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Marley AR, Ryder JR, Turcotte LM, Spector LG. Maternal obesity and acute lymphoblastic leukemia risk in offspring: A summary of trends, epidemiological evidence, and possible biological mechanisms. Leuk Res 2022; 121:106924. [PMID: 35939888 DOI: 10.1016/j.leukres.2022.106924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 10/16/2022]
Abstract
Acute lymphoblastic leukemia, a heterogenous malignancy characterized by uncontrolled proliferation of lymphoid progenitors and generally initiated in utero, is the most common pediatric cancer. Although incidence of ALL has been steadily increasing in recent decades, no clear reason for this trend has been identified. Rising concurrently with ALL incidence, increasing maternal obesity rates may be partially contributing to increasing ALL prevelance. Epidemiological studies, including a recent meta-analysis, have found an association between maternal obesity and leukemogenesis in offspring, although mechanisms underlying this association remain unknown. Therefore, the purpose of this review is to propose possible mechanisms connecting maternal obesity to ALL risk in offspring, including changes to fetal/neonatal epigenetics, altered insulin-like growth factor profiles and insulin resistance, modified adipokine production and secretion, changes to immune cell populations, and impacts on birthweight and childhood obesity/adiposity. We describe how each proposed mechanism is biologically plausible due to their connection with maternal obesity, presence in neonatal and/or fetal tissue, observation in pediatric ALL patients at diagnosis, and association with leukemogenesis, A description of ALL and maternal obesity trends, a summary of epidemiological evidence, a discussion of the pathway from intrauterine environment to subsequent malignancy, and propositions for future directions are also presented.
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Affiliation(s)
- Andrew R Marley
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, 420 Delaware St SE MMC 715, Minneapolis, MN 55455, USA.
| | - Justin R Ryder
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, 420 Delaware St SE MMC 715, Minneapolis, MN 55455, USA; Center for Pediatric Obesity Medicine, Department of Pediatrics, University of Minnesota, 2450 Riverside Ave S AO-102, Minneapolis, MN 55454, USA
| | - Lucie M Turcotte
- Division of Hematology/Oncology, Department of Pediatrics, University of Minnesota, 420 Delaware St SE MMC 484, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, 425 East River Parkway, Minneapolis, MN 55455, USA
| | - Logan G Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, 420 Delaware St SE MMC 715, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, 425 East River Parkway, Minneapolis, MN 55455, USA
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52
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Yang J, Wang Q, Zhang ZY, Long L, Ezhilarasan R, Karp JM, Tsirigos A, Snuderl M, Wiestler B, Wick W, Miao Y, Huse JT, Sulman EP. DNA methylation-based epigenetic signatures predict somatic genomic alterations in gliomas. Nat Commun 2022; 13:4410. [PMID: 35906213 PMCID: PMC9338285 DOI: 10.1038/s41467-022-31827-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/05/2022] [Indexed: 02/06/2023] Open
Abstract
Molecular classification has improved diagnosis and treatment for patients with malignant gliomas. However, classification has relied on individual assays that are both costly and slow, leading to frequent delays in treatment. Here, we propose the use of DNA methylation, as an emerging clinical diagnostic platform, to classify gliomas based on major genomic alterations and provide insight into subtype characteristics. We show that using machine learning models, DNA methylation signatures can accurately predict somatic alterations and show improvement over existing classifiers. The established Unified Diagnostic Pipeline (UniD) we develop is rapid and cost-effective for genomic alterations and gene expression subtypes diagnostic at early clinical phase and improves over individual assays currently in clinical use. The significant relationship between genetic alteration and epigenetic signature indicates broad applicability of our approach to other malignancies. No clinical assay currently exists to classify glioma tumours based on gene expression. Here, the authors develop a DNA methylation-based classifier, Unified Diagnostic Pipeline (UniD) that identifies genomic alterations and gene expression subtypes of gliomas.
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Affiliation(s)
- Jie Yang
- Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA.,Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.,Quantitative Science Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Qianghu Wang
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Ze-Yan Zhang
- Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA.,Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lihong Long
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravesanker Ezhilarasan
- Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA.,Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Jerome M Karp
- Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA.,Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratory, NYU Grossman School of Medicine, New York, NY, USA
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Benedikt Wiestler
- Department of Neuroradiology, Technical University of Munich, Munich, Germany
| | - Wolfgang Wick
- German Cancer Research Center (DKFZ) and Department of Neurology and NCT Neurooncology Program, University of Heidelberg, Heidelberg, Germany
| | - Yinsen Miao
- Department of Statistics, Rice University, Houston, TX, USA
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik P Sulman
- Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA. .,Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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53
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Derakhshan M, Kessler NJ, Ishida M, Demetriou C, Brucato N, Moore G, Fall CHD, Chandak GR, Ricaut FX, Prentice A, Hellenthal G, Silver M. Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo. Nucleic Acids Res 2022; 50:6735-6752. [PMID: 35713545 PMCID: PMC9749461 DOI: 10.1093/nar/gkac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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Affiliation(s)
| | - Noah J Kessler
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK
| | - Miho Ishida
- UCL Great Ormond Street Institute of Child Health, UK
| | | | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton,
Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular
and Molecular Biology,Hyderabad, India
| | - Francois-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London,
Gower Street, London WC1E 6BT, UK
| | - Matt J Silver
- London School of Hygiene and Tropical Medicine, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
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54
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Xie A, Ensink E, Li P, Gordevičius J, Marshall LL, George S, Pospisilik JA, Aho VTE, Houser MC, Pereira PAB, Rudi K, Paulin L, Tansey MG, Auvinen P, Brundin P, Brundin L, Labrie V, Scheperjans F. Bacterial Butyrate in Parkinson's Disease Is Linked to Epigenetic Changes and Depressive Symptoms. Mov Disord 2022; 37:1644-1653. [PMID: 35723531 PMCID: PMC9545646 DOI: 10.1002/mds.29128] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/08/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The gut microbiome and its metabolites can impact brain health and are altered in Parkinson's disease (PD) patients. It has been recently demonstrated that PD patients have reduced fecal levels of the potent epigenetic modulator butyrate and its bacterial producers. OBJECTIVES Here, we investigate whether the changes in the gut microbiome and associated metabolites are related to PD symptoms and epigenetic markers in leucocytes and neurons. METHODS Stool, whole blood samples, and clinical data were collected from 55 PD patients and 55 controls. We performed DNA methylation analysis on whole blood samples and analyzed the results in relation to fecal short-chain fatty acid concentrations and microbiota composition. In another cohort, prefrontal cortex neurons were isolated from control and PD brains. We identified genome-wide DNA methylation by targeted bisulfite sequencing. RESULTS We show that lower fecal butyrate and reduced counts of genera Roseburia, Romboutsia, and Prevotella are related to depressive symptoms in PD patients. Genes containing butyrate-associated methylation sites include PD risk genes and significantly overlap with sites epigenetically altered in PD blood leucocytes, predominantly neutrophils, and in brain neurons, relative to controls. Moreover, butyrate-associated methylated-DNA regions in PD overlap with those altered in gastrointestinal (GI), autoimmune, and psychiatric diseases. CONCLUSIONS Decreased levels of bacterially produced butyrate are related to epigenetic changes in leucocytes and neurons from PD patients and to the severity of their depressive symptoms. PD shares common butyrate-dependent epigenetic changes with certain GI and psychiatric disorders, which could be relevant for their epidemiological relation. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Aoji Xie
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Elizabeth Ensink
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Peipei Li
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Juozas Gordevičius
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Lee L Marshall
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Sonia George
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA
| | | | - Velma T E Aho
- Department of Neurology, Helsinki University Hospital, and Clinicum, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Madelyn C Houser
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA.,Department of Physiology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Pedro A B Pereira
- Department of Neurology, Helsinki University Hospital, and Clinicum, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science (KBM), Norwegian University of Life Sciences, Ås, Norway
| | - Lars Paulin
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Malú G Tansey
- Department of Physiology, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Neuroscience and Neurology, Center for Translational Research in Neurodegenerative Disease, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Petri Auvinen
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Patrik Brundin
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Lena Brundin
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Viviane Labrie
- Department for Neurodegenerative Science, Parkinson's Disease Center, Van Andel Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Filip Scheperjans
- Department of Neurology, Helsinki University Hospital, and Clinicum, University of Helsinki, Helsinki, Finland
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55
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Wang X, Cho HY, Campbell MR, Panduri V, Coviello S, Caballero MT, Sambandan D, Kleeberger SR, Polack FP, Ofman G, Bell DA. Epigenome-wide association study of bronchopulmonary dysplasia in preterm infants: results from the discovery-BPD program. Clin Epigenetics 2022; 14:57. [PMID: 35484630 PMCID: PMC9052529 DOI: 10.1186/s13148-022-01272-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants caused by therapeutic oxygen supplemental and characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD have been increasing with limited therapeutic options for prevention and treatment. This study was designed to explore the relationship between gestational age (GA), birth weight, and estimated blood cell-type composition in premature infants and to elucidate early epigenetic biomarkers associated with BPD. METHODS Cord blood DNA from preterm neonates that went on to develop BPD (n = 14) or not (non-BPD, n = 93) was applied to Illumina 450 K methylation arrays. Blood cell-type compositions were estimated using DNA methylation profiles. Multivariable robust regression analysis elucidated CpGs associated with BPD risk. cDNA microarray analysis of cord blood RNA identified differentially expressed genes in neonates who later developed BPD. RESULTS The development of BPD and the need for oxygen supplementation were strongly associated with GA (BPD, p < 1.0E-04; O2 supplementation, p < 1.0E-09) and birth weight (BPD, p < 1.0E-02; O2 supplementation, p < 1.0E-07). The estimated nucleated red blood cell (NRBC) percent was negatively associated with birth weight and GA, positively associated with hypomethylation of the tobacco smoke exposure biomarker cg05575921, and high-NRBC blood samples displayed a hypomethylation profile. Epigenome-wide association study (EWAS) identified 38 (Bonferroni) and 275 (false discovery rate 1%) differentially methylated CpGs associated with BPD. BPD-associated CpGs in cord blood were enriched for lung maturation and hematopoiesis pathways. Stochastic epigenetic mutation burden at birth was significantly elevated among those who developed BPD (adjusted p = 0.02). Transcriptome changes in cord blood cells reflected cell cycle, development, and pulmonary disorder events in BPD. CONCLUSIONS While results must be interpreted with caution because of the small size of this study, NRBC content strongly impacted DNA methylation profiles in preterm cord blood and EWAS analysis revealed potential insights into biological pathways involved in BPD pathogenesis.
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Affiliation(s)
- Xuting Wang
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Hye-Youn Cho
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Michelle R Campbell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Vijayalakshmi Panduri
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | | | - Mauricio T Caballero
- Fundación INFANT, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Deepa Sambandan
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
- The Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - Steven R Kleeberger
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Fernando P Polack
- Fundación INFANT, Buenos Aires, Argentina
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gaston Ofman
- Fundación INFANT, Buenos Aires, Argentina
- Section of Neonatal-Perinatal Medicine, Center for Pregnancy and Newborn Research, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Douglas A Bell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA.
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56
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Bartsch L, Schroeder MP, Hänzelmann S, Bastian L, Lázaro-Navarro J, Schlee C, Tanchez JO, Schulze V, Isaakidis K, Rieger MA, Gökbuget N, Eckert C, Serve H, Horstmann M, Schrappe M, Brüggemann M, Baldus CD, Neumann M. An alternative CYB5A transcript is expressed in aneuploid ALL and enriched in relapse. BMC Genom Data 2022; 23:30. [PMID: 35436854 PMCID: PMC9014596 DOI: 10.1186/s12863-022-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a genetically heterogenous malignancy with poor prognosis in relapsed adult patients. The genetic basis for relapse in aneuploid subtypes such as near haploid (NH) and high hyperdiploid (HeH) BCP-ALL is only poorly understood. Pathogenic genetic alterations remain to be identified. To this end, we investigated the dynamics of genetic alterations in a matched initial diagnosis-relapse (ID-REL) BCP-ALL cohort. Here, we firstly report the identification of the novel genetic alteration CYB5Aalt, an alternative transcript of CYB5A, in two independent cohorts. METHODS We identified CYB5alt in the RNAseq-analysis of a matched ID-REL BCP-ALL cohort with 50 patients and quantified its expression in various molecular BCP-ALL subtypes. Findings were validated in an independent cohort of 140 first diagnosis samples from adult BCP-ALL patients. Derived from patient material, the alternative open reading frame of CYB5Aalt was cloned (pCYB5Aalt) and pCYB5Aalt or the empty vector were stably overexpressed in NALM-6 cells. RNA sequencing was performed of pCYB5Aalt clones and empty vector controls followed by differential expression analysis, gene set enrichment analysis and complementing cell death and viability assays to determine functional implications of CYB5Aalt. RESULTS RNAseq data analysis revealed non-canonical exon usage of CYB5Aalt starting from a previously undescribed transcription start site. CYB5Aalt expression was increased in relapsed BCP-ALL and its occurrence was specific towards the shared gene expression cluster of NH and HeH BCP-ALL in independent cohorts. Overexpression of pCYB5Aalt in NALM-6 cells induced a distinct transcriptional program compared to empty vector controls with downregulation of pathways related to reported functions of CYB5A wildtype. Interestingly, CYB5A wildtype expression was decreased in CYB5Aalt samples in silico and in vitro. Additionally, pCYB5Aalt NALM-6 elicited a more resistant drug response. CONCLUSIONS Across all age groups, CYB5Aalt was the most frequent secondary genetic event in relapsed NH and HeH BCP-ALL. In addition to its high subgroup specificity, CYB5Aalt is a novel candidate to be potentially implicated in therapy resistance in NH and HeH BCP-ALL. This is underlined by overexpressing CYB5Aalt providing first evidence for a functional role in BCL2-mediated apoptosis.
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Affiliation(s)
- Lorenz Bartsch
- Department of Hematology and Oncology, Charité, University Hospital Berlin, Campus Benjamin Franklin, 12203, Berlin, Germany.
| | - Michael P Schroeder
- Department of Hematology and Oncology, Charité, University Hospital Berlin, Campus Benjamin Franklin, 12203, Berlin, Germany
| | - Sonja Hänzelmann
- Research Institute Children's Cancer Center, Department of Pediatric Hematology and Oncology, University Medical Center Hamburg, 20251, Hamburg, Germany
| | - Lorenz Bastian
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Juan Lázaro-Navarro
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Hematology/Oncology, Charité, University Hospital Berlin, Campus Rudolf Virchow, 13353, Berlin, Germany
| | - Cornelia Schlee
- Core Unit Genomics, Berlin Institute of Health, 13353, Berlin, Germany
| | - Jutta Ortiz Tanchez
- Department of Hematology and Oncology, Charité, University Hospital Berlin, Campus Benjamin Franklin, 12203, Berlin, Germany
| | - Veronika Schulze
- Department of Hematology and Oncology, Charité, University Hospital Berlin, Campus Benjamin Franklin, 12203, Berlin, Germany
| | - Konstandina Isaakidis
- Department of Hematology and Oncology, Charité, University Hospital Berlin, Campus Benjamin Franklin, 12203, Berlin, Germany
| | - Michael A Rieger
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Medicine, Department of Hematology/Oncology, Goethe University Hospital, 60590, Frankfurt/M, Germany
- Frankfurt Cancer Institute, 60590, Frankfurt/M, Germany
| | - Nicola Gökbuget
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Medicine, Department of Hematology/Oncology, Goethe University Hospital, 60590, Frankfurt/M, Germany
| | - Cornelia Eckert
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Hematology/Oncology, Charité, University Hospital Berlin, Campus Rudolf Virchow, 13353, Berlin, Germany
| | - Hubert Serve
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Medicine, Department of Hematology/Oncology, Goethe University Hospital, 60590, Frankfurt/M, Germany
| | - Martin Horstmann
- Research Institute Children's Cancer Center, Department of Pediatric Hematology and Oncology, University Medical Center Hamburg, 20251, Hamburg, Germany
| | - Martin Schrappe
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Monika Brüggemann
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Claudia D Baldus
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Martin Neumann
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
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Mariani MP, Chen JA, Zhang Z, Pike SC, Salas LA. MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions. FRONTIERS IN BIOINFORMATICS 2022; 2:859828. [PMID: 35573871 PMCID: PMC9098103 DOI: 10.3389/fbinf.2022.859828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation-based copy number variation (CNV) calling software offers the advantages of providing both genetic (copy-number) and epigenetic (methylation) state information from a single genomic library. This method is advantageous when looking at large-scale chromosomal rearrangements such as the loss of the short arm of chromosome 3 (3p) in renal cell carcinoma and the codeletion of the short arm of chromosome 1 and the long arm of chromosome 19 (1p/19q) commonly seen in histologically defined oligodendrogliomas. Herein, we present MethylMasteR: a software framework that facilitates the standardization and customization of methylation-based CNV calling algorithms in a single R package deployed using the Docker software framework. This framework allows for the easy comparison of the performance and the large-scale CNV event identification capability of four common methylation-based CNV callers. Additionally, we incorporated our custom routine, which was among the best performing routines. We employed the Affymetrix 6.0 SNP Chip results as a gold standard against which to compare large-scale event recall. As there are disparities within the software calling algorithms themselves, no single software is likely to perform best for all samples and all combinations of parameters. The employment of a standardized software framework via creating a Docker image and its subsequent deployment as a Docker container allows researchers to efficiently compare algorithms and lends itself to the development of modified workflows such as the custom workflow we have developed. Researchers can now use the MethylMasteR software for their methylation-based CNV calling needs and follow our software deployment framework. We will continue to refine our methodology in the future with a specific focus on identifying large-scale chromosomal rearrangements in cancer methylation data.
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Affiliation(s)
- Michael P. Mariani
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
- Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, Hanover, NH, United States
| | - Jennifer A. Chen
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
| | - Ze Zhang
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
- Guarini School of Graduate and Advanced Studies, Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH, United States
| | - Steven C. Pike
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
- Guarini School of Graduate and Advanced Studies, Integrative Neuroscience at Dartmouth, Dartmouth College, Hanover, NH, United States
| | - Lucas A. Salas
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
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Lucia RM, Huang WL, Pathak KV, McGilvrey M, David-Dirgo V, Alvarez A, Goodman D, Masunaka I, Odegaard AO, Ziogas A, Pirrotte P, Norden-Krichmar TM, Park HL. Association of Glyphosate Exposure with Blood DNA Methylation in a Cross-Sectional Study of Postmenopausal Women. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:47001. [PMID: 35377194 PMCID: PMC8978648 DOI: 10.1289/ehp10174] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Glyphosate is the most commonly used herbicide in the world and is purported to have a variety of health effects, including endocrine disruption and an elevated risk of several types of cancer. Blood DNA methylation has been shown to be associated with many other environmental exposures, but to our knowledge, no studies to date have examined the association between blood DNA methylation and glyphosate exposure. OBJECTIVE We conducted an epigenome-wide association study to identify DNA methylation loci associated with urinary glyphosate and its metabolite aminomethylphosphonic acid (AMPA) levels. Secondary goals were to determine the association of epigenetic age acceleration with glyphosate and AMPA and develop blood DNA methylation indices to predict urinary glyphosate and AMPA levels. METHODS For 392 postmenopausal women, white blood cell DNA methylation was measured using the Illumina Infinium MethylationEPIC BeadChip array. Glyphosate and AMPA were measured in two urine samples per participant using liquid chromatography-tandem mass spectrometry. Methylation differences at the probe and regional level associated with glyphosate and AMPA levels were assessed using a resampling-based approach. Probes and regions that had an false discovery rate q < 0.1 in ≥ 90 % of 1,000 subsamples of the study population were considered differentially methylated. Differentially methylated sites from the probe-specific analysis were combined into a methylation index. Epigenetic age acceleration from three epigenetic clocks and an epigenetic measure of pace of aging were examined for associations with glyphosate and AMPA. RESULTS We identified 24 CpG sites whose methylation level was associated with urinary glyphosate concentration and two associated with AMPA. Four regions, within the promoters of the MSH4, KCNA6, ABAT, and NDUFAF2/ERCC8 genes, were associated with glyphosate levels, along with an association between ESR1 promoter hypomethylation and AMPA. The methylation index accurately predicted glyphosate levels in an internal validation cohort. AMPA, but not glyphosate, was associated with greater epigenetic age acceleration. DISCUSSION Glyphosate and AMPA exposure were associated with DNA methylation differences that could promote the development of cancer and other diseases. Further studies are warranted to replicate our results, determine the functional impact of glyphosate- and AMPA-associated differential DNA methylation, and further explore whether DNA methylation could serve as a biomarker of glyphosate exposure. https://doi.org/10.1289/EHP10174.
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Affiliation(s)
- Rachel M. Lucia
- Department of Epidemiology and Biostatistics, University of California, Irvine, California, USA
| | - Wei-Lin Huang
- Department of Epidemiology and Biostatistics, University of California, Irvine, California, USA
| | - Khyatiben V. Pathak
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, California, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Marissa McGilvrey
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, California, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Victoria David-Dirgo
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, California, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Andrea Alvarez
- Department of Medicine, University of California, Irvine, California, USA
| | - Deborah Goodman
- Department of Epidemiology and Biostatistics, University of California, Irvine, California, USA
| | - Irene Masunaka
- Department of Medicine, University of California, Irvine, California, USA
| | - Andrew O. Odegaard
- Department of Epidemiology and Biostatistics, University of California, Irvine, California, USA
| | - Argyrios Ziogas
- Department of Medicine, University of California, Irvine, California, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, California, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - Hannah Lui Park
- Department of Epidemiology and Biostatistics, University of California, Irvine, California, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, USA
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Seyres D, Cabassi A, Lambourne JJ, Burden F, Farrow S, McKinney H, Batista J, Kempster C, Pietzner M, Slingsby O, Cao TH, Quinn PA, Stefanucci L, Sims MC, Rehnstrom K, Adams CL, Frary A, Ergüener B, Kreuzhuber R, Mocciaro G, D'Amore S, Koulman A, Grassi L, Griffin JL, Ng LL, Park A, Savage DB, Langenberg C, Bock C, Downes K, Wareham NJ, Allison M, Vacca M, Kirk PDW, Frontini M. Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes. Clin Epigenetics 2022; 14:39. [PMID: 35279219 PMCID: PMC8917653 DOI: 10.1186/s13148-022-01257-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND This work is aimed at improving the understanding of cardiometabolic syndrome pathophysiology and its relationship with thrombosis by generating a multi-omic disease signature. METHODS/RESULTS We combined classic plasma biochemistry and plasma biomarkers with the transcriptional and epigenetic characterisation of cell types involved in thrombosis, obtained from two extreme phenotype groups (morbidly obese and lipodystrophy) and lean individuals to identify the molecular mechanisms at play, highlighting patterns of abnormal activation in innate immune phagocytic cells. Our analyses showed that extreme phenotype groups could be distinguished from lean individuals, and from each other, across all data layers. The characterisation of the same obese group, 6 months after bariatric surgery, revealed the loss of the abnormal activation of innate immune cells previously observed. However, rather than reverting to the gene expression landscape of lean individuals, this occurred via the establishment of novel gene expression landscapes. NETosis and its control mechanisms emerge amongst the pathways that show an improvement after surgical intervention. CONCLUSIONS We showed that the morbidly obese and lipodystrophy groups, despite some differences, shared a common cardiometabolic syndrome signature. We also showed that this could be used to discriminate, amongst the normal population, those individuals with a higher likelihood of presenting with the disease, even when not displaying the classic features.
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Affiliation(s)
- Denis Seyres
- National Institute for Health Research BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.
| | - Alessandra Cabassi
- MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John J Lambourne
- National Institute for Health Research BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Frances Burden
- National Institute for Health Research BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Samantha Farrow
- National Institute for Health Research BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Harriet McKinney
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Joana Batista
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Carly Kempster
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Oliver Slingsby
- Department of Cardiovascular Sciences, Glenfield Hospital, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Thong Huy Cao
- Department of Cardiovascular Sciences, Glenfield Hospital, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Paulene A Quinn
- Department of Cardiovascular Sciences, Glenfield Hospital, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Luca Stefanucci
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge, UK
| | - Matthew C Sims
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- Oxford Haemophilia and Thrombosis Centre, Oxford University Hospitals NHS Foundation Trust, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Karola Rehnstrom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Claire L Adams
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amy Frary
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Bekir Ergüener
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Roman Kreuzhuber
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Gabriele Mocciaro
- Department of Biochemistry and the Cambridge Systems Biology Centre, University of Cambridge, The Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Simona D'Amore
- Addenbrooke's Hospital, NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124, Bari, Italy
- National Cancer Research Center, IRCCS Istituto Tumori 'Giovanni Paolo II', Viale Orazio Flacco, 65, 70124, Bari, Italy
| | - Albert Koulman
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- MRC Elsie Widdowson Laboratory, Cambridge, UK
- National Institute for Health Research Biomedical Research Centres Core Nutritional Biomarker Laboratory, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- National Institute for Health Research Biomedical Research Centres Core Metabolomics and Lipidomics Laboratory, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Luigi Grassi
- National Institute for Health Research BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Julian L Griffin
- Department of Biochemistry and the Cambridge Systems Biology Centre, University of Cambridge, The Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Leong Loke Ng
- Department of Cardiovascular Sciences, Glenfield Hospital, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Adrian Park
- Addenbrooke's Hospital, NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David B Savage
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Kate Downes
- National Institute for Health Research BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- East Midlands and East of England Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Michael Allison
- Addenbrooke's Hospital, NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michele Vacca
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Department of Biochemistry and the Cambridge Systems Biology Centre, University of Cambridge, The Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Paul D W Kirk
- MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, CB2 0AW, UK.
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge, UK.
- Institute of Biomedical & Clinical Science, College of Medicine and Health, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW, UK.
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Accelerated epigenetic aging and inflammatory/immunological profile (ipAGE) in patients with chronic kidney disease. GeroScience 2022; 44:817-834. [PMID: 35237926 DOI: 10.1007/s11357-022-00540-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease (CKD) is defined by a reduced estimated glomerular filtration rate (eGFR). This failure can be related to a phenotype of accelerated aging. In this work, we considered 76 patients with end-stage renal disease (ESRD) and 83 healthy controls. We concomitantly evaluated for the first time two measures that can be informative of the rate of aging, i.e., whole blood DNA methylation using the Illumina Infinium EPIC array and plasma levels of a selection of inflammatory/immunological proteins using multiplex immunoassays. First of all, we demonstrated accelerated aging in terms of the most common epigenetic age estimators in CKD patients. Moreover, we developed a new clock/predictor of age based on the inflammatory/immunological profile (ipAGE) and identified the inflammatory/immunological biomarkers differentially expressed between cases and controls. IpAGE appeared to be more sensitive than epigenetic clocks in quantifying the accelerated aging phenotype of ESRD patients. Interestingly, we did not find any correlation between the age acceleration evaluated according to the epigenetic clocks and ipAGE in either the ESRD group or the control group. On the whole, our data show a consistent accelerated aging phenotype in ESRD patients, which is better appreciated by quantifying the underlying inflammatory processes (inflammaging) by ipAGE than by using epigenetic clocks.
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Jedynak P, Tost J, Calafat AM, Bourova-Flin E, Broséus L, Busato F, Forhan A, Heude B, Jakobi M, Schwartz J, Slama R, Vaiman D, Lepeule J, Philippat C. Pregnancy exposure to phthalates and DNA methylation in male placenta - An epigenome-wide association study. ENVIRONMENT INTERNATIONAL 2022; 160:107054. [PMID: 35032864 PMCID: PMC8972089 DOI: 10.1016/j.envint.2021.107054] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Exposure to phthalates during pregnancy may alter DNA methylation in the placenta, a crucial organ for the growth and development of the fetus. OBJECTIVES We studied associations between urinary concentrations of phthalate biomarkers during pregnancy and placental DNA methylation. METHODS We measured concentrations of 11 phthalate metabolites in maternal spot urine samples collected between 22 and 29 gestational weeks in 202 pregnant women. We analyzed DNA methylation levels in placental tissue (fetal side) collected at delivery. We first investigated changes in global DNA methylation of repetitive elements Alu and LINE-1. We then performed an adjusted epigenome-wide association study using IlluminaHM450 BeadChips and identified differentially methylated regions (DMRs) associated with phthalate exposure. RESULTS Monobenzyl phthalate concentration was inversely associated with placental methylation of Alu repeats. Moreover, all phthalate biomarkers except for monocarboxy-iso-octyl phthalate and mono(2-ethyl-5-hydroxyhexyl) phthalate were associated with at least one DMR. All but three DMRs showed increased DNA methylation with increased phthalate exposure. The largest identified DMR (22 CpGs) was positively associated with monocarboxy-iso-nonyl phthalate and encompassed heat shock proteins (HSPA1A, HSPA1L). The remaining DMRs encompassed transcription factors and nucleotide exchange factors, among other genes. CONCLUSIONS This is the first description of genome-wide modifications of placental DNA methylation in association with pregnancy exposure to phthalates. Our results suggest epigenetic mechanisms by which exposure to these compounds could affect fetal development. Of interest, four identified DMRs had been previously associated with maternal smoking, which may suggest particular sensitivity of these genomic regions to the effect of environmental contaminants.
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Affiliation(s)
- Paulina Jedynak
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Antonia M Calafat
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ekaterina Bourova-Flin
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Lucile Broséus
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004 Paris, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004 Paris, France
| | - Milan Jakobi
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rémy Slama
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Vaiman
- Genomics, Epigenetics and Physiopathology of Reproduction, Institut Cochin, U1016 Inserm - UMR 8104 CNRS - Paris-Descartes University, Paris, France
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Claire Philippat
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
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Kular L, Ewing E, Needhamsen M, Pahlevan Kakhki M, Covacu R, Gomez-Cabrero D, Brundin L, Jagodic M. DNA methylation changes in glial cells of the normal-appearing white matter in Multiple Sclerosis patients. Epigenetics 2022; 17:1311-1330. [PMID: 35094644 PMCID: PMC9586622 DOI: 10.1080/15592294.2021.2020436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Multiple Sclerosis (MS), the leading cause of non-traumatic neurological disability in young adults, is a chronic inflammatory and neurodegenerative disease of the central nervous system (CNS). Due to the poor accessibility to the target organ, CNS-confined processes underpinning the later progressive form of MS remain elusive thereby limiting treatment options. We aimed to examine DNA methylation, a stable epigenetic mark of genome activity, in glial cells to capture relevant molecular changes underlying MS neuropathology. We profiled DNA methylation in nuclei of non-neuronal cells, isolated from 38 post-mortem normal-appearing white matter (NAWM) specimens of MS patients (n = 8) in comparison to white matter of control individuals (n = 14), using Infinium MethylationEPIC BeadChip. We identified 1,226 significant (genome-wide adjusted P-value < 0.05) differentially methylated positions (DMPs) between MS patients and controls. Functional annotation of the altered DMP-genes uncovered alterations of processes related to cellular motility, cytoskeleton dynamics, metabolic processes, synaptic support, neuroinflammation and signaling, such as Wnt and TGF-β pathways. A fraction of the affected genes displayed transcriptional differences in the brain of MS patients, as reported by publically available transcriptomic data. Cell type-restricted annotation of DMP-genes attributed alterations of cytoskeleton rearrangement and extracellular matrix remodelling to all glial cell types, while some processes, including ion transport, Wnt/TGF-β signaling and immune processes were more specifically linked to oligodendrocytes, astrocytes and microglial cells, respectively. Our findings strongly suggest that NAWM glial cells are highly altered, even in the absence of lesional insult, collectively exhibiting a multicellular reaction in response to diffuse inflammation.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ruxandra Covacu
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - David Gomez-Cabrero
- Department of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
- Mucosal and Salivary Biology Division, King’s College London Dental Institute, London, UK
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (Chn), Universidad Pública de Navarra (Upna), IdiSNA, Pamplona, Spain
- Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Lou Brundin
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Newell F, Pires da Silva I, Johansson PA, Menzies AM, Wilmott JS, Addala V, Carlino MS, Rizos H, Nones K, Edwards JJ, Lakis V, Kazakoff SH, Mukhopadhyay P, Ferguson PM, Leonard C, Koufariotis LT, Wood S, Blank CU, Thompson JF, Spillane AJ, Saw RPM, Shannon KF, Pearson JV, Mann GJ, Hayward NK, Scolyer RA, Waddell N, Long GV. Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance. Cancer Cell 2022; 40:88-102.e7. [PMID: 34951955 DOI: 10.1016/j.ccell.2021.11.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 09/15/2021] [Accepted: 11/29/2021] [Indexed: 02/06/2023]
Abstract
We concurrently examine the whole genome, transcriptome, methylome, and immune cell infiltrates in baseline tumors from 77 patients with advanced cutaneous melanoma treated with anti-PD-1 with or without anti-CTLA-4. We show that high tumor mutation burden (TMB), neoantigen load, expression of IFNγ-related genes, programmed death ligand expression, low PSMB8 methylation (therefore high expression), and T cells in the tumor microenvironment are associated with response to immunotherapy. No specific mutation correlates with therapy response. A multivariable model combining the TMB and IFNγ-related gene expression robustly predicts response (89% sensitivity, 53% specificity, area under the curve [AUC], 0.84); tumors with high TMB and a high IFNγ signature show the best response to immunotherapy. This model validates in an independent cohort (80% sensitivity, 59% specificity, AUC, 0.79). Except for a JAK3 loss-of-function mutation, for patients who did not respond as predicted there is no obvious biological mechanism that clearly explained their outlier status, consistent with intratumor and intertumor heterogeneity in response to immunotherapy.
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Affiliation(s)
- Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Ines Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Cancer Centre, Blacktown Hospital, Sydney, NSW 2148, Australia
| | - Peter A Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia; Mater Hospital, Sydney, NSW 2060, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Venkateswar Addala
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia; Department of Medical Oncology, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Helen Rizos
- Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Jarem J Edwards
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Stephen H Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Camperdown, NSW 2050, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Christian U Blank
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Mater Hospital, Sydney, NSW 2060, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Andrew J Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Mater Hospital, Sydney, NSW 2060, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Mater Hospital, Sydney, NSW 2060, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Mater Hospital, Sydney, NSW 2060, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia; John Curtin School of Medical Research, Australian National University, ACT 2601, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Camperdown, NSW 2050, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Department of Medical Oncology, Royal North Shore Hospital, Sydney, NSW 2065, Australia; Mater Hospital, Sydney, NSW 2060, Australia.
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DNA methylation pattern of hypertriglyceridemic subjects. CLINICA E INVESTIGACION EN ARTERIOSCLEROSIS : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ARTERIOSCLEROSIS 2022; 34:27-32. [PMID: 34879978 DOI: 10.1016/j.arteri.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND Chylomicronemias are generally diagnosed genetically by genomic sequencing or screening for mutations in causal genes with a large phenotypic effect. This strategy has allowed to improve the characterization of these patients, but we still have 30% of the patients without a conclusive genetic diagnosis. This is why we hypothesize that by adding the epigenetic component we can improve the genetic diagnosis, and for this we have explored the degree of methylation in the DNA of hypertriglyceridemic patients. METHODOLOGY Blood cell DNA was obtained from 16 hypertriglyceridemic patients and from 16 age- and sex-matched control subjects. The degree of methylation in genome-wide DNA was determined using the Illumina® Infinium Methylation EPIC Array Analysis. RESULTS We identified 31 differentially methylated cytosines by comparing the methylation patterns presented by hypertriglyceridemic patients vs. control subjects. The cg03636183 in the F2RL3 gene was 10% hypomethylated in hypertriglyceridemic patients, and has previously been associated with an increased cardiovascular risk. Cg13824500 is 10% hypomethylated in hypertriglyceridemic patients and is located in VTI1A, which is a limiting gene in the transit of chylomicrons in the enterocyte through the endoplasmic reticulum and the Golgi apparatus. Cg26468118 in the RAB20 gene (13% hypomethylated) and cg21560722 in the SBF2 gene (33% hypermethylated) are involved in the regulation of Golgi apparatus vesicles. CONCLUSIONS Our results suggest that there are differentially methylated regions related to the formation of chylomicrons in hypertriglyceridemic patients.
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Kasuga Y, Kawai T, Miyakoshi K, Hori A, Tamagawa M, Hasegawa K, Ikenoue S, Ochiai D, Saisho Y, Hida M, Tanaka M, Hata K. DNA methylation analysis of cord blood samples in neonates born to gestational diabetes mothers diagnosed before 24 gestational weeks. BMJ Open Diabetes Res Care 2022; 10:10/1/e002539. [PMID: 35046013 PMCID: PMC8772407 DOI: 10.1136/bmjdrc-2021-002539] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION Genome-wide methylation analyses of gestational diabetes mellitus (GDM) diagnosed after 24 gestational weeks (late GDM (L-GDM)) using cord blood have been reported. However, epigenetic changes in neonates born to mothers with GDM diagnosed before 24 gestational weeks (early GDM (E-GDM)) have not been reported. We investigated DNA methylation in neonates born to mothers with E-GDM using cord blood samples. RESEARCH DESIGN AND METHODS Genome-wide DNA methylation analysis was performed using an Illumina EPIC array to compare methylation rates of 754 255 autosomal sites in cord blood samples from term neonates born to 162 mothers with GDM (E-GDM: n=84, L-GDM: n=78) and 60 normal glucose tolerance (normal OGTT) pregnancies. GDM was diagnosed based on Japan Society of Obstetrics and Gynecology criteria modified with International Association of Diabetes in Pregnancy Study Group criteria. In this study, all GDM mothers underwent dietary management, while self-monitoring of blood glucose and insulin administration was initiated when dietary modification did not achieve glycemic control. RESULTS There were no significant differences in genome-wide DNA methylation of cord blood samples between the GDM (E-GDM and L-GDM) groups and normal OGTT group or between the E-GDM and normal OGTT groups, L-GDM and normal OGTT groups, and E-GDM and L-GDM groups. CONCLUSIONS This is the first report to determine the DNA methylation patterns in neonates born to mothers with E-GDM. Neonates born to mothers with GDM, who were diagnosed based on Japan Society of Obstetrics and Gynecology criteria, may not differ in DNA methylation compared with those born to normal OGTT mothers.
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Affiliation(s)
- Yoshifumi Kasuga
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Tomoko Kawai
- Division of Fetal Development, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Kei Miyakoshi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Asuka Hori
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
- Department of Medical Genetics and Genomics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
| | - Masumi Tamagawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Keita Hasegawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Satoru Ikenoue
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Daigo Ochiai
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yoshifumi Saisho
- Department of Internal Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Mariko Hida
- Department of Pediatrics, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Mamoru Tanaka
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
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Dzobo K. The Role of Natural Products as Sources of Therapeutic Agents for Innovative Drug Discovery. COMPREHENSIVE PHARMACOLOGY 2022. [PMCID: PMC8016209 DOI: 10.1016/b978-0-12-820472-6.00041-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Emerging threats to human health require a concerted effort in search of both preventive and treatment strategies, placing natural products at the center of efforts to obtain new therapies and reduce disease spread and associated mortality. The therapeutic value of compounds found in plants has been known for ages, resulting in their utilization in homes and in clinics for the treatment of many ailments ranging from common headache to serious conditions such as wounds. Despite the advancement observed in the world, plant based medicines are still being used to treat many pathological conditions or are used as alternatives to modern medicines. In most cases, these natural products or plant-based medicines are used in an un-purified state as extracts. A lot of research is underway to identify and purify the active compounds responsible for the healing process. Some of the current drugs used in clinics have their origins as natural products or came from plant extracts. In addition, several synthetic analogues are natural product-based or plant-based. With the emergence of novel infectious agents such as the SARS-CoV-2 in addition to already burdensome diseases such as diabetes, cancer, tuberculosis and HIV/AIDS, there is need to come up with new drugs that can cure these conditions. Natural products offer an opportunity to discover new compounds that can be converted into drugs given their chemical structure diversity. Advances in analytical processes make drug discovery a multi-dimensional process involving computational designing and testing and eventual laboratory screening of potential drug candidates. Lead compounds will then be evaluated for safety, pharmacokinetics and efficacy. New technologies including Artificial Intelligence, better organ and tissue models such as organoids allow virtual screening, automation and high-throughput screening to be part of drug discovery. The use of bioinformatics and computation means that drug discovery can be a fast and efficient process and enable the use of natural products structures to obtain novel drugs. The removal of potential bottlenecks resulting in minimal false positive leads in drug development has enabled an efficient system of drug discovery. This review describes the biosynthesis and screening of natural products during drug discovery as well as methods used in studying natural products.
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Campagna MP, Xavier A, Lechner-Scott J, Maltby V, Scott RJ, Butzkueven H, Jokubaitis VG, Lea RA. Epigenome-wide association studies: current knowledge, strategies and recommendations. Clin Epigenetics 2021; 13:214. [PMID: 34863305 PMCID: PMC8645110 DOI: 10.1186/s13148-021-01200-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
The aetiology and pathophysiology of complex diseases are driven by the interaction between genetic and environmental factors. The variability in risk and outcomes in these diseases are incompletely explained by genetics or environmental risk factors individually. Therefore, researchers are now exploring the epigenome, a biological interface at which genetics and the environment can interact. There is a growing body of evidence supporting the role of epigenetic mechanisms in complex disease pathophysiology. Epigenome-wide association studies (EWASes) investigate the association between a phenotype and epigenetic variants, most commonly DNA methylation. The decreasing cost of measuring epigenome-wide methylation and the increasing accessibility of bioinformatic pipelines have contributed to the rise in EWASes published in recent years. Here, we review the current literature on these EWASes and provide further recommendations and strategies for successfully conducting them. We have constrained our review to studies using methylation data as this is the most studied epigenetic mechanism; microarray-based data as whole-genome bisulphite sequencing remains prohibitively expensive for most laboratories; and blood-based studies due to the non-invasiveness of peripheral blood collection and availability of archived DNA, as well as the accessibility of publicly available blood-cell-based methylation data. Further, we address multiple novel areas of EWAS analysis that have not been covered in previous reviews: (1) longitudinal study designs, (2) the chip analysis methylation pipeline (ChAMP), (3) differentially methylated region (DMR) identification paradigms, (4) methylation quantitative trait loci (methQTL) analysis, (5) methylation age analysis and (6) identifying cell-specific differential methylation from mixed cell data using statistical deconvolution.
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Affiliation(s)
- Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexandre Xavier
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Jeannette Lechner-Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Department of Neurology, Division of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Vicky Maltby
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Rodney J Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Division of Molecular Medicine, New South Wales Health Pathology North, Newcastle, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Vilija G Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Rodney A Lea
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia.
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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Pan X, Zhang C, Wang J, Wang P, Gao Y, Shang S, Guo S, Li X, Zhi H, Ning S. Epigenome signature as an immunophenotype indicator prompts durable clinical immunotherapy benefits in lung adenocarcinoma. Brief Bioinform 2021; 23:6447679. [PMID: 34864866 DOI: 10.1093/bib/bbab481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Intertumoral immune heterogeneity is a critical reason for distinct clinical benefits of immunotherapy in lung adenocarcinoma (LUAD). Tumor immunophenotype (immune 'Hot' or 'Cold') suggests immunological individual differences and potential clinical treatment guidelines. However, employing epigenome signatures to determine tumor immunophenotypes and responsive treatment is not well understood. To delineate the tumor immunophenotype and immune heterogeneity, we first distinguished the immune 'Hot' and 'Cold' tumors of LUAD based on five immune expression signatures. In terms of clinical presentation, the immune 'Hot' tumors usually had higher immunoactivity, lower disease stages and better survival outcomes than 'Cold' tumors. At the epigenome levels, we observed that distinct DNA methylation patterns between immunophenotypes were closely associated with LUAD development. Hence, we identified a set of five CpG sites as the immunophenotype-related methylation signature (iPMS) for tumor immunophenotyping and further confirmed its efficiency based on a machine learning framework. Furthermore, we found iPMS and immunophenotype-related immune checkpoints (IPCPs) could contribute to the risk of tumor progression, implying IPCP has the potential to be a novel immunotherapy blockade target. After further parsing of the role of iPMS-predicted immunophenotypes, we found immune 'Hot' was a protective factor leading to better survival outcomes when patients received the anti-PD-1/PD-L1 immunotherapy. And iPMS was also a well-performed signature (AUC = 0.752) for predicting the durable/nondurable clinical benefits. In summary, our study explored the role of epigenome signature in clinical tumor immunophenotyping. Utilizing iPMS to characterize tumor immunophenotypes will facilitate developing personalized epigenetic anticancer approaches.
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Affiliation(s)
- Xu Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Caiyu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Junwei Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Corley MJ, Pang APS, Rasmussen TA, Tolstrup M, Søgaard OS, Ndhlovu LC. Candidate host epigenetic marks predictive for HIV reservoir size, responsiveness to latency reversal, and viral rebound. AIDS 2021; 35:2269-2279. [PMID: 34482353 PMCID: PMC8563431 DOI: 10.1097/qad.0000000000003065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE This study aimed to identify candidate host epigenetic biomarkers predicting latency reversal agents (LRA) efficacy and HIV-1 rebound kinetics during analytical treatment interruption (ATI). DESIGN Retrospective longitudinal epigenetic profiling study from 13 people with HIV (PWH) on virologically suppressive antiretroviral therapy (ART) that participated in a LRA (HDAC inhibitor) clinical trial (NCT01680094) and a subsequent optional ATI to monitor for viral recrudescence after ART cessation. METHODS Genome-wide DNA methylation (DNAm) in purified CD4+ T cells was measured at single-nucleotide resolution using the Infinium MethylationEPIC array. HIV-1 DNA and RNA measures were previously assessed by PCR-based methods and the association of DNAm levels at regulatory sites of the human genome were examined with reservoir size, responsiveness to LRA, and time to viral rebound following ATI. RESULTS A distinct set of 15 candidate DNAm sites in purified CD4+ T cells at baseline pre-LRA and pre-ATI significantly correlated with time to viral rebound. Eight of these DNAm sites occurred in genes linked to HIV-1 replication dynamics including (SEPSECS, cg19113954), (MALT1, cg15968021), (CPT1C, cg14318858), (CRTAM, cg10977115), (B4GALNT4, cg04663285), (IL10, cg16284789), (TFPI2, cg19645693), and (LIFR, cg26437306); with the remaining sites at intergenic regions containing regulatory elements. Moreover, baseline DNAm states related to total HIV-1 DNA levels and the fold change in unspliced cell-associated HIV RNA following LRA treatment. CONCLUSION Preexisting host epigenetic states may determine HIV-1 rebound kinetics and reservoir maintenance. These findings suggest integrating a suite of DNA methylation markers to improve optimal participant selection and drug regimen in future HIV cure clinical trials.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Thomas A. Rasmussen
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Ole S. Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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Diedrich JD, Dong Q, Ferguson DC, Bergeron BP, Autry RJ, Qian M, Yang W, Smith C, Papizan JB, Connelly JP, Hagiwara K, Crews KR, Pruett-Miller SM, Pui CH, Yang JJ, Relling MV, Evans WE, Savic D. Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks. Leukemia 2021; 35:3078-3091. [PMID: 33714976 PMCID: PMC8435544 DOI: 10.1038/s41375-021-01209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/03/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematopoietic malignancy comprised of molecular subtypes largely characterized by aneuploidy or recurring chromosomal rearrangements. Despite extensive information on the ALL transcriptome and methylome, there is limited understanding of the ALL chromatin landscape. We therefore mapped accessible chromatin in 24 primary ALL cell biospecimens comprising three common molecular subtypes (DUX4/ERG, ETV6-RUNX1 and hyperdiploid) from patients treated at St. Jude Children's Research Hospital. Our findings highlight extensive chromatin reprogramming in ALL, including the identification ALL subtype-specific chromatin landscapes that are additionally modulated by genetic variation. Chromatin accessibility differences between ALL and normal B-cells implicate the activation of B-cell repressed chromatin domains and detail the disruption of normal B-cell development in ALL. Among ALL subtypes, we uncovered roles for basic helix-loop-helix, homeodomain and activator protein 1 transcription factors in promoting subtype-specific chromatin accessibility and distinct gene regulatory networks. In addition to chromatin subtype-specificity, we further identified over 3500 DNA sequence variants that alter the ALL chromatin landscape and contribute to inter-individual variability in chromatin accessibility. Collectively, our data suggest that subtype-specific chromatin landscapes and gene regulatory networks impact ALL biology and contribute to transcriptomic differences among ALL subtypes.
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Affiliation(s)
- Jonathan D Diedrich
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Dong
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Maoxiang Qian
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colton Smith
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James B Papizan
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Hematological Malignancies Program and Center for Precision Medicine in Leukemia, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA.
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TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis. Nat Commun 2021; 12:6061. [PMID: 34663818 PMCID: PMC8523747 DOI: 10.1038/s41467-021-26093-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023] Open
Abstract
Mutations in the epigenetic modifier TET2 are frequent in myeloid malignancies and clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS). Here, we investigate associations between TET2 mutations and DNA methylation in whole blood in 305 elderly twins, 15 patients with CCUS and 18 healthy controls. We find that TET2 mutations are associated with DNA hypermethylation at enhancer sites in whole blood in CHIP and in both granulocytes and mononuclear cells in CCUS. These hypermethylated sites are associated with leukocyte function and immune response and ETS-related and C/EBP-related transcription factor motifs. While the majority of TET2-associated hypermethylation sites are shared between CHIP and in AML, we find a set of AML-specific hypermethylated loci at active enhancer elements in hematopoietic stem cells. In summary, we show that TET2 mutations is associated with hypermethylated enhancers involved in myeloid differentiation in both CHIP, CCUS and AML patients.
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Shorey-Kendrick LE, McEvoy CT, O'Sullivan SM, Milner K, Vuylsteke B, Tepper RS, Haas DM, Park B, Gao L, Vu A, Morris CD, Spindel ER. Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes. Clin Epigenetics 2021; 13:177. [PMID: 34538263 PMCID: PMC8451157 DOI: 10.1186/s13148-021-01161-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/28/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Maternal smoking during pregnancy (MSDP) affects development of multiple organ systems including the placenta, lung, brain, and vasculature. In particular, children exposed to MSDP show lifelong deficits in pulmonary function and increased risk of asthma and wheeze. Our laboratory has previously shown that vitamin C supplementation during pregnancy prevents some of the adverse effects of MSDP on offspring respiratory outcomes. Epigenetic modifications, including DNA methylation (DNAm), are a likely link between in utero exposures and adverse health outcomes, and MSDP has previously been associated with DNAm changes in blood, placenta, and buccal epithelium. Analysis of placental DNAm may reveal critical targets of MSDP and vitamin C relevant to respiratory health outcomes. RESULTS DNAm was measured in placentas obtained from 72 smokers enrolled in the VCSIP RCT: NCT03203603 (37 supplemented with vitamin C, 35 with placebo) and 24 never-smokers for reference. Methylation at one CpG, cg20790161, reached Bonferroni significance and was hypomethylated in vitamin C supplemented smokers versus placebo. Analysis of spatially related CpGs identified 93 candidate differentially methylated regions (DMRs) between treatment groups, including loci known to be associated with lung function, oxidative stress, fetal development and growth, and angiogenesis. Overlap of nominally significant differentially methylated CpGs (DMCs) in never-smokers versus placebo with nominally significant DMCs in vitamin C versus placebo identified 9059 candidate "restored CpGs" for association with placental transcript expression and respiratory outcomes. Methylation at 274 restored candidate CpG sites was associated with expression of 259 genes (FDR < 0.05). We further identified candidate CpGs associated with infant lung function (34 CpGs) and composite wheeze (1 CpG) at 12 months of age (FDR < 0.05). Increased methylation in the DIP2C, APOH/PRKCA, and additional candidate gene regions was associated with improved lung function and decreased wheeze in offspring of vitamin C-treated smokers. CONCLUSIONS Vitamin C supplementation to pregnant smokers ameliorates changes associated with maternal smoking in placental DNA methylation and gene expression in pathways potentially linked to improved placental function and offspring respiratory health. Further work is necessary to validate candidate loci and elucidate the causal pathway between placental methylation changes and outcomes of offspring exposed to MSDP. Clinical trial registration ClinicalTrials.gov, NCT01723696. Registered November 6, 2012. https://clinicaltrials.gov/ct2/show/record/NCT01723696 .
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA.
| | - Cindy T McEvoy
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Shannon M O'Sullivan
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
| | - Kristin Milner
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Brittany Vuylsteke
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Robert S Tepper
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byung Park
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA
- School of Public Health, Oregon Health and Science University-Portland State University, Portland, OR, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Annette Vu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Cynthia D Morris
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
- Oregon Clinical and Translational Research Institute, Oregon Health and Science, Portland, OR, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
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Gomez-Verjan JC, Esparza-Aguilar M, Martín-Martín V, Salazar-Perez C, Cadena-Trejo C, Gutierrez-Robledo LM, Martínez-Magaña JJ, Nicolini H, Arroyo P. Years of Schooling Could Reduce Epigenetic Aging: A Study of a Mexican Cohort. Genes (Basel) 2021; 12:1408. [PMID: 34573390 PMCID: PMC8469534 DOI: 10.3390/genes12091408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 12/03/2022] Open
Abstract
Adverse conditions in early life, including environmental, biological and social influences, are risk factors for ill-health during aging and the onset of age-related disorders. In this context, the recent field of social epigenetics offers a valuable method for establishing the relationships among them However, current clinical studies on environmental changes and lifespan disorders are limited. In this sense, the Tlaltizapan (Mexico) cohort, who 52 years ago was exposed to infant malnutrition, low income and poor hygiene conditions, represents a vital source for exploring such factors. Therefore, in the present study, 52 years later, we aimed to explore differences in clinical/biochemical/anthropometric and epigenetic (DNA methylation) variables between individuals from such a cohort, in comparison with an urban-raised sample. Interestingly, only cholesterol levels showed significant differences between the cohorts. On the other hand, individuals from the Tlaltizapan cohort with more years of schooling had a lower epigenetic age in the Horvath (p-value = 0.0225) and PhenoAge (p-value = 0.0353) clocks, compared to those with lower-level schooling. Our analysis indicates 12 differentially methylated sites associated with the PI3-Akt signaling pathway and galactose metabolism in individuals with different durations of schooling. In conclusion, our results suggest that longer durations of schooling could promote DNA methylation changes that may reduce epigenetic age; nevertheless, further studies are needed.
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Affiliation(s)
- Juan Carlos Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico City 10200, Mexico; (C.C.-T.); (P.A.)
| | - Marcelino Esparza-Aguilar
- Departamento de Investigación en Epidemiología, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.E.-A.); (C.S.-P.)
| | - Verónica Martín-Martín
- Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Mexico City 04530, Mexico;
| | - Cecilia Salazar-Perez
- Departamento de Investigación en Epidemiología, Instituto Nacional de Pediatría, Mexico City 04530, Mexico; (M.E.-A.); (C.S.-P.)
| | - Cinthya Cadena-Trejo
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico City 10200, Mexico; (C.C.-T.); (P.A.)
| | | | - José Jaime Martínez-Magaña
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 04809, Mexico; (J.J.M.-M.); (H.N.)
| | - Humberto Nicolini
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 04809, Mexico; (J.J.M.-M.); (H.N.)
| | - Pedro Arroyo
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico City 10200, Mexico; (C.C.-T.); (P.A.)
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Canouil M, Khamis A, Keikkala E, Hummel S, Lobbens S, Bonnefond A, Delahaye F, Tzala E, Mustaniemi S, Vääräsmäki M, Jarvelin MR, Sebert S, Kajantie E, Froguel P, Andrew T. Epigenome-Wide Association Study Reveals Methylation Loci Associated With Offspring Gestational Diabetes Mellitus Exposure and Maternal Methylome. Diabetes Care 2021; 44:1992-1999. [PMID: 34116986 PMCID: PMC8740918 DOI: 10.2337/dc20-2960] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/26/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Gestational diabetes mellitus (GDM) is associated with an increased risk of obesity and insulin resistance in offspring later in life, which might be explained by epigenetic changes in response to maternal hyperglycemic exposure. RESEARCH DESIGN AND METHODS We explored the association between GDM exposure and maternal blood and newborn cord blood methylation in 536 mother-offspring pairs from the prospective FinnGeDi cohort using Illumina MethylationEPIC 850K BeadChip arrays. We assessed two hypotheses. First, we tested for shared maternal and offspring epigenetic effects resulting from GDM exposure. Second, we tested whether GDM exposure and maternal methylation had an epigenetic effect on the offspring. RESULTS We did not find any epigenetic marks (differentially methylated CpG probes) with shared and consistent effects between mothers and offspring. After including maternal methylation in the model, we identified a single significant (false discovery rate 1.38 × 10-2) CpG at the cg22790973 probe (TFCP2) associated with GDM. We identified seven additional FDR-significant interactions of maternal methylation and GDM status, with the strongest association at the same cg22790973 probe (TFCP2), as well as cg03456133, cg24440941 (H3C6), cg20002843 (LOC127841), cg19107264, and cg11493553 located within the UBE3C gene and cg17065901 in FAM13A, both susceptibility genes for type 2 diabetes and BMI, and cg23355087 within the DLGAP2 gene, known to be involved in insulin resistance during pregnancy. CONCLUSIONS Our study reveals the potential complexity of the epigenetic transmission between mothers with GDM and their offspring, likely determined by not only GDM exposure but also other factors indicated by maternal epigenetic status, such as maternal metabolic history.
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Affiliation(s)
- Mickaël Canouil
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- Lille University Hospital, University of Lille, Lille, France
| | - Amna Khamis
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- Lille University Hospital, University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Elina Keikkala
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology (PEDEGO), Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
- Forschergruppe Diabetes e.V., Munich-Neuherberg, Germany
| | - Stephane Lobbens
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- Lille University Hospital, University of Lille, Lille, France
| | - Amélie Bonnefond
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- Lille University Hospital, University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Fabien Delahaye
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- Lille University Hospital, University of Lille, Lille, France
| | - Evangelia Tzala
- Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England Centre for Environment and Health, School of Public Health, Imperial College London, London, U.K
| | - Sanna Mustaniemi
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology (PEDEGO), Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Marja Vääräsmäki
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology (PEDEGO), Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England Centre for Environment and Health, School of Public Health, Imperial College London, London, U.K
- Center for Lifecourse Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, U.K
| | - Sylvain Sebert
- Center for Lifecourse Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Eero Kajantie
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology (PEDEGO), Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children's Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Philippe Froguel
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- Lille University Hospital, University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Toby Andrew
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- Lille University Hospital, University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
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TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia. Proc Natl Acad Sci U S A 2021; 118:2110758118. [PMID: 34413196 PMCID: PMC8403940 DOI: 10.1073/pnas.2110758118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy in need of novel targeted therapies to prevent relapse and lessen treatment toxicity. We reveal frequent (∼88%) transcriptional silencing or repression of the tumor suppressor TET2 in T-ALL. We show that loss of TET2 in T-ALL is correlated with hypermethylation of the TET2 promoter and that TET2 expression can be rescued by treatment with the DNA demethylating agent, 5-azacytidine (5-aza). We further reveal that the TET2 cofactor vitamin C exerts a strong synergistic effect on global transcriptional changes when added to 5-aza treatment. Importantly, 5-aza treatment results in increased cell death, specifically in T-ALL cells lacking TET2. Thus, we clearly identify 5-aza as a potentially targeted therapy for TET2-silenced T-ALL. Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy resulting from overproduction of immature T-cells in the thymus and is typified by widespread alterations in DNA methylation. As survival rates for relapsed T-ALL remain dismal (10 to 25%), development of targeted therapies to prevent relapse is key to improving prognosis. Whereas mutations in the DNA demethylating enzyme TET2 are frequent in adult T-cell malignancies, TET2 mutations in T-ALL are rare. Here, we analyzed RNA-sequencing data of 321 primary T-ALLs, 20 T-ALL cell lines, and 25 normal human tissues, revealing that TET2 is transcriptionally repressed or silenced in 71% and 17% of T-ALL, respectively. Furthermore, we show that TET2 silencing is often associated with hypermethylation of the TET2 promoter in primary T-ALL. Importantly, treatment with the DNA demethylating agent, 5-azacytidine (5-aza), was significantly more toxic to TET2-silenced T-ALL cells and resulted in stable re-expression of the TET2 gene. Additionally, 5-aza led to up-regulation of methylated genes and human endogenous retroviruses (HERVs), which was further enhanced by the addition of physiological levels of vitamin C, a potent enhancer of TET activity. Together, our results clearly identify 5-aza as a potential targeted therapy for TET2-silenced T-ALL.
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76
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Wang P, Wang B, Zhang Z, Wang Z. Identification of inflammation-related DNA methylation biomarkers in periodontitis patients based on weighted co-expression analysis. Aging (Albany NY) 2021; 13:19678-19695. [PMID: 34347624 PMCID: PMC8386560 DOI: 10.18632/aging.203378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/04/2021] [Indexed: 04/18/2023]
Abstract
Evidence from past research has shown that DNA methylation plays a key role in the pathogenesis of periodontitis, regulating gene expression levels and thereby affecting the occurrence of various diseases. Three sample sets of methylation data and gene expression data were downloaded from Gene Expression Omnibus (GEO) database. A diagnostic classifier is established based on gene expression data and CpG methylation data. Abnormal expression of immune-related pathways and methyltransferase-related genes in patients with periodontitis was detected. A total of 8,029 differentially expressed CpG (DMP) was annotated to the promoter region of 4,940 genes, of which 295 immune genes were significantly enriched. The CpG sites of 23 differentially co-expressed immune gene promoter regions were identified, and 13 CpG were generally hypermethylated in healthy group samples, while some were methylated in most patients. Five CpGs were screened as robust periodontitis biomarkers. The accuracy in the training data set, the two external verification data sets, and in the transcriptome was 95.5%, 80% and 78.3%, and 82.6%, respectively. This study provided new features for the diagnosis of periodontitis, and contributed to the personalized treatment of periodontitis.
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Affiliation(s)
- Pengcheng Wang
- Department of Stomatology, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Bingbing Wang
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Department of Oncology, Capital Medical University, Beijing 100069, China
| | - Zheng Zhang
- Department of Periodontology, Tianjin Stomatological Hospital and Tianjin Key Laboratory of Oral Function Reconstruction, Hospital of Stomatology, Nankai University, Tianjin 300041, China
| | - Zuomin Wang
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
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77
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Li M, Li Y, Qin H, Tubbs JD, Li M, Qiao C, Lin J, Li Q, Fan F, Gou M, Huang J, Tong J, Yang F, Tan Y, Yao Y. Genome-wide DNA methylation analysis of peripheral blood cells derived from patients with first-episode schizophrenia in the Chinese Han population. Mol Psychiatry 2021; 26:4475-4485. [PMID: 33279932 DOI: 10.1038/s41380-020-00968-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/03/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a severe neuropsychiatric disorder with core features including hallucinations, delusions, and cognition deficits. Accumulating evidence has implicated abnormal DNA methylation in the development of schizophrenia. However, the mechanisms by which DNA methylation changes alter the risk for schizophrenia remain largely unknown. We recently carried out a DNA methylome study of peripheral blood samples from 469 first-episode patients with schizophrenia and 476 age- and gender-matched healthy controls of Han Chinese origin. Genomic DNA methylation patterns were quantified using an Illumina Infinium Human MethylationEPIC BeadChip. We identified multiple differentially methylated positions (DMPs) and regions between patients and controls. The most significant DMPs were annotated to genes C17orf53, THAP1 and KCNQ4 (KV7.4), with Bonferroni-adjusted P values of [Formula: see text], [Formula: see text], and [Formula: see text], respectively. In particular, KCNQ4 encodes a voltage-gated potassium channel of the KV7 family, which is linked to neuronal excitability. The genes associated with top-ranked DMPs also included many genes involved in nervous system development, such as LIMK2 and TMOD2. Gene ontology analysis of the differentially methylated genes further identified strong enrichment of neuronal networks, including neuron projection extension, axonogenesis and neuron apoptotic process. Finally, we provided evidence that schizophrenia-associated epigenetic alterations co-localize with genetic susceptibility loci. By focusing on first-episode schizophrenia patients, our investigation lends particularly strong support for an important role of DNA methylation in schizophrenia pathogenesis unconfounded by the effects of long-term antipsychotic medication or disease progression. The observed DNA methylation aberrations in schizophrenia patients could potentially provide a valuable resource for identifying diagnostic biomarkers and developing novel therapeutic targets to benefit schizophrenia patients.
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Affiliation(s)
- Mingrui Li
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Yanli Li
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Haide Qin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, PR China
| | - Justin D Tubbs
- Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, 999077, PR China
| | - Minghui Li
- Sinotech Genomics Ltd, Shanghai, 210000, PR China
| | - Chunhong Qiao
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.,Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, 201203, PR China
| | - Jinran Lin
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Qingyang Li
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Fengmei Fan
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Mengzhuang Gou
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Junchao Huang
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Jinghui Tong
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Fude Yang
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Yunlong Tan
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China.
| | - Yin Yao
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.
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78
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Schwalbe EC, H L, Lafta F, Barrow TM, Strathdee G. Integration of genome-level data to allow identification of subtype-specific vulnerability genes as novel therapeutic targets. Oncogene 2021; 40:5213-5223. [PMID: 34230614 PMCID: PMC8376645 DOI: 10.1038/s41388-021-01923-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023]
Abstract
The identification of cancer-specific vulnerability genes is one of the most promising approaches for developing more effective and less toxic cancer treatments. Cancer genomes exhibit thousands of changes in DNA methylation and gene expression, with the vast majority likely to be passenger changes. We hypothesised that, through integration of genome-wide DNA methylation/expression data, we could exploit this inherent variability to identify cancer subtype-specific vulnerability genes that would represent novel therapeutic targets that could allow cancer-specific cell killing. We developed a bioinformatics pipeline integrating genome-wide DNA methylation/gene expression data to identify candidate subtype-specific vulnerability partner genes for the genetic drivers of individual genetic/molecular subtypes. Using acute lymphoblastic leukaemia as an initial model, 21 candidate subtype-specific vulnerability genes were identified across the five common genetic subtypes, with at least one per subtype. To confirm the approach was applicable across cancer types, we also assessed medulloblastoma, identifying 15 candidate subtype-specific vulnerability genes across three of four established subtypes. Almost all identified genes had not previously been implicated in these diseases. Functional analysis of seven candidate subtype-specific vulnerability genes across the two tumour types confirmed that siRNA-mediated knockdown induced significant inhibition of proliferation/induction of apoptosis, which was specific to the cancer subtype in which the gene was predicted to be specifically lethal. Thus, we present a novel approach that integrates genome-wide DNA methylation/expression data to identify cancer subtype-specific vulnerability genes as novel therapeutic targets. We demonstrate this approach is applicable to multiple cancer types and identifies true functional subtype-specific vulnerability genes with high efficiency.
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Affiliation(s)
- Edward C Schwalbe
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
- Department of Applied Sciences, Northumbria University, Newcastle, UK
| | - Lalchungnunga H
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
| | - Fadhel Lafta
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
- Department of Biology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Timothy M Barrow
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, UK
| | - Gordon Strathdee
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK.
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Chen S, Liu T, Bu D, Zhu J, Wang X, Pan Y, Liu Y, Lu ZJ, Wang P. Methylome profiling identifies TCHH methylation in CfDNA as a noninvasive marker of liver metastasis in colorectal cancer. FASEB J 2021; 35:e21720. [PMID: 34110642 DOI: 10.1096/fj.202100266r] [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: 02/10/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 11/11/2022]
Abstract
Methylation of circulating free DNA (CfDNA) has emerged as an efficient marker of tumor screening and prognostics. However, no efficient methylation marker has been developed for monitoring liver metastasis (LM) in colorectal cancer (CRC). Utilizing methylome profiling and bisulfite sequencing polymerase chain reaction of paired primary and LM sites, significantly increased methylation of TCHH was identified in the process of LM in CRC in the present study. Methylight analysis of TCHH methylation in CfDNA displayed a promisingly discriminative power between CRC with and without LM. Besides, significant coefficient of TCHH methylation and LM tumor volume was also validated. Together, these results indicated the potential of TCHH methylation in CfDNA as a monitoring marker of LM in CRC.
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Affiliation(s)
- Shanwen Chen
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Tao Liu
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Dingfang Bu
- Central laboratory, Peking University First Hospital, Beijing, China
| | - Jing Zhu
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Xin Wang
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Yisheng Pan
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Yucun Liu
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pengyuan Wang
- Division of General Surgery, Peking University First Hospital, Beijing, China
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80
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Touzart A, Mayakonda A, Smith C, Hey J, Toth R, Cieslak A, Andrieu GP, Tran Quang C, Latiri M, Ghysdael J, Spicuglia S, Dombret H, Ifrah N, Macintyre E, Lutsik P, Boissel N, Plass C, Asnafi V. Epigenetic analysis of patients with T-ALL identifies poor outcomes and a hypomethylating agent-responsive subgroup. Sci Transl Med 2021; 13:13/595/eabc4834. [PMID: 34039737 DOI: 10.1126/scitranslmed.abc4834] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/10/2020] [Accepted: 05/07/2021] [Indexed: 12/14/2022]
Abstract
Adult "T cell" acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that is associated with poor outcomes, requiring additional therapeutic options. The DNA methylation landscapes of adult T-ALL remain undercharacterized. Here, we systematically analyzed the DNA methylation profiles of normal thymic-sorted T cell subpopulations and 143 primary adult T-ALLs as part of the French GRAALL 2003-2005 trial. Our results indicated that T-ALL is epigenetically heterogeneous consisting of five subtypes (C1-C5), which were either associated with co-occurring DNA methyltransferase 3 alpha (DNMT3A)/isocitrate dehydrogenase [NADP(+)] 2 (IDH2) mutations (C1), TAL bHLH transcription factor 1, erythroid differentiation factor (TAL1) deregulation (C2), T cell leukemia homeobox 3 (TLX3) (C3), TLX1/in cis-homeobox A9 (HOXA9) (C4), or in trans-HOXA9 overexpression (C5). Integrative analysis of DNA methylation and gene expression identified potential cluster-specific oncogenes and tumor suppressor genes. In addition to an aggressive hypomethylated subgroup (C1), our data identified an unexpected subset of hypermethylated T-ALL (C5) associated with poor outcome and primary therapeutic response. Using mouse xenografts, we demonstrated that hypermethylated T-ALL samples exhibited therapeutic responses to the DNA hypomethylating agent 5-azacytidine, which significantly (survival probability; P = 0.001 for C3, 0.01 for C4, and 0.0253 for C5) delayed tumor progression. These findings suggest that epigenetic-based therapies may provide an alternative treatment option in hypermethylated T-ALL.
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Affiliation(s)
- Aurore Touzart
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Université de Paris (Descartes), Institut Necker -Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France
| | - Anand Mayakonda
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker -Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France
| | - Joschka Hey
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.,Germany-Israeli Helmholtz Research School in Cancer Biology, 69120 Heidelberg, Germany
| | - Reka Toth
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker -Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France
| | - Guillaume P Andrieu
- Université de Paris (Descartes), Institut Necker -Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France
| | - Christine Tran Quang
- Institut Curie, Orsay, France.,CNRS UMR3348, Institut Curie, Orsay, France.,INSERM 1278, Centre Universitaire, Orsay, France.,PSL Research University, Paris, France.,Paris-Saclay, 91400 Orsay, France
| | - Mehdi Latiri
- Université de Paris (Descartes), Institut Necker -Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France
| | - Jacques Ghysdael
- Institut Curie, Orsay, France.,CNRS UMR3348, Institut Curie, Orsay, France.,INSERM 1278, Centre Universitaire, Orsay, France.,PSL Research University, Paris, France.,Paris-Saclay, 91400 Orsay, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), Equipe labellisée Ligue, UMR1090, 13288 Marseille, France
| | - Hervé Dombret
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, 75010 Paris, France
| | - Norbert Ifrah
- PRES LUNAM, CHU Angers service des Maladies du Sang et INSERM U 892, 49933 Angers, France
| | - Elizabeth Macintyre
- Université de Paris (Descartes), Institut Necker -Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France
| | - Pavlo Lutsik
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Research Consortium (DKTK), 69120 Heidelberg, Germany
| | - Nicolas Boissel
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, 75010 Paris, France
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. .,German Cancer Research Consortium (DKTK), 69120 Heidelberg, Germany
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker -Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75743 Paris, France.
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81
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Zhu W, Jiang L, Pan C, Sun J, Huang X, Ni W. Deoxyribonucleic acid methylation signatures in sperm deoxyribonucleic acid fragmentation. Fertil Steril 2021; 116:1297-1307. [PMID: 34253331 DOI: 10.1016/j.fertnstert.2021.06.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/05/2021] [Accepted: 06/10/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To evaluate Deoxyribonucleic acid (DNA) methylation patterns in sperm from men with differential levels of sperm DNA fragmentation index (DFI). DESIGN Prospective study. SETTING University-affiliated reproductive medicine center. PATIENT(S) A total of 278 male patients consulting for couple infertility were recruited from the First Affiliated Hospital of Wenzhou Medical University. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Genome-wide DNA methylation analysis was performed using Infinium MethylationEPIC BeadChip on spermatozoal DNA from 20 male patients. Differentially methylated regions (DMRs) were identified and validated using targeted bisulfite amplicon sequencing in spermatozoal DNA from 266 males. RESULT(S) Unsupervised hierarchical clustering analysis revealed three main clusters corresponding to sperm DFI levels (low, medium, or high). Between-cluster comparisons identified 959 (medium-low), 738 (high-medium), and 937 (high-low) DMRs. Sixty-six DMRs were validated in the 266-sample cohort, of which nine CpG fragments corresponding to nine genes (BLCAP, DIRAS3, FAM50B, GNAS, MEST, TSPAN32, PSMA8, SYCP1, and TEX12) exhibited significantly altered methylation in those with high DFI (≥25%) compared with those with low DFI (<25%). CONCLUSION(S) We identified and validated a distinct DNA methylation signature associated with sperm DNA damage in a large, unselected cohort. These results indicate that sperm DNA damage may affect DNA methylation patterns in human sperm.
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Affiliation(s)
- Weijian Zhu
- Central Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Lei Jiang
- Central Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Chengshuang Pan
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Junhui Sun
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xuefeng Huang
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Wuhua Ni
- Reproductive Medicine Center, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
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82
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Bozack AK, Boileau P, Wei L, Hubbard AE, Sillé FCM, Ferreccio C, Acevedo J, Hou L, Ilievski V, Steinmaus CM, Smith MT, Navas-Acien A, Gamble MV, Cardenas A. Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes. Environ Health 2021; 20:79. [PMID: 34243768 PMCID: PMC8272372 DOI: 10.1186/s12940-021-00754-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Arsenic (As) exposure through drinking water is a global public health concern. Epigenetic dysregulation including changes in DNA methylation (DNAm), may be involved in arsenic toxicity. Epigenome-wide association studies (EWAS) of arsenic exposure have been restricted to single populations and comparison across EWAS has been limited by methodological differences. Leveraging data from epidemiological studies conducted in Chile and Bangladesh, we use a harmonized data processing and analysis pipeline and meta-analysis to combine results from four EWAS. METHODS DNAm was measured among adults in Chile with and without prenatal and early-life As exposure in PBMCs and buccal cells (N = 40, 850K array) and among men in Bangladesh with high and low As exposure in PBMCs (N = 32, 850K array; N = 48, 450K array). Linear models were used to identify differentially methylated positions (DMPs) and differentially variable positions (DVPs) adjusting for age, smoking, cell type, and sex in the Chile cohort. Probes common across EWAS were meta-analyzed using METAL, and differentially methylated and variable regions (DMRs and DVRs, respectively) were identified using comb-p. KEGG pathway analysis was used to understand biological functions of DMPs and DVPs. RESULTS In a meta-analysis restricted to PBMCs, we identified one DMP and 23 DVPs associated with arsenic exposure; including buccal cells, we identified 3 DMPs and 19 DVPs (FDR < 0.05). Using meta-analyzed results, we identified 11 DMRs and 11 DVRs in PBMC samples, and 16 DMRs and 19 DVRs in PBMC and buccal cell samples. One region annotated to LRRC27 was identified as a DMR and DVR. Arsenic-associated KEGG pathways included lysosome, autophagy, and mTOR signaling, AMPK signaling, and one carbon pool by folate. CONCLUSIONS Using a two-step process of (1) harmonized data processing and analysis and (2) meta-analysis, we leverage four DNAm datasets from two continents of individuals exposed to high levels of As prenatally and during adulthood to identify DMPs and DVPs associated with arsenic exposure. Our approach suggests that standardizing analytical pipelines can aid in identifying biological meaningful signals.
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Affiliation(s)
- Anne K Bozack
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA.
| | - Philippe Boileau
- Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Linqing Wei
- Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Alan E Hubbard
- Graduate Group in Biostatistics, University of California, Berkeley, Berkeley, CA, USA
| | - Fenna C M Sillé
- Department of Environmental Health and Engineering, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Catterina Ferreccio
- Advanced Center for Chronic Diseases (ACCDiS), School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Johanna Acevedo
- Department of Public Health, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Health Planning Division in the Ministry of Health, Santiago, Chile
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Vesna Ilievski
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Craig M Steinmaus
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA
| | - Ana Navas-Acien
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Mary V Gamble
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, Berkeley, CA, 94720, USA
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83
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Tejedor JR, Bueno C, Vinyoles M, Petazzi P, Agraz-Doblas A, Cobo I, Torres-Ruiz R, Bayón GF, Pérez RF, López-Tamargo S, Gutierrez-Agüera F, Santamarina-Ojeda P, Ramírez-Orellana M, Bardini M, Cazzaniga G, Ballerini P, Schneider P, Stam RW, Varela I, Fraga MF, Fernández AF, Menéndez P. Integrative methylome-transcriptome analysis unravels cancer cell vulnerabilities in infant MLL-rearranged B cell acute lymphoblastic leukemia. J Clin Invest 2021; 131:138833. [PMID: 33983906 DOI: 10.1172/jci138833] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/11/2021] [Indexed: 01/04/2023] Open
Abstract
B cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. As predicted by its prenatal origin, infant B-ALL (iB-ALL) shows an exceptionally silent DNA mutational landscape, suggesting that alternative epigenetic mechanisms may substantially contribute to its leukemogenesis. Here, we have integrated genome-wide DNA methylome and transcriptome data from 69 patients with de novo MLL-rearranged leukemia (MLLr) and non-MLLr iB-ALL leukemia uniformly treated according to the Interfant-99/06 protocol. iB-ALL methylome signatures display a plethora of common and specific alterations associated with chromatin states related to enhancer and transcriptional control in normal hematopoietic cells. DNA methylation, gene expression, and gene coexpression network analyses segregated MLLr away from non-MLLr iB-ALL and identified a coordinated and enriched expression of the AP-1 complex members FOS and JUN and RUNX factors in MLLr iB-ALL, consistent with the significant enrichment of hypomethylated CpGs in these genes. Integrative methylome-transcriptome analysis identified consistent cancer cell vulnerabilities, revealed a robust iB-ALL-specific gene expression-correlating dmCpG signature, and confirmed an epigenetic control of AP-1 and RUNX members in reshaping the molecular network of MLLr iB-ALL. Finally, pharmacological inhibition or functional ablation of AP-1 dramatically impaired MLLr-leukemic growth in vitro and in vivo using MLLr-iB-ALL patient-derived xenografts, providing rationale for new therapeutic avenues in MLLr-iB-ALL.
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Affiliation(s)
- Juan Ramón Tejedor
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and.,RICORS-TERAV Network, ISCIII, Madrid, Spain
| | - Meritxell Vinyoles
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and
| | - Paolo Petazzi
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Isabel Cobo
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Raúl Torres-Ruiz
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,RICORS-TERAV Network, ISCIII, Madrid, Spain.,Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Gustavo F Bayón
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Raúl F Pérez
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Sara López-Tamargo
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Francisco Gutierrez-Agüera
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,RICORS-TERAV Network, ISCIII, Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Manuel Ramírez-Orellana
- RICORS-TERAV Network, ISCIII, Madrid, Spain.,Hematology Diagnostic Laboratory, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Michela Bardini
- Centro Ricerca Tettamanti, Department of Paediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Department of Paediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Paola Ballerini
- Pediatric Hematology, Armand Trousseau Hospital, Paris, France
| | - Pauline Schneider
- Princess Maxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Ronald W Stam
- Princess Maxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Mario F Fraga
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Agustín F Fernández
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and.,RICORS-TERAV Network, ISCIII, Madrid, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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84
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Lucia RM, Huang WL, Alvarez A, Masunaka I, Ziogas A, Goodman D, Odegaard AO, Norden-Krichmar TM, Park HL. Association of mammographic density with blood DNA methylation. Epigenetics 2021; 17:531-546. [PMID: 34116608 PMCID: PMC9067527 DOI: 10.1080/15592294.2021.1928994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background: Altered DNA methylation may be an intermediate phenotype between breast cancer risk factors and disease. Mammographic density is a strong risk factor for breast cancer. However, no studies to date have identified an epigenetic signature of mammographic density. We performed an epigenome-wide association study of mammographic density. Methods: White blood cell DNA methylation was measured for 385 postmenopausal women using the Illumina Infinium MethylationEPIC BeadChip array. Differential methylation was assessed using genome-wide, probe-level, and regional analyses. We implemented a resampling-based approach to improve the stability of our findings. Results: On average, women with elevated mammographic density exhibited DNA hypermethylation within CpG islands and gene promoters compared to women with lower mammographic density. We identified 250 CpG sites for which DNA methylation was significantly associated with mammographic density. The top sites were located within genes associated with cancer, including HDLBP, TGFB2, CCT4, and PAX8, and were more likely to be located in regulatory regions of the genome. We also identified differential DNA methylation in 37 regions, including within the promoters of PAX8 and PF4, a gene involved in the regulation of angiogenesis. Overall, our results paint a picture of epigenetic dysregulation associated with mammographic density. Conclusion: Mammographic density is associated with differential DNA methylation throughout the genome, including within genes associated with cancer. Our results suggest the potential involvement of several genes in the biological mechanisms behind differences in breast density between women. Further studies are warranted to explore these potential mechanisms and potential links to breast cancer risk.
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Affiliation(s)
- Rachel M Lucia
- Department of Epidemiology, University of California, Irvine, USA
| | - Wei-Lin Huang
- Department of Epidemiology, University of California, Irvine, USA
| | - Andrea Alvarez
- Department of Medicine, University of California, Irvine, USA
| | - Irene Masunaka
- Department of Medicine, University of California, Irvine, USA
| | - Argyrios Ziogas
- Department of Medicine, University of California, Irvine, USA
| | - Deborah Goodman
- Department of Epidemiology, University of California, Irvine, USA
| | | | | | - Hannah Lui Park
- Department of Epidemiology, University of California, Irvine, USA.,Department of Pathology and Laboratory Medicine, University of California, Irvine, USA
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85
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Krali O, Palle J, Bäcklin CL, Abrahamsson J, Norén-Nyström U, Hasle H, Jahnukainen K, Jónsson ÓG, Hovland R, Lausen B, Larsson R, Palmqvist L, Staffas A, Zeller B, Nordlund J. DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML). Genes (Basel) 2021; 12:895. [PMID: 34200630 PMCID: PMC8229099 DOI: 10.3390/genes12060895] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Pediatric acute myeloid leukemia (AML) is a heterogeneous disease composed of clinically relevant subtypes defined by recurrent cytogenetic aberrations. The majority of the aberrations used in risk grouping for treatment decisions are extensively studied, but still a large proportion of pediatric AML patients remain cytogenetically undefined and would therefore benefit from additional molecular investigation. As aberrant epigenetic regulation has been widely observed during leukemogenesis, we hypothesized that DNA methylation signatures could be used to predict molecular subtypes and identify signatures with prognostic impact in AML. To study genome-wide DNA methylation, we analyzed 123 diagnostic and 19 relapse AML samples on Illumina 450k DNA methylation arrays. We designed and validated DNA methylation-based classifiers for AML cytogenetic subtype, resulting in an overall test accuracy of 91%. Furthermore, we identified methylation signatures associated with outcome in t(8;21)/RUNX1-RUNX1T1, normal karyotype, and MLL/KMT2A-rearranged subgroups (p < 0.01). Overall, these results further underscore the clinical value of DNA methylation analysis in AML.
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Affiliation(s)
- Olga Krali
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden;
| | - Josefine Palle
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden;
- Department of Women’s and Children’s Health, Uppsala University, 752 37 Uppsala, Sweden
| | - Christofer L. Bäcklin
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 751 85 Uppsala, Sweden; (C.L.B.); (R.L.)
| | - Jonas Abrahamsson
- Department of Pediatrics, Queen Silvia Children’s Hospital, 416 85 Gothenburg, Sweden;
| | - Ulrika Norén-Nyström
- Department of Clinical Sciences, Pediatrics, Umeå University Hospital, 901 85 Umeå, Sweden;
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital, DK-8200 Aarhus, Denmark;
| | - Kirsi Jahnukainen
- Children’s Hospital, Helsinki University Central Hospital, Helsinki, and University of Helsinki, 00290 Helsinki, Finland;
| | - Ólafur Gísli Jónsson
- Department of Pediatrics, Landspitali University Hospital, 101 Reykjavík, Iceland;
| | - Randi Hovland
- Center of Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5009 Bergen, Norway;
| | - Birgitte Lausen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Rolf Larsson
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 751 85 Uppsala, Sweden; (C.L.B.); (R.L.)
| | - Lars Palmqvist
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, 41346 Gothenburg, Sweden; (L.P.); (A.S.)
| | - Anna Staffas
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, 41346 Gothenburg, Sweden; (L.P.); (A.S.)
| | - Bernward Zeller
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway;
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden;
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86
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Epigenetic Modification of Death Receptor Genes for TRAIL and TRAIL Resistance in Childhood B-Cell Precursor Acute Lymphoblastic Leukemia. Genes (Basel) 2021; 12:genes12060864. [PMID: 34198757 PMCID: PMC8229974 DOI: 10.3390/genes12060864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
Immunotherapies specific for B-cell precursor acute lymphoblastic leukemia (BCP-ALL), such as anti-CD19 chimeric antigen receptor (CAR) T-cells and blinatumomab, have dramatically improved the therapeutic outcome in refractory cases. In the anti-leukemic activity of those immunotherapies, TNF-related apoptosis-inducing ligand (TRAIL) on cytotoxic T-cells plays an essential role by inducing apoptosis of the target leukemia cells through its death receptors (DR4 and DR5). Since there are CpG islands in the promoter regions, hypermethylation of the DR4 and DR5 genes may be involved in resistance of leukemia cells to immunotherapies due to TRAIL-resistance. We analyzed the DR4 and DR5 methylation status in 32 BCP-ALL cell lines by sequencing their bisulfite PCR products with a next-generation sequencer. The DR4 and DR5 methylation status was significantly associated with the gene and cell-surface expression levels and the TRAIL-sensitivities. In the clinical samples at diagnosis (459 cases in the NOPHO study), both DR4 and DR5 genes were unmethylated in the majority of cases, whereas methylated in several cases with dic(9;20), MLL-rearrangement, and hypodiploidy, suggesting that evaluation of methylation status of the DR4 and DR5 genes might be clinically informative to predict efficacy of immunotherapy in certain cases with such unfavorable karyotypes. These observations provide an epigenetic rational for clinical efficacy of immunotherapy in the vast majority of BCP-ALL cases.
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87
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Chen D, Camponeschi A, Nordlund J, Marincevic‐Zuniga Y, Abrahamsson J, Lönnerholm G, Fogelstrand L, Mårtensson I. RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children. Cancer Med 2021; 10:3997-4003. [PMID: 33987955 PMCID: PMC8209579 DOI: 10.1002/cam4.3928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 12/05/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) can be classified into subtypes according to the genetic aberrations they display. For instance, the translocation t(12;21)(p13;q22), representing the ETV6-RUNX1 fusion gene (ER), is present in a quarter of BCP-ALL cases. However, around 10% of the cases lack classifying chromosomal abnormalities (B-other). In pediatric ER BCP-ALL, rearrangement mediated by RAG (recombination-activating genes) has been proposed as the predominant driver of oncogenic rearrangement. Herein we analyzed almost 1600 pediatric BCP-ALL samples to determine which subtypes express RAG. We demonstrate that RAG1 mRNA levels are especially high in the ETV6-RUNX1 (ER) subtype and in a subset of B-other samples. We also define 31 genes that are co-expressed with RAG1 (RAG1-signature) in the ER subtype, a signature that also identifies this subset of B-other samples. Moreover, this subset also shares leukemia and pro-B gene expression signatures as well as high levels of the ETV6 target genes (BIRC7, WBP1L, CLIC5, ANGPTL2) with the ER subtype, indicating that these B-other cases are the recently identified ER-like subtype. We validated our results in a cohort where ER-like has been defined, which confirmed expression of the RAG1-signature in this recently described subtype. Taken together, our results demonstrate that the RAG1-signature identifies the ER-like subtype. As there are no definitive genetic markers to identify this novel subtype, the RAG1-signature represents a means to screen for this leukemia in children.
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Affiliation(s)
- Dongfeng Chen
- Institute of Life SciencesJiangsu UniversityZhenjiangChina
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Alessandro Camponeschi
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Jessica Nordlund
- Department of Medical SciencesMolecular Medicine and Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Yanara Marincevic‐Zuniga
- Department of Medical SciencesMolecular Medicine and Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Jonas Abrahamsson
- Department of PediatricsInstitute of Clinical SciencesSahlgrenska University HospitalGothenburgSweden
| | - Gudmar Lönnerholm
- Department of Women and Children’s HealthUppsala UniversityUppsalaSweden
| | - Linda Fogelstrand
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden
- Department of Clinical Chemistry and Transfusion MedicineUniversity of GothenburgGothenburgSweden
| | - Inga‐Lill Mårtensson
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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88
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Cao VT, Lea RA, Sutherland HG, Benton MC, Pishva RS, Haupt LM, Griffiths LR. A genome-wide methylation study of body fat traits in the Norfolk Island isolate. Nutr Metab Cardiovasc Dis 2021; 31:1556-1563. [PMID: 33810959 DOI: 10.1016/j.numecd.2021.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND AIMS Natural variation in body fat is explained by both genetic and environmental effects. Epigenetic mechanisms such as DNA methylation can mediate these effects causing changes in gene expression leading to onset of obesity. Studies of genetic isolates have the potential to provide new epigenetic insights with advantages such as reduced genetic diversity and environmental exposures. METHODS AND RESULTS This was an exploratory study of genome-wide DNA methylation in relation to body fat traits in 47 healthy adults from the genetic isolate of Norfolk Island. Quantitative body fat traits (body fat percentage, body mass index, hip circumference, waist circumference, waist-hip-ratio and weight) were carefully measured. DNA methylation data was obtained from peripheral blood using Illumina 450K arrays. Multi-trait analysis was performed using Principal Component Analysis (PCA). CpG by trait association testing was performed using stepwise linear regressions. Two components were identified that explained approximately 89% of the phenotypic variance. In total, 5 differential methylated positions (DMPs) were identified at genome-wide significance (P≤ 2.4 × 10-7), which mapped to GOT2-CDH8, LYSMD3, HIBADH, ADGRD1 and EBF4 genes. Gene set enrichment analysis of 848 genes containing suggestive DMPs (P≤ 1.0 × 10-4) implicated the Cadherin (28 genes, Padj = 6.76 × 10-7) and Wnt signaling pathways (38 genes, Padj = 7.78 × 10-6). CONCLUSION This study provides new insights into the epigenetically influenced genes and pathways underlying body fat variation in a healthy cohort and provides targets for consideration in future studies of obesity risk.
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Affiliation(s)
- Van T Cao
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Rodney A Lea
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Heidi G Sutherland
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Miles C Benton
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia; Human Genomics, Institute of Environmental Science and Research, Kenepuru, Wellington, New Zealand.
| | - Reza S Pishva
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
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89
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Velasco G, Ulveling D, Rondeau S, Marzin P, Unoki M, Cormier-Daire V, Francastel C. Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders. Int J Mol Sci 2021; 22:3735. [PMID: 33916664 PMCID: PMC8038329 DOI: 10.3390/ijms22073735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation (DNAme) profiling is used to establish specific biomarkers to improve the diagnosis of patients with inherited neurodevelopmental disorders and to guide mutation screening. In the specific case of mendelian disorders of the epigenetic machinery, it also provides the basis to infer mechanistic aspects with regard to DNAme determinants and interplay between histone and DNAme that apply to humans. Here, we present comparative methylomes from patients with mutations in the de novo DNA methyltransferases DNMT3A and DNMT3B, in their catalytic domain or their N-terminal parts involved in reading histone methylation, or in histone H3 lysine (K) methylases NSD1 or SETD2 (H3 K36) or KMT2D/MLL2 (H3 K4). We provide disease-specific DNAme signatures and document the distinct consequences of mutations in enzymes with very similar or intertwined functions, including at repeated sequences and imprinted loci. We found that KMT2D and SETD2 germline mutations have little impact on DNAme profiles. In contrast, the overlapping DNAme alterations downstream of NSD1 or DNMT3 mutations underlines functional links, more specifically between NSD1 and DNMT3B at heterochromatin regions or DNMT3A at regulatory elements. Together, these data indicate certain discrepancy with the mechanisms described in animal models or the existence of redundant or complementary functions unforeseen in humans.
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Affiliation(s)
- Guillaume Velasco
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
| | - Damien Ulveling
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
| | - Sophie Rondeau
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Pauline Marzin
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
| | - Valérie Cormier-Daire
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Claire Francastel
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
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90
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Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL. Blood 2021; 136:2319-2333. [PMID: 32573712 DOI: 10.1182/blood.2019004090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
Karyotype is an important prognostic factor in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but the underlying pharmacogenomics remain unknown. Asparaginase is an integral component in current chemotherapy for childhood BCP-ALL. Asparaginase therapy depletes serum asparagine. Normal hematopoietic cells can produce asparagine by asparagine synthetase (ASNS) activity, but ALL cells are unable to synthesize adequate amounts of asparagine. The ASNS gene has a typical CpG island in its promoter. Thus, methylation of the ASNS CpG island could be one of the epigenetic mechanisms for ASNS gene silencing in BCP-ALL. To gain deep insights into the pharmacogenomics of asparaginase therapy, we investigated the association of ASNS methylation status with asparaginase sensitivity. The ASNS CpG island is largely unmethylated in normal hematopoietic cells, but it is allele-specifically methylated in BCP-ALL cells. The ASNS gene is located at 7q21, an evolutionally conserved imprinted gene cluster. ASNS methylation in childhood BCP-ALL is associated with an aberrant methylation of the imprinted gene cluster at 7q21. Aberrant methylation of mouse Asns and a syntenic imprinted gene cluster is also confirmed in leukemic spleen samples from ETV6-RUNX1 knockin mice. In 3 childhood BCP-ALL cohorts, ASNS is highly methylated in BCP-ALL patients with favorable karyotypes but is mostly unmethylated in BCP-ALL patients with poor prognostic karyotypes. Higher ASNS methylation is associated with higher L-asparaginase sensitivity in BCP-ALL through lower ASNS gene and protein expression levels. These observations demonstrate that silencing of the ASNS gene as a result of aberrant imprinting is a pharmacogenetic mechanism for the leukemia-specific activity of asparaginase therapy in BCP-ALL.
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91
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Koldobskiy MA, Jenkinson G, Abante J, Rodriguez DiBlasi VA, Zhou W, Pujadas E, Idrizi A, Tryggvadottir R, Callahan C, Bonifant CL, Rabin KR, Brown PA, Ji H, Goutsias J, Feinberg AP. Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nat Biomed Eng 2021; 5:360-376. [PMID: 33859388 PMCID: PMC8370714 DOI: 10.1038/s41551-021-00703-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/18/2021] [Indexed: 02/02/2023]
Abstract
In cancer, linking epigenetic alterations to drivers of transformation has been difficult, in part because DNA methylation analyses must capture epigenetic variability, which is central to tumour heterogeneity and tumour plasticity. Here, by conducting a comprehensive analysis, based on information theory, of differences in methylation stochasticity in samples from patients with paediatric acute lymphoblastic leukaemia (ALL), we show that ALL epigenomes are stochastic and marked by increased methylation entropy at specific regulatory regions and genes. By integrating DNA methylation and single-cell gene-expression data, we arrived at a relationship between methylation entropy and gene-expression variability, and found that epigenetic changes in ALL converge on a shared set of genes that overlap with genetic drivers involved in chromosomal translocations across the disease spectrum. Our findings suggest that an epigenetically driven gene-regulation network, with UHRF1 (ubiquitin-like with PHD and RING finger domains 1) as a central node, links genetic drivers and epigenetic mediators in ALL.
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Affiliation(s)
- Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garrett Jenkinson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Varenka A Rodriguez DiBlasi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim, Ridgefield, CT, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elisabet Pujadas
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Challice L Bonifant
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen R Rabin
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Patrick A Brown
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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92
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Visco ZR, Sfakianos G, Grenier C, Boudreau MH, Simpson S, Rodriguez I, Whitaker R, Yao DY, Berchuck A, Murphy SK, Huang Z. Epigenetic Regulation of Claudin-1 in the Development of Ovarian Cancer Recurrence and Drug Resistance. Front Oncol 2021; 11:620873. [PMID: 33828978 PMCID: PMC8019902 DOI: 10.3389/fonc.2021.620873] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022] Open
Abstract
Over 21,000 women are diagnosed with ovarian cancer (OC) in the United States each year and over half that number succumb to this disease annually, often due to recurrent disease. A deeper understanding of the molecular events associated with recurrent disease is needed to identify potential targets. Using genome-scale DNA methylation and gene expression data for 16 matched primary-recurrent advanced stage serous epithelial OCs, we discovered that Claudin-1 (CLDN1), a tight junction protein, shows a stronger correlation between expression and methylation in recurrent versus primary OC at multiple CpG sites (R= –0.47 to −0.64 versus R= -0.32 to −0.57, respectively). An independent dataset showed that this correlation is stronger in tumors from short-term (<3y) survivors than in tumors from long-term (>7y) survivors (R= −0.41 to −0.46 versus R= 0.06 to −0.19, respectively). The presence of this inverse correlation in short-term survivors and recurrent tumors suggests an important role for this relationship and potential predictive value for disease prognosis. CLDN1 expression increased following pharmacologic inhibition of DNA methyltransferase activity (p< 0.001), thus validating the role of methylation in CLDN1 gene inhibition. CLDN1 knockdown enhanced chemosensitivity and suppressed cell proliferation, migration, and wound healing (p< 0.05). Stable CLDN1 knockdown in vivo resulted in reduced xenograft tumor growth but did not reach significance. Our results indicate that the relationship between CLDN1 methylation and expression plays an important role in OC aggressiveness and recurrence.
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Affiliation(s)
- Zachary R Visco
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Gregory Sfakianos
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Carole Grenier
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States.,Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Marie-Helene Boudreau
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Sabrina Simpson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Isabel Rodriguez
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Regina Whitaker
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Derek Y Yao
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Susan K Murphy
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States.,Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Zhiqing Huang
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States.,Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
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93
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de Barrios O, Parra M. Epigenetic Control of Infant B Cell Precursor Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22063127. [PMID: 33803872 PMCID: PMC8003172 DOI: 10.3390/ijms22063127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a highly aggressive malignancy, with poorer prognosis in infants than in adults. A genetic signature has been associated with this outcome but, remarkably, leukemogenesis is commonly triggered by genetic alterations of embryonic origin that involve the deregulation of chromatin remodelers. This review considers in depth how the alteration of epigenetic profiles (at DNA and histone levels) induces an aberrant phenotype in B lymphocyte progenitors by modulating the oncogenic drivers and tumor suppressors involved in key cancer hallmarks. DNA methylation patterns have been widely studied in BCP-ALL and their correlation with survival has been established. However, the effect of methylation on histone residues can be very different. For instance, methyltransferase KMT2A gene participates in chromosomal rearrangements with several partners, imposing an altered pattern of methylated H3K4 and H3K79 residues, enhancing oncogene promoter activation, and conferring a worse outcome on affected infants. In parallel, acetylation processes provide an additional layer of epigenetic regulation and can alter the chromatin conformation, enabling the binding of regulatory factors. Therefore, an integrated knowledge of all epigenetic disorders is essential to understand the molecular basis of BCP-ALL and to identify novel entry points that can be exploited to improve therapeutic options and disease prognosis.
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Affiliation(s)
- Oriol de Barrios
- Correspondence: (O.d.B.); (M.P.); Tel.: +34-93-557-28-00 (ext. 4222) (O.d.B.); +34-93-557-28-00 (ext. 4210) (M.P.)
| | - Maribel Parra
- Correspondence: (O.d.B.); (M.P.); Tel.: +34-93-557-28-00 (ext. 4222) (O.d.B.); +34-93-557-28-00 (ext. 4210) (M.P.)
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94
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A novel DNA methylation-based model that effectively predicts prognosis in hepatocellular carcinoma. Biosci Rep 2021; 41:227938. [PMID: 33634306 PMCID: PMC7955104 DOI: 10.1042/bsr20203945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To build a novel predictive model for hepatocellular carcinoma (HCC) patients based on DNA methylation data. METHODS Four independent DNA methylation datasets for HCC were used to screen for common differentially methylated genes (CDMGs). Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to explore the biological roles of CDMGs in HCC. Univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox analysis were performed to identify survival-related CDMGs (SR-CDMGs) and to build a predictive model. The importance of this model was assessed using Cox regression analysis, propensity score-matched (PSM) analysis and stratification analysis. A validation group from the Cancer Genome Atlas (TCGA) was constructed to further validate the model. RESULTS Four SR-CDMGs were identified and used to build the predictive model. The risk score of this model was calculated as follows: risk score = (0.01489826 × methylation level of WDR69) + (0.15868618 × methylation level of HOXB4) + (0.16674959 × methylation level of CDKL2) + (0.16689301 × methylation level of HOXA10). Kaplan-Meier analysis demonstrated that patients in the low-risk group had a significantly longer overall survival (OS; log-rank P-value =0.00071). The Cox model multivariate analysis and PSM analysis identified the risk score as an independent prognostic factor (P<0.05). Stratified analysis results further confirmed this model performed well. By analyzing the validation group, the results of receiver operating characteristic (ROC) curve analysis and survival analysis further validated this model. CONCLUSION Our DNA methylation-based prognosis predictive model is effective and reliable in predicting prognosis for patients with HCC.
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95
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Lin CH, Lee YS, Huang YY, Tsai CN. Methylation status of vault RNA 2-1 promoter is a predictor of glycemic response to glucagon-like peptide-1 analog therapy in type 2 diabetes mellitus. BMJ Open Diabetes Res Care 2021; 9:9/1/e001416. [PMID: 33674278 PMCID: PMC7938984 DOI: 10.1136/bmjdrc-2020-001416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 01/28/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Therapeutic efficiency of glucagon-like peptide-1 (GLP-1) analog is about 50%-70% in type 2 diabetes mellitus (T2DM). Discovery of potential genetic biomarkers for prediction of treatment efficiency of GLP-1 analog before therapy is still necessary. We assess whether DNA methylation was associated with glycemic response to GLP-1 analog therapy in patients with poorly controlled T2DM. RESEARCH DESIGN AND METHODS Genomic DNA was extracted from the peripheral blood of training (n=10) and validation (n=128) groups of patients with T2DM receiving GLP-1 analogs. DNA methylome was analyzed using Infinium Human Methylation EPIC Bead Chip in the training group. The candidate genes were examined using a pyrosequencing platform in the validation group. The association between DNA methylation status and glycemic response to GLP-1 was analyzed in these patients. RESULTS The most differential methylation region between those with a good (responsive) and poor (unresponsive) glycemic response to GLP-1 analog therapy was located on chromosome 5q31.1 (135415693 to 135416613), the promoter of VTRNA2-1 in the training group. The methylation status of the VTRNA2-1 promoter was examined in the validation group via pyrosequencing reaction, and the hypomethylation of VTRNA2-1 (<40% methylation) was significantly associated with poor glycemic response to GLP-1 treatment (OR 2.757, 95% CI 1.240 to 6.130, p=0.011). Since the VTRNA2-1 promoter region was previously reported maternal imprinting extended to the adjacent centromeric CCCTC-binding factor site that contained an A/C polymorphism (rs2346018), which was associated with methylation density of VTRNA2-1, this A/C polymorphism was also integrated to analyze association with glycemic response to GLP-1 analog therapy. In patients with the A allele of rs2346018 and hypomethylation (<40%) on the VTRNA2-1 promoter, the OR increased to 4.048 (95% CI 1.438 to 11.389, p=0.007). CONCLUSIONS The glycemic response to GLP-1 analog treatment is associated with the methylation status of the VTRNA2-1 promoter and polymorphism of rs2346018.
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Affiliation(s)
- Chia-Hung Lin
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yun-Shien Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou Main Branch, Taoyuan, Taiwan
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan
| | - Yu-Yao Huang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
- Department of Surgery, New Taipei Municipal Tucheng Hospital, New Taipei City, Taiwan
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96
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Whalley C, Payne K, Domingo E, Blake A, Richman S, Brooks J, Batis N, Spruce R, Mehanna H, Nankivell P, Beggs AD. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA. EPIGENOMES 2021; 5:6. [PMID: 33777442 PMCID: PMC7610445 DOI: 10.3390/epigenomes5010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/06/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022] Open
Abstract
Abnormal CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide coverage. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA is challenging at the genome-wide level because of lack of available input. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples. METHODS For all experiments, the Infinium HD assay for methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50 ng); eighteen blood derived specimens (lowest input 10 ng) and six matched ctDNA input (lowest input 10 ng)/fresh tumour specimens (lowest input 250 ng) were processed. Downstream analysis was performed in R/Bioconductor for quality control metrics and differential methylation analysis as well as copy number calls. RESULTS Correlation coefficients for CpG methylation were high at the probe level averaged R2 = 0.99 for blood derived samples and R2 > 0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared, R2 > 0.91 between the two. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample with good concordance via DQ plot. CONCLUSIONS The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to an input of 10 ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA. These findings demonstrate that these samples can now be accessed by methylation array technology, allowing analysis of these important sample types.
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Affiliation(s)
- Celina Whalley
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Karl Payne
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Enric Domingo
- Department of Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (E.D.); (A.B.)
| | - Andrew Blake
- Department of Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (E.D.); (A.B.)
| | - Susan Richman
- Pathology and Data Analytics, Leeds Institute of Medical Research, St James University Hospital, Leeds LS2 9JT, UK;
| | - Jill Brooks
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Nikolaos Batis
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Rachel Spruce
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | | | - Hisham Mehanna
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Paul Nankivell
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Andrew D. Beggs
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
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97
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Kashima K, Kawai T, Nishimura R, Shiwa Y, Urayama KY, Kamura H, Takeda K, Aoto S, Ito A, Matsubara K, Nagamatsu T, Fujii T, Omori I, Shimizu M, Hyodo H, Kugu K, Matsumoto K, Shimizu A, Oka A, Mizuguchi M, Nakabayashi K, Hata K, Takahashi N. Identification of epigenetic memory candidates associated with gestational age at birth through analysis of methylome and transcriptional data. Sci Rep 2021; 11:3381. [PMID: 33564054 PMCID: PMC7873311 DOI: 10.1038/s41598-021-83016-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/28/2021] [Indexed: 11/09/2022] Open
Abstract
Preterm birth is known to be associated with chronic disease risk in adulthood whereby epigenetic memory may play a mechanistic role in disease susceptibility. Gestational age (GA) is the most important prognostic factor for preterm infants, and numerous DNA methylation alterations associated with GA have been revealed by epigenome-wide association studies. However, in human preterm infants, whether the methylation changes relate to transcription in the fetal state and persist after birth remains to be elucidated. Here, we identified 461 transcripts associated with GA (range 23-41 weeks) and 2093 candidate CpG sites for GA-involved epigenetic memory through analysis of methylome (110 cord blood and 47 postnatal blood) and transcriptional data (55 cord blood). Moreover, we discovered the trends of chromatin state, such as polycomb-binding, among these candidate sites. Fifty-four memory candidate sites showed correlation between methylation and transcription, and the representative corresponding gene was UCN, which encodes urocortin.
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Affiliation(s)
- Kohei Kashima
- Department of Pediatrics, The University of Tokyo Hospital, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. .,Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Riki Nishimura
- Department of Pediatrics, The University of Tokyo Hospital, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yuh Shiwa
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Iwate, Japan
| | - Kevin Y Urayama
- Department of Social Medicine, National Research Institute for Child Health and Development, Tokyo, Japan.,Graduate School of Public Health, St. Luke's International University, Tokyo, Japan
| | - Hiromi Kamura
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazue Takeda
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Saki Aoto
- Medical Genome Center, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Ito
- Department of Pediatrics, The University of Tokyo Hospital, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takeshi Nagamatsu
- Department of Obstetrics and Gynecology, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomoyuki Fujii
- Department of Obstetrics and Gynecology, The University of Tokyo Hospital, Tokyo, Japan
| | - Isaku Omori
- Department of Neonatology, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Mitsumasa Shimizu
- Department of Neonatology, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Hironobu Hyodo
- Department of Obstetrics and Gynecology, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Koji Kugu
- Department of Obstetrics and Gynecology, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Iwate, Japan.,Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Iwate, Japan
| | - Akira Oka
- Department of Pediatrics, The University of Tokyo Hospital, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Masashi Mizuguchi
- Department of Developmental Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Naoto Takahashi
- Department of Pediatrics, The University of Tokyo Hospital, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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98
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Fathi E, Farahzadi R, Montazersaheb S, Bagheri Y. Epigenetic Modifications in Acute Lymphoblastic Leukemia: From Cellular Mechanisms to Therapeutics. Curr Gene Ther 2021; 21:60-71. [PMID: 33183201 DOI: 10.2174/1566523220999201111194554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Epigenetic modification pattern is considered as a characteristic feature in blood malignancies. Modifications in the DNA methylation modulators are recurrent in lymphoma and leukemia, so that the distinct methylation pattern defines different types of leukemia. Generally, the role of epigenetics is less understood, and most investigations are focused on genetic abnormalities and cytogenic studies to develop novel treatments for patients with hematologic disorders. Recently, understanding the underlying mechanism of acute lymphoblastic leukemia (ALL), especially epigenetic alterations as a driving force in the development of ALL opens a new era of investigation for developing promising strategy, beyond available conventional therapy. OBJECTIVE This review will focus on a better understanding of the epigenetic mechanisms in cancer development and progression, with an emphasis on epigenetic alterations in ALL including, DNA methylation, histone modification, and microRNA alterations. Other topics that will be discussed include the use of epigenetic alterations as a promising therapeutic target in order to develop novel, well-suited approaches against ALL. CONCLUSION According to the literature review, leukemogenesis of ALL is extensively influenced by epigenetic modifications, particularly DNA hyper-methylation, histone modification, and miRNA alteration.
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Affiliation(s)
- Ezzatollah Fathi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Raheleh Farahzadi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yasin Bagheri
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
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99
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Lakis V, Lawlor RT, Newell F, Patch AM, Mafficini A, Sadanandam A, Koufariotis LT, Johnston RL, Leonard C, Wood S, Rusev B, Corbo V, Luchini C, Cingarlini S, Landoni L, Salvia R, Milella M, Chang D, Bailey P, Jamieson NB, Duthie F, Gingras MC, Muzny DM, Wheeler DA, Gibbs RA, Milione M, Pederzoli P, Samra JS, Gill AJ, Johns AL, Pearson JV, Biankin AV, Grimmond SM, Waddell N, Nones K, Scarpa A. DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association. Commun Biol 2021; 4:155. [PMID: 33536587 PMCID: PMC7859232 DOI: 10.1038/s42003-020-01469-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Here we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX, DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent loss of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs.
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Affiliation(s)
- Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rita T Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrea Mafficini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Rebecca L Johnston
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Borislav Rusev
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
| | - Vincenzo Corbo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Sara Cingarlini
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - David Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Baden-Württemberg, Germany
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, UK
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of Pathology, Queen Elizabeth University Hospital, Greater Glasgow & Clyde NHS, Glasgow, G51 4TF, UK
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Michael E. DeBakey Department of Surgery and The Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030-3411, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas, 77030-3411, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Massimo Milione
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | | | | | - Anthony J Gill
- University of Sydney, Sydney, New South Wales, 2006, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - Amber L Johns
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, New South Wales, 2010, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, Victoria, 3000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, Queensland, 4006, Australia.
| | - Aldo Scarpa
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, 37134, Italy.
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.
- ENETS Center of Excellence, University and Hospital Trust of Verona, Verona, Italy.
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100
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Zhao Y, Wang P, Zhou Y, Xia B, Zhu Q, Ge W, Li J, Shi H, Xiao X, Zhang Y. Prenatal fine particulate matter exposure, placental DNA methylation changes, and fetal growth. ENVIRONMENT INTERNATIONAL 2021; 147:106313. [PMID: 33341587 DOI: 10.1016/j.envint.2020.106313] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/26/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
This study was designed to examine the impact of prenatal fine particulate matter (PM2.5) exposure on fetal growth and the underlying placental epigenetic mechanism in a cohort of Chinese women. Within the prospective Shanghai Mother-Child Pairs cohort (Shanghai MCPC), 329 women carrying singleton pregnancy with a due date in 2018 were recruited between 2017 and 2018. Maternal PM2.5 exposure levels were estimated using gestational exposure prediction model combining satellite-driven ambient concentrations and personal air sampling. Fetal growth characteristics were evaluated by prenatal ultrasound examinations and anthropometric measurements at birth. In a discovery phase, whole-genome DNA methylation analysis was performed using the Infinium 850 K array. In a validation phase, placental DNA methylation was measured using bisulfite pyrosequencing for five candidate genes that showed the most significant alterations and function relevance in our methylation array screen, including BID (BH3 interacting domain death agonist), FOXN3 (Forkhead box N3), FOXP1 (Forkhead box P1), IGF2 (Insulin-like growth factor 2) and HSD11B2 (Hydroxysteroid 11-beta dehydrogenase 2). Multivariate linear regression models were applied to examine the associations among PM2.5 exposure, fetal growth characteristics and DNA methylation on placental candidate genes. Sobel tests were used to evaluate the mediating role of DNA methylation in multivariable models. After excluding women who withdrew or failed to provide placenta, a total of 287 pregnant women with an average age of 30 entered the final analysis. Increased PM2.5 exposure was significantly associated with reduced biparietal diameter (BPD) (β: -0.136 mm, 95% CI: -0.228 to -0.043), head circumference (HC) (β: -0.462 mm, 95% CI: -0.782 to -0.142), femur length (FL) (β: -0.113 mm, 95% CI: -0.185 to -0.041) and abdominal circumference (AC) (β: -0.371 mm, 95% CI: -0.672 to -0.071) in the second trimester and birth length (β: -0.013 cm, 95% CI: -0.025 to -0.001). Prenatal PM2.5 exposure could lead to aberrant changes in DNA methylation profile of placenta genome, which were mainly enriched in reproductive development, energy metabolism and immune response. DNA methylation of IGF2 and BID showed significant associations with PM2.5 exposures during all exposure windows. In addition, BID methylation was negatively correlated with HC (β: -1.396 mm, 95% CI: -2.582 to -0.209) and BPD (β: -0.330 mm, 95% CI: -0.635 to -0.026) in the second trimester. Further mediation analysis indicated that BID methylation mediated about 30% of the effects of PM2.5 exposure on HC. These findings collectively suggested that prenatal PM2.5 exposure may cause adverse effects on fetal growth by modifying placental DNA methylation.
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Affiliation(s)
- Yingya Zhao
- Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China (Fudan University), China; Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China
| | - Pengpeng Wang
- Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China
| | - Yuhan Zhou
- Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China
| | - Bin Xia
- Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China (Fudan University), China
| | - Qingyang Zhu
- Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China (Fudan University), China
| | - Wenzhen Ge
- Regeneron Pharmaceuticals Inc., New York, NY, USA
| | - Jialin Li
- Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China
| | - Huijing Shi
- Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China (Fudan University), China; Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China
| | - Xirong Xiao
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200032, China.
| | - Yunhui Zhang
- Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China (Fudan University), China; Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China.
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