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Hernangomez-Laderas A, Cilleros-Portet A, Martínez Velasco S, Marí S, Legarda M, González-García BP, Tutau C, García-Santisteban I, Irastorza I, Fernandez-Jimenez N, Bilbao JR. Sex bias in celiac disease: XWAS and monocyte eQTLs in women identify TMEM187 as a functional candidate gene. Biol Sex Differ 2023; 14:86. [PMID: 38072919 PMCID: PMC10712119 DOI: 10.1186/s13293-023-00572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Celiac disease (CeD) is an immune-mediated disorder that develops in genetically predisposed individuals upon gluten consumption. HLA risk alleles explain 40% of the genetic component of CeD, so there have been continuing efforts to uncover non-HLA loci that can explain the remaining heritability. As in most autoimmune disorders, the prevalence of CeD is significantly higher in women. Here, we investigated the possible involvement of the X chromosome on the sex bias of CeD. METHODS We performed a X chromosome-wide association study (XWAS) and a gene-based association study in women from the CeD Immunochip (7062 cases, 5446 controls). We also constructed a database of X chromosome cis-expression quantitative trait loci (eQTLs) in monocytes from unstimulated (n = 226) and lipopolysaccharide (LPS)-stimulated (n = 130) female donors and performed a Summary-data-based MR (SMR) analysis to integrate XWAS and eQTL information. We interrogated the expression of the potentially causal gene (TMEM187) in peripheral blood mononuclear cells (PBMCs) from celiac patients at onset, on a gluten-free diet, potential celiac patients and non-celiac controls. RESULTS The XWAS and gene-based analyses identified 13 SNPs and 25 genes, respectively, 22 of which had not been previously associated with CeD. The X chromosome cis-eQTL analysis found 18 genes with at least one cis-eQTL in naïve female monocytes and 8 genes in LPS-stimulated female monocytes, 2 of which were common to both situations and 6 were unique to LPS stimulation. SMR identified a potentially causal association of TMEM187 expression in naïve monocytes with CeD in women, regulated by CeD-associated, eQTL-SNPs rs7350355 and rs5945386. The CeD-risk alleles were correlated with lower TMEM187 expression. These results were replicated using eQTLs from LPS-stimulated monocytes. We observed higher levels of TMEM187 expression in PBMCs from female CeD patients at onset compared to female non-celiac controls, but not in male CeD individuals. CONCLUSION Using X chromosome genotypes and gene expression data from female monocytes, SMR has identified TMEM187 as a potentially causal candidate in CeD. Further studies are needed to understand the implication of the X chromosome in the higher prevalence of CeD in women.
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Affiliation(s)
- Alba Hernangomez-Laderas
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Silvia Martínez Velasco
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - María Legarda
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Bárbara Paola González-García
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Carlos Tutau
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Iñaki Irastorza
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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Soler-Blasco R, Llop S, Riutort-Mayol G, Lozano M, Vallejo-Ortega J, Murcia M, Ballester F, Irizar A, Andiarena A, Fernandez-Jimenez N, Braeuer S, Harari F. Genetic Susceptibility to Neurotoxicity Related to Prenatal Inorganic Arsenic Exposure in Young Spanish Children. Environ Sci Technol 2023; 57:15366-15378. [PMID: 37787746 DOI: 10.1021/acs.est.3c03336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
We explored the influence of child and maternal single nucleotide polymorphisms (SNPs) in genes related to neurological function and arsenic metabolism (i.e., ABCA1, ABCB1, PON1, CYP3A, BDNF, GSTP1, MT2A, and APOE as well as AS3MT) on the association between prenatal arsenic (As) exposure and methylation efficiency and neuropsychological development in 4-5-year-old children. Participants were 549 mother-child pairs from the INMA (Environment and Childhood) Spanish Project. We measured inorganic arsenic (iAs) and the metabolites monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA) in urine samples collected during pregnancy. Neuropsychological development was assessed at the age of 4-5 years using the McCarthy Scales of Children's Abilities (MSCA). Several SNPs were determined in maternal and child DNA; AS3MT and APOE haplotypes were inferred. The median ∑As (sum of iAs, DMA, and MMA) was 7.08 μg/g creatinine. Statistically significant interactions for children's APOE haplotype were observed. Specifically, ε4-carrier children had consistently lower MSCA scores in several scales with increasing ∑As and MMA concentrations. These results provide evidence regarding the neurotoxic effects of early life exposure to As, observing that the APOE ε4 allele could make children more vulnerable to this exposure.
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Affiliation(s)
- Raquel Soler-Blasco
- Department of Nursing, Universitat de València, 46010 Valencia, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, 46020 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Sabrina Llop
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, 46020 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Gabriel Riutort-Mayol
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, 46020 Valencia, Spain
| | - Manuel Lozano
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, 46020 Valencia, Spain
- Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, 46010 Valencia, Spain
| | - Jorge Vallejo-Ortega
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, 46020 Valencia, Spain
| | - Mario Murcia
- Health Policy Planning and Evaluation Service, Conselleria de Sanitat Universal i Salut Pública, Generalitat Valenciana, 46010 Valencia, Spain
| | - Ferran Ballester
- Department of Nursing, Universitat de València, 46010 Valencia, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, 46020 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Amaia Irizar
- Biodonostia Health Research Institute, 20014 San Sebastian, Spain
- Department of Preventive Medicine and Public Health of the University of the Basque Country, UPV/EHU, 48940 Leioa, Spain
| | - Ainara Andiarena
- Biodonostia Health Research Institute, 20014 San Sebastian, Spain
- Faculty of Psychology, University of the Basque Country, UPV/EHU, 20018 San Sebastian, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), 48903 Leioa, Spain
| | - Simone Braeuer
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, Vienna 1090, Austria
- Institute of Chemistry, University of Graz, 8010 Graz, Austria
| | - Florencia Harari
- Occupational and Environmental Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, 40530 Gothenburg, Sweden
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Badia-Bringué G, Canive M, Fernandez-Jimenez N, Lavín JL, Casais R, Blanco-Vázquez C, Vázquez P, Fernández A, Bilbao JR, Garrido JM, Juste RA, González-Recio O, Alonso-Hearn M. Summary-data based Mendelian randomization identifies gene expression regulatory polymorphisms associated with bovine paratuberculosis by modulation of the nuclear factor Kappa β (NF-κß)-mediated inflammatory response. BMC Genomics 2023; 24:605. [PMID: 37821814 PMCID: PMC10568764 DOI: 10.1186/s12864-023-09710-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified host genetic variants associated with paratuberculosis (PTB) susceptibility. Most of the GWAS-identified SNPs are in non-coding regions. Connecting these non-coding variants and downstream affected genes is a challenge and, up to date, only a few functional mutations or expression quantitative loci (cis-eQTLs) associated with PTB susceptibility have been identified. In the current study, the associations between imputed whole-genome sequence genotypes and whole RNA-Sequencing data from peripheral blood (PB) and ileocecal valve (ICV) samples of Spanish Holstein cows (N = 16) were analyzed with TensorQTL. This approach allowed the identification of 88 and 37 cis-eQTLs regulating the expression levels of 90 and 37 genes in PB and ICV samples, respectively (False discorey rate, FDR ≤ 0.05). Next, we applied summary-based data Mendelian randomization (SMR) to integrate the cis-eQTL dataset with GWAS data obtained from a cohort of 813 culled cattle that were classified according to the presence or absence of PTB-associated histopathological lesions in gut tissues. After multiple testing corrections (FDR ≤ 0.05), we identified two novel cis-eQTLs affecting the expression of the early growth response factor 4 (EGR4) and the bovine neuroblastoma breakpoint family member 6-like protein isoform 2 (MGC134040) that showed pleiotropic associations with the presence of multifocal and diffuse lesions in gut tissues; P = 0.002 and P = 0.017, respectively. While EGR4 acts as a brake on T-cell proliferation and cytokine production through interaction with the nuclear factor Kappa β (NF-κß), MGC134040 is a target gene of NF-κß. Our findings provide a better understanding of the genetic factors influencing PTB outcomes, confirm that the multifocal lesions are localized/confined lesions that have different underlying host genetics than the diffuse lesions, and highlight regulatory SNPs and regulated-gene targets to design future functional studies.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
- Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - Maria Canive
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - José Luis Lavín
- Department of Applied Mathematics, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Rosa Casais
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Cristina Blanco-Vázquez
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Jose Ramón Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - Joseba M Garrido
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ramón A Juste
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.
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González-García BP, Marí S, Cilleros-Portet A, Hernangomez-Laderas A, Fernandez-Jimenez N, García-Santisteban I, Bilbao JR. Two-Sample Mendelian Randomization detects bidirectional causality between gut microbiota and celiac disease in individuals with high genetic risk. Front Immunol 2023; 14:1082862. [PMID: 37457693 PMCID: PMC10347381 DOI: 10.3389/fimmu.2023.1082862] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Background Celiac Disease (CeD) is an autoimmune disorder triggered by gluten intake in genetically susceptible individuals. Highest risk individuals are homozygous for the Human Leucocyte Antigen (HLA) DQ2.5 haplotype or DQ2.5/DQ2.2 heterozygous. Both the HLA-DQ2-positive high genetic risk individuals and those that have developed the disease have altered intestinal microbiota, but it remains unclear whether these alterations are a cause or a consequence of CeD. Objective To investigate a potential bidirectional causality between gut microbiota (GM) and CeD in HLA-DQ2 high genetic risk individuals. Materials and Methods We performed a bidirectional Two-Sample Mendelian Randomization (2SMR) test using summary statistics from the largest publicly available Genome-Wide Association Study (GWAS) of GM and the summary statistics of the Immunochip CeD study of those individuals with the HLA-DQ2 high-risk haplotype. To test whether changes in GM composition were causally linked to CeD, GM data were used as exposure and CeD data as outcome; to test for reverse causation, the exposure and outcome datasets were inverted. Results We identified several bacteria from Ruminococcaceae and Lachnospiraceae families of the Firmicutes phylum as potentially causal in both directions. In addition, our results suggest that changes in the abundance of Veillonellaceae family might be causal in the development of CeD, while alterations in Pasteurellaceae family might be a consequence of the disease itself. Conclusion Our results suggest that the relationship between GM and HLA-DQ2 high risk individuals is highly complex and bidirectional.
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Affiliation(s)
- Bárbara P. González-García
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces Bizkaia Health Research Institute, Leioa, Spain
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces Bizkaia Health Research Institute, Leioa, Spain
| | - Alba Hernangomez-Laderas
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces Bizkaia Health Research Institute, Leioa, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces Bizkaia Health Research Institute, Leioa, Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces Bizkaia Health Research Institute, Leioa, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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5
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Cilleros-Portet A, Lesseur C, Marí S, Cosin-Tomas M, Lozano M, Irizar A, Burt A, García-Santisteban I, Martín DG, Escaramís G, Hernangomez-Laderas A, Soler-Blasco R, Breeze CE, Gonzalez-Garcia BP, Santa-Marina L, Chen J, Llop S, Fernández MF, Vrijhed M, Ibarluzea J, Guxens M, Marsit C, Bustamante M, Bilbao JR, Fernandez-Jimenez N. Potentially causal associations between placental DNA methylation and schizophrenia and other neuropsychiatric disorders. medRxiv 2023:2023.03.07.23286905. [PMID: 36945560 PMCID: PMC10029044 DOI: 10.1101/2023.03.07.23286905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Increasing evidence supports the role of placenta in neurodevelopment and potentially, in the later onset of neuropsychiatric disorders. Recently, methylation quantitative trait loci (mQTL) and interaction QTL (iQTL) maps have proven useful to understand SNP-genome wide association study (GWAS) relationships, otherwise missed by conventional expression QTLs. In this context, we propose that part of the genetic predisposition to complex neuropsychiatric disorders acts through placental DNA methylation (DNAm). We constructed the first public placental cis-mQTL database including nearly eight million mQTLs calculated in 368 fetal placenta DNA samples from the INMA project, ran cell type- and gestational age-imQTL models and combined those data with the summary statistics of the largest GWAS on 10 neuropsychiatric disorders using Summary-based Mendelian Randomization (SMR) and colocalization. Finally, we evaluated the influence of the DNAm sites identified on placental gene expression in the RICHS cohort. We found that placental cis-mQTLs are highly enriched in placenta-specific active chromatin regions, and useful to map the etiology of neuropsychiatric disorders at prenatal stages. Specifically, part of the genetic burden for schizophrenia, bipolar disorder and major depressive disorder confers risk through placental DNAm. The potential causality of several of the observed associations is reinforced by secondary association signals identified in conditional analyses, regional pleiotropic methylation signals associated to the same disorder, and cell type-imQTLs, additionally associated to the expression levels of relevant immune genes in placenta. In conclusion, the genetic risk of several neuropsychiatric disorders could operate, at least in part, through DNAm and associated gene expression in placenta.
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Affiliation(s)
- Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Marta Cosin-Tomas
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Lozano
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de Valéncia, Valencia, Spain
- Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain
| | - Amaia Irizar
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Department of Preventive Medicine and Public Health, University of the Basque Country (UPV/EHU), Leioa, Spain
- Biodonostia Health Research Institute, 20013, San Sebastian, Spain
| | - Amber Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Diego Garrido Martín
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona (UB), 08028 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Geòrgia Escaramís
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Casanova 143, Barcelona, Spain
| | - Alba Hernangomez-Laderas
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Raquel Soler-Blasco
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de Valéncia, Valencia, Spain
- Department of Nursing, Universitat de València, Valencia, Spain
| | - Charles E. Breeze
- UCL Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, United Kingdom
| | - Bárbara P. Gonzalez-Garcia
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Loreto Santa-Marina
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Biodonostia Health Research Institute, 20013, San Sebastian, Spain
- Department of Health of the Basque Government, Subdirectorate of Public Health of Gipuzkoa, Avenida Navarra 4, 20013, San Sebastian, Spain
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina Llop
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de Valéncia, Valencia, Spain
| | - Mariana F. Fernández
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Biomedical Research Center (CIBM) & Department of Radiology and Physical Medicine, School of Medicine University of Granada, 18016 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Martine Vrijhed
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jesús Ibarluzea
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Biodonostia Health Research Institute, 20013, San Sebastian, Spain
- Department of Health of the Basque Government, Subdirectorate of Public Health of Gipuzkoa, Avenida Navarra 4, 20013, San Sebastian, Spain
| | - Mònica Guxens
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - Carmen Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), Leioa, Spain
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Fernandez-Jimenez N, Fore R, Cilleros-Portet A, Lepeule J, Perron P, Kvist T, Tian FY, Lesseur C, Binder AM, Lozano M, Martorell-Marugán J, Loke YJ, Bakulski KM, Zhu Y, Forhan A, Sammallahti S, Everson TM, Chen J, Michels KB, Belmonte T, Carmona-Sáez P, Halliday J, Daniele Fallin M, LaSalle JM, Tost J, Czamara D, Fernández MF, Gómez-Martín A, Craig JM, Gonzalez-Alzaga B, Schmidt RJ, Dou JF, Muggli E, Lacasaña M, Vrijheid M, Marsit CJ, Karagas MR, Räikkönen K, Bouchard L, Heude B, Santa-Marina L, Bustamante M, Hivert MF, Bilbao JR. A meta-analysis of pre-pregnancy maternal body mass index and placental DNA methylation identifies 27 CpG sites with implications for mother-child health. Commun Biol 2022; 5:1313. [PMID: 36446949 PMCID: PMC9709064 DOI: 10.1038/s42003-022-04267-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
Higher maternal pre-pregnancy body mass index (ppBMI) is associated with increased neonatal morbidity, as well as with pregnancy complications and metabolic outcomes in offspring later in life. The placenta is a key organ in fetal development and has been proposed to act as a mediator between the mother and different health outcomes in children. The overall aim of the present work is to investigate the association of ppBMI with epigenome-wide placental DNA methylation (DNAm) in 10 studies from the PACE consortium, amounting to 2631 mother-child pairs. We identify 27 CpG sites at which we observe placental DNAm variations of up to 2.0% per 10 ppBMI-unit. The CpGs that are differentially methylated in placenta do not overlap with CpGs identified in previous studies in cord blood DNAm related to ppBMI. Many of the identified CpGs are located in open sea regions, are often close to obesity-related genes such as GPX1 and LGR4 and altogether, are enriched in cancer and oxidative stress pathways. Our findings suggest that placental DNAm could be one of the mechanisms by which maternal obesity is associated with metabolic health outcomes in newborns and children, although further studies will be needed in order to corroborate these findings.
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Affiliation(s)
- Nora Fernandez-Jimenez
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country Spain
| | - Ruby Fore
- grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Ariadna Cilleros-Portet
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country Spain
| | - Johanna Lepeule
- grid.418110.d0000 0004 0642 0153University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, Grenoble, France
| | - Patrice Perron
- grid.411172.00000 0001 0081 2808Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC Canada
| | - Tuomas Kvist
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Fu-Ying Tian
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA USA
| | - Corina Lesseur
- grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Alexandra M. Binder
- grid.410445.00000 0001 2188 0957Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA ,grid.19006.3e0000 0000 9632 6718Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA USA
| | - Manuel Lozano
- grid.5338.d0000 0001 2173 938XEpidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain ,grid.5338.d0000 0001 2173 938XPreventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain
| | - Jordi Martorell-Marugán
- grid.4489.10000000121678994Department of Statistics and Operations Research, University of Granada, Granada, Spain ,grid.4489.10000000121678994Bioinformatics Unit. GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Yuk J. Loke
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Kelly M. Bakulski
- grid.214458.e0000000086837370Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Yihui Zhu
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA USA
| | - Anne Forhan
- grid.508487.60000 0004 7885 7602Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Sara Sammallahti
- grid.5645.2000000040459992XDepartment of Child and Adolescent Psychiatry and Psychology, Erasmus MC Rotterdam, The Netherlands
| | - Todd M. Everson
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Epidemiology, Rollins School of Public health at Emory University, Atlanta, GA USA
| | - Jia Chen
- grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Karin B. Michels
- grid.19006.3e0000 0000 9632 6718Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA USA ,grid.5963.9Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Thalia Belmonte
- grid.411342.10000 0004 1771 1175Health Research Institute of Asturias, ISPA and Biomedical Research and Innovation Institute of Cadiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cadiz, Spain
| | - Pedro Carmona-Sáez
- grid.4489.10000000121678994Department of Statistics and Operations Research, University of Granada, Granada, Spain ,grid.4489.10000000121678994Bioinformatics Unit. GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jane Halliday
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - M. Daniele Fallin
- grid.21107.350000 0001 2171 9311Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Janine M. LaSalle
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA USA
| | - Jorg Tost
- grid.418135.a0000 0004 0641 3404Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Darina Czamara
- grid.419548.50000 0000 9497 5095Max-Planck-Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Mariana F. Fernández
- grid.4489.10000000121678994University of Granada, Center for Biomedical Research (CIBM), Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antonio Gómez-Martín
- grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.413740.50000 0001 2186 2871Andalusian School of Public Health (EASP), Granada, Spain
| | - Jeffrey M. Craig
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1021.20000 0001 0526 7079Deakin University, IMPACT – the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Beatriz Gonzalez-Alzaga
- grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.413740.50000 0001 2186 2871Andalusian School of Public Health (EASP), Granada, Spain
| | - Rebecca J. Schmidt
- grid.27860.3b0000 0004 1936 9684Department of Public Health Sciences and the MIND Institute, University of California Davis School of Medicine, Davis, CA USA
| | - John F. Dou
- grid.214458.e0000000086837370Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Evelyne Muggli
- grid.1058.c0000 0000 9442 535XMurdoch Children’s Research Institute, Parkville, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Marina Lacasaña
- grid.507088.2Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain ,grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.413740.50000 0001 2186 2871Andalusian School of Public Health (EASP), Granada, Spain
| | - Martine Vrijheid
- grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.434607.20000 0004 1763 3517ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmen J. Marsit
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Epidemiology, Rollins School of Public health at Emory University, Atlanta, GA USA
| | - Margaret R. Karagas
- grid.86715.3d0000 0000 9064 6198Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, QC Canada
| | - Katri Räikkönen
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Luigi Bouchard
- grid.86715.3d0000 0000 9064 6198Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, QC Canada ,grid.459278.50000 0004 4910 4652Department of Laboratory Medicine, CIUSSS du Saguenay–Lac-St-Jean – Hôpital Universitaire de Chicoutimi, Chicoutimi, QC Canada
| | - Barbara Heude
- grid.508487.60000 0004 7885 7602Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Loreto Santa-Marina
- grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.432380.eBiodonostia, Epidemiology and Public Health Area, Environmental Epidemiology and Child Development Group, 20014 San Sebastian, Basque Country Spain ,Health Department of Basque Government, Sub-directorate of Public Health of Gipuzkoa, San Sebastian, Basque Country Spain
| | - Mariona Bustamante
- grid.466571.70000 0004 1756 6246CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain ,grid.434607.20000 0004 1763 3517ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marie-France Hivert
- grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA USA ,grid.411172.00000 0001 0081 2808Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC Canada ,grid.32224.350000 0004 0386 9924Diabetes Unit, Massachusetts General Hospital, Boston, MA USA
| | - Jose Ramon Bilbao
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country Spain ,grid.512890.7CIBER of diabetes and associated metabolic disorders (CIBERDEM), Madrid, Spain
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Cosin-Tomas M, Cilleros-Portet A, Aguilar-Lacasaña S, Fernandez-Jimenez N, Bustamante M. Prenatal Maternal Smoke, DNA Methylation, and Multi-omics of Tissues and Child Health. Curr Environ Health Rep 2022; 9:502-512. [PMID: 35670920 PMCID: PMC9363403 DOI: 10.1007/s40572-022-00361-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Maternal tobacco smoking during pregnancy is of public health concern, and understanding the biological mechanisms can help to promote smoking cessation campaigns. This non-systematic review focuses on the effects of maternal smoking during pregnancy on offspring's epigenome, consistent in chemical modifications of the genome that regulate gene expression. RECENT FINDINGS Recent meta-analyses of epigenome-wide association studies have shown that maternal smoking during pregnancy is consistently associated with offspring's DNA methylation changes, both in the placenta and blood. These studies indicate that effects on blood DNA methylation can persist for years, and that the longer the duration of the exposure and the higher the dose, the larger the effects. Hence, DNA methylation scores have been developed to estimate past exposure to maternal smoking during pregnancy as biomarkers. There is robust evidence for DNA methylation alterations associated with maternal smoking during pregnancy; however, the role of sex, ethnicity, and genetic background needs further exploration. Moreover, there are no conclusive studies about exposure to low doses or during the preconception period. Similarly, studies on tissues other than the placenta and blood are scarce, and cell-type specificity within tissues needs further investigation. In addition, biological interpretation of DNA methylation findings requires multi-omics data, poorly available in epidemiological settings. Finally, although several mediation analyses link DNA methylation changes with health outcomes, they do not allow causal inference. For this, a combination of data from multiple study designs will be essential in the future to better address this topic.
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Affiliation(s)
- Marta Cosin-Tomas
- ISGlobal, Institute for Global Health, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,CIBER Epidemiología Y Salud Pública, Madrid, Spain.
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Sofía Aguilar-Lacasaña
- ISGlobal, Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología Y Salud Pública, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología Y Salud Pública, Madrid, Spain
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8
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Sarzo B, Ballesteros V, Iñiguez C, Manzano-Salgado CB, Casas M, Llop S, Murcia M, Guxens M, Vrijheid M, Santa Marina L, Schettgen T, Espada M, Irizar A, Fernandez-Jimenez N, Ballester F, Lopez-Espinosa MJ. Response to "Comment on Maternal Perfluoroalkyl Substances, Thyroid Hormones, and DIO Genes: A Spanish Cross-sectional Study: Predictability of Multiple Imputations for Large Amounts of Missing Data". Environ Sci Technol 2022; 56:5278-5282. [PMID: 35263543 DOI: 10.1021/acs.est.2c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Blanca Sarzo
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-Universitat de València, 46020, València, Spain
- Department of Microbiology and Ecology, University of Valencia, 46019, Burjasot, Spain
- School of Mathematics, University of Edinburgh, EH9 3FD, Edinburgh, U.K
| | - Virginia Ballesteros
- Andalusian Health and Environment Observatory (OSMAN), Andalusian School of Public Health, 18011, Granada, Spain
| | - Carmen Iñiguez
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-Universitat de València, 46020, València, Spain
- Department of Statistics and Operational Research, University of Valencia, 46100, Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | | | - Maribel Casas
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- ISGlobal, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Sabrina Llop
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-Universitat de València, 46020, València, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Mario Murcia
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-Universitat de València, 46020, València, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Health Information Systems Analysis Service, Conselleria de Sanitat, Generalitat Valenciana, 46010, Valencia, Spain
| | - Mónica Guxens
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- ISGlobal, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Martine Vrijheid
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- ISGlobal, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Loreto Santa Marina
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Department of Health of the Basque Government, Subdirectorate of Public Health of Gipuzkoa, 20013, Donostia-San Sebastian, Spain
- Biodonostia Health Research Institute, Environmental Epidemiology and Child Development Group, 20014, Donostia-San Sebastian, Spain
| | - Thomas Schettgen
- Institute for Occupational, Social and Environmental Medicine, RWTH Aachen University, 52074, Aachen, Germany
| | - Mercedes Espada
- Clinical Chemistry Unit, Public Health Laboratory of Bilbao, 48160, Bilbao, Spain
| | - Amaia Irizar
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Biodonostia Health Research Institute, Environmental Epidemiology and Child Development Group, 20014, Donostia-San Sebastian, Spain
- Department of Preventive Medicine and Public Health, University of the Basque Country (UPV-EHU), 20018, San Sebastian, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Ferran Ballester
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-Universitat de València, 46020, València, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Faculty of Nursing and Chiropody, University of Valencia, 46010, Valencia, Spain
| | - Maria-Jose Lopez-Espinosa
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-Universitat de València, 46020, València, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Faculty of Nursing and Chiropody, University of Valencia, 46010, Valencia, Spain
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Canive M, Fernandez-Jimenez N, Casais R, Vázquez P, Lavín JL, Bilbao JR, Blanco-Vázquez C, Garrido JM, Juste RA, Alonso-Hearn M. Author Correction: Identification of loci associated with susceptibility to bovine paratuberculosis and with the dysregulation of the MECOM, eEF1A2, and U1 spliceosomal RNA expression. Sci Rep 2021; 11:21337. [PMID: 34697373 PMCID: PMC8546122 DOI: 10.1038/s41598-021-00840-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Maria Canive
- Department of Animal Health, NEIKER- Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.,Doctoral Program in Immunology, Microbiology and Parasitology, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - Rosa Casais
- SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Grupo NySA, Deva, Asturias, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER- Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.,SALUVET‑Innova S.L., Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - José Luis Lavín
- Department of Applied Mathematics, NEIKER-Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - José Ramón Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - Cristina Blanco-Vázquez
- SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Grupo NySA, Deva, Asturias, Spain
| | - Joseba M Garrido
- Department of Animal Health, NEIKER- Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ramón A Juste
- Department of Animal Health, NEIKER- Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER- Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.
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Olaechea-Lázaro S, García-Santisteban I, Pineda JR, Badiola I, Alonso S, Bilbao JR, Fernandez-Jimenez N. shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study. BMC Bioinformatics 2021; 22:476. [PMID: 34602053 PMCID: PMC8487674 DOI: 10.1186/s12859-021-04392-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Quantitative, reverse transcription PCR (qRT-PCR) is currently the gold-standard for SARS-CoV-2 detection and it is also used for detection of other virus. Manual data analysis of a small number of qRT-PCR plates per day is a relatively simple task, but automated, integrative strategies are needed if a laboratory is dealing with hundreds of plates per day, as is being the case in the COVID-19 pandemic. RESULTS Here we present shinyCurves, an online shiny-based, free software to analyze qRT-PCR amplification data from multi-plate and multi-platform formats. Our shiny application does not require any programming experience and is able to call samples Positive, Negative or Undetermined for viral infection according to a number of user-defined settings, apart from providing a complete set of melting and amplification curve plots for the visual inspection of results. CONCLUSIONS shinyCurves is a flexible, integrative and user-friendly software that speeds-up the analysis of massive qRT-PCR data from different sources, with the possibility of automatically producing and evaluating melting and amplification curve plots.
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Affiliation(s)
- S Olaechea-Lázaro
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
| | - I García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
- Biocruces-Bizkaia Health Research Institute, Plaza de Cruces, 48903, Barakaldo, Spain
| | - J R Pineda
- Achucarro Basque Center for Neuroscience, Barrio Sarriena s/n, 48940, Leioa, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
| | - I Badiola
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
| | - S Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
- Biocruces-Bizkaia Health Research Institute, Plaza de Cruces, 48903, Barakaldo, Spain.
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
- Biocruces-Bizkaia Health Research Institute, Plaza de Cruces, 48903, Barakaldo, Spain.
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11
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Everson TM, Vives-Usano M, Seyve E, Cardenas A, Lacasaña M, Craig JM, Lesseur C, Baker ER, Fernandez-Jimenez N, Heude B, Perron P, Gónzalez-Alzaga B, Halliday J, Deyssenroth MA, Karagas MR, Íñiguez C, Bouchard L, Carmona-Sáez P, Loke YJ, Hao K, Belmonte T, Charles MA, Martorell-Marugán J, Muggli E, Chen J, Fernández MF, Tost J, Gómez-Martín A, London SJ, Sunyer J, Marsit CJ, Lepeule J, Hivert MF, Bustamante M. Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth. Nat Commun 2021; 12:5095. [PMID: 34429407 PMCID: PMC8384884 DOI: 10.1038/s41467-021-24558-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Maternal smoking during pregnancy (MSDP) contributes to poor birth outcomes, in part through disrupted placental functions, which may be reflected in the placental epigenome. Here we present a meta-analysis of the associations between MSDP and placental DNA methylation (DNAm) and between DNAm and birth outcomes within the Pregnancy And Childhood Epigenetics (PACE) consortium (N = 1700, 344 with MSDP). We identify 443 CpGs that are associated with MSDP, of which 142 associated with birth outcomes, 40 associated with gene expression, and 13 CpGs are associated with all three. Only two CpGs have consistent associations from a prior meta-analysis of cord blood DNAm, demonstrating substantial tissue-specific responses to MSDP. The placental MSDP-associated CpGs are enriched for environmental response genes, growth-factor signaling, and inflammation, which play important roles in placental function. We demonstrate links between placental DNAm, MSDP and poor birth outcomes, which may better inform the mechanisms through which MSDP impacts placental function and fetal growth.
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Affiliation(s)
- Todd M Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA.
| | - Marta Vives-Usano
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Emie Seyve
- University Grenoble Alpes, Inserm, CNRS, IAB, Grenoble, France
| | - Andres Cardenas
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Marina Lacasaña
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Andalusian School of Public Health, Granada, Spain
- Instituto de Investigación Biosantaria (ibs.GRANADA), Granada, Spain
| | - Jeffrey M Craig
- Epigenetics Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- IMPACT - the Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily R Baker
- Department of Obstetrics & Gynecology, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Nora Fernandez-Jimenez
- University of the Basque Country (UPV/EHU), Leioa, Spain
- Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
- Public Health Division of Gipuzkoa, Basque Government, San Sebastian, Spain
| | - Barbara Heude
- Université de Paris, CRESS, INSERM, INRAE, Paris, France
| | - Patrice Perron
- Department of Medicine, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Beatriz Gónzalez-Alzaga
- Andalusian School of Public Health, Granada, Spain
- Instituto de Investigación Biosantaria (ibs.GRANADA), Granada, Spain
| | - Jane Halliday
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Reproductive Epidemiology, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Maya A Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Carmen Íñiguez
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Statistics and Computational Research, Universitat de València, València, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Pedro Carmona-Sáez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Statistics, Faculty of Sciences, University of Granada, Granada, Spain
| | - Yuk J Loke
- Epigenetics Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Jordi Martorell-Marugán
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Atrys Health S.A., Barcelona, Spain
| | - Evelyne Muggli
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Reproductive Epidemiology, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mariana F Fernández
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Instituto de Investigación Biosantaria (ibs.GRANADA), Granada, Spain
- Biomedical Research Centre (CIBM) and School of Medicine, University of Granada, Granada, Spain
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Evry, France
| | - Antonio Gómez-Martín
- Genomics Unit, GENYO. Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC, USA
| | - Jordi Sunyer
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public health at Emory University, Atlanta, GA, USA
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, IAB, Grenoble, France
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mariona Bustamante
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.
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12
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Sarzo B, Ballesteros V, Iñiguez C, Manzano-Salgado CB, Casas M, Llop S, Murcia M, Guxens M, Vrijheid M, Marina LS, Schettgen T, Espada M, Irizar A, Fernandez-Jimenez N, Ballester F, Lopez-Espinosa MJ. Maternal Perfluoroalkyl Substances, Thyroid Hormones, and DIO Genes: A Spanish Cross-sectional Study. Environ Sci Technol 2021; 55:11144-11154. [PMID: 34314170 DOI: 10.1021/acs.est.1c01452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Results of studies on perfluoroalkyl substances (PFASs) and thyroid hormones (THs) are heterogeneous, and the mechanisms underlying the action of PFASs to target THs have not been fully characterized. We examined the relation between first-trimester maternal PFAS and TH levels and the role played by polymorphisms in the iodothyronine deiodinase 1 (DIO1) and 2 (DIO2) genes in this association. Our sample comprised 919 pregnant Spanish women (recruitment = 2003-2008) with measurements of perfluorohexanesulfonic acid (PFHxS), perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), perfluorononanoic acid (PFNA), thyroid-stimulating hormone (TSH), total triiodothyronine (TT3), and free thyroxine (FT4), and we genotyped for single-nucleotide polymorphisms in the DIO1 (rs2235544) and DIO2 (rs12885300) genes. We performed multivariate regression analyses between PFASs and THs and included the interaction term PFAS-genotypes in the models. PFHxS was associated with an increase in TSH (% change in outcome [95% CI] per 2-fold PFAS increase = 6.09 [-0.71, 13.4]), and PFOA and PFNA were associated with a decrease in TT3 (-7.17 [-13.5, -0.39] and -6.28 [-12.3, 0.12], respectively). We found stronger associations between PFOA, PFNA, and TT3 for DIO1-CC and DIO2-CT genotypes, although interaction p-values were not significant. In conclusion, this study found evidence of an inverse association between PFOA and TT3 levels. No clear effect modification by DIO enzyme genes was observed.
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Affiliation(s)
- Blanca Sarzo
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-University of Valencia, 46019 Valencia, Spain
| | - Virginia Ballesteros
- Andalusian Health and Environment Observatory (OSMAN), Andalusian School of Public Health, 18011 Granada, Spain
| | - Carmen Iñiguez
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-University of Valencia, 46019 Valencia, Spain
- Department of Statistics and Operational Research, University of Valencia, 46100 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | | | - Maribel Casas
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- ISGlobal, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Sabrina Llop
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-University of Valencia, 46019 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Mario Murcia
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-University of Valencia, 46019 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Health Information Systems Analysis Service, Conselleria de Sanitat, Generalitat Valenciana, 46010 Valencia, Spain
| | - Mònica Guxens
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- ISGlobal, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Martine Vrijheid
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- ISGlobal, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Loreto Santa Marina
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Health of the Basque Government, Subdirectorate of Public Health of Gipuzkoa, 20013 Donostia-San Sebastian, Spain
- Biodonostia Health Research Institute, Environmental Epidemiology and Child Development Group, 20014 Donostia-San Sebastian, Spain
| | - Thomas Schettgen
- Institute for Occupational, Social and Environmental Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Mercedes Espada
- Clinical Chemistry Unit, Public Health Laboratory of Bilbao, 8160 Bilbao, Spain
| | - Amaia Irizar
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Biodonostia Health Research Institute, Environmental Epidemiology and Child Development Group, 20014 Donostia-San Sebastian, Spain
- Department of Preventive Medicine and Public Health, University of the Basque Country (UPV-EHU), 20018 San Sebastian, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, Biocruces-Bizkaia Health Research Institute and University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Ferran Ballester
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-University of Valencia, 46019 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Faculty of Nursing and Chiropody, University of Valencia, 46010 Valencia, Spain
| | - Maria-Jose Lopez-Espinosa
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-University Jaume I-University of Valencia, 46019 Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Faculty of Nursing and Chiropody, University of Valencia, 46010 Valencia, Spain
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13
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Rueda-Martínez A, Garitazelaia A, Cilleros-Portet A, Marí S, Arauzo R, de Miguel J, González-García BP, Fernandez-Jimenez N, Bilbao JR, García-Santisteban I. Genetic Contribution of Endometriosis to the Risk of Developing Hormone-Related Cancers. Int J Mol Sci 2021; 22:6083. [PMID: 34199930 PMCID: PMC8200110 DOI: 10.3390/ijms22116083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/02/2021] [Indexed: 01/10/2023] Open
Abstract
Endometriosis is a common gynecological disorder that has been associated with endometrial, breast and epithelial ovarian cancers in epidemiological studies. Since complex diseases are a result of multiple environmental and genetic factors, we hypothesized that the biological mechanism underlying their comorbidity might be explained, at least in part, by shared genetics. To assess their potential genetic relationship, we performed a two-sample mendelian randomization (2SMR) analysis on results from public genome-wide association studies (GWAS). This analysis confirmed previously reported genetic pleiotropy between endometriosis and endometrial cancer. We present robust evidence supporting a causal genetic association between endometriosis and ovarian cancer, particularly with the clear cell and endometrioid subtypes. Our study also identified genetic variants that could explain those associations, opening the door to further functional experiments. Overall, this work demonstrates the value of genomic analyses to support epidemiological data, and to identify targets of relevance in multiple disorders.
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Affiliation(s)
- Aintzane Rueda-Martínez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Aiara Garitazelaia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Rebeca Arauzo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Jokin de Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Bárbara P. González-García
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, 48940 Leioa, Spain; (A.R.-M.); (A.G.); (A.C.-P.); (S.M.); (R.A.); (J.d.M.); (B.P.G.-G.); (N.F.-J.); (J.R.B.)
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14
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Sebastian-delaCruz M, Olazagoitia-Garmendia A, Huerta Madrigal A, Garcia-Etxebarria K, Mendoza L, Fernandez-Jimenez N, Garcia Casales Z, de la Calle Navarro E, Calvo A, Legarda M, Tutau C, Irastorza I, Bujanda L, Bilbao J, Castellanos-Rubio A. A Novel Noninvasive Method Based on Salivary Inflammatory Biomarkers for the Screening of Celiac Disease. Cell Mol Gastroenterol Hepatol 2021; 12:1511-1513.e2. [PMID: 34062280 PMCID: PMC8531944 DOI: 10.1016/j.jcmgh.2021.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 12/10/2022]
Affiliation(s)
- M. Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - A. Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | | | - K. Garcia-Etxebarria
- Biodonostia, Gastrointestinal Genetics Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, San Sebastian, Spain
| | - L.M. Mendoza
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - N. Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | | | | | - A.E. Calvo
- Hospital de Txagorritxu, Vitoria-Gasteiz, Spain
| | - M. Legarda
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Pediatrics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - C. Tutau
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Pediatrics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - I. Irastorza
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Pediatrics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - L. Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Universidad del País Vasco, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, San Sebastian, Spain
| | - J.R. Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain
| | - A. Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Gastroenterology, Biodonostia Health Research Institute, Universidad del País Vasco, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, San Sebastian, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain,Corresponding author: Ainara Castellanos-Rubio, PhD, Department of Genetics, Physical Anthropology and Animal Physiology Maria Goyri building, Lab 1.11 University of the Basque Country (UPV/EHU) Leioa, 48940, Spain
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15
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García-Santisteban I, Romero-Garmendia I, Cilleros-Portet A, Bilbao JR, Fernandez-Jimenez N. Celiac disease susceptibility: The genome and beyond. Int Rev Cell Mol Biol 2020; 358:1-45. [PMID: 33707051 DOI: 10.1016/bs.ircmb.2020.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Celiac Disease (CeD) is an immune-mediated complex disease that is triggered by the ingestion of gluten and develops in genetically susceptible individuals. It has been known for a long time that the Human Leucocyte Antigen (HLA) molecules DQ2 and DQ8 are necessary, although not sufficient, for the disease development, and therefore other susceptibility genes and (epi)genetic events must participate in CeD pathogenesis. The advances in Genomics during the last 15 years have made CeD one of the immune-related disorders with the best-characterized genetic component. In the present work, we will first review the main Genome-Wide Association Studies (GWAS) carried out in the disorder, and emphasize post-GWAS discoveries, including diverse integrative strategies, SNP prioritization approaches, and insights into the Microbiome through the host Genomics. Second, we will explore CeD-related Epigenetics and Epigenomics, mostly focusing on the emerging knowledge of the celiac methylome, and the vast but yet under-explored non-coding RNA (ncRNA) landscape. We conclude that much has been done in the field although there are still completely unvisited areas in the post-Genomics of CeD. Chromatin conformation and accessibility, and Epitranscriptomics are promising domains that need to be unveiled to complete the big picture of the celiac Genome.
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Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain; Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders, CIBERDEM, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain.
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16
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Agliata I, Fernandez-Jimenez N, Goldsmith C, Marie JC, Bilbao JR, Dante R, Hernandez-Vargas H. The DNA methylome of inflammatory bowel disease (IBD) reflects intrinsic and extrinsic factors in intestinal mucosal cells. Epigenetics 2020; 15:1068-1082. [PMID: 32281463 PMCID: PMC7518701 DOI: 10.1080/15592294.2020.1748916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abnormal DNA methylation has been described in human inflammatory conditions of the gastrointestinal tract, such as inflammatory bowel disease (IBD). As other complex diseases, IBD results from the balance between genetic predisposition and environmental exposures. As such, DNA methylation may be the consequence (and potential effector) of both, genetic susceptibility variants and/or environmental signals such as cytokine exposure. We attempted to discern between these two non-excluding possibilities by performing a combined analysis of published DNA methylation data in intestinal mucosal cells of IBD and control samples. We identified abnormal DNA methylation at different levels: deviation from mean methylation signals at site and region levels, and differential variability. A fraction of such changes is associated with genetic polymorphisms linked to IBD susceptibility. In addition, by comparing with another intestinal inflammatory condition (i.e., coeliac disease) we propose that aberrant DNA methylation can also be the result of unspecific processes such as chronic inflammation. Our characterization suggests that IBD methylomes combine intrinsic and extrinsic responses in intestinal mucosal cells, and could point to knowledge-based biomarkers of IBD detection and progression.
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Affiliation(s)
- Iolanda Agliata
- Department of Medicine and Health Sciences, University of Molise , Campobasso, Italy
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa, Spain
| | - Chloe Goldsmith
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France
| | - Julien C Marie
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France
| | - Jose R Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa, Spain.,Ciber de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) , Madrid, Spain
| | - Robert Dante
- Department of Signaling of Tumoral Escape, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon , Lyon, France
| | - Hector Hernandez-Vargas
- Department of Immunity, Virus and Inflammation, Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard , Lyon, France.,Department of Translational Research and Innovation, Centre Léon Bérard , Lyon, France
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17
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Fernandez-Jimenez N, Bilbao JR. Mendelian randomization analysis of celiac GWAS reveals a blood expression signature with diagnostic potential in absence of gluten consumption. Hum Mol Genet 2020; 28:3037-3042. [PMID: 31127932 PMCID: PMC6737291 DOI: 10.1093/hmg/ddz113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/10/2019] [Accepted: 05/20/2019] [Indexed: 12/26/2022] Open
Abstract
Celiac disease (CeD) is an immune-mediated enteropathy with a strong genetic component where the main environmental trigger is dietary gluten, and currently a correct diagnosis of the disease is impossible if gluten-free diet (GFD) has already been started. We hypothesized that merging different levels of genomic information through Mendelian randomization (MR) could help discover genetic biomarkers useful for CeD diagnosis. MR was performed using public databases of expression quantitative trait loci (QTL) and methylation QTL as exposures and the largest CeD genome-wide association study conducted to date as the outcome, in order to identify potential causal genes. As a result, we identified UBE2L3, an ubiquitin ligase located in a CeD-associated region. We interrogated the expression of UBE2L3 in an independent data set of peripheral blood mononuclear cells (PBMCs) and found that its expression is altered in CeD patients on GFD when compared to non-celiac controls. The relative expression of UBE2L3 isoforms predicts CeD with 100% specificity and sensitivity and could be used as a diagnostic marker, especially in the absence of gluten consumption. This approach could be applicable to other diseases where diagnosis of asymptomatic patients can be complicated.
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Affiliation(s)
- Nora Fernandez-Jimenez
- University of the Basque Country (UPV/EHU), BioCruces-Bizkaia Health Research Institute, Leioa, Basque Country, Spain
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV/EHU), BioCruces-Bizkaia Health Research Institute, Leioa, Basque Country, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) Madrid, Spain
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18
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Koroknai V, Szász I, Hernandez-Vargas H, Fernandez-Jimenez N, Cuenin C, Herceg Z, Vízkeleti L, Ádány R, Ecsedi S, Balázs M. DNA hypermethylation is associated with invasive phenotype of malignant melanoma. Exp Dermatol 2020; 29:39-50. [PMID: 31602702 DOI: 10.1111/exd.14047] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/29/2019] [Accepted: 10/06/2019] [Indexed: 01/01/2023]
Abstract
Tumor cell invasion is one of the key processes during cancer progression, leading to life-threatening metastatic lesions in melanoma. As methylation of cancer-related genes plays a fundamental role during tumorigenesis and may lead to cellular plasticity which promotes invasion, our aim was to identify novel epigenetic markers on selected invasive melanoma cells. Using Illumina BeadChip assays and Affymetrix Human Gene 1.0 microarrays, we explored the DNA methylation landscape of selected invasive melanoma cells and examined the impact of DNA methylation on gene expression patterns. Our data revealed predominantly hypermethylated genes in the invasive cells affecting the neural crest differentiation pathway and regulation of the actin cytoskeleton. Integrative analysis of the methylation and gene expression profiles resulted in a cohort of hypermethylated genes (IL12RB2, LYPD6B, CHL1, SLC9A3, BAALC, FAM213A, SORCS1, GPR158, FBN1 and ADORA2B) with decreased expression. On the other hand, hypermethylation in the gene body of the EGFR and RBP4 genes was positively correlated with overexpression of the genes. We identified several methylation changes that can have role during melanoma progression, including hypermethylation of the promoter regions of the ARHGAP22 and NAV2 genes that are commonly altered in locally invasive primary melanomas as well as during metastasis. Interestingly, the down-regulation of the methylcytosine dioxygenase TET2 gene, which regulates DNA methylation, was associated with hypermethylated promoter region of the gene. This can probably lead to the observed global hypermethylation pattern of invasive cells and might be one of the key changes during the development of malignant melanoma cells.
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Affiliation(s)
- Viktória Koroknai
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - István Szász
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | | | | | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Laura Vízkeleti
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Róza Ádány
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Szilvia Ecsedi
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Margit Balázs
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
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Patil V, Cuenin C, Chung F, Aguilera JR, Fernandez-Jimenez N, Romero-Garmendia I, Bilbao JR, Cahais V, Rothwell J, Herceg Z. Human mitochondrial DNA is extensively methylated in a non-CpG context. Nucleic Acids Res 2019; 47:10072-10085. [PMID: 31665742 PMCID: PMC6821263 DOI: 10.1093/nar/gkz762] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowly methylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.
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Affiliation(s)
- Vibha Patil
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Felicia Chung
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | | | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country 48940, Spain
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Joseph Rothwell
- Nutritional Epidemiology Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon Cedex 08, France
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20
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Ochoa E, Zuber V, Fernandez-Jimenez N, Bilbao JR, Clark GR, Maher ER, Bottolo L. MethylCal: Bayesian calibration of methylation levels. Nucleic Acids Res 2019; 47:e81. [PMID: 31049595 PMCID: PMC6698668 DOI: 10.1093/nar/gkz325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/24/2019] [Accepted: 04/20/2019] [Indexed: 12/16/2022] Open
Abstract
Bisulfite amplicon sequencing has become the primary choice for single-base methylation quantification of multiple targets in parallel. The main limitation of this technology is a preferential amplification of an allele and strand in the PCR due to methylation state. This effect, known as 'PCR bias', causes inaccurate estimation of the methylation levels and calibration methods based on standard controls have been proposed to correct for it. Here, we present a Bayesian calibration tool, MethylCal, which can analyse jointly all CpGs within a CpG island (CGI) or a Differentially Methylated Region (DMR), avoiding 'one-at-a-time' CpG calibration. This enables more precise modeling of the methylation levels observed in the standard controls. It also provides accurate predictions of the methylation levels not considered in the controlled experiment, a feature that is paramount in the derivation of the corrected methylation degree. We tested the proposed method on eight independent assays (two CpG islands and six imprinting DMRs) and demonstrated its benefits, including the ability to detect outliers. We also evaluated MethylCal's calibration in two practical cases, a clinical diagnostic test on 18 patients potentially affected by Beckwith-Wiedemann syndrome, and 17 individuals with celiac disease. The calibration of the methylation levels obtained by MethylCal allows a clearer identification of patients undergoing loss or gain of methylation in borderline cases and could influence further clinical or treatment decisions.
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Affiliation(s)
- Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Verena Zuber
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
- CIBERDEM Diabetes and Associated Metabolic Diseases, Spain
| | - Graeme R Clark
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
- The Alan Turing Institute, London NW1 2DB, UK
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21
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Cielo D, Galatola M, Fernandez-Jimenez N, De Leo L, Garcia-Etxebarria K, Loganes C, Tommasini A, Not T, Auricchio R, Greco L, Bilbao JR. Combined Analysis of Methylation and Gene Expression Profiles in Separate Compartments of Small Bowel Mucosa Identified Celiac Disease Patients' Signatures. Sci Rep 2019; 9:10020. [PMID: 31292504 PMCID: PMC6620355 DOI: 10.1038/s41598-019-46468-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/14/2019] [Indexed: 02/07/2023] Open
Abstract
By GWAS studies on celiac disease, gene expression was studied at the level of the whole intestinal mucosa, composed by two different compartments: epithelium and lamina propria. Our aim is to analyse the gene-expression and DNA methylation of candidate genes in each of these compartments. Epithelium was separated from lamina propria in biopsies of CeD patients and CTRs using magnetic beads. Gene-expression was analysed by RT-PC; methylation analysis required bisulfite conversion and NGS. Reverse modulation of gene-expression and methylation in the same cellular compartment was observed for the IL21 and SH2B3 genes in CeD patients relative to CTRs. Bioinformatics analysis highlighted the regulatory elements in the genomic region of SH2B3 that altered methylation levels. The cREL and TNFAIP3 genes showed methylation patterns that were significantly different between CeD patients and CTRs. In CeD, the genes linked to inflammatory processes are up-regulated, whereas the genes involved in the cell adhesion/integrity of the intestinal barrier are down-regulated. These findings suggest a correlation between gene-expression and methylation profile for the IL21 and SH2B3 genes. We identified a “gene-expression phenotype” of CeD and showed that the abnormal response to dietary antigens in CeD might be related not to abnormalities of gene structure but to the regulation of molecular pathways.
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Affiliation(s)
- D Cielo
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - M Galatola
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy. .,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy.
| | - N Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - L De Leo
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - K Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - C Loganes
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - A Tommasini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - T Not
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain.,Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - R Auricchio
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - L Greco
- Department of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Naples, Italy
| | - J R Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
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Fernandez-Jimenez N, Allard C, Bouchard L, Perron P, Bustamante M, Bilbao JR, Hivert MF. Comparison of Illumina 450K and EPIC arrays in placental DNA methylation. Epigenetics 2019; 14:1177-1182. [PMID: 31250700 DOI: 10.1080/15592294.2019.1634975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Illumina HumanMethylation450 BeadChip (450K) has been commonly used to investigate DNA methylation in human tissues. Recently, it has been replaced by Illumina HumanMethylationEPIC BeadChip (EPIC) covering over 850,000 CpGs distributed genome-wide. Many consortia have now datasets coming from both arrays and aspire to analyze the two together. The placenta shows a high number of intermediate methylation levels and is often investigated for obstetric/birth outcomes, and potentially for long-term programming in offspring. We performed a systematic comparison between the two arrays using 108 duplicate placental samples from Gen3G birth cohort. We find that placenta shows a high per-sample correlation between the arrays, and higher median correlations at individual CpGs than those reported for blood. We identify 26,340 probes with absolute difference in per cent methylation >10%. We conclude that EPIC and 450K placental data can be combined, and we provide two lists of CpGs that should be excluded to avoid misleading results.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa , Spain
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS) , Sherbrooke , Canada
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS) , Sherbrooke , Canada.,Department of Biochemistry, Faculty of medicine and life sciences, Université de Sherbrooke , Sherbrooke , Canada.,Department of Medical Biology, CIUSSS Saguenay-Lac-Saint-Jean - Hôpital de Chicoutimi , Saguenay , Canada
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS) , Sherbrooke , Canada.,Department of Medicine, Faculty of Medicine and Life Sciences, Université de Sherbrooke , Sherbrooke , Canada
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health , Barcelona , Spain.,University Pompeu Fabra (UPF) , Barcelona , Spain.,CIBER of Epidemiology and Public Health (CIBERESP) , Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute , Leioa , Spain.,CIBER of diabetes and associated metabolic disorders (CIBERDEM) , Madrid , Spain
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS) , Sherbrooke , Canada.,Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School , Boston , USA.,Diabetes Unit, Massachusetts General Hospital , Boston , MA , USA
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23
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Fernandez-Jimenez N, Garcia-Etxebarria K, Plaza-Izurieta L, Romero-Garmendia I, Jauregi-Miguel A, Legarda M, Ecsedi S, Castellanos-Rubio A, Cahais V, Cuenin C, Degli Esposti D, Irastorza I, Hernandez-Vargas H, Herceg Z, Bilbao JR. The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region. Sci Rep 2019; 9:1298. [PMID: 30718669 PMCID: PMC6362130 DOI: 10.1038/s41598-018-37746-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022] Open
Abstract
The Human Leucocyte Antigen (HLA) locus and other DNA sequence variants identified in Genome-Wide Association (GWA) studies explain around 50% of the heritability of celiac disease (CD). However, the pathogenesis of CD could be driven by other layers of genomic information independent from sequence variation, such as DNA methylation, and it is possible that allele-specific methylation explains part of the SNP associations. Since the DNA methylation landscape is expected to be different among cell types, we analyzed the methylome of the epithelial and immune cell populations of duodenal biopsies in CD patients and controls separately. We found a cell type-specific methylation signature that includes genes mapping to the HLA region, namely TAP1 and HLA-B. We also performed Immunochip SNP genotyping of the same samples and interrogated the expression of some of the affected genes. Our analysis revealed that the epithelial methylome is characterized by the loss of CpG island (CGI) boundaries, often associated to altered gene expression, and by the increased variability of the methylation across the samples. The overlap between differentially methylated positions (DMPs) and CD-associated SNPs or variants contributing to methylation quantitative trait loci (mQTLs) is minimal. In contrast, there is a notable enrichment of mQTLs among the most significant CD-associated SNPs. Our results support the notion that DNA methylation alterations constitute a genotype-independent event and confirm its role in the HLA region (apart from the well-known, DQ allele-specific effect). Finally, we find that a fraction of the CD-associated variants could exert its phenotypic effect through DNA methylation.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Koldo Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, Donostia, Basque Country, Spain
| | - Leticia Plaza-Izurieta
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Amaia Jauregi-Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, 48903, Spain
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Universite Côte d'Azur, INSERM, CNRS, iBV, Nice, France
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain
- Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Irstea - Laboratoire d'écotoxicologie, UR "Milieux aquatiques, écologie et pollutions", Villeurbanne, France
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, 48903, Spain
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
- Department of Immunology, Virology and Inflammation; TGF beta and Immune Evasion Group; Cancer Research Center of Lyon; INSERM, CNRS, Centre Léon Bérard Hospital, Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, Lyon, France
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Basque Country, 48940, Spain.
- Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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Woo HD, Fernandez-Jimenez N, Ghantous A, Degli Esposti D, Cuenin C, Cahais V, Choi IJ, Kim YI, Kim J, Herceg Z. Genome-wide profiling of normal gastric mucosa identifies Helicobacter pylori- and cancer-associated DNA methylome changes. Int J Cancer 2018; 143:597-609. [PMID: 29574700 DOI: 10.1002/ijc.31381] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/12/2018] [Accepted: 03/02/2018] [Indexed: 12/11/2022]
Abstract
The large geographic variations in the incidence of gastric cancer (GC) are likely due to differential environmental exposures, in particular to Helicobacter pylori (H. pylori) infection. We aimed to investigate the impact of H. pylori on the epigenome in normal gastric mucosa and methylation changes associated with cancer risk independent of H. pylori. A discovery set of normal gastric mucosa from GC cases (n = 42) and controls (n = 42), nested in a large case-control study and stratified by H. pylori status, were subjected to genome-wide methylation profiling. Single-nucleotide polymorphism arrays from peripheral blood leukocytes were used to conduct methylation quantitative trait loci (mQTL) analysis. A validation set of gastric mucosa samples (n = 180) was used in the replication phase. We found 1,924 differentially methylated positions (DMPs) and 438 differentially methylated regions (DMRs) associated with H. pylori infection, most of which were hypermethylated. Significant methylation alterations identified in the initial set were successfully replicated. Furthermore, the H. pylori-associated DMP/Rs showed marked stability ('epigenetic memory') after H. pylori clearance. Interestingly, we found 152 DMRs associated with cancer risk independent of the H. pylori status in normal gastric mucosa. The methylation score derived from three biomarkers was a strong predictor of GC. Finally, the mQTL analysis indicated that the H. pylori- and cancer-specific methylation signatures were minimally affected by genetic variation. The comprehensively characterized methylome changes associated with H. pylori infection and GC risk in our study might serve as potential biomarkers for early cancer progression in tumour-free gastric mucosa.
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Affiliation(s)
- Hae Dong Woo
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, 69372, France
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, 69372, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, 69372, France
| | - Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, 69372, France
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, 69372, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, 69372, France
| | - Il Ju Choi
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Young-Il Kim
- Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, 69372, France
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Romero-Garmendia I, Garcia-Etxebarria K, Hernandez-Vargas H, Santin I, Jauregi-Miguel A, Plaza-Izurieta L, Cros MP, Legarda M, Irastorza I, Herceg Z, Fernandez-Jimenez N, Bilbao JR. Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease. Genes (Basel) 2018; 9:E245. [PMID: 29748492 PMCID: PMC5977185 DOI: 10.3390/genes9050245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.
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Affiliation(s)
- Irati Romero-Garmendia
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Koldo Garcia-Etxebarria
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Izortze Santin
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
| | - Amaia Jauregi-Miguel
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Leticia Plaza-Izurieta
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Nora Fernandez-Jimenez
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
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26
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Fernandez-Jimenez N, Sklias A, Ecsedi S, Cahais V, Degli-Esposti D, Jay A, Ancey PB, Woo HD, Hernandez-Vargas H, Herceg Z. Lowly methylated region analysis identifies EBF1 as a potential epigenetic modifier in breast cancer. Epigenetics 2017; 12:964-972. [PMID: 29099283 PMCID: PMC5788421 DOI: 10.1080/15592294.2017.1373919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/21/2017] [Accepted: 08/28/2017] [Indexed: 01/03/2023] Open
Abstract
Breast cancer (BC) encompasses heterogeneous pathologies with different subtypes exhibiting distinct molecular changes, including those related to DNA methylation. However, the role of these changes in mediating BC heterogeneity is poorly understood. Lowly methylated regions (LMRs), non-CpG island loci that usually contain transcription factor (TF) binding sites, have been suggested to act as regulatory elements that define cellular identity. In this study, we aimed to identify the key subtype-specific TFs that may lead to LMR generation and shape the BC methylome and transcription program. We initially used whole-genome bisulfite sequencing (WGBS) data available at The Cancer Genome Atlas (TCGA) portal to identify subtype-specific LMRs. Differentially methylated regions (DMRs) within the BC PAM50 subtype-specific LMRs were selected by comparing tumors and normal tissues in a larger TCGA cohort assessed by HumanMethylation450 BeadChip (450K) arrays and TF enrichment analyses were performed. To assess the impact of LMRs on gene expression, TCGA RNA sequencing data were downloaded and Pearson correlations between methylation levels of loci presenting subtype-specific TF motifs and expression of the nearest genes were calculated. WGBS methylome data revealed a large number of LMRs for each of the BC subtypes. Analysis of these LMRs in the 450K datasets available for a larger sample set identified 7,765, 5,657, and 19 differentially methylated positions (DMPs) between normal adjacent tissues and tumor tissues from basal, luminal, and HER2-enriched subtypes, respectively. Unsupervised clustering showed that the discriminatory power of the top DMPs was remarkably strong for basal BC. Interestingly, in this particular subtype, we found 4,409 differentially hypomethylated positions grouped into 1,185 DMRs with a strong enrichment for the early B-cell factor 1 (EBF1) motifs. The methylation levels of the DMRs containing EBF1 motifs showed a strong negative correlation with the expression of 719 nearby genes, including BTS2 and CD74, two oncogenes known to be specific for basal BC subtype and for poor outcome. This study identifies LMRs specific to the three main BC subtypes and reveals EBF1 as a potentially important regulator of BC subtype-specific methylation and gene expression program.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Athena Sklias
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Davide Degli-Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Antonin Jay
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Pierre Benoit Ancey
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Hae Dong Woo
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon Cedex 08, France
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Degli Esposti D, Sklias A, Lima SC, Beghelli-de la Forest Divonne S, Cahais V, Fernandez-Jimenez N, Cros MP, Ecsedi S, Cuenin C, Bouaoun L, Byrnes G, Accardi R, Sudaka A, Giordanengo V, Hernandez-Vargas H, Pinto LFR, Van Obberghen-Schilling E, Herceg Z. Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas. Genome Med 2017; 9:33. [PMID: 28381277 PMCID: PMC5382363 DOI: 10.1186/s13073-017-0419-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/24/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermethylation in HPV(+) oropharyngeal cancers, but only few consistent target genes have been so far described, and the evidence of a functional impact on gene expression is still limited. METHODS We performed global and stratified pooled analyses of epigenome-wide data in HNSCCs based on the Illumina HumanMethylation450 bead-array data in order to identify tissue-specific components and common viral epigenetic targets in HPV-associated tumours. RESULTS We identified novel differentially methylated CpGs and regions associated with viral infection that are independent of the anatomic site. In particular, most hypomethylated regions were characterized by a marked loss of CpG island boundaries, which showed significant correlations with expression of neighbouring genes. Moreover, a subset of only five CpGs in a few hypomethylated regions predicted HPV status with a high level of specificity in different cohorts. Finally, this signature was a better predictor of survival compared with HPV status determined by viral gene expression by RNA sequencing in The Cancer Genome Atlas cohort. CONCLUSIONS We identified a novel epigenetic signature of HPV infection in HNSCCs which is independent of the anatomic site, is functionally correlated with gene expression and may be leveraged for improved stratification of prognosis in HNSCCs.
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Affiliation(s)
- Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France.
| | - Athena Sklias
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Sheila C Lima
- Instituto Nacional de Cancer, Rio de Janeiro, Brazil
| | | | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Nora Fernandez-Jimenez
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
- MTA-DE Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Liacine Bouaoun
- Environment Section, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Graham Byrnes
- Environment Section, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Rosita Accardi
- Infection Cancer Biology Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Anne Sudaka
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose (iBV), 06100, Nice, France
- Centre Antoine Lacassagne, Nice, 06189, France
| | - Valérie Giordanengo
- Université Côte d'Azur, Laboratoire de Virologie, CHU Nice-Archet, 06202, Nice, France
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | | | - Ellen Van Obberghen-Schilling
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose (iBV), 06100, Nice, France.
- Centre Antoine Lacassagne, Nice, 06189, France.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France.
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28
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Esposti DD, Hernandez-Vargas H, Voegele C, Fernandez-Jimenez N, Forey N, Bancel B, Calvez-Kelm FL, McKay J, Merle P, Herceg Z. Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing. Oncotarget 2016; 7:31862-77. [PMID: 26887054 PMCID: PMC5077982 DOI: 10.18632/oncotarget.7364] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/20/2016] [Indexed: 12/27/2022] Open
Abstract
Functional characterization of long non-coding RNAs (lncRNAs) and their pathological relevance is still a challenging task. Abnormal expression of a few long non-coding RNAs have been found associated with hepatocellular carcinoma, with potential implications to both improve our understanding of molecular mechanism of liver carcinogenesis and to discover biomarkers for early diagnosis or therapy. However, the understanding of the global role of lncRNAs during HCC development is still in its infancy. In this study, we produced RNA-Seq data from 23 liver tissues (controls, cirrhotic and HCCs) and applied statistical and gene network analysis approaches to identify and characterize expressed lncRNAs. We detected 5,525 lncRNAs across different tissue types and identified 57 differentially expressed lncRNAs in HCC compared with adjacent non-tumour tissues using stringent criteria (FDR<0.05, Fold Change>2). Using weighted gene co-expression network analysis (WGCNA), we found that differentially expressed lncRNAs are co-expressed with genes involved in cell cycle regulation, TGF-β signalling and liver metabolism. Furthermore, we found that more than 20% of differentially expressed lncRNAs are associated to actively transcribed enhancers and that the co-expression patterns with their closest genes change dramatically during HCC development. Our study provides the most comprehensive compendium of lncRNAs expressed in HCC, as well as in control or cirrhotic livers. Our results identified both known oncogenic lncRNAs (such as H19 and CRNDE) and novel lncRNAs involved in cell cycle deregulation and liver metabolism deficits occurring during HCC development.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Male
- Middle Aged
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Sequence Analysis, RNA
- Signal Transduction
- Transcriptome
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Affiliation(s)
- Davide Degli Esposti
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Catherine Voegele
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Nathalie Forey
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Brigitte Bancel
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex, France
- Hospices Civils de Lyon, Service d'Anatomopathologie, Groupement Hospitalier Lyon Nord, Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - James McKay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Philippe Merle
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex, France
- Hospices Civils de Lyon, Service d'Hépatologie et de Gastroentérologie, Groupement Hospitalier Lyon Nord, Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
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29
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Castellanos-Rubio A, Fernandez-Jimenez N, Kratchmarov R, Luo X, Bhagat G, Green PHR, Schneider R, Kiledjian M, Bilbao JR, Ghosh S. A long noncoding RNA associated with susceptibility to celiac disease. Science 2016; 352:91-5. [PMID: 27034373 DOI: 10.1126/science.aad0467] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/18/2016] [Indexed: 12/15/2022]
Abstract
Recent studies have implicated long noncoding RNAs (lncRNAs) as regulators of many important biological processes. Here we report on the identification and characterization of a lncRNA, lnc13, that harbors a celiac disease-associated haplotype block and represses expression of certain inflammatory genes under homeostatic conditions. Lnc13 regulates gene expression by binding to hnRNPD, a member of a family of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). Upon stimulation, lnc13 levels are reduced, thereby allowing increased expression of the repressed genes. Lnc13 levels are significantly decreased in small intestinal biopsy samples from patients with celiac disease, which suggests that down-regulation of lnc13 may contribute to the inflammation seen in this disease. Furthermore, the lnc13 disease-associated variant binds hnRNPD less efficiently than its wild-type counterpart, thus helping to explain how these single-nucleotide polymorphisms contribute to celiac disease.
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Affiliation(s)
- Ainara Castellanos-Rubio
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Research Institute, Leioa 48940, Basque Country, Spain
| | - Radomir Kratchmarov
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Xiaobing Luo
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Govind Bhagat
- Center for Celiac Disease, Department of Medicine, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA. Alexandria Center for Life Sciences, New York University School of Medicine, New York, NY 10016, USA
| | - Peter H R Green
- Alexandria Center for Life Sciences, New York University School of Medicine, New York, NY 10016, USA
| | - Robert Schneider
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Megerditch Kiledjian
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Research Institute, Leioa 48940, Basque Country, Spain
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA.
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30
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Axpe E, Lopez-Euba T, Castellanos-Rubio A, Merida D, Garcia JA, Plaza-Izurieta L, Fernandez-Jimenez N, Plazaola F, Bilbao JR. Detection of atomic scale changes in the free volume void size of three-dimensional colorectal cancer cell culture using positron annihilation lifetime spectroscopy. PLoS One 2014; 9:e83838. [PMID: 24392097 PMCID: PMC3879280 DOI: 10.1371/journal.pone.0083838] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 11/17/2013] [Indexed: 11/18/2022] Open
Abstract
Positron annihilation lifetime spectroscopy (PALS) provides a direct measurement of the free volume void sizes in polymers and biological systems. This free volume is critical in explaining and understanding physical and mechanical properties of polymers. Moreover, PALS has been recently proposed as a potential tool in detecting cancer at early stages, probing the differences in the subnanometer scale free volume voids between cancerous/healthy skin samples of the same patient. Despite several investigations on free volume in complex cancerous tissues, no positron annihilation studies of living cancer cell cultures have been reported. We demonstrate that PALS can be applied to the study in human living 3D cell cultures. The technique is also capable to detect atomic scale changes in the size of the free volume voids due to the biological responses to TGF-β. PALS may be developed to characterize the effect of different culture conditions in the free volume voids of cells grown in vitro.
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Affiliation(s)
- Eneko Axpe
- Department of Electricity and Electronics, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
- * E-mail:
| | - Tamara Lopez-Euba
- Immunogenetics Research Laboratory, BioCruces Research Institute, Barakaldo, Basque Country, Spain
| | - Ainara Castellanos-Rubio
- Immunogenetics Research Laboratory, BioCruces Research Institute, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
| | - David Merida
- Department of Applied Physics II, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
| | - Jose Angel Garcia
- Department of Applied Physics II, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
| | - Leticia Plaza-Izurieta
- Immunogenetics Research Laboratory, BioCruces Research Institute, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
| | - Nora Fernandez-Jimenez
- Immunogenetics Research Laboratory, BioCruces Research Institute, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
| | - Fernando Plazaola
- Department of Electricity and Electronics, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
| | - Jose Ramon Bilbao
- Immunogenetics Research Laboratory, BioCruces Research Institute, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country - UPV/EHU, Leioa, Basque Country, Spain
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31
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Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Irastorza I, Elcoroaristizabal X, Jauregi-Miguel A, Lopez-Euba T, Tutau C, de Pancorbo MM, Vitoria JC, Bilbao JR. Coregulation and modulation of NFκB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation. Hum Mol Genet 2013; 23:1298-310. [PMID: 24163129 PMCID: PMC3919015 DOI: 10.1093/hmg/ddt520] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
It is known that the NFκB route is constitutively upregulated in celiac disease (CD), an immune-mediated disorder of the gut caused by intolerance to ingested gluten. Our aim was to scrutinize the expression patterns of several of the most biologically relevant components of the NFκB route in intestinal biopsies from active and treated patients and after in vitro gliadin challenge, and to assess normalization of the expression using an inhibitor of the MALT1 paracaspase. The expression of 93 NFκB genes was measured by RT-PCR in a set of uncultured active and treated CD and control biopsies, and in cultured biopsy series challenged with gliadin, the NFκB modulator, both compounds and none. Methylation of eight genes involved in NFκB signaling was analyzed by conventional pyrosequencing. Groups were compared and Pearson's correlation matrixes were constructed to check for coexpression and co-methylation. Our results confirm the upregulation of the NFκB pathway and show that constitutively altered genes usually belong to the core of the pathway and have central roles, whereas genes overexpressed only in active CD are more peripheral. Additionally, this is the first work to detect methylation level changes in celiac intestinal mucosa. Coexpression is very common in controls, whereas gliadin challenge and especially chronic inflammation present in untreated CD result in the disruption of the regulatory equilibrium. In contrast, co-methylation occurs more often in active CD. Importantly, NFκB modulation partially restores coregulation, opening the door to future therapeutic possibilities and targets.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, BioCruces Health Research Institute, University of the Basque Country-UPV/EHU, Leioa, Basque Country, Spain
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Bondar C, Plaza-Izurieta L, Fernandez-Jimenez N, Irastorza I, Withoff S, Wijmenga C, Chirdo F, Bilbao JR. THEMIS and PTPRK in celiac intestinal mucosa: coexpression in disease and after in vitro gliadin challenge. Eur J Hum Genet 2013; 22:358-62. [PMID: 23820479 DOI: 10.1038/ejhg.2013.136] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/29/2013] [Accepted: 05/23/2013] [Indexed: 12/20/2022] Open
Abstract
Celiac disease (CD) is an immune mediated, polygenic disorder, where HLA-DQ2/DQ8 alleles contribute around 35% to genetic risk, but several other genes are also involved. Genome-wide association studies (GWASs) and the more recent immunochip genotyping projects have fine-mapped 39 regions of genetic susceptibility to the disease, most of which harbor candidate genes that could participate in this disease process. We focused our attention to the GWAS peak on chr6: 127.99-128.38 Mb, a region including two genes, thymocyte-expressed molecule involved in selection (THEMIS) and protein tyrosine phosphatase, receptor type, kappa (PTPRK), both of which have immune-related functions. The aim of this work was to evaluate the expression levels of these two genes in duodenal mucosa of active and treated CD patients and in controls, and to determine whether SNPs (rs802734, rs55743914, rs72975916, rs10484718 and rs9491896) associated with CD have any influence on gene expression. THEMIS showed higher expression in active CD compared with treated patients and controls, whereas PTPRK showed lower expression. Our study confirmed the association of this region with CD in our population, but only the genotype of rs802734 showed some influence in the expression of THEMIS. On the other hand, we found a significant positive correlation between THEMIS and PTPRK mRNA levels in CD patients but not in controls. Our results suggest a possible role for both candidate genes in CD pathogenesis and the existence of complex, regulatory relationships that reside in the vast non-coding, functional intergenic regions of the genome. Further investigation is needed to clarify the impact of the disease-associated SNPs on gene function.
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Fernandez-Jimenez N, Plaza-Izurieta L, Lopez-Euba T, Jauregi-Miguel A, Ramon Bilbao J. Cubic regression-based degree of correction predicts the performance of whole bisulfitome amplified DNA methylation analysis. Epigenetics 2012; 7:1349-54. [PMID: 23154537 PMCID: PMC3528690 DOI: 10.4161/epi.22846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Epigenetic mechanisms, including DNA methylation, are important determinants in development and disease. There is a need for technologies capable of detecting small variations in methylation levels in an accurate and reproducible manner, even if only limited amounts of DNA are available (which is the case in many studies in humans). Quantitative methylation analysis of minute DNA amounts after whole bisulfitome amplification (qMAMBA) has been proposed as an alternative, but this technique has not been adequately standardized and no comparative study against conventional methods has been performed, that includes a wide range of methylation percentages and different target assays. We designed an experiment to compare the performance of qMAMBA and bisulfite-treated genomic (non-amplified) DNA pyrosequencing. Reactions were performed in duplicate for each technique in eight different target genes, using nine artificially constructed DNA samples with methylation levels ranging between 0% and 100% with intervals of 12.5%. Cubic polynomial curves were plotted from the experimental results and the real methylation values and the resulting equation was used to estimate new corrected data points. The use of the cubic regression-based correction benefits the accuracy and the power of discrimination in methylation studies. Additionally, dispersion of the new estimated data around a y = x line (R ( 2) ) served to fix a cutoff that can discriminate, with a single 9-point curve experiment, whether whole bisulfitome amplification and subsequent qMAMBA can produce accurate methylation results. Finally, even with an optimized reagent kit, DNA samples subjected to whole bisulfitome amplification enhance the preferential amplification of unmethylated alleles, and subtle changes in methylation levels cannot be detected confidently.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, BioCruces Health Research Institute, University of the Basque Country UPV/EHU, Leioa, Basque Country, Spain
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Castellanos-Rubio A, Caja S, Irastorza I, Fernandez-Jimenez N, Plaza-Izurieta L, Vitoria JC, Maki M, Lindfors K, Bilbao JR. Angiogenesis-related gene expression analysis in celiac disease. Autoimmunity 2012; 45:264-70. [PMID: 22136669 DOI: 10.3109/08916934.2011.637531] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Celiac disease (CD) involves disturbance of the small-bowel mucosal vascular network, and transglutaminase autoantibodies (TGA) have been related to angiogenesis disturbance, a complex phenomenon probably also influenced by common genetic variants in angiogenesis-related genes. A set of genes with "angiogenesis" GO term identified in a previous expression microarray experiment (SCG2, STAB1, TGFA, ANG, ERBB2, GNA13, PML, CASP8, ECGF1, JAG1, HIF1A, TNFSF13 and TGM2) was selected for genetic and functional studies. SNPs that showed a trend for association with CD in the first GWAS were genotyped in 555 patients and 541 controls. Gene expression of all genes was quantified in 15 pairs of intestinal biopsies (diagnosis vs. GFD) and in three-dimensional HUVEC and T84 cell cultures incubated with TGA-positive and negative serum. A regulatory SNP in TNFSF13 (rs11552708) is associated with CD (p = 0.01, OR = 0.7). Expression changes in biopsies pointed to TGM2 and PML as up-regulated antiangiogenic genes and to GNA13, TGFA, ERBB2 and SCG2 as down-regulated proangiogenic factors in CD. TGA seem to enhance TGM2 expression in both cell models, but PML expression was induced only in T84 enterocytes while GNA13 and ERBB2 were repressed in HUVEC endothelial cells, with several genes showing discordant effects in each model, highlighting the complexity of gene interactions in the pathogenesis of CD. Finally, cell culture models are useful tools to help dissect complex responses observed in human explants.
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Affiliation(s)
- Ainara Castellanos-Rubio
- Immunogenetics Research Laboratory, Endocrinology, Diabetes and Nutrition Research Group, Hospital de Cruces, Barakaldo, Basque Country
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Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Gutierrez G, Irastorza I, Castaño L, Vitoria JC, Bilbao JR. Accuracy in copy number calling by qPCR and PRT: a matter of DNA. PLoS One 2011; 6:e28910. [PMID: 22174923 PMCID: PMC3236783 DOI: 10.1371/journal.pone.0028910] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/17/2011] [Indexed: 02/01/2023] Open
Abstract
The possible implication of copy number variation (CNV) in the genetic susceptibility to human disease needs to be assessed using robust methods that can be applied at a population scale. In this report, we analyze the performance of the two major techniques, quantitative PCR (qPCR) and paralog ratio test (PRT), and investigate the influence of input DNA amount and template integrity on the reliability of both methods. Analysis of three genes (PRELID1, SYNPO and DEFB4) in a large sample set showed that both methods are prone to false copy number assignments if sufficient attention is not paid to DNA concentration and quality. Accurate normalization of samples is essential for reproducible qPCR because it avoids the effect of differential amplification efficiencies between target and control assays, whereas PRT is generally more sensitive to template degradation due to the fact that longer amplicons are usually needed to optimize sensitivity and specificity of paralog sequence PCR. The use of normalized, high quality genomic DNA yields comparable results with both methods.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Basque Country, Spain
| | - Ainara Castellanos-Rubio
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Basque Country, Spain
| | - Leticia Plaza-Izurieta
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Basque Country, Spain
| | - Galder Gutierrez
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Iñaki Irastorza
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
- Department of Pediatrics, University of the Basque Country, Bilbao, Basque Country, Spain
| | - Luis Castaño
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
- Department of Pediatrics, University of the Basque Country, Bilbao, Basque Country, Spain
| | - Juan Carlos Vitoria
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
- Department of Pediatrics, University of the Basque Country, Bilbao, Basque Country, Spain
| | - Jose Ramon Bilbao
- Immunogenetics Research Laboratory, Cruces University Hospital, Barakaldo, Basque Country, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Basque Country, Spain
- * E-mail:
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Fernandez-Jimenez N, Santín I, Irastorza I, Plaza-Izurieta L, Castellanos-Rubio A, Vitoria JC, Bilbao JR. Upregulation of KIR3DL1 gene expression in intestinal mucosa in active celiac disease. Hum Immunol 2011; 72:617-20. [DOI: 10.1016/j.humimm.2011.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/04/2011] [Accepted: 04/26/2011] [Indexed: 12/11/2022]
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Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Gutierrez G, Castaño L, Vitoria JC, Bilbao JR. Analysis of beta-defensin and Toll-like receptor gene copy number variation in celiac disease. Hum Immunol 2010; 71:833-6. [PMID: 20483368 DOI: 10.1016/j.humimm.2010.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 05/06/2010] [Accepted: 05/12/2010] [Indexed: 12/18/2022]
Abstract
Celiac disease (CD) is an immune-mediated disorder of the gut in which innate and adaptive responses are involved. Toll-like receptor (TLR) 2 and TLR4 participate in host defense through antigen recognition, and show altered expression in CD gut mucosa. beta-defensins are inducible antimicrobial peptides, and DEFB gene copy number polymorphisms have been associated with autoimmune and inflammatory disorders. We performed copy number analysis of TLR2, TLR4, and the beta-defensin cluster (DEFB4, DEFB103 and DEFB104) by gene-specific, real-time polymerase chain reaction (PCR) in 376 CD patients and 376 controls. TLR genes did not show copy number variation, and all samples presented with two copies. beta-defensin clusters varied between 2 and 9 copies per genome, and when grouped into bins, high copy numbers (>4) were underrepresented among patients (p = 0.023; odds ratio = 0.69, 95% CI = 0.50-0.96), suggesting that increased copy numbers could protect from CD, possibly by impeding bacterial infiltration more efficiently and preserving gut epithelial integrity.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Endocrinology, Diabetes and Nutrition Research Group, Hospital de Cruces, Barakaldo-Bizkaia, Basque Country, Spain
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