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Integrative Analysis of Genome-Wide Association Studies and DNA Methylation Profile Identified Genetic Control Genes of DNA Methylation for Kashin-Beck Disease.
Cartilage. 2019 Jun 20 [Online ahead of print]C

Abstract

OBJECTIVE

Epigenetic modifications of DNA are regarded as a crucial factor for understanding the molecular basis of complex phenotypes. This study aims to uncover insight into the epigenetic modifications for Kashin-Beck disease (KBD) by integrating genome-wide association studies (GWAS), methylation quantitative trait loci (meQTLs), and DNA methylation profiles data.

DESIGN

The knee articular cartilages of 5 KBD patients and 5 healthy controls were collected for DNA methylation profiling, using Illumina Infinium HumanMethylation450 BeadChip. Mass spectrograph validation of identified differently methylated genes was conducted using independent samples of 4 KBD patients and 3 healthy controls, together with a previous sample of 2743 Han Chinese individuals of GWAS study for KBD and a study of 697 normal subjects for meQTLs annotation datasets. KBD GWAS single nucleotide polymorphisms (SNPs) and normal meQTLs SNPs were integrated with DNA methylation profiles of KBD articular cartilage to identify genetic control (GC) genes of DNA methylation for KBD. Quantitative polymerase chain reaction (qPCR) was performed to validate the mRNA expression of several identified candidate genes.

RESULTS

A total of 162 CpG sites, 253 SNPs, and 123 GC genes for KBD were identified. Enrichment analysis detected 642 marked GO terms and 19 KEGG pathways (P < 0.05). Six potential key GC genes were conducted for qPCR experiment (ERG, MN1, MITF, WISP1, TRIO, and NOSTRIN).

CONCLUSIONS

The results suggest that GC genes of DNA methylation may lead to the erosion of cartilage in KBD, which may help us in understanding the epigenetic alteration of KBD.

Authors+Show Affiliations

1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.1 Key Laboratory of Trace Elements and Endemic Disease of National Health Commission of the People's Republic of China, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31220921

Citation

Li, Ping, et al. "Integrative Analysis of Genome-Wide Association Studies and DNA Methylation Profile Identified Genetic Control Genes of DNA Methylation for Kashin-Beck Disease." Cartilage, 2019, p. 1947603519858748.
Li P, Wu C, Guo X, et al. Integrative Analysis of Genome-Wide Association Studies and DNA Methylation Profile Identified Genetic Control Genes of DNA Methylation for Kashin-Beck Disease. Cartilage. 2019.
Li, P., Wu, C., Guo, X., Wen, Y., Liu, L., Liang, X., Du, Y., Zhang, L., Ma, M., Cheng, S., Cheng, B., Wang, S., & Zhang, F. (2019). Integrative Analysis of Genome-Wide Association Studies and DNA Methylation Profile Identified Genetic Control Genes of DNA Methylation for Kashin-Beck Disease. Cartilage, 1947603519858748. https://doi.org/10.1177/1947603519858748
Li P, et al. Integrative Analysis of Genome-Wide Association Studies and DNA Methylation Profile Identified Genetic Control Genes of DNA Methylation for Kashin-Beck Disease. Cartilage. 2019 Jun 20;1947603519858748. PubMed PMID: 31220921.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Integrative Analysis of Genome-Wide Association Studies and DNA Methylation Profile Identified Genetic Control Genes of DNA Methylation for Kashin-Beck Disease. AU - Li,Ping, AU - Wu,Cuiyan, AU - Guo,Xiong, AU - Wen,Yan, AU - Liu,Li, AU - Liang,Xiao, AU - Du,Yanan, AU - Zhang,Lu, AU - Ma,Mei, AU - Cheng,Shiqiang, AU - Cheng,Bolun, AU - Wang,Sen, AU - Zhang,Feng, Y1 - 2019/06/20/ PY - 2019/6/22/entrez PY - 2019/6/22/pubmed PY - 2019/6/22/medline KW - DNA methylation KW - GWAS KW - Kashin-Beck disease KW - genetic control genes KW - meQTLs SP - 1947603519858748 EP - 1947603519858748 JF - Cartilage JO - Cartilage N2 - OBJECTIVE: Epigenetic modifications of DNA are regarded as a crucial factor for understanding the molecular basis of complex phenotypes. This study aims to uncover insight into the epigenetic modifications for Kashin-Beck disease (KBD) by integrating genome-wide association studies (GWAS), methylation quantitative trait loci (meQTLs), and DNA methylation profiles data. DESIGN: The knee articular cartilages of 5 KBD patients and 5 healthy controls were collected for DNA methylation profiling, using Illumina Infinium HumanMethylation450 BeadChip. Mass spectrograph validation of identified differently methylated genes was conducted using independent samples of 4 KBD patients and 3 healthy controls, together with a previous sample of 2743 Han Chinese individuals of GWAS study for KBD and a study of 697 normal subjects for meQTLs annotation datasets. KBD GWAS single nucleotide polymorphisms (SNPs) and normal meQTLs SNPs were integrated with DNA methylation profiles of KBD articular cartilage to identify genetic control (GC) genes of DNA methylation for KBD. Quantitative polymerase chain reaction (qPCR) was performed to validate the mRNA expression of several identified candidate genes. RESULTS: A total of 162 CpG sites, 253 SNPs, and 123 GC genes for KBD were identified. Enrichment analysis detected 642 marked GO terms and 19 KEGG pathways (P < 0.05). Six potential key GC genes were conducted for qPCR experiment (ERG, MN1, MITF, WISP1, TRIO, and NOSTRIN). CONCLUSIONS: The results suggest that GC genes of DNA methylation may lead to the erosion of cartilage in KBD, which may help us in understanding the epigenetic alteration of KBD. SN - 1947-6043 UR - https://www.unboundmedicine.com/medline/citation/31220921/Integrative_Analysis_of_Genome-Wide_Association_Studies_and_DNA_Methylation_Profile_Identified_Genetic_Control_Genes_of_DNA_Methylation_for_Kashin-Beck_Disease L2 - https://journals.sagepub.com/doi/10.1177/1947603519858748?url_ver=Z39.88-2003&amp;rfr_id=ori:rid:crossref.org&amp;rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -
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