51
|
Yamada Y, Sasaki S. A method for identifying allele-specific hydroxymethylation. Epigenetics 2019; 15:231-250. [PMID: 31533538 DOI: 10.1080/15592294.2019.1664228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We previously identified sequence-dependent allele-specific methylation (sd-ASM) in adult human peripheral blood leukocytes, in which ASM occurs in cis depending on adjacent polymorphic sequences. A number of groups have identified sd-ASM sites in the human and mouse genomes, illustrating the prevalence of sd-ASM in mammalian genomes. In addition, sd-ASM can lead to sequence-dependent allele-specific expression of neighbouring genes. Imprinted genes also often exhibit parent-of-origin-dependent allele-specific methylation (pd-ASM), which causes parent-of-origin-dependent allele-specific expression. However, whether most of the already known sd-ASM and pd-ASM sites are methylated or hydroxymethylated remains unclear due to technical restrictions. Accordingly, a novel method that enables examination of allelic methylation and hydroxymethylation status and also overcomes the drawbacks of conventional methods is needed. Such a method could also be used to elucidate the mechanisms underlying polymorphism-associated inter-individual differences in disease susceptibility and the mechanism of genomic imprinting. Here, we developed a simple method to determine allelic hydroxymethylation status and identified novel sequence- and parent-of-origin-dependent allele-specific hydroxymethylation sites. Correlation analyses of TF binding sequences and methylation or hydroxymethylation between three mouse strains revealed the involvement of Pax5 in strain-specific methylation and hydroxymethylation in exon 7 of Pdgfrb.
Collapse
Affiliation(s)
- Yoichi Yamada
- Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Sho Sasaki
- Division of Electrical and Computer Engineering, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
52
|
Vandiedonck C. Genetic association of molecular traits: A help to identify causative variants in complex diseases. Clin Genet 2019; 93:520-532. [PMID: 29194587 DOI: 10.1111/cge.13187] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022]
Abstract
In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies. The genetic variants that modulate them are called expression quantitative trait loci. Their study has been extended to other molecular quantitative trait loci (molQTLs) that regulate gene expression at the various levels, from chromatin state to cellular responses. Altogether, these studies have generated a wealth of basic information on the genome-wide patterns of gene expression and their inter-individual variation. Most importantly, molQTLs have become an invaluable asset in the genetic study of complex diseases. Although the identification of the disease-causing variants on the basis of their overlap with molQTLs requires caution, molQTLs can help to prioritize the relevant candidate gene(s) in the disease-associated regions and bring a functional interpretation of the associated variants, therefore, bridging the gap between genotypes and clinical phenotypes.
Collapse
Affiliation(s)
- C Vandiedonck
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
53
|
Gong J, Tian J, Lou J, Wang X, Ke J, Li J, Yang Y, Gong Y, Zhu Y, Zou D, Peng X, Yang N, Mei S, Zhong R, Chang J, Miao X. A polymorphic MYC response element in KBTBD11 influences colorectal cancer risk, especially in interaction with an MYC-regulated SNP rs6983267. Ann Oncol 2019; 29:632-639. [PMID: 29267898 DOI: 10.1093/annonc/mdx789] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background MYC is a well-established cancer driver gene regulating the expression of numerous genes, indicating that polymorphisms in MYC response elements could affect tumorigenesis through altering MYC regulation. We performed integrative multistage study to evaluate the effects of variants in MYC response elements and colorectal cancer (CRC) risk. Patients and methods We systematically integrated ChIP-Seq, DNase-Seq and transcription factor motif data to screen variants with potential ability to affect the MYC binding affinity. Then, we conducted a two-stage case-control study, totally consisting of 4830 CRC cases and 4759 controls in Chinese population to identify risk polymorphisms and interactions. The effects of risk variants were confirmed by functional assays in CRC LoVo, SW480 and HCT15 cells. Results We identified a novel polymorphism rs11777210 in KBTBD11 significantly associated with CRC susceptibility (P = 2.43 × 10-12). Notably, we observed a significant interaction between rs11777210 and MYC nearby rs6983267 (P-multi = 0.003, P-add = 0.005), subjects carrying rs6983267 GG and rs11777210 CC genotypes showing higher susceptibility to CRC (2.83-fold) than those carrying rs6983267 TT and rs11777210 TT genotypes. We further demonstrated that rs6983267 T > G increased MYC expression, and MYC bound to and negatively regulated KBTBD11 expression when the rs11777210 C risk allele was present. KBTBD11 was downregulated in tumor tissues, and KBTBD11 knockdown promoted cell proliferation and inhibited cell apoptosis. Conclusion The rs11777210 is a potential predictive biomarker of CRC susceptibility, and KBTBD11 functions as a putative tumor suppressor in tumorigenesis. Our study highlighted the high CRC risk of people carrying rs6983267 G and rs11777210 C alleles, and provided possible biological mechanism of the interaction.
Collapse
Affiliation(s)
- J Gong
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - J Tian
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - J Lou
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - X Wang
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - J Ke
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - J Li
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Y Yang
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Y Gong
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Y Zhu
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - D Zou
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - X Peng
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - N Yang
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - S Mei
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - R Zhong
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - J Chang
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - X Miao
- Department of Epidemiology and Biostatistics, Huazhong University of Science and Technology, Wuhan, China; State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
54
|
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] [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.
Collapse
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.
| |
Collapse
|
55
|
Relationship between Alzheimer's disease-associated SNPs within the CLU gene, local DNA methylation and episodic verbal memory in healthy and schizophrenia subjects. Psychiatry Res 2019; 272:380-386. [PMID: 30599442 DOI: 10.1016/j.psychres.2018.12.134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/16/2018] [Accepted: 12/24/2018] [Indexed: 11/24/2022]
Abstract
Genetic variation may impact on local DNA methylation patterns. Therefore, information about allele-specific DNA methylation (ASM) within disease-related loci has been proposed to be useful for the interpretation of GWAS results. To explore mechanisms that may underlie associations between Alzheimer's disease (AD) and schizophrenia risk CLU gene and verbal memory, one of the most affected cognitive domains in both conditions, we studied DNA methylation in a region between AD-associated SNPs rs9331888 and rs9331896 in 72 healthy individuals and 73 schizophrenia patients. Using single-molecule real-time bisulfite sequencing we assessed the haplotype-dependent ASM in this region. We then investigated whether its methylation could influence episodic verbal memory measured with the Rey Auditory Verbal Learning Test in these two cohorts. The region showed a complex methylation pattern, which was similar in healthy and schizophrenia individuals and unrelated to haplotypes. The pattern predicted memory scores in controls. The results suggest that epigenetic modifications within the CLU locus may play a role in memory variation, independent of ASM.
Collapse
|
56
|
Wang H, Lou D, Wang Z. Crosstalk of Genetic Variants, Allele-Specific DNA Methylation, and Environmental Factors for Complex Disease Risk. Front Genet 2019; 9:695. [PMID: 30687383 PMCID: PMC6334214 DOI: 10.3389/fgene.2018.00695] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 12/12/2018] [Indexed: 01/04/2023] Open
Abstract
Over the past decades, genome-wide association studies (GWAS) have identified thousands of phenotype-associated DNA sequence variants for potential explanations of inter-individual phenotypic differences and disease susceptibility. However, it remains a challenge for translating the associations into causative mechanisms for complex diseases, partially due to the involved variants in the noncoding regions and the inconvenience of functional studies in human population samples. So far, accumulating evidence has suggested a complex crosstalk among genetic variants, allele-specific binding of transcription factors (ABTF), and allele-specific DNA methylation patterns (ASM), as well as environmental factors for disease risk. This review aims to summarize the current studies regarding the interactions of the aforementioned factors with a focus on epigenetic insights. We present two scenarios of single nucleotide polymorphisms (SNPs) in coding regions and non-coding regions for disease risk, via potentially impacting epigenetic patterns. While a SNP in a coding region may confer disease risk via altering protein functions, a SNP in non-coding region may cause diseases, via SNP-altering ABTF, ASM, and allele-specific gene expression (ASE). The allelic increases or decreases of gene expression are key for disease risk during development. Such ASE can be achieved via either a "SNP-introduced ABTF to ASM" or a "SNP-introduced ASM to ABTF." Together with our additional in-depth review on insulator CTCF, we are convinced to propose a working model that the small effect of a SNP acts through altered ABTF and/or ASM, for ASE and eventual disease outcome (named as a "SNP intensifier" model). In summary, the significance of complex crosstalk among genetic factors, epigenetic patterns, and environmental factors requires further investigations for disease susceptibility.
Collapse
Affiliation(s)
- Huishan Wang
- Laboratory of Human Environmental Epigenome, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
- Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dan Lou
- Laboratory of Human Environmental Epigenome, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Zhibin Wang
- Laboratory of Human Environmental Epigenome, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| |
Collapse
|
57
|
Mother-child transmission of epigenetic information by tunable polymorphic imprinting. Proc Natl Acad Sci U S A 2018; 115:E11970-E11977. [PMID: 30509985 PMCID: PMC6304996 DOI: 10.1073/pnas.1815005115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
First, our work provides critical biological interpretation of intermediate DNA methylation readouts at the nc886 differentially methylated region (DMR). nc886 was identified in multiple large-scale epigenome-wide association studies (EWAS) that did not recognize that this region acts as a contiguous DMR imposed by genomic imprinting, highlighting the need to reexamine several 450k data sets. Second, strict control of genomic imprinting was thought to be required for organismal viability. Reports of polymorphic imprinting are limited to specific tissue types such as placenta and brain. In blood and somatic tissues, we show nc886 imprinting is mosaic in the population and influenced by maternal environment. Genomic imprinting mediated by DNA methylation restricts gene expression to a single allele determined by parental origin and is not generally considered to be under genetic or environmental influence. Here, we focused on a differentially methylated region (DMR) of approximately 1.9 kb that includes a 101-bp noncoding RNA gene (nc886/VTRNA2-1), which is maternally imprinted in ∼75% of humans. This is unlike other imprinted genes, which demonstrate monoallelic methylation in 100% of individuals. The DMR includes a CTCF binding site on the centromeric side defining the DMR boundary and is flanked by a CTCF binding site on the telomeric side. The centromeric CTCF binding site contains an A/C polymorphism (rs2346018); the C allele is associated with less imprinting. The frequency of imprinting of the nc886 DMR in infants was linked to at least two nongenetic factors, maternal age at delivery and season of conception. In a separate cohort, nc886 imprinting was associated with lower body mass index in children at 5 y of age. Thus, we propose that the imprinting status of the nc886 DMR is “tunable” in that it is associated with maternal haplotype and prenatal environment. This provides a potential mechanism for transmitting information, with phenotypic consequences, from mother to child.
Collapse
|
58
|
Genetic variants influence on the placenta regulatory landscape. PLoS Genet 2018; 14:e1007785. [PMID: 30452450 PMCID: PMC6277118 DOI: 10.1371/journal.pgen.1007785] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 12/03/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
From genomic association studies, quantitative trait loci analysis, and epigenomic mapping, it is evident that significant efforts are necessary to define genetic-epigenetic interactions and understand their role in disease susceptibility and progression. For this reason, an analysis of the effects of genetic variation on gene expression and DNA methylation in human placentas at high resolution and whole-genome coverage will have multiple mechanistic and practical implications. By producing and analyzing DNA sequence variation (n = 303), DNA methylation (n = 303) and mRNA expression data (n = 80) from placentas from healthy women, we investigate the regulatory landscape of the human placenta and offer analytical approaches to integrate different types of genomic data and address some potential limitations of current platforms. We distinguish two profiles of interaction between expression and DNA methylation, revealing linear or bimodal effects, reflecting differences in genomic context, transcription factor recruitment, and possibly cell subpopulations. These findings help to clarify the interactions of genetic, epigenetic, and transcriptional regulatory mechanisms in normal human placentas. They also provide strong evidence for genotype-driven modifications of transcription and DNA methylation in normal placentas. In addition to these mechanistic implications, the data and analytical methods presented here will improve the interpretability of genome-wide and epigenome-wide association studies for human traits and diseases that involve placental functions. The placenta is a critical organ playing multiple roles including oxygen and metabolite transfer from mother to fetus, hormone production, and vascular perfusion. With this study, we aimed to deliver a placenta-specific regulatory map based on a combination of publicly available and newly generated data. To complete this reference, we obtained genotype information (n = 303), DNA methylation (n = 303) and expression data (n = 80) for placentas from healthy women. Our analysis of methylation and expression quantitative trait loci (QTLs) and correlations between methylation and expression data were designed to identify fundamental associations between genome, transcriptome, and epigenome in this key fetal organ. The results provide high-resolution genetic and epigenetic maps specific to the placenta based on a representative ethnically diverse cohort. As interest and efforts are growing to better understand the etiology of placental disease and the impact of the environment on placental function these data will provide a reference and enhance future investigations.
Collapse
|
59
|
Friedman JE. Developmental Programming of Obesity and Diabetes in Mouse, Monkey, and Man in 2018: Where Are We Headed? Diabetes 2018; 67:2137-2151. [PMID: 30348820 PMCID: PMC6198344 DOI: 10.2337/dbi17-0011] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022]
Abstract
Childhood obesity and its comorbidities continue to accelerate across the globe. Two-thirds of pregnant women are obese/overweight, as are 20% of preschoolers. Gestational diabetes mellitus (GDM) is escalating, affecting up to 1 in 5 pregnant women. The field of developmental origins of health and disease has begun to move beyond associations to potential causal mechanisms for developmental programming. Evidence across species compellingly demonstrates that maternal obesity, diabetes, and Western-style diets create a long-lasting signature on multiple systems, including infant stem cells, the early immune system, and gut microbiota. Such exposures accelerate adipogenesis, disrupt mitochondrial metabolism, and impair energy sensing, affecting neurodevelopment, liver, pancreas, and skeletal muscle. Attempts to prevent developmental programming have met with very limited success. A challenging level of complexity is involved in how the host genome, metabolome, and microbiome throughout pregnancy and lactation increase the offspring's risk of metabolic diseases across the life span. Considerable gaps in knowledge include the timing of exposure(s) and permanence or plasticity of the response, encompassing effects from both maternal and paternal dysmetabolism. Basic, translational, and human intervention studies targeting pathways that connect diet, microbiota, and metabolism in mothers with obesity/GDM and their infants are a critical unmet need and present new challenges for disease prevention in the next generation.
Collapse
Affiliation(s)
- Jacob E Friedman
- Section of Neonatology, Department of Pediatrics; Department of Biochemistry & Molecular Genetics; Division of Endocrinology, Metabolism & Diabetes, Department of Medicine; and Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
60
|
Frequent monoallelic or skewed expression for developmental genes in CNS-derived cells and evidence for balancing selection. Proc Natl Acad Sci U S A 2018; 115:E10379-E10386. [PMID: 30322913 PMCID: PMC6217436 DOI: 10.1073/pnas.1808652115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cellular mosaicism due to monoallelic autosomal expression (MAE), with cell selection during development, is becoming increasingly recognized as prevalent in mammals, leading to interest in understanding its extent and mechanism(s). We report here use of clonal cell lines derived from the CNS of adult female [Formula: see text] hybrid (C57BL/6 X JF1) mice to characterize MAE as neural stem cells (nscs) differentiate to astrocyte-like cells (asls). We found that different subsets of genes show MAE in the two populations of cells; in each case, there is strong enrichment for genes specific to the respective developmental state. Genes that exhibit MAE are 22% of nsc-specific genes and 26% of asl-specific genes. Moreover, the promoters of genes with MAE have reduced CpG dinucleotides but increased CpG differences between the two parental mouse strains. Extending the study of variability to wild populations of mice, we found evidence for balancing selection as a contributing force in evolution of those genes showing developmental specificity (i.e., expressed in either nsc or asl), not just for genes showing MAE. Furthermore, we found that genes showing skewed allelic expression (SKE) were similarly enriched among cell type-specific genes and also showed a heightened probability of balancing selection. Thus, developmental stage-specific genes and genes with MAE or SKE seem to make up overlapping classes subject to selection for increased diversity. The implications of these results for development and evolution are discussed in the context of a model with stochastic epigenetic modifications taking place only during a relatively brief developmental window.
Collapse
|
61
|
Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science 2018; 361:eaar3146. [PMID: 30139913 PMCID: PMC6198826 DOI: 10.1126/science.aar3146] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/07/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
To assess the impact of genetic variation in regulatory loci on human health, we constructed a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes revealed sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, which is defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provided a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated genetic variation.
Collapse
Affiliation(s)
- Vitor Onuchic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Eugene Lurie
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Ivenise Carrero
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Piotr Pawliczek
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Ronak Y Patel
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Zhuoyi Huang
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert C Altshuler
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhizhuo Zhang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - R Alan Harris
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Cristian Coarfa
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Lillian Ashmore
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Jessica W Bertol
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Walid D Fakhouri
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Fuli Yu
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Manolis Kellis
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Aleksandar Milosavljevic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA.
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| |
Collapse
|
62
|
Kessler NJ, Waterland RA, Prentice AM, Silver MJ. Establishment of environmentally sensitive DNA methylation states in the very early human embryo. SCIENCE ADVANCES 2018; 4:eaat2624. [PMID: 30009262 PMCID: PMC6040841 DOI: 10.1126/sciadv.aat2624] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/01/2018] [Indexed: 05/04/2023]
Abstract
The molecular mechanisms responsible for the developmental origins of later disease are currently unknown. We previously demonstrated that women's periconceptional nutrition predicts their offspring's DNA methylation at metastable epialleles (MEs). We present a genome-wide screen yielding 687 MEs and track their trajectories across nine developmental stages in human in vitro fertilization embryos. MEs exhibit highly unusual methylation dynamics across the implantation-gastrulation transition, producing a large excess of intermediate methylation states, suggesting the potential for differential programming in response to external signals. Using a natural experiment in rural Gambia, we show that genomic regions sensitive to season of conception are highly enriched for MEs and show similar atypical methylation patterns. MEs are enriched for proximal enhancers and transcription start sites and are influenced by genotype. Together, these observations position MEs as distinctive epigenomic features programmed in the early embryo, sensitive to genetic and periconceptional environment, and with the potential to influence phenotype.
Collapse
Affiliation(s)
- Noah J. Kessler
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Robert A. Waterland
- U.S. Department of Agriculture/Agricultural Research Service Children’s Nutrition Research Center, Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| |
Collapse
|
63
|
DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis. Nat Commun 2018; 9:2397. [PMID: 29921915 PMCID: PMC6008330 DOI: 10.1038/s41467-018-04732-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
The human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-sensitive regulatory properties in vitro. Causal inference and Mendelian randomization provide evidence that HLA variants mediate risk for MS via changes in the HLA-DRB1 DMR that modify HLA-DRB1 expression. Meta-analysis of 14,259 cases and 171,347 controls confirms that these variants confer risk from DRB1*15:01 and also identifies a protective variant (rs9267649, p < 3.32 × 10-8, odds ratio = 0.86) after conditioning for all MS-associated variants in the region. rs9267649 is associated with increased DNA methylation at the HLA-DRB1 DMR and reduced expression of HLA-DRB1, suggesting a modulation of the DRB1*15:01 effect. Our integrative approach provides insights into the molecular mechanisms of MS susceptibility and suggests putative therapeutic strategies targeting a methylation-mediated regulation of the major risk gene.
Collapse
|
64
|
Wu HC, Do C, Andrulis IL, John EM, Daly MB, Buys SS, Chung WK, Knight JA, Bradbury AR, Keegan THM, Schwartz L, Krupska I, Miller RL, Santella RM, Tycko B, Terry MB. Breast cancer family history and allele-specific DNA methylation in the legacy girls study. Epigenetics 2018; 13:240-250. [PMID: 29436922 DOI: 10.1080/15592294.2018.1435243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Family history, a well-established risk factor for breast cancer, can have both genetic and environmental contributions. Shared environment in families as well as epigenetic changes that also may be influenced by shared genetics and environment may also explain familial clustering of cancers. Epigenetic regulation, such as DNA methylation, can change the activity of a DNA segment without a change in the sequence; environmental exposures experienced across the life course can induce such changes. However, genetic-epigenetic interactions, detected as methylation quantitative trait loci (mQTLs; a.k.a. meQTLs) and haplotype-dependent allele-specific methylation (hap-ASM), can also contribute to inter-individual differences in DNA methylation patterns. To identify differentially methylated regions (DMRs) associated with breast cancer susceptibility, we examined differences in white blood cell DNA methylation in 29 candidate genes in 426 girls (ages 6-13 years) from the LEGACY Girls Study, 239 with and 187 without a breast cancer family history (BCFH). We measured methylation by targeted massively parallel bisulfite sequencing (bis-seq) and observed BCFH DMRs in two genes: ESR1 (Δ4.9%, P = 0.003) and SEC16B (Δ3.6%, P = 0.026), each of which has been previously implicated in breast cancer susceptibility and pubertal development. These DMRs showed high inter-individual variability in methylation, suggesting the presence of mQTLs/hap-ASM. Using single nucleotide polymorphisms data in the bis-seq amplicon, we found strong hap-ASM in SEC16B (with allele specific-differences ranging from 42% to 74%). These findings suggest that differential methylation in genes relevant to breast cancer susceptibility may be present early in life, and that inherited genetic factors underlie some of these epigenetic differences.
Collapse
Affiliation(s)
- Hui-Chen Wu
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY
| | - Catherine Do
- c John Theurer Cancer Center , Hackensack University Medical Center , Hackensack NJ
| | - Irene L Andrulis
- d Lunenfeld-Tanenbaum Research Institute , Sinai Health System , Toronto , Ontario.,e Departments of Molecular Genetics and Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Esther M John
- f Cancer Prevention Institute of California , Fremont CA.,g Department of Health Research & Policy (Epidemiology) , and Stanford Cancer Institute, Stanford University School of Medicine , Stanford , CA
| | - Mary B Daly
- h Department of Clinical Genetics , Fox Chase Cancer Center , Philadelphia , PA
| | - Saundra S Buys
- i Department of Medicine and , Huntsman Cancer Institute, University of Utah Health Sciences Center , UT
| | - Wendy K Chung
- j Departments of Pediatrics ; Department of Medicine , Columbia University College of Physicians and Surgeons , New York , NY
| | - Julia A Knight
- d Lunenfeld-Tanenbaum Research Institute , Sinai Health System , Toronto , Ontario.,k Dalla Lana School of Public Health , University of Toronto , Toronto
| | - Angela R Bradbury
- l Departments of Medicine, Division of Hematology/Oncology, Department of Medical Ethics and Health Policy, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA
| | - Theresa H M Keegan
- m Center for Oncology Hematology Outcomes Research and Training (COHORT).,n Division of Hematology and Oncology , University of California Davis School of Medicine , Sacramento , CA
| | - Lisa Schwartz
- o Department of Pediatrics, Division of Oncology, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA.,p The Children's Hospital of Philadelphia , Philadelphia , PA
| | - Izabela Krupska
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY
| | - Rachel L Miller
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,j Departments of Pediatrics ; Department of Medicine , Columbia University College of Physicians and Surgeons , New York , NY
| | - Regina M Santella
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY
| | - Benjamin Tycko
- c John Theurer Cancer Center , Hackensack University Medical Center , Hackensack NJ.,q Lombardi Comprehensive Cancer Center , Georgetown University , Washington , DC
| | - Mary Beth Terry
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY.,r Imprints Center , Columbia University Medical Center , New York , NY.,s Department of Epidemiology , Mailman School of Public Health of Columbia University , New York , NY
| |
Collapse
|
65
|
Chiba H, Kakuta Y, Kinouchi Y, Kawai Y, Watanabe K, Nagao M, Naito T, Onodera M, Moroi R, Kuroha M, Kanazawa Y, Kimura T, Shiga H, Endo K, Negoro K, Nagasaki M, Unno M, Shimosegawa T. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease. PLoS One 2018; 13:e0194036. [PMID: 29547621 PMCID: PMC5856270 DOI: 10.1371/journal.pone.0194036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 02/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. METHODS CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score ([Formula: see text]) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing [Formula: see text] >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. RESULTS We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of [Formula: see text] (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 ([Formula: see text] = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). CONCLUSIONS We confirmed the existence of cis-regulated ASM around IBD susceptibility genes and the association between ASM SNP (rs36221701) genotype and SMAD3 expression, a susceptibility gene for IBD. These results give us supporting evidence that DNA methylation mediates genetic effects on disease susceptibility.
Collapse
Affiliation(s)
- Hirofumi Chiba
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Kinouchi
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuhiro Watanabe
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Munenori Nagao
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeo Naito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Motoyuki Onodera
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Rintaro Moroi
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masatake Kuroha
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitake Kanazawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoya Kimura
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hisashi Shiga
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsuya Endo
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kenichi Negoro
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masao Nagasaki
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| |
Collapse
|
66
|
de Sá Machado Araújo G, da Silva Francisco Junior R, Dos Santos Ferreira C, Mozer Rodrigues PT, Terra Machado D, Louvain de Souza T, Teixeira de Souza J, Figueiredo Osorio da Silva C, Alves da Silva AF, Andrade CCF, da Silva AT, Ramos V, Garcia AB, Machado FB, Medina-Acosta E. Maternal 5 mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. Front Genet 2018; 9:36. [PMID: 29545821 PMCID: PMC5838017 DOI: 10.3389/fgene.2018.00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5mC) of alleles at CpG islands (CGIs) in their promoter regions. This 5mCpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion. iDMRs function as regulatory platforms, built through the recruitment of chemical modifications to histones to achieve differential, parent-of-origin-dependent chromatin segmentation states. Here, we used a comparative computational data mining approach to identify 125 novel constitutive candidate iDMRs that integrate the maximal number of allele-specific methylation region records overlapping CGIs in human methylomes. Twenty-nine candidate iDMRs display gametic 5mCpG asymmetry, and another 96 are candidate secondary iDMRs. We established the maternal origin of the 5mCpG imprints of one gametic (PARD6G-AS1) and one secondary (GCSAML) iDMRs. We also found a constitutively hemimethylated, nonimprinted domain at the PWWP2AP1 promoter CGI with oocyte-derived methylation asymmetry. Given that the 5mCpG level at the iDMRs is not a sufficient criterion to predict active or silent locus states and that iDMRs can regulate genes from a distance of more than 1 Mb, we used RNA-Seq experiments from the Genotype-Tissue Expression project and public archives to assess the transcriptional expression profiles of SNPs across 4.6 Mb spans around the novel maternal iDMRs. We showed that PARD6G-AS1 and GCSAML are expressed biallelically in multiple tissues. We found evidence of tissue-specific monoallelic expression of ZNF124 and OR2L13, located 363 kb upstream and 419 kb downstream, respectively, of the GCSAML iDMR. We hypothesize that the GCSAML iDMR regulates the tissue-specific, monoallelic expression of ZNF124 but not of OR2L13. We annotated the non-coding epigenomic marks in the two maternal iDMRs using data from the Roadmap Epigenomics project and showed that the PARD6G-AS1 and GCSAML iDMRs achieve contrasting activation and repression chromatin segmentations. Lastly, we found that the maternal 5mCpG imprints are perturbed in several hematopoietic cancers. We conclude that the maternal 5mCpG imprints at PARD6G-AS1 and GCSAML iDMRs are decoupled from parent-of-origin transcriptional expression effects in multiple tissues.
Collapse
Affiliation(s)
- Graziela de Sá Machado Araújo
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Ronaldo da Silva Francisco Junior
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Cristina Dos Santos Ferreira
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Pedro Thyago Mozer Rodrigues
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thais Louvain de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade de Medicina de Campos, Campos dos Goytacazes, Brazil
| | - Jozimara Teixeira de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Cleiton Figueiredo Osorio da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Antônio Francisco Alves da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Claudia Caixeta Franco Andrade
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade Metropolitana São Carlos, Bom Jesus do Itabapoana, Brazil
| | - Alan Tardin da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Victor Ramos
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Beatriz Garcia
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Filipe Brum Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| |
Collapse
|
67
|
Kachroo P, Szymczak S, Heinsen FA, Forster M, Bethune J, Hemmrich-Stanisak G, Baker L, Schrappe M, Stanulla M, Franke A. NGS-based methylation profiling differentiates TCF3-HLF and TCF3-PBX1 positive B-cell acute lymphoblastic leukemia. Epigenomics 2018; 10:133-147. [DOI: 10.2217/epi-2017-0080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To determine whether methylation differences between mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes can be associated with differential gene expression and remission. Materials & methods: Five (extremely rare) TCF3-HLF versus five (very similar) TCF3-PBX1 patients were sampled before and after remission and analyzed using reduced representation bisulfite sequencing and RNA-sequencing. Results: We identified 7000 differentially methylated CpG sites between subtypes, of which 78% had lower methylation levels in TCF3-HLF. Gene expression was negatively correlated with CpG sites in 23 genes. KBTBD11 clearly differed in methylation and expression between subtypes and before and after remission in TCF3-HLF samples. Conclusion: KBTBD11 hypomethylation may be a promising potential target for further experimental validation especially for the TCF3-HLF subtype.
Collapse
Affiliation(s)
- Priyadarshini Kachroo
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
- Channing Laboratory, Department of Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Silke Szymczak
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
- Institute of Medical Informatics & Statistics, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Femke-Anouska Heinsen
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Jörn Bethune
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Lewis Baker
- Department of Applied Mathematics, University of Colorado, Boulder, CO 80309, USA
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Martin Stanulla
- Pediatric Hematology & Oncology, Hannover Medical School, Hannover 30625, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| |
Collapse
|
68
|
Van Baak TE, Coarfa C, Dugué PA, Fiorito G, Laritsky E, Baker MS, Kessler NJ, Dong J, Duryea JD, Silver MJ, Saffari A, Prentice AM, Moore SE, Ghantous A, Routledge MN, Gong YY, Herceg Z, Vineis P, Severi G, Hopper JL, Southey MC, Giles GG, Milne RL, Waterland RA. Epigenetic supersimilarity of monozygotic twin pairs. Genome Biol 2018; 19:2. [PMID: 29310692 PMCID: PMC5759268 DOI: 10.1186/s13059-017-1374-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/06/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to be largely due to their genetic identity. RESULTS Here, by analyzing data from a genome-scale study of DNA methylation in monozygotic and dizygotic twins, we identified genomic regions at which the epigenetic similarity of monozygotic twins is substantially greater than can be explained by their genetic identity. This "epigenetic supersimilarity" apparently results from locus-specific establishment of epigenotype prior to embryo cleavage during twinning. Epigenetically supersimilar loci exhibit systemic interindividual epigenetic variation and plasticity to periconceptional environment and are enriched in sub-telomeric regions. In case-control studies nested in a prospective cohort, blood DNA methylation at these loci years before diagnosis is associated with risk of developing several types of cancer. CONCLUSIONS These results establish a link between early embryonic epigenetic development and adult disease. More broadly, epigenetic supersimilarity is a previously unrecognized phenomenon that may contribute to the phenotypic similarity of monozygotic twins.
Collapse
Affiliation(s)
- Timothy E Van Baak
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Giovanni Fiorito
- Department of Medical Sciences, University of Torino and Italian Institute for Genomic Medicine, Torino, Italy
| | - Eleonora Laritsky
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria S Baker
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Noah J Kessler
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Jianrong Dong
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jack D Duryea
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Matt J Silver
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Ayden Saffari
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Andrew M Prentice
- MRC Unit The Gambia, Keneba, Gambia
- MRC International Nutrition Group at LSHTM, London, UK
| | - Sophie E Moore
- MRC Unit The Gambia, Keneba, Gambia
- Division of Women's Health, King's College London, London, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | | | - Yun Yun Gong
- School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
- Italian Institute for Genomic Medicine, Torino, Italy
| | - Gianluca Severi
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
- Italian Institute for Genomic Medicine, Torino, Italy
- CESP Inserm, Facultés de medicine Université Paris-Sud, Paris, France
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School for Global and Population Health, University of Melbourne, Melbourne, VIC, Australia
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
69
|
Bell CG, Gao F, Yuan W, Roos L, Acton RJ, Xia Y, Bell J, Ward K, Mangino M, Hysi PG, Wang J, Spector TD. Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci. Nat Commun 2018; 9:8. [PMID: 29295990 PMCID: PMC5750212 DOI: 10.1038/s41467-017-01586-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
Integrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly encoding the DNA methylome. Therefore, genetic polymorphism impacts on the observed epigenome. Furthermore, large genetic variants alter epigenetic signal dosage. Here, we identify DNA methylation variability between GWAS-SNP risk and non-risk haplotypes. In three subsets comprising 3128 MeDIP-seq peripheral-blood DNA methylomes, we find 7173 consistent and functionally enriched Differentially Methylated Regions. 36.8% can be attributed to common non-SNP genetic variants. CpG-SNPs, as well as facilitative TFBS-motifs, are also enriched. Highlighting their functional potential, CpG-SNPs strongly associate with allele-specific DNase-I hypersensitivity sites. Our results demonstrate strong DNA methylation allelic differences driven by obligatory or facilitative genetic effects, with potential direct or regional disease-related repercussions. These allelic variations require disentangling from pure tissue-specific modifications, may influence array studies, and imply underestimated population variability in current reference epigenomes. Genomic polymorphisms affect the epigenome, which in turn influences how epigenome- and genome-wide analysis are interpreted. Here, the authors characterise allelic differences in DNA methylation driven by obligatory or facilitative genetic effects, which may affect disease-related loci.
Collapse
Affiliation(s)
- Christopher G Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK. .,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK. .,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, SO17 1BJ, UK. .,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK.
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Leonie Roos
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Richard J Acton
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK.,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, SO17 1BJ, UK.,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | | | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Kirsten Ward
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jun Wang
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| |
Collapse
|
70
|
Thurner M, van de Bunt M, Torres JM, Mahajan A, Nylander V, Bennett AJ, Gaulton KJ, Barrett A, Burrows C, Bell CG, Lowe R, Beck S, Rakyan VK, Gloyn AL, McCarthy MI. Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci. eLife 2018; 7:31977. [PMID: 29412141 PMCID: PMC5828664 DOI: 10.7554/elife.31977] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/06/2018] [Indexed: 12/30/2022] Open
Abstract
Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n = 17) and DNA methylation (whole-genome bisulphite sequencing, n = 10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.
Collapse
Affiliation(s)
- Matthias Thurner
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Martijn van de Bunt
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Jason M Torres
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Anubha Mahajan
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Kyle J Gaulton
- Department of PediatricsUniversity of California, San DiegoSan DiegoUnited States
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Carla Burrows
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
| | - Christopher G Bell
- Department of Twin Research and Genetic EpidemiologyKings College LondonLondonUnited Kingdom,MRC Lifecourse Epidemiology UnitUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Robert Lowe
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUnited Kingdom
| | - Stephan Beck
- Department of Cancer Biology, UCL Cancer InstituteUniversity College LondonLondonUnited Kingdom
| | - Vardhman K Rakyan
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUnited Kingdom
| | - Anna L Gloyn
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom,Oxford NIHR Biomedical Research CentreChurchill HospitalOxfordUnited Kingdom
| | - Mark I McCarthy
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom,Oxford NIHR Biomedical Research CentreChurchill HospitalOxfordUnited Kingdom
| |
Collapse
|
71
|
Genome-Wide MicroRNA Analysis Implicates miR-30b/d in the Etiology of Alopecia Areata. J Invest Dermatol 2017; 138:549-556. [PMID: 29080678 DOI: 10.1016/j.jid.2017.09.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/11/2022]
Abstract
Alopecia areata (AA) is one of the most common forms of human hair loss. Although genetic studies have implicated autoimmune processes in AA etiology, understanding of the etiopathogenesis is incomplete. Recent research has implicated microRNAs, a class of small noncoding RNAs, in diverse autoimmune diseases. To our knowledge, no study has investigated the role of microRNAs in AA. In this study, gene-based analyses were performed for microRNAs using data of the largest genome-wide association meta-analysis of AA to date. Nominally, significant P-values were obtained for 78 of the 617 investigated microRNAs. After correction for multiple testing, three of the 78 microRNAs remained significant. Of these, miR-30b/d was the most significant microRNA for the follow-up analyses, which also showed lower expression in the hair follicle of AA patients. Target gene analyses for the three microRNAs showed 42 significantly associated target genes. These included IL2RA, TNXB, and ERBB3, which had been identified as susceptibility loci in previous genome-wide association studies. Using luciferase assay, site-specific miR-30b regulation of the AA risk genes IL2RA, STX17, and TNXB was validated. This study implicates microRNAs in the pathogenesis of AA. This finding may facilitate the development of future treatment strategies.
Collapse
|
72
|
Wilson AL, Moffitt LR, Duffield N, Rainczuk A, Jobling TW, Plebanski M, Stephens AN. Autoantibodies against HSF1 and CCDC155 as Biomarkers of Early-Stage, High-Grade Serous Ovarian Cancer. Cancer Epidemiol Biomarkers Prev 2017; 27:183-192. [PMID: 29141850 DOI: 10.1158/1055-9965.epi-17-0752] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/23/2017] [Accepted: 11/09/2017] [Indexed: 11/16/2022] Open
Abstract
Background: Tumor-directed circulating autoantibodies (AAb) are a well-established feature of many solid tumor types, and are often observed prior to clinical disease manifestation. As such, they may provide a good indicator of early disease development. We have conducted a pilot study to identify novel AAbs as markers of early-stage HGSOCs.Methods: A rare cohort of patients with early (FIGO stage Ia-c) HGSOCs for IgG, IgA, and IgM-mediated AAb reactivity using high-content protein arrays (containing 9,184 individual proteins). AAb reactivity against selected antigens was validated by ELISA in a second, independent cohort of individual patients.Results: A total of 184 antigens were differentially detected in early-stage HGSOC patients compared with all other patient groups assessed. Among the six most highly detected "early-stage" antigens, anti-IgA AAbs against HSF1 and anti-IgG AAbs CCDC155 (KASH5; nesprin 5) were significantly elevated in patients with early-stage malignancy. Receiver operating characteristic (ROC) analysis suggested that AAbs against HSF1 provided better detection of early-stage malignancy than CA125 alone. Combined measurement of anti-HSF1, anti-CCDC155, and CA125 also improved efficacy at higher sensitivity.Conclusions: The combined measurement of anti-HSF1, anti-CCDC155, and CA125 may be useful for early-stage HGSOC detection.Impact: This is the first study to specifically identify AAbs associated with early-stage HGSOC. The presence and high frequency of specific AAbs in early-stage cancer patients warrants a larger scale examination to define their value for early disease detection at primary diagnosis and/or recurrence. Cancer Epidemiol Biomarkers Prev; 27(2); 183-92. ©2017 AACR.
Collapse
Affiliation(s)
- Amy L Wilson
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Laura R Moffitt
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Nadine Duffield
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Adam Rainczuk
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia.,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia
| | - Tom W Jobling
- Obstetrics and Gynaecology, Monash Medical Centre, Clayton, Victoria, Australia.,Epworth Research Institute, Epworth HealthCare, Richmond, Victoria, Australia
| | - Magdalena Plebanski
- Department of Immunology and Pathology, Monash University, Melbourne, Australia.,School of Health and Biomedical Sciences, RMIT, Bundoora, Victoria, Australia
| | - Andrew N Stephens
- Department of Molecular and Translational Sciences, Monash University, Victoria, Australia. .,Centre for Cancer Research, Hudson Institute of Medical Research, Victoria, Australia.,Epworth Research Institute, Epworth HealthCare, Richmond, Victoria, Australia
| |
Collapse
|
73
|
Pirini F, Rodriguez-Torres S, Ayandibu BG, Orera-Clemente M, Gonzalez-de la Vega A, Lawson F, Thorpe RJ, Sidransky D, Guerrero-Preston R. INSIG2 rs7566605 single nucleotide variant and global DNA methylation index levels are associated with weight loss in a personalized weight reduction program. Mol Med Rep 2017; 17:1699-1709. [PMID: 29138870 PMCID: PMC5780113 DOI: 10.3892/mmr.2017.8039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/17/2017] [Indexed: 12/27/2022] Open
Abstract
Single nucleotide polymorphisms associated with lipid metabolism and energy balance are implicated in the weight loss response caused by nutritional interventions. Diet-induced weight loss is also associated with differential global DNA methylation. DNA methylation has been proposed as a predictive biomarker for weight loss response. Personalized biomarkers for successful weight loss may inform clinical decisions when deciding between behavioral and surgical weight loss interventions. The aim of the present study was to investigate the association between global DNA methylation, genetic variants associated with energy balance and lipid metabolism, and weight loss following a non-surgical weight loss regimen. The present study included 105 obese participants that were enrolled in a personalized weight loss program based on their allelic composition of the following five energy balance and lipid metabolism-associated loci: Near insulin-induced gene 2 (INSIG2); melanocortin 4 receptor; adrenoceptor β2; apolipoprotein A5; and G-protein subunit β3. The present study investigated the association between a global DNA methylation index (GDMI), the allelic composition of the five energy balance and lipid metabolism-associated loci, and weight loss during a 12 month program, after controlling for age, sex and body mass index (BMI). The results demonstrated a significant association between the GDMI and near INSIG2 locus, after adjusting for BMI and weight loss, and significant trends were observed when stratifying by gender. In conclusion, a combination of genetic and epigenetic biomarkers may be used to design personalized weight loss interventions, enabling adherence and ensuring improved outcomes for obesity treatment programs. Precision weight loss programs designed based on molecular information may enable the creation of personalized interventions for patients, that use genomic biomarkers for treatment design and for treatment adherence monitoring, thus improving response to treatment.
Collapse
Affiliation(s)
- Francesca Pirini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, I‑47014 Meldola, Italy
| | | | - Bola Grace Ayandibu
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - María Orera-Clemente
- Genetic Laboratory, University General Hospital Gregorio Marañón, 28007 Madrid, Spain
| | | | - Fahcina Lawson
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Roland J Thorpe
- Johns Hopkins University Centre for Health Disparities Solutions, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David Sidransky
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| |
Collapse
|
74
|
Jakubowski JL, Labrie V. Epigenetic Biomarkers for Parkinson's Disease: From Diagnostics to Therapeutics. JOURNAL OF PARKINSONS DISEASE 2017; 7:1-12. [PMID: 27792016 PMCID: PMC5302044 DOI: 10.3233/jpd-160914] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Parkinson’s disease (PD) is a prevalent neurodegenerative illness that is often diagnosed after significant pathology and neuronal cell loss has occurred. Biomarkers of PD are greatly needed for early diagnosis, as well as for the prediction of disease progression and treatment outcome. In this regard, the epigenome, which is partially dynamic, holds considerable promise for the development of molecular biomarkers for PD. Epigenetic marks are modified by both DNA sequence and environmental factors associated with PD, and such marks could serve as a unifying predictor of at-risk individuals. Epigenetic abnormalities have been detected in PD and other age-dependent neurodegenerative diseases, some of which were reported to occur early on and were reversible by PD medications. Emerging reports indicate that certain epigenetic differences observed in the PD brain are detectable in more easily accessible tissues. In this review, we examine epigenetic-based strategies for the development of PD biomarkers. Despite the complexities and challenges faced, the epigenome offers a new source of biomarkers with potential etiological relevance to PD, and may expand opportunities for personalized therapies.
Collapse
Affiliation(s)
- Jennifer L Jakubowski
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Viviane Labrie
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA.,Center for Addiction and Mental Health, Toronto, ON, Canada
| |
Collapse
|
75
|
DNA methylation at enhancers identifies distinct breast cancer lineages. Nat Commun 2017; 8:1379. [PMID: 29123100 PMCID: PMC5680222 DOI: 10.1038/s41467-017-00510-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancers exhibit genome-wide aberrant DNA methylation patterns. To investigate how these affect the transcriptome and which changes are linked to transformation or progression, we apply genome-wide expression-methylation quantitative trait loci (emQTL) analysis between DNA methylation and gene expression. On a whole genome scale, in cis and in trans, DNA methylation and gene expression have remarkably and reproducibly conserved patterns of association in three breast cancer cohorts (n = 104, n = 253 and n = 277). The expression-methylation quantitative trait loci associations form two main clusters; one relates to tumor infiltrating immune cell signatures and the other to estrogen receptor signaling. In the estrogen related cluster, using ChromHMM segmentation and transcription factor chromatin immunoprecipitation sequencing data, we identify transcriptional networks regulated in a cell lineage-specific manner by DNA methylation at enhancers. These networks are strongly dominated by ERα, FOXA1 or GATA3 and their targets were functionally validated using knockdown by small interfering RNA or GRO-seq analysis after transcriptional stimulation with estrogen.
Collapse
|
76
|
Ng B, White CC, Klein H, Sieberts SK, McCabe C, Patrick E, Xu J, Yu L, Gaiteri C, Bennett DA, Mostafavi S, De Jager PL. An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. Nat Neurosci 2017; 20:1418-1426. [PMID: 28869584 PMCID: PMC5785926 DOI: 10.1038/nn.4632] [Citation(s) in RCA: 270] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/02/2017] [Indexed: 12/15/2022]
Abstract
We report a multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types. We identify SNPs significantly associated with gene expression, DNA methylation and histone modification levels. Many of these SNPs influence multiple molecular features, and we demonstrate that SNP effects on RNA expression are fully mediated by epigenetic features in 9% of these loci. Further, we illustrate the utility of our new resource, xQTL Serve, by using it to prioritize the cell type(s) most affected by an xQTL. We also reanalyze published genome wide association studies using an xQTL-weighted analysis approach and identify 18 new schizophrenia and 2 new bipolar susceptibility variants, which is more than double the number of loci that can be discovered with a larger blood-based expression eQTL resource.
Collapse
Affiliation(s)
- B Ng
- Department of Statistics and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - CC White
- Broad Institute, Cambridge, Massachusetts, USA
| | - H Klein
- Broad Institute, Cambridge, Massachusetts, USA
- Center for Translational & Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | | | - C McCabe
- Broad Institute, Cambridge, Massachusetts, USA
| | - E Patrick
- Broad Institute, Cambridge, Massachusetts, USA
| | - J Xu
- Broad Institute, Cambridge, Massachusetts, USA
| | - L Yu
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - C Gaiteri
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - DA Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - S Mostafavi
- Department of Statistics and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research, CIFAR program in Child and Brain Development, Toronto, Canada
| | - PL De Jager
- Broad Institute, Cambridge, Massachusetts, USA
- Center for Translational & Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, New York, USA
| |
Collapse
|
77
|
Schröder C, Leitão E, Wallner S, Schmitz G, Klein-Hitpass L, Sinha A, Jöckel KH, Heilmann-Heimbach S, Hoffmann P, Nöthen MM, Steffens M, Ebert P, Rahmann S, Horsthemke B. Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function. Epigenetics Chromatin 2017; 10:37. [PMID: 28747224 PMCID: PMC5530492 DOI: 10.1186/s13072-017-0144-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/20/2017] [Indexed: 01/23/2023] Open
Abstract
Background There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. Results We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before. The DMRs fall into different chromatin states, where methylation is inversely correlated with active, but not repressive histone marks. However, methylation is not correlated with the expression of associated genes. High-resolution single nucleotide polymorphism (SNP) genotyping of the five donors revealed evidence for a role of cis-acting genetic variation in establishing methylation patterns. To validate this finding in a larger cohort, we performed genome-wide association studies (GWAS) using SNP genotypes and 450k array methylation data from blood samples of 1128 individuals. Only 30/157 (19%) DMRs include at least one 450k CpG, which shows that these arrays miss a large proportion of DNA methylation variation. In most cases, the GWAS peak overlapped the CpG position, and these regions are enriched for CREB group, NF-1, Sp100 and CTCF binding motifs. In two cases, there was tentative evidence for a trans-effect by KRAB zinc finger proteins. Conclusions Allele-specific DNA methylation occurs in discrete chromosomal regions and is driven by genetic variation in cis and trans, but in general has little effect on gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0144-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Christopher Schröder
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Stefan Wallner
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Anupam Sinha
- Institute of Clinical Molecular Biology, Kiel University, University Hospital, Kiel, Germany
| | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - Peter Ebert
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarland Informatics Campus, Saarbrücken, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany.
| |
Collapse
|
78
|
Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B. Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biol 2017. [PMID: 28629478 PMCID: PMC5477265 DOI: 10.1186/s13059-017-1250-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS). Sequence variants in CCCTC-binding factor (CTCF) and transcription factor binding sites have been mechanistically linked to mQTLs and hap-ASM. Identifying these sites can point to disease-associated transcriptional pathways, with implications for targeted treatment and prevention.
Collapse
Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Alyssa Shearer
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neurobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Taub Institute for Research on Alzheimer's disease and the Aging Brain, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
| |
Collapse
|
79
|
Yotova I, Hsu E, Do C, Gaba A, Sczabolcs M, Dekan S, Kenner L, Wenzl R, Tycko B. Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis. PLoS One 2017; 12:e0170859. [PMID: 28125717 PMCID: PMC5268815 DOI: 10.1371/journal.pone.0170859] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. Genes found to have DM included examples encoding transporters (SLC22A23), signaling components (BDNF, DAPK1, ROR1, and WNT5A) and transcription factors (GATA family, HAND2, HOXA cluster, NR5A1, OSR2, TBX3). Intriguingly, among the TF genes with DM we also found JAZF1, a proto-oncogene affected by chromosomal translocations in endometrial stromal tumors. Using RNA-Seq we identified a subset of the DM genes showing differential expression (DE), with the likelihood of DE increasing with the extent of the DM and its location in enhancer elements. Supporting functional relevance, treatment of stromal cells with the hypomethylating drug 5aza-dC led to activation of DAPK1 and SLC22A23 and repression of HAND2, JAZF1, OSR2, and ROR1 mRNA expression. We found that global 5hmC is decreased in endometriotic versus normal epithelial but not stroma cells, and for JAZF1 and BDNF examined by oxidative bis-seq, found that when 5hmC is detected, patterns of 5hmC paralleled those of 5mC. Together with prior studies, these results define a consistent epigenetic signature in endometriosis stromal cells and nominate specific transcriptional and signaling pathways as therapeutic targets.
Collapse
Affiliation(s)
- Iveta Yotova
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
- * E-mail:
| | - Emily Hsu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Catherine Do
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Aulona Gaba
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Matthias Sczabolcs
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Sabine Dekan
- Department of Experimental Pathology, Clinical Institute of Pathology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Department of Experimental Pathology, Clinical Institute of Pathology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
- Pathology Laboratory Animal Pathology University of Veterinary Medicine Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Rene Wenzl
- Department of Gynecology and Gynecological Oncology, University Clinic of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| |
Collapse
|
80
|
Do C, Xing Z, Yu YE, Tycko B. Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models. Epigenomics 2016; 9:189-207. [PMID: 27911079 PMCID: PMC5549717 DOI: 10.2217/epi-2016-0138] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An important line of postgenomic research seeks to understand how genetic factors can influence epigenetic patterning. Here we review epigenetic effects of chromosomal aneuploidies, focusing on findings in Down syndrome (DS, trisomy 21). Recent work in human DS and mouse models has shown that the extra chromosome 21 acts in trans to produce epigenetic changes, including differential CpG methylation (DS-DM), in specific sets of downstream target genes, mostly on other chromosomes. Mechanistic hypotheses emerging from these data include roles of chromosome 21-linked methylation pathway genes (DNMT3L and others) and transcription factor genes (RUNX1, OLIG2, GABPA, ERG and ETS2) in shaping the patterns of DS-DM. The findings may have broader implications for trans-acting epigenetic effects of chromosomal and subchromosomal aneuploidies in other human developmental and neuropsychiatric disorders, and in cancers.
Collapse
Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Taub Institute for Research on Alzheimer's disease & the Aging Brain, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| |
Collapse
|