritashvili Centre of Experimental Biomedicine, Tbilisi, Georgia
| | - Eka Lepsveridze
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Kevin M. Kelly
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States
- Department of Neurology, Philadelphia, PA, United States
- Department of Neurology, Allegheny General Hospital, Pittsburgh, PA, United States
- Center for Neuroscience Research, Allegheny Health Network Research Institute, Pittsburgh, PA, United States, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Revaz Solomonia
- School of Natural Sciences and Medicine, Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
- Iv. Beritashvili Centre of Experimental Biomedicine, Tbilisi, Georgia
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31
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Gonzalez-Latapi P, Bustos B, Dong S, Lubbe S, Simuni T, Krainc D. Alterations in Blood Methylome as Potential Epigenetic Biomarker in Sporadic Parkinson's Disease. Ann Neurol 2024; 95:1162-1172. [PMID: 38563317 DOI: 10.1002/ana.26923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE To characterize DNA methylation (DNAm) differences between sporadic Parkinson's disease (PD) and healthy control (HC) individuals enrolled in the Parkinson's Progression Markers Initiative (PPMI). METHODS Using whole blood, we characterized longitudinal differences in DNAm between sporadic PD patients (n = 196) and HCs (n = 86) enrolled in PPMI. RNA sequencing (RNAseq) was used to conduct gene expression analyses for genes mapped to differentially methylated cytosine-guanine sites (CpGs). RESULTS At the time of patient enrollment, 5,178 CpGs were differentially methylated (2,683 hypermethylated and 2,495 hypomethylated) in PD compared to HC. Of these, 579 CpGs underwent significant methylation changes over 3 years. Several differentially methylated CpGs were found near the cytochrome P450 family 2 subfamily E member 1 (CYP2E1) gene. Additionally, multiple hypermethylated CpGs were associated with the N-myc downregulated gene family member 4 (NDRG4) gene. RNA-Seq analyses showed 75 differentially expressed genes in PD patients compared to controls. An integrative analysis of both differentially methylated sites and differentially expressed genes revealed 20 genes that exhibited hypomethylation concomitant with overexpression. Additionally, 1 gene, cathepsin H (CTSH), displayed hypermethylation that was associated with its decreased expression. INTERPRETATION We provide initial evidence of alterations in DNAm in blood of PD patients that may serve as potential epigenetic biomarker of disease. To evaluate the significance of these changes throughout the progression of PD, additional profiling at longer intervals and during the prodromal stages of disease will be necessary. ANN NEUROL 2024;95:1162-1172.
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Affiliation(s)
- Paulina Gonzalez-Latapi
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bernabe Bustos
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Siyuan Dong
- Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Steven Lubbe
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tanya Simuni
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Sibilio P, Conte F, Huang Y, Castaldi PJ, Hersh CP, DeMeo DL, Silverman EK, Paci P. Correlation-based network integration of lung RNA sequencing and DNA methylation data in chronic obstructive pulmonary disease. Heliyon 2024; 10:e31301. [PMID: 38807864 PMCID: PMC11130701 DOI: 10.1016/j.heliyon.2024.e31301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/30/2024] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous, chronic inflammatory process of the lungs and, like other complex diseases, is caused by both genetic and environmental factors. Detailed understanding of the molecular mechanisms of complex diseases requires the study of the interplay among different biomolecular layers, and thus the integration of different omics data types. In this study, we investigated COPD-associated molecular mechanisms through a correlation-based network integration of lung tissue RNA-seq and DNA methylation data of COPD cases (n = 446) and controls (n = 346) derived from the Lung Tissue Research Consortium. First, we performed a SWIM-network based analysis to build separate correlation networks for RNA-seq and DNA methylation data for our case-control study population. Then, we developed a method to integrate the results into a coupled network of differentially expressed and differentially methylated genes to investigate their relationships across both molecular layers. The functional enrichment analysis of the nodes of the coupled network revealed a strikingly significant enrichment in Immune System components, both innate and adaptive, as well as immune-system component communication (interleukin and cytokine-cytokine signaling). Our analysis allowed us to reveal novel putative COPD-associated genes and to analyze their relationships, both at the transcriptomics and epigenomics levels, thus contributing to an improved understanding of COPD pathogenesis.
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Affiliation(s)
- Pasquale Sibilio
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Yichen Huang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- Karolinska Institutet, 17177, Stockholm, Sweden
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Ohi K, Fujikane D, Takai K, Kuramitsu A, Muto Y, Sugiyama S, Shioiri T. Epigenetic signatures of social anxiety, panic disorders and stress experiences: Insights from genome-wide DNA methylation risk scores. Psychiatry Res 2024; 337:115984. [PMID: 38820651 DOI: 10.1016/j.psychres.2024.115984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/15/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Social anxiety disorder (SAD) and panic disorder (PD) are prevalent anxiety disorders characterized by a complex interplay of genetic and environmental factors. Both disorders share overlapping features and often coexist, despite displaying distinct characteristics. Childhood life adversity, overall stressful life events, and genetic factors contribute to the development of these disorders. DNA methylation, an epigenetic modification, has been implicated in the pathogenesis of these diseases. In this study, we investigated whether whole-genome DNA methylation risk scores (MRSs) for SAD risk, severity of social anxiety, childhood life adversity, PD risk, and overall stressful life events were associated with SAD or PD case‒control status. Preliminary epigenome-wide association studies (EWASs) for SAD risk, severity of social anxiety, and childhood life adversity were conducted in 66 SAD individuals and 77 healthy controls (HCs). Similarly, EWASs for PD risk and overall stressful life events were performed in 182 PD individuals and 81 HCs. MRSs were calculated from these EWASs. MRSs derived from the EWASs of SAD risk and severity of social anxiety were greater in PD patients than in HCs. Additionally, MRSs derived from the EWASs of overall stressful life events, particularly in PD individuals, were lower in SAD individuals than in HCs. In contrast, MRSs for childhood life adversity or PD risk were not significantly associated with PD or SAD case‒control status. These findings highlight the epigenetic features shared in both disorders and the distinctive epigenetic features related to social avoidance in SAD patients, helping to elucidate the epigenetic basis of these disorders.
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Affiliation(s)
- Kazutaka Ohi
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan; Department of General Internal Medicine, Kanazawa Medical University, Ishikawa, Japan.
| | - Daisuke Fujikane
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kentaro Takai
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ayumi Kuramitsu
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yukimasa Muto
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Shunsuke Sugiyama
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Toshiki Shioiri
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
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Irizar H, Chun Y, Hsu HHL, Li YC, Zhang L, Arditi Z, Grishina G, Grishin A, Vicencio A, Pandey G, Bunyavanich S. Multi-omic integration reveals alterations in nasal mucosal biology that mediate air pollutant effects on allergic rhinitis. Allergy 2024. [PMID: 38796780 DOI: 10.1111/all.16174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/12/2024] [Accepted: 03/30/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Allergic rhinitis is a common inflammatory condition of the nasal mucosa that imposes a considerable health burden. Air pollution has been observed to increase the risk of developing allergic rhinitis. We addressed the hypotheses that early life exposure to air toxics is associated with developing allergic rhinitis, and that these effects are mediated by DNA methylation and gene expression in the nasal mucosa. METHODS In a case-control cohort of 505 participants, we geocoded participants' early life exposure to air toxics using data from the US Environmental Protection Agency, assessed physician diagnosis of allergic rhinitis by questionnaire, and collected nasal brushings for whole-genome DNA methylation and transcriptome profiling. We then performed a series of analyses including differential expression, Mendelian randomization, and causal mediation analyses to characterize relationships between early life air toxics, nasal DNA methylation, nasal gene expression, and allergic rhinitis. RESULTS Among the 505 participants, 275 had allergic rhinitis. The mean age of the participants was 16.4 years (standard deviation = 9.5 years). Early life exposure to air toxics such as acrylic acid, phosphine, antimony compounds, and benzyl chloride was associated with developing allergic rhinitis. These air toxics exerted their effects by altering the nasal DNA methylation and nasal gene expression levels of genes involved in respiratory ciliary function, mast cell activation, pro-inflammatory TGF-β1 signaling, and the regulation of myeloid immune cell function. CONCLUSIONS Our results expand the range of air pollutants implicated in allergic rhinitis and shed light on their underlying biological mechanisms in nasal mucosa.
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Affiliation(s)
- Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hsiao-Hsien Leon Hsu
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yan-Chak Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lingdi Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zoe Arditi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Galina Grishina
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Grishin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alfin Vicencio
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Shu J, Jelinek J, Chen H, Zhang Y, Qin T, Li M, Liu L, Issa JPJ. Genome-wide screening and functional validation of methylation barriers near promoters. Nucleic Acids Res 2024; 52:4857-4871. [PMID: 38647050 PMCID: PMC11109949 DOI: 10.1093/nar/gkae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
CpG islands near promoters are normally unmethylated despite being surrounded by densely methylated regions. Aberrant hypermethylation of these CpG islands has been associated with the development of various human diseases. Although local genetic elements have been speculated to play a role in protecting promoters from methylation, only a limited number of methylation barriers have been identified. In this study, we conducted an integrated computational and experimental investigation of colorectal cancer methylomes. Our study revealed 610 genes with disrupted methylation barriers. Genomic sequences of these barriers shared a common 41-bp sequence motif (MB-41) that displayed homology to the chicken HS4 methylation barrier. Using the CDKN2A (P16) tumor suppressor gene promoter, we validated the protective function of MB-41 and showed that loss of such protection led to aberrant hypermethylation. Our findings highlight a novel sequence signature of cis-acting methylation barriers in the human genome that safeguard promoters from silencing.
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Affiliation(s)
- Jingmin Shu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Cooper Medical School at Rowan University, Camden, NJ 08103, USA
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Hai Chen
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yan Zhang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Taichun Qin
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Ming Li
- Phoenix VA Health Care System, Phoenix, AZ 85012, USA
- University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Cooper Medical School at Rowan University, Camden, NJ 08103, USA
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
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Salama OE, Hizon N, Del Vecchio M, Kolsun K, Fonseca MA, Lin DTS, Urtatiz O, MacIsaac JL, Kobor MS, Sellers EAC, Dolinsky VW, Dart AB, Jones MJ, Wicklow BA. DNA methylation signatures of youth-onset type 2 diabetes and exposure to maternal diabetes. Clin Epigenetics 2024; 16:65. [PMID: 38741114 DOI: 10.1186/s13148-024-01675-1] [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: 01/12/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
OBJECTIVE Youth-onset type 2 diabetes (T2D) is physiologically distinct from adult-onset, but it is not clear how the two diseases differ at a molecular level. In utero exposure to maternal type 2 diabetes (T2D) is known to be a specific risk factor for youth-onset T2D. DNA methylation (DNAm) changes associated with T2D but which differ between youth- and adult-onset might delineate the impacts of T2D development at different ages and could also determine the contribution of exposure to in utero diabetes. METHODS We performed an epigenome-wide analysis of DNAm on whole blood from 218 youth with T2D and 77 normoglycemic controls from the iCARE (improving renal Complications in Adolescents with type 2 diabetes through REsearch) cohort. Associations were tested using multiple linear regression models while adjusting for maternal diabetes, sex, age, BMI, smoking status, second-hand smoking exposure, cell-type proportions and genetic ancestry. RESULTS We identified 3830 differentially methylated sites associated with youth T2D onset, of which 3794 were moderately (adjusted p-value < 0.05 and effect size estimate > 0.01) associated and 36 were strongly (adjusted p-value < 0.05 and effect size estimate > 0.05) associated. A total of 3725 of these sites were not previously reported in the EWAS Atlas as associated with T2D, adult obesity or youth obesity. Moreover, three CpGs associated with youth-onset T2D in the PFKFB3 gene were also associated with maternal T2D exposure (FDR < 0.05 and effect size > 0.01). This is the first study to link PFKFB3 and T2D in youth. CONCLUSION Our findings support that T2D in youth has different impacts on DNAm than adult-onset, and suggests that changes in DNAm could provide an important link between in utero exposure to maternal diabetes and the onset of T2D.
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Affiliation(s)
- Ola E Salama
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Nikho Hizon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Melissa Del Vecchio
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Kurt Kolsun
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Mario A Fonseca
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada
| | - David T S Lin
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Oscar Urtatiz
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
- Edwin S.H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth A C Sellers
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Vernon W Dolinsky
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada
| | - Allison B Dart
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
| | - Brandy A Wicklow
- Diabetes Research Envision and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.
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Islam M, Behura SK. Molecular Regulation of Fetal Brain Development in Inbred and Congenic Mouse Strains Differing in Longevity. Genes (Basel) 2024; 15:604. [PMID: 38790233 PMCID: PMC11121069 DOI: 10.3390/genes15050604] [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: 04/19/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The objective of this study was to investigate gene regulation of the developing fetal brain from congenic or inbred mice strains that differed in longevity. Gene expression and alternative splice variants were analyzed in a genome-wide manner in the fetal brain of C57BL/6J mice (long-lived) in comparison to B6.Cg-Cav1tm1Mls/J (congenic, short-lived) and AKR/J (inbred, short-lived) mice on day(d) 12, 15, and 17 of gestation. The analysis showed a contrasting gene expression pattern during fetal brain development in these mice. Genes related to brain development, aging, and the regulation of alternative splicing were significantly differentially regulated in the fetal brain of the short-lived compared to long-lived mice during development from d15 and d17. A significantly reduced number of splice variants was observed on d15 compared to d12 or d17 in a strain-dependent manner. An epigenetic clock analysis of d15 fetal brain identified DNA methylations that were significantly associated with single-nucleotide polymorphic sites between AKR/J and C57BL/6J strains. These methylations were associated with genes that show epigenetic changes in an age-correlated manner in mice. Together, the finding of this study suggest that fetal brain development and longevity are epigenetically linked, supporting the emerging concept of the early-life origin of longevity.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Susanta K. Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, USA
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Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590171. [PMID: 38746367 PMCID: PMC11092597 DOI: 10.1101/2024.05.01.590171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to traditional averaging, rPCs leverage principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrated a 54% improvement in sensitivity over averaging in simulations, offering a robust framework for identifying subtle epigenetic variations. Applying rPCs to the AD brain methylation data in ROSMAP, combined with cell type deconvolution, we uncovered 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci (meQTL) with genome-wide association studies (GWAS) identified 17 genes with potential causal roles in AD, including MS4A4A and PICALM. Our approach is available in the Bioconductor package regionalpcs, opening avenues for research and facilitating a deeper understanding of the epigenetic landscape in complex diseases.
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Affiliation(s)
- Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Olivier Gevaert
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Greicius
- Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
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Yusupov N, Roeh S, Sotillos Elliott L, Chang S, Loganathan S, Urbina-Treviño L, Fröhlich AS, Sauer S, Ködel M, Matosin N, Czamara D, Deussing JM, Binder EB. DNA methylation patterns of FKBP5 regulatory regions in brain and blood of humanized mice and humans. Mol Psychiatry 2024; 29:1510-1520. [PMID: 38317011 PMCID: PMC11189813 DOI: 10.1038/s41380-024-02430-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: 07/20/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024]
Abstract
Humanized mouse models can be used to explore human gene regulatory elements (REs), which frequently lie in non-coding and less conserved genomic regions. Epigenetic modifications of gene REs, also in the context of gene x environment interactions, have not yet been explored in humanized mouse models. We applied high-accuracy measurement of DNA methylation (DNAm) via targeted bisulfite sequencing (HAM-TBS) to investigate DNAm in three tissues/brain regions (blood, prefrontal cortex and hippocampus) of mice carrying the human FK506-binding protein 5 (FKBP5) gene, an important candidate gene associated with stress-related psychiatric disorders. We explored DNAm in three functional intronic glucocorticoid-responsive elements (at introns 2, 5, and 7) of FKBP5 at baseline, in cases of differing genotype (rs1360780 single nucleotide polymorphism), and following application of the synthetic glucocorticoid dexamethasone. We compared DNAm patterns in the humanized mouse (N = 58) to those in human peripheral blood (N = 447 and N = 89) and human postmortem brain prefrontal cortex (N = 86). Overall, DNAm patterns in the humanized mouse model seem to recapitulate DNAm patterns observed in human tissue. At baseline, this was to a higher extent in brain tissue. The animal model also recapitulated effects of dexamethasone on DNAm, especially in peripheral blood and to a lesser extent effects of genotype on DNAm. The humanized mouse model could thus assist in reverse translation of human findings in psychiatry that involve genetic and epigenetic regulation in non-coding elements.
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Affiliation(s)
- Natan Yusupov
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | - Simone Roeh
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Laura Sotillos Elliott
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Simon Chang
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Srivaishnavi Loganathan
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | | | - Anna S Fröhlich
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | - Susann Sauer
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Maik Ködel
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Natalie Matosin
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Darina Czamara
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
| | - Jan M Deussing
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany.
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Ao X, Parisien M, Fillingim RB, Ohrbach R, Slade GD, Diatchenko L, Smith SB. Whole-genome methylation profiling reveals regions associated with painful temporomandibular disorders and active recovery processes. Pain 2024; 165:1060-1073. [PMID: 38015635 PMCID: PMC11018476 DOI: 10.1097/j.pain.0000000000003104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/24/2023] [Indexed: 11/30/2023]
Abstract
ABSTRACT Temporomandibular disorders (TMDs), collectively representing one of the most common chronic pain conditions, have a substantial genetic component, but genetic variation alone has not fully explained the heritability of TMD risk. Reasoning that the unexplained heritability may be because of DNA methylation, an epigenetic phenomenon, we measured genome-wide DNA methylation using the Illumina MethylationEPIC platform with blood samples from participants in the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) study. Associations with chronic TMD used methylation data from 496 chronic painful TMD cases and 452 TMD-free controls. Changes in methylation between enrollment and a 6-month follow-up visit were determined for a separate sample of 62 people with recent-onset painful TMD. More than 750,000 individual CpG sites were examined for association with chronic painful TMD. Six differentially methylated regions were significantly ( P < 5 × 10 -8 ) associated with chronic painful TMD, including loci near genes involved in the regulation of inflammatory and neuronal response. A majority of loci were similarly differentially methylated in acute TMD consistent with observed transience or persistence of symptoms at follow-up. Functional characterization of the identified regions found relationships between methylation at these loci and nearby genetic variation contributing to chronic painful TMD and with gene expression of proximal genes. These findings reveal epigenetic contributions to chronic painful TMD through methylation of the genes FMOD , PM20D1 , ZNF718 , ZFP57 , and RNF39 , following the development of acute painful TMD. Epigenetic regulation of these genes likely contributes to the trajectory of transcriptional events in affected tissues leading to resolution or chronicity of pain.
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Affiliation(s)
- Xiang Ao
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Marc Parisien
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Roger B. Fillingim
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, Florida; Pain Research and Intervention Center of Excellence, Department of Community Dentistry and Behavioral Science, College of Dentistry, University of Florida, Gainesville, Florida
| | - Richard Ohrbach
- Department of Oral Diagnostic Sciences, University at Buffalo, Buffalo, New York
| | - Gary D. Slade
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Luda Diatchenko
- Faculty of Dental Medicine and Oral Health Sciences; Department of Anesthesia, Faculty of Medicine and Health Sciences; Alan Edwards Centre for Research on Pain; McGill University, Montreal, Canada
| | - Shad B. Smith
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University, Durham, North Carolina, USA
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41
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Watanabe LM, Pereira VAB, Noronha NY, de Souza Pinhel MA, Wolf LS, de Oliveira CC, Plaça JR, Noma IHY, da Silva Rodrigues G, de Souza VCO, Júnior FB, Nonino CB. The influence of serum selenium in differential epigenetic and transcriptional regulation of CPT1B gene in women with obesity. J Trace Elem Med Biol 2024; 83:127376. [PMID: 38183920 DOI: 10.1016/j.jtemb.2023.127376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
INTRODUCTION The increasing prevalence of obesity has become a major health problem worldwide. The causes of obesity are multifactorial and could be influenced by dietary patterns and genetic factors. Obesity has been associated with a decrease in micronutrient intake and consequently decreased blood concentrations. Selenium is an essential micronutrient for human health, and its metabolism could be affected by obesity, especially severe obesity. This study aimed to identify differential methylation genes associated with serum selenium concentration in women with and without obesity. METHODOLOGY Thirty-four patients were enrolled in the study and divided into two groups: Obese (Ob) n = 20 and Non-Obese (NOb) n = 14, according to the Body Mass Index (BMI). Anthropometry, body composition, serum selenium, selenium intake, and biochemical parameters were evaluated. DNA extraction and bisulfite conversion were performed to hybridize the samples on the 450k Methylation Chip Infinium Beadchip (Illumina). Bioinformatics analysis was performed using the R program and the Champ package. The differentially methylated regions (DMRs) were identified using the Bumphunter method. In addition, logarithmic conversion was performed for the analysis of serum selenium and methylation. RESULTS In the Ob group, the body weight, BMI, fat mass, and free fat mass were higher than in the NOb group, as expected. Interestingly, the serum selenium was lower in the Ob than in the NOb group without differences in selenium intake. One DMR corresponding to the CPT1B gene, involved in lipid oxidation, was related to selenium levels. This region was hypermethylated in the Ob group, indicating that the intersection between selenium deficiency and hypermethylation could influence the expression of the CPT1B gene. The transcriptional analysis confirmed the lower expression of the CPT1B gene in the Ob group. CONCLUSION Studies connecting epigenetics to environmental factors could offer insights into the mechanisms involving the expression of genes related to obesity and its comorbidities. Here we demonstrated that the mineral selenium might play an essential role in lipid oxidation via epigenetic and transcriptional regulation of the CPT1B gene in obesity.
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Affiliation(s)
- Lígia Moriguchi Watanabe
- Department of Health Sciences, Division of Nutrition and Metabolism, Ribeirão Preto Medical School, University of São Paulo, FMRP/USP, Brazil.
| | - Vanessa Aparecida Batista Pereira
- Department of Health Sciences, Division of Nutrition and Metabolism, Ribeirão Preto Medical School, University of São Paulo, FMRP/USP, Brazil
| | - Natalia Yumi Noronha
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, FMRP/USP, Brazil
| | - Marcela Augusta de Souza Pinhel
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, FMRP/USP, Brazil; Departament of Molecular Biology - São Jose do Rio Preto Medical School, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Leticia Santana Wolf
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, FMRP/USP, Brazil
| | | | - Jessica Rodrigues Plaça
- National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, São Paulo, Brazil
| | - Isabella Harumi Yonehara Noma
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | | | - Vanessa Cristina Oliveira de Souza
- Department of Clinical and Toxicological Analyses and Bromatology, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, FCFRP/USP, Brazil
| | - Fernando Barbosa Júnior
- Department of Clinical and Toxicological Analyses and Bromatology, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, FCFRP/USP, Brazil
| | - Carla Barbosa Nonino
- Department of Health Sciences, Division of Nutrition and Metabolism, Ribeirão Preto Medical School, University of São Paulo, FMRP/USP, Brazil; Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, FMRP/USP, Brazil
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42
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Becker AP, Becker V, McElroy J, Webb A, Han C, Guo Y, Bell EH, Fleming J, Popp I, Staszewski O, Prinz M, Otero JJ, Haque SJ, Grosu AL, Chakravarti A. Proteomic Analysis of Spatial Heterogeneity Identifies HMGB2 as Putative Biomarker of Tumor Progression in Adult-Type Diffuse Astrocytomas. Cancers (Basel) 2024; 16:1516. [PMID: 38672598 PMCID: PMC11049315 DOI: 10.3390/cancers16081516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Although grading is defined by the highest histological grade observed in a glioma, most high-grade gliomas retain areas with histology reminiscent of their low-grade counterparts. We sought to achieve the following: (i) identify proteins and molecular pathways involved in glioma evolution; and (ii) validate the high mobility group protein B2 (HMGB2) as a key player in tumor progression and as a prognostic/predictive biomarker for diffuse astrocytomas. We performed liquid chromatography tandem mass spectrometry (LC-MS/MS) in multiple areas of adult-type astrocytomas and validated our finding in multiplatform-omics studies and high-throughput IHC analysis. LC-MS/MSdetected proteomic signatures characterizing glioma evolution towards higher grades associated with, but not completely dependent, on IDH status. Spatial heterogeneity of diffuse astrocytomas was associated with dysregulation of specific molecular pathways, and HMGB2 was identified as a putative driver of tumor progression, and an early marker of worse overall survival in grades 2 and 3 diffuse gliomas, at least in part regulated by DNA methylation. In grade 4 astrocytomas, HMGB2 expression was strongly associated with proliferative activity and microvascular proliferation. Grounded in proteomic findings, our results showed that HMGB2 expression assessed by IHC detected early signs of tumor progression in grades 2 and 3 astrocytomas, as well as identified GBMs that had a better response to the standard chemoradiation with temozolomide.
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Affiliation(s)
- Aline P. Becker
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Valesio Becker
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Joseph McElroy
- Center for Biostatistics, The Ohio State University, Columbus, OH 43210, USA;
| | - Amy Webb
- School of Biomedical Science-Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA;
| | - Chunhua Han
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Yingshi Guo
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Erica H. Bell
- Department of Neurology, The Ohio State University, Columbus, OH 43210, USA;
| | - Jessica Fleming
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Ilinca Popp
- Department of Radiation Oncology, University of Freiburg, 79110 Freiburg, Germany; (I.P.); (A.-L.G.)
| | - Ori Staszewski
- Institute of Neuropathology, Medical Faculty of the Saarland University, 66421 Homburg, Germany;
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany;
- Signalling Research Centres BIOSS & CIBSS, University of Freiburg, 79098 Freiburg, Germany
| | - Jose J. Otero
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA;
| | - Saikh Jaharul Haque
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Anca-Ligia Grosu
- Department of Radiation Oncology, University of Freiburg, 79110 Freiburg, Germany; (I.P.); (A.-L.G.)
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
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Hannon ER, Marsit CJ, Dent AE, Embury P, Ogolla S, Midem D, Williams SM, Kazura JW. Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation. RESEARCH SQUARE 2024:rs.3.rs-3992113. [PMID: 38645047 PMCID: PMC11030537 DOI: 10.21203/rs.3.rs-3992113/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs). Methods Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively. Results Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils. Conclusion Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.
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Roberts JB, Boldvig OLG, Aubourg G, Kanchenapally ST, Deehan DJ, Rice SJ, Loughlin J. Specific isoforms of the ubiquitin ligase gene WWP2 are targets of osteoarthritis genetic risk via a differentially methylated DNA sequence. Arthritis Res Ther 2024; 26:78. [PMID: 38570801 PMCID: PMC10988806 DOI: 10.1186/s13075-024-03315-8] [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: 11/30/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Transitioning from a genetic association signal to an effector gene and a targetable molecular mechanism requires the application of functional fine-mapping tools such as reporter assays and genome editing. In this report, we undertook such studies on the osteoarthritis (OA) risk that is marked by single nucleotide polymorphism (SNP) rs34195470 (A > G). The OA risk-conferring G allele of this SNP associates with increased DNA methylation (DNAm) at two CpG dinucleotides within WWP2. This gene encodes a ubiquitin ligase and is the host gene of microRNA-140 (miR-140). WWP2 and miR-140 are both regulators of TGFβ signaling. METHODS Nucleic acids were extracted from adult OA (arthroplasty) and foetal cartilage. Samples were genotyped and DNAm quantified by pyrosequencing at the two CpGs plus 14 flanking CpGs. CpGs were tested for transcriptional regulatory effects using a chondrocyte cell line and reporter gene assay. DNAm was altered using epigenetic editing, with the impact on gene expression determined using RT-qPCR. In silico analysis complemented laboratory experiments. RESULTS rs34195470 genotype associates with differential methylation at 14 of the 16 CpGs in OA cartilage, forming a methylation quantitative trait locus (mQTL). The mQTL is less pronounced in foetal cartilage (5/16 CpGs). The reporter assay revealed that the CpGs reside within a transcriptional regulator. Epigenetic editing to increase their DNAm resulted in altered expression of the full-length and N-terminal transcript isoforms of WWP2. No changes in expression were observed for the C-terminal isoform of WWP2 or for miR-140. CONCLUSIONS As far as we are aware, this is the first experimental demonstration of an OA association signal targeting specific transcript isoforms of a gene. The WWP2 isoforms encode proteins with varying substrate specificities for the components of the TGFβ signaling pathway. Future analysis should focus on the substrates regulated by the two WWP2 isoforms that are the targets of this genetic risk.
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Affiliation(s)
- Jack B Roberts
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
| | - Olivia L G Boldvig
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Guillaume Aubourg
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - S Tanishq Kanchenapally
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - David J Deehan
- Freeman Hospital, Newcastle University Teaching Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
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45
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Shi Z, Guo X, Hu X, Li R, Li X, Lu J, Jin M, Jiang X. DNA methylation profiling identifies epigenetic signatures of early gastric cancer. Virchows Arch 2024; 484:687-695. [PMID: 38507065 DOI: 10.1007/s00428-024-03765-0] [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: 08/20/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Research on the DNA methylation status of gastric cancer (GC) has primarily focused on identifying invasive GC to develop biomarkers for diagnostic. However, DNA methylation in noninvasive GC remains unclear. We conducted a comprehensive DNA methylation profiling study of differentiated-type intramucosal GCs (IMCs). Illumina 850K microarrays were utilized to assess the DNA methylation profiles of formalin-fixed paraffin-embedded tissues from eight patients who were Epstein-Barr virus-negative and DNA mismatch repair proficient, including IMCs and paired adjacent nontumor mucosa. Gene expression profiling microarray data from the GEO database were analyzed via bioinformatics to identify candidate methylation genes. The final validation was conducted using quantitative real-time PCR, the TCGA methylation database, and single-sample gene set enrichment analysis (GSEA). Genome-wide DNA methylation profiling revealed a global decrease in methylation in IMCs compared with nontumor tissues. Differential methylation analysis between IMCs and nontumor tissues identified 449 differentially methylated probes, with a majority of sites showing hypomethylation in IMCs compared with nontumor tissues (66.1% vs 33.9%). Integrating two RNA-seq microarray datasets, we found one hypomethylation-upregulated gene: eEF1A2, overlapped with our DNA methylation data. The mRNA expression of eEF1A2 was higher in twenty-four IMC tissues than in their paired adjacent nontumor tissues. GSEA indicated that the functions of eEF1A2 were associated with the development of IMCs. Furthermore, TCGA data indicated that eEF1A2 is hypomethylated in advanced GC. Our study illustrates the implications of DNA methylation alterations in IMCs and suggests that aberrant hypomethylation and high mRNA expression of eEF1A2 might play a role in IMCs development.
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Affiliation(s)
- Zhongyue Shi
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xinmeng Guo
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xiumei Hu
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ruiqi Li
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xue Li
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jun Lu
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Mulan Jin
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
| | - Xingran Jiang
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
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46
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Liang B, Wang Y, Huang J, Lin S, Mao G, Zhou Z, Yan W, Shan C, Wu H, Etcheverry A, He Y, Liu F, Kang H, Yin A, Zhang S. Genome-wide DNA methylation analysis identifies potent CpG signature for temzolomide response in non-G-CIMP glioblastomas with unmethylated MGMT promoter: MGMT-dependent roles of GPR81. CNS Neurosci Ther 2024; 30:e14465. [PMID: 37830163 PMCID: PMC11017469 DOI: 10.1111/cns.14465] [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: 08/09/2022] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 10/14/2023] Open
Abstract
PURPOSES To identify potent DNA methylation candidates that could predict response to temozolomide (TMZ) in glioblastomas (GBMs) that do not have glioma-CpGs island methylator phenotype (G-CIMP) but have an unmethylated promoter of O-6-methylguanine-DNA methyltransferase (unMGMT). METHODS The discovery-validation approach was planned incorporating a series of G-CIMP-/unMGMT GBM cohorts with DNA methylation microarray data and clinical information, to construct multi-CpG prediction models. Different bioinformatic and experimental analyses were performed for biological exploration. RESULTS By analyzing discovery sets with radiotherapy (RT) plus TMZ versus RT alone, we identified a panel of 64 TMZ efficacy-related CpGs, from which a 10-CpG risk signature was further constructed. Both the 64-CpG panel and the 10-CpG risk signature were validated showing significant correlations with overall survival of G-CIMP-/unMGMT GBMs when treated with RT/TMZ, rather than RT alone. The 10-CpG risk signature was further observed for aiding TMZ choice by distinguishing differential outcomes to RT/TMZ versus RT within each risk subgroup. Functional studies on GPR81, the gene harboring one of the 10 CpGs, indicated its distinct impacts on TMZ resistance in GBM cells, which may be dependent on the status of MGMT expression. CONCLUSIONS The 64 TMZ efficacy-related CpGs and in particular the 10-CpG risk signature may serve as promising predictive biomarker candidates for guiding optimal usage of TMZ in G-CIMP-/unMGMT GBMs.
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Affiliation(s)
- Bao‐Bao Liang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Yu‐Hong Wang
- The Emergency DepartmentThe Seventh Medical Center of Chinese PLA General HospitalBeijingChina
| | - Jing‐Jing Huang
- Department of Pediatric SurgeryThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Shuai Lin
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Guo‐Chao Mao
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Zhang‐Jian Zhou
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Wan‐Jun Yan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Chang‐You Shan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Hui‐Zi Wu
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Amandine Etcheverry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR)RennesFrance
| | - Ya‐Long He
- Department of Neurosurgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Fang‐Fang Liu
- Institute of Neurosciences, College of Basic MedicineAir Force Medical UniversityXi'anChina
| | - Hua‐Feng Kang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - An‐An Yin
- Department of Biochemistry and Molecular BiologyAir Force Medical UniversityXi'anChina
- Department of Plastic and Reconstructive Surgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Shu‐Qun Zhang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
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47
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Shaw TI, Pounds S, Cao X, Ma J, Palacios G, Mason J, Perkins S, Wu G, Fan Y, Wang J, Zhou X, Obermayer A, Kinney MC, Kraveka J, Gross T, Sandlund J, Zhang J, Mullighan C, Lim MS, Leventaki V. Comprehensive genomic analysis reveals molecular heterogeneity in pediatric ALK-positive anaplastic large cell lymphoma. RESEARCH SQUARE 2024:rs.3.rs-4145750. [PMID: 38585847 PMCID: PMC10996813 DOI: 10.21203/rs.3.rs-4145750/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Anaplastic large cell lymphoma (ALCL) is a mature T-cell lymphoma that accounts for for 10-15% of childhood lymphomas. Despite the observation that more than 90% of pediatric cases harbor the anaplastic lymphoma kinase (ALK) rearrangement resulting in aberrant ALK kinase expression, there is significant clinical, morphologic, and biological heterogeneity. To gain insights into the genomic aberrations and molecular heterogeneity within ALK-positive ALCL(ALK+ ALCL), we analyzed 46 pediatric ALK+ ALCLs by whole-exome sequencing, RNA-sequencing, and DNA methylation profiling. Whole-exome sequencing found on average 25 SNV/Indel events per sample with recurring genetic events in regulators of DNA damage (TP53, MDM4), transcription (JUNB), and epigenetic regulators (TET1, KMT2B, KMT2A, KMT2C, KMT2E). Gene expression and methylation profiling consistently subclassified ALK+ ALCLs into two groups characterized by diferential ALK expression levels. The ALK-low group showed enrichment of pathways associated with immune response, cytokine signaling, and a hypermethylated predominant pattern compared to the ALK- high group, which had more frequent copy number changes, and was enriched with pathways associated with cell growth, proliferation, metabolic pathways, and. Taken together, these findings suggest that there is molecular heterogeneity within pediatric ALK+ALCL, predicting distinct biological mechanisms that may provide novel insights into disease pathogenesis and represent prognostic markers.
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Affiliation(s)
- Timothy I. Shaw
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Health Promotion and Disease Prevention, University of Tennessee Health Science Center, Memphis, TN
| | - Jing Ma
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Gustavo Palacios
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
| | - John Mason
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Sherrie Perkins
- Department of Pathology, University of Utah Health Sciences, Salt Lake City, UT
| | - Gang Wu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jian Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Alyssa Obermayer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL
| | - Marsha C. Kinney
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, at San Antonio, San Antonio, TX
| | - Jacqueline Kraveka
- Division of Pediatric Hematology-Oncology, Medical University of South Carolina, Charleston, SC
| | - Thomas Gross
- Department of Pediatric Hematology-Oncology, Nationwide Children’s Hospital, Columbus, OH
| | - John Sandlund
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Megan S. Lim
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vasiliki Leventaki
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
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48
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Huang H, Li Q, Tu X, Yu D, Zhou Y, Ma L, Wei K, Gao Y, Zhao G, Han R, Ye F, Ke C. DNA hypomethylation patterns and their impact on the tumor microenvironment in colorectal cancer. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00933-x. [PMID: 38520647 DOI: 10.1007/s13402-024-00933-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Recent research underscores the pivotal role of immune checkpoints as biomarkers in colorectal cancer (CRC) therapy, highlighting the dynamics of resistance and response to immune checkpoint inhibitors. The impact of epigenetic alterations in CRC, particularly in relation to immune therapy resistance, is not fully understood. METHODS We integrated a comprehensive dataset encompassing TCGA-COAD, TCGA-READ, and multiple GEO series (GSE14333, GSE37892, GSE41258), along with key epigenetic datasets (TCGA-COAD, TCGA-READ, GSE77718). Hierarchical clustering, based on Euclidean distance and Ward's method, was applied to 330 primary tumor samples to identify distinct clusters. The immune microenvironment was assessed using MCPcounter. Machine learning algorithms were employed to predict DNA methylation patterns and their functional enrichment, in addition to transcriptome expression analysis. Genomic mutation profiles and treatment response assessments were also conducted. RESULTS Our analysis delineated a specific tumor cluster with CpG Island (CGI) methylation, termed the Demethylated Phenotype (DMP). DMP was associated with metabolic pathways such as oxidative phosphorylation, implicating increased ATP production efficiency in mitochondria, which contributes to tumor aggressiveness. Furthermore, DMP showed activation of the Myc target pathway, known for tumor immune suppression, and exhibited downregulation in key immune-related pathways, suggesting a tumor microenvironment characterized by diminished immunity and increased fibroblast infiltration. Six potential therapeutic agents-lapatinib, RDEA119, WH.4.023, MG.132, PD.0325901, and AZ628-were identified as effective for the DMP subtype. CONCLUSION This study unveils a novel epigenetic phenotype in CRC linked to resistance against immune checkpoint inhibitors, presenting a significant step toward personalized medicine by suggesting epigenetic classifications as a means to identify ideal candidates for immunotherapy in CRC. Our findings also highlight potential therapeutic agents for the DMP subtype, offering new avenues for tailored CRC treatment strategies.
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Grants
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- 2021YDZ03 Medical Products Administration of Guangdong Province
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- QN2021012 Science and Technology Research Project of Hebei Higher Education Institutions
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 81902498,H2022405002 National Natural Science Foundation of China
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- 2019CFB177 Hubei Provincial Natural Science Foundation
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- Q20182105 Natural Science Foundation of Hubei Provincial Department of Education
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- CXPJJH11800001-2018333 Chen Xiao-ping Foundation for the development of science and technology of Hubei Provincial
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- WJ2021Q007 The Foundation of Health and Family planning Commission of Hubei Province
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 201810929005, 201810929009, 201810929068, 201813249010, S201910929009, S201910929045, S202013249005, S202013249008 and 202010929009 Innovation and entrepreneurship training program
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
- 2021JJXM009 The Scientific and Technological Project of Taihe hospital
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Affiliation(s)
- He Huang
- Department of General Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510630, China
| | - Qian Li
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Xusheng Tu
- Department of Emergency Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510630, China
| | - Dongyue Yu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yundong Zhou
- Shanghai Medical Innovation Fusion Biomedical Research Center, Shanghai, China
| | - Lifei Ma
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
- College of Lab Medicine, Hebei North University, Zhangjiakou, Hebei, 075000, China
| | - Kongyuan Wei
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Im Neuenheimer Feld 420, 69120, Heidelberg, Germany
| | - Yuzhen Gao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Guodong Zhao
- Faculty of Hepatopancreatobiliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, China
| | - Ruiqin Han
- State Key Laboratory of Common Mechanism Research for Major Diseas, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200000, China.
| | - Chunlian Ke
- Department of General Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510630, China.
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49
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Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024; 12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [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] [Indexed: 03/24/2024] Open
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Ludger JE Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Julie Y Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kerry A Pierce
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Clary B Clish
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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50
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Li Z, Wang W, Li W, Duan H, Xu C, Tian X, Ning F, Zhang D. Co-methylation analyses identify CpGs associated with lipid traits in Chinese discordant monozygotic twins. Hum Mol Genet 2024; 33:583-593. [PMID: 38142287 DOI: 10.1093/hmg/ddad207] [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: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/25/2023] Open
Abstract
To control genetic background and early life milieu in genome-wide DNA methylation analysis for blood lipids, we recruited Chinese discordant monozygotic twins to explore the relationships between DNA methylations and total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). 132 monozygotic (MZ) twins were included with discordant lipid levels and completed data. A linear mixed model was conducted in Epigenome-wide association study (EWAS). Generalized estimating equation model was for gene expression analysis. We conducted Weighted correlation network analysis (WGCNA) to build co-methylated interconnected network. Additional Qingdao citizens were recruited for validation. Inference about Causation through Examination of Familial Confounding (ICE FALCON) was used to infer the possible direction of these relationships. A total of 476 top CpGs reached suggestively significant level (P < 10-4), of which, 192 CpGs were significantly associated with TG (FDR < 0.05). They were used to build interconnected network and highlight crucial genes from WGCNA. Finally, four CpGs in GATA4 were validated as risk factors for TC; six CpGs at ITFG2-AS1 were negatively associated with TG; two CpGs in PLXND1 played protective roles in HDL-C. ICE FALCON indicated abnormal TC was regarded as the consequence of DNA methylation in CpGs at GATA4, rather than vice versa. Four CpGs in ITFG2-AS1 were both causes and consequences of modified TG levels. Our results indicated that DNA methylation levels of 12 CpGs in GATA4, ITFG2-AS1, and PLXND1 were relevant to TC, TG, and HDL-C, respectively, which might provide new epigenetic insights into potential clinical treatment of dyslipidemia.
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Affiliation(s)
- Zhaoying Li
- Department of Epidemiology and Health Statistics, The College of Public Health of Qingdao University, No. 308 Ning Xia Street, Qingdao 266071, Shandong Province, People's Republic of China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, The College of Public Health of Qingdao University, No. 308 Ning Xia Street, Qingdao 266071, Shandong Province, People's Republic of China
| | - Weilong Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9 B, st. tv. Odense C DK-5000, Denmark
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Feng Ning
- Qingdao Municipal Center for Disease Control and Prevention, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
- Qingdao Institute of Preventive Medicine, No. 175 Shandong Road, Qingdao 266000, Shandong Province, People's Republic of China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, The College of Public Health of Qingdao University, No. 308 Ning Xia Street, Qingdao 266071, Shandong Province, People's Republic of China
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