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Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips.
Biomed Environ Sci. 2016 07; 29(7):539-43.BE

Abstract

To understand how differentially methylated genes (DMGs) might affect the pathogenesis of Kashin-Beck disease (KBD). Genome-wide methylation profiling of whole blood from 12 matched KBD and controls pairs was performed using a high-resolution Infinium 450 K methylation array. In total, 97 CpG sites were differentially methylated in KBD compared to the normal controls; of these sites, 36 sites were significantly hypermethylated (covering 22 genes) and 61 sites were significantly hypomethylated (covering 34 genes). Of these genes, 14 significant pathways were identified, the most significant P value pathway was type I diabetes mellitus pathway and pathways associated with autoimmune diseases and inflammatory diseases were included in this study. Subsequently, 4 CpG sites in HLA-DRB1 were validated using bisulfite sequencing polymerase chain reaction (BSP) in articular cartilage, and the results showed significant differences in the methylation status between KBD and controls, consistent with the results of the high-resolution array. These results suggested that differences in genome-wide DNA methylation exist between KBD and the controls, and the biological pathways support the autoimmune disease and inflammatory disease hypothesis of KBD.

Authors+Show Affiliations

Department of Pediatrics, The First Affiliated Hospital of the Medical College of Xi'an Jiaotong University, Xi'an 710061, Shannxi, China.Department of Oncosurgery, The First Affiliated Hospital of the Medical College of Xi'an Jiaotong University, Xi'an 710061, Shannxi, China.School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Environment and Gene Related Diseases of Ministry of Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, Xi'an 710061, Shannxi, China.School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Environment and Gene Related Diseases of Ministry of Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, Xi'an 710061, Shannxi, China.School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Environment and Gene Related Diseases of Ministry of Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, Xi'an 710061, Shannxi, China.School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Environment and Gene Related Diseases of Ministry of Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, Xi'an 710061, Shannxi, China.

Pub Type(s)

Letter

Language

eng

PubMed ID

27554126

Citation

Shi, Xiao Wei, et al. "Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips." Biomedical and Environmental Sciences : BES, vol. 29, no. 7, 2016, pp. 539-43.
Shi XW, Shi BH, Lyu AL, et al. Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips. Biomed Environ Sci. 2016;29(7):539-43.
Shi, X. W., Shi, B. H., Lyu, A. L., Zhang, F., Zhou, T. T., & Guo, X. (2016). Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips. Biomedical and Environmental Sciences : BES, 29(7), 539-43. https://doi.org/10.3967/bes2016.072
Shi XW, et al. Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips. Biomed Environ Sci. 2016;29(7):539-43. PubMed PMID: 27554126.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Exploring Genome-wide DNA Methylation Profiles Altered in Kashin-Beck Disease Using Infinium Human Methylation 450 Bead Chips. AU - Shi,Xiao Wei, AU - Shi,Bo Hui, AU - Lyu,Ai Li, AU - Zhang,Feng, AU - Zhou,Tian Tian, AU - Guo,Xiong, PY - 2015/12/10/received PY - 2016/05/05/accepted PY - 2016/8/25/entrez PY - 2016/8/25/pubmed PY - 2017/1/28/medline SP - 539 EP - 43 JF - Biomedical and environmental sciences : BES JO - Biomed. Environ. Sci. VL - 29 IS - 7 N2 - To understand how differentially methylated genes (DMGs) might affect the pathogenesis of Kashin-Beck disease (KBD). Genome-wide methylation profiling of whole blood from 12 matched KBD and controls pairs was performed using a high-resolution Infinium 450 K methylation array. In total, 97 CpG sites were differentially methylated in KBD compared to the normal controls; of these sites, 36 sites were significantly hypermethylated (covering 22 genes) and 61 sites were significantly hypomethylated (covering 34 genes). Of these genes, 14 significant pathways were identified, the most significant P value pathway was type I diabetes mellitus pathway and pathways associated with autoimmune diseases and inflammatory diseases were included in this study. Subsequently, 4 CpG sites in HLA-DRB1 were validated using bisulfite sequencing polymerase chain reaction (BSP) in articular cartilage, and the results showed significant differences in the methylation status between KBD and controls, consistent with the results of the high-resolution array. These results suggested that differences in genome-wide DNA methylation exist between KBD and the controls, and the biological pathways support the autoimmune disease and inflammatory disease hypothesis of KBD. SN - 0895-3988 UR - https://www.unboundmedicine.com/medline/citation/27554126/Exploring_Genome_wide_DNA_Methylation_Profiles_Altered_in_Kashin_Beck_Disease_Using_Infinium_Human_Methylation_450_Bead_Chips_ L2 - https://doi.org/10.3967/bes2016.072 DB - PRIME DP - Unbound Medicine ER -