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Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor J, Xu Z, Lie RT, Gjessing HK, Jugessur A. Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. NAR Genom Bioinform 2021; 3:lqab035. [PMID: 33987535 PMCID: PMC8092375 DOI: 10.1093/nargab/lqab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/04/2022] Open
Abstract
DNA methylation is the most widely studied epigenetic mark in humans and plays an essential role in normal biological processes as well as in disease development. More focus has recently been placed on understanding functional aspects of methylation, prompting the development of methods to investigate the relationship between heterogeneity in methylation patterns and disease risk. However, most of these methods are limited in that they use simplified models that may rely on arbitrarily chosen parameters, they can only detect differentially methylated regions (DMRs) one at a time, or they are computationally intensive. To address these shortcomings, we present a wavelet-based method called 'Wavelet Screening' (WS) that can perform an epigenome-wide association study (EWAS) of thousands of individuals on a single CPU in only a matter of hours. By detecting multiple DMRs located near each other, WS identifies more complex patterns that can differentiate between different methylation profiles. We performed an extensive set of simulations to demonstrate the robustness and high power of WS, before applying it to a previously published EWAS dataset of orofacial clefts (OFCs). WS identified 82 associated regions containing several known genes and loci for OFCs, while other findings are novel and warrant replication in other OFCs cohorts.
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Affiliation(s)
- William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, 0450, Oslo, Norway
| | - Jack A Taylor
- Epidemiology Branch and Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
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Lou S, Ma L, Kan S, Yu X, Wang Y, Yang F, Zhu G, Fan L, Li D, Wang H, Wang W, Zhang W, Wang L, Pan Y. Association Study of Genetic Variants in Autophagy Pathway and Risk of Non-syndromic Cleft Lip With or Without Cleft Palate. Front Cell Dev Biol 2020; 8:576. [PMID: 32766242 PMCID: PMC7381156 DOI: 10.3389/fcell.2020.00576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/15/2020] [Indexed: 11/13/2022] Open
Abstract
Although genetic variants in autophagy pathway genes were associated with the risk of oral cancers and early development in embryos, their associations with non-syndromic cleft lip with or without cleft palate (NSCL/P) risk remained unclear. A two-stage case-control study (2,027 NSCL/P cases and 1,843 controls) was performed to investigate the associations between single nucleotide polymorphisms (SNPs) in 23 autophagy pathway genes and NSCL/P susceptibility. The logistic regression model was used to calculate effects of SNPs on NSCL/P susceptibility. Gene-based analysis was performed via the sequence kernel association test (SKAT) and multi-marker analysis of genomic annotation (MAGMA) methods. Expression quantitative trait loci (eQTL) analysis was conducted using NSCL/P lip tissue samples. Gene expression during embryonic development was evaluated using RNA-Seq. Functional roles were explored by luciferase activity assay, cell apoptosis, proliferation, and cycle in vitro. Rs2301104 in HIF1A was significantly associated with NSCL/P susceptibility in the combined analysis (OR: 1.29, 95% CI: 1.09-1.29, P = 3.39 × 10-03), and showed strong evidence of association heterogeneity (P = 9.06 × 10-03) with obvious association in the female (OR: 1.80; 95% CI: 1.32-2.45; P = 1.79 × 10-04). The G allele of rs2301104 was associated with enhanced transcription activity and high expression of HIF1A compared with that of C allele. Moreover, rs2301104 exhibited an eQTL effect for HIF1A with its GC/CC genotypes associated with decreased HIF1A expression compared with those with GG genotypes (P = 3.1 × 10-2). Knockdown of HIF1A induced cell apoptosis and inhibited cell proliferation in human embryonic palate mesenchyme (HEPM) and human oral epithelium cells (HOEC). This study demonstrated that rs2301104 in autophagy pathway gene HIF1A was associated with susceptibility of NSCL/P.
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Affiliation(s)
- Shu Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shiyi Kan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Xin Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yuting Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Liwen Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Hua Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Wei Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Weibing Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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