Efficient detection of differentially methylated regions in the genome of patients with thoracic aortic dissection and association with MMP2 hypermethylation

Li,Ni; Lin,Hangjuan; Zhou,Hua; Zheng,Dawei; Xu,Guodong; Shi,Huoshun; Zhu,Xiuying; Gao,Jianqing; Shao,Guofeng; Sun,Lebo

doi:10.3892/etm.2020.8753

Efficient detection of differentially methylated regions in the genome of patients with thoracic aortic dissection and association with MMP2 hypermethylation

Authors:
- Ni Li
- Hangjuan Lin
- Hua Zhou
- Dawei Zheng
- Guodong Xu
- Huoshun Shi
- Xiuying Zhu
- Jianqing Gao
- Guofeng Shao
- Lebo Sun
View Affiliations

Affiliations: Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China, Department of Pharmacy, Ningbo Traditional Chinese Medicine Hospital, Ningbo, Zhejiang 315041, P.R. China, Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
Published online on: May 15, 2020 https://doi.org/10.3892/etm.2020.8753
Pages: 1073-1081
Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

DNA methylation is known to regulate the expression of numerous genes but its role in the pathogenesis of thoracic aortic dissection (TAD) has remained largely elusive. In the present study, the DNA methylome of patients with TAD was analyzed using a methylation microarray and bisulfite pyrosequencing was used to determine whether the hypermethylation of matrix metalloproteinase 2 (MMP2) specifically is associated with TAD. Chip‑based whole‑DNA methylome analysis was performed on 4 male patients with TAD and 4 male healthy controls using an Illumina HumanMethylation EPIC 850K BeadChip. The resulting data were analyzed by clustering and principal component analysis, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the differentially methylated genes to interrogate their biological functions. Compared to the healthy controls, 3,362 loci were differentially methylated in the patients with TAD with a statistical significance of P<0.05, while 1,223 loci had a significance of P<0.01. Among these loci, 2,019 were hypermethylated and 1,343 were hypomethylated. From GO analysis within the biological process category, the MMP2, MMP14 and WNT2B genes were identified. enrichment was observed for loci involved in cellular component organization, enzyme‑linked receptor protein signaling pathways (potentially having a key role in the development of cardiopulmonary function disorders) and vascular reconstruction. Bisulfite pyrosequencing of plasma samples indicated significantly increased methylation (P<0.01) of the CpG site at position 2 in the promoter of MMP2 in the TAD group relative to the healthy controls, and the mean methylation level of four CpG sites on the MMP2 gene in the TAD group was slightly higher than that in the control group, but not significantly. Hypermethylation of the MMP2 promoter may be a promising novel diagnostic and prognostic biomarker for TAD. Future studies on the epigenetics of biomarkers linked to vascular reconstruction and immune function may provide further insight into the pathogenesis and progression of TAD.

View Figures

View References

1	Ohle R: Diagnosing acute aortic dissection: Both an artery and a science. Acad Emerg Med. 25(1186)2018.PubMed/NCBI View Article : Google Scholar
2	Zhao H, Wen D, Duan W, An R, Li J and Zheng M: Identification of CTA-Based predictive findings for temporary and permanent neurological dysfunction after repair in acute type a aortic dissection. Sci Rep. 8(9740)2018.PubMed/NCBI View Article : Google Scholar
3	Strzyz P: A sugar rush of DNA methylation. Nat Rev Mol Cell Biol. 19(617)2018.PubMed/NCBI View Article : Google Scholar
4	Pan S, Lai H, Shen Y, Breeze C, Beck S, Hong T, Wang C and Teschendorff AE: DNA methylome analysis reveals distinct epigenetic patterns of ascending aortic dissection and bicuspid aortic valve. Cardiovasc Res. 113:692–704. 2017.PubMed/NCBI View Article : Google Scholar
5	Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, et al: Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 49:359–367. 2013.PubMed/NCBI View Article : Google Scholar
6	Longo GM, Xiong W, Greiner TC, Zhao Y, Fiotti N and Baxter BT: Matrix metalloproteinases 2 and 9 work in concert to produce aortic aneurysms. J Clin Invest. 110:625–632. 2002.PubMed/NCBI View Article : Google Scholar
7	Moran S, Arribas C and Esteller M: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics. 8:389–399. 2016.PubMed/NCBI View Article : Google Scholar
8	Nasu T, Satoh M, Ohmomo H, Shiwa Y, Komaki S, Ono K, Shimizu A, Taguchi S, Takahashi Y, Osaki T, et al: Epigenome-wide association study identifies a novel DNA methylation in patients with severe aortic valve stenosis. Circ Genom Precis Med. 13(e002649)2020.PubMed/NCBI View Article : Google Scholar
9	Xu H, Du S, Fang B, Li C, Jia X, Zheng S, Wang S, Li Q, Su W, Wang N, et al: VSMC-specific EP4 deletion exacerbates angiotensin II-induced aortic dissection by increasing vascular inflammation and blood pressure. Proc Natl Acad Sci USA. 116(8457)2019.PubMed/NCBI View Article : Google Scholar
10	Xu L, Zheng D, Wang L, Jiang D, Liu H, Xu L, Liao Q, Zhang L, Liu P, Shi X, et al: GCK gene-body hypomethylation is associated with the risk of coronary heart disease. Biomed Res Int. 2014(151723)2014.PubMed/NCBI View Article : Google Scholar
11	Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, Van Djik S, Muhlhausler B, Stirzaker C and Clark SJ: Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biol. 17(208)2016.PubMed/NCBI View Article : Google Scholar
12	Kirby MK, Ramaker RC, Roberts BS, Lasseigne BN, Gunther DS, Burwell TC, Davis NS, Gulzar ZG, Absher DM, Cooper SJ, et al: Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns. BMC Cancer. 17(273)2017.PubMed/NCBI View Article : Google Scholar
13	Silva-Martinez GA, Zaina S and Lund G: Array probe density and pathobiological relevant CpG calling bias in human disease and physiological DNA methylation profiling. Brief Funct Genomics. 17:42–48. 2018.PubMed/NCBI View Article : Google Scholar
14	Taylor JY, Wright ML, Crusto CA and Sun YV: The intergenerational impact of genetic and psychological factors on blood pressure (InterGEN) study: Design and methods for complex DNA analysis. Biol Res Nurs. 18:521–530. 2016.PubMed/NCBI View Article : Google Scholar
15	Zheng D, Chen X, Li N, Sun L, Zhou Q, Shi H, Xu G, Liu J, Xu L, Duan S and Shao G: Differentially methylated regions in patients with rheumatic heart disease and secondary pulmonary arterial hypertension. Exp Ther Med. 14:1367–1372. 2017.PubMed/NCBI View Article : Google Scholar
16	Nagata H, Kozaki KI, Muramatsu T, Hiramoto H, Tanimoto K, Fujiwara N, Imoto S, Ichikawa D, Otsuji E, Miyano S, et al: Genome-wide screening of DNA methylation associated with lymph node metastasis in esophageal squamous cell carcinoma. Oncotarget. 8:37740–37750. 2017.PubMed/NCBI View Article : Google Scholar
17	Chen X, Shen LH, Gui LX, Yang F, Li J, Cao SZ, Zuo ZC, Ma XP, Deng JL, Ren ZH, et al: Genome-wide DNA methylation profile of prepubertal porcine testis. Reprod Fertil Dev. 30:349–358. 2018.PubMed/NCBI View Article : Google Scholar
18	Liu O, Xie W, Qin Y, Jia L, Zhang J, Xin Y, Guan X, Li H, Gong M, Liu Y, et al: MMP-2 gene polymorphisms are associated with type A aortic dissection and aortic diameters in patients. Medicine (Baltimore). 95(e5175)2016.PubMed/NCBI View Article : Google Scholar
19	Shalata A, Mahroom M, Milewicz DM, Limin G, Kassum F, Badarna K, Tarabeih N, Assy N, Fell R, Cohen H, et al: Fatal thoracic aortic aneurysm and dissection in a large family with a novel MYLK gene mutation: Delineation of the clinical phenotype. Orphanet J Rare Dis. 13(41)2018.PubMed/NCBI View Article : Google Scholar
20	Tang W, Yao L, Hoogeveen RC, Alonso A, Couper DJ, Lutsey PL, Steenson CC, Guan W, Hunter DW, Lederle FA and Folsom AR: The association of biomarkers of inflammation and extracellular matrix degradation with the risk of abdominal aortic aneurysm: The ARIC Study. Angiology. 70:130–140. 2019.PubMed/NCBI View Article : Google Scholar
21	Li H, Chan YC and Cheng SW: Contemporary endovascular treatment of type B aortic dissection in China. Asian Cardiovasc Thorac Ann. 24:739–749. 2016.PubMed/NCBI View Article : Google Scholar
22	Bhandari R, Aatre RD and Kanthi Y: Diagnostic approach and management of genetic aortopathies. Vasc Med. 25:63–77. 2020.PubMed/NCBI View Article : Google Scholar
23	Liao M, Zou S, Bao Y, Jin J, Yang J, Liu Y, Green M, Yang F and Qu L: Matrix metalloproteinases are regulated by MicroRNA 320 in macrophages and are associated with aortic dissection. Exp Cell Res. 370:98–102. 2018.PubMed/NCBI View Article : Google Scholar
24	Li T, Lv Z, Jing JJ, Yang J and Yuan Y: Matrix metalloproteinase family polymorphisms and the risk of aortic aneurysmal diseases: A systematic review and meta-analysis. Clin Genet. 93:15–32. 2018.PubMed/NCBI View Article : Google Scholar
25	Lin X, Tan JYL, The AL, Lim IY, Liew SJ, MacIsaac JL, Chong YS, Gluckman PD, Kobor MS, Cheong CY and Karnani N: Cell type-specific DNA methylation in neonatal cord tissue and cord blood: A 850K-reference panel and comparison of cell-types. Epigenetics. 13:941–958. 2018.PubMed/NCBI View Article : Google Scholar
26	Li YH, Li XM, Lu MS, LV MF and JIN X: The expression of the BRM and MMP2 genes in thoracic aortic aneurysm and aortic dissection. Eur Rev Med Pharmacol Sci. 21:2743–2748. 2017.PubMed/NCBI