Journal of Shandong University (Health Sciences) ›› 2019, Vol. 57 ›› Issue (11): 1-8.doi: 10.6040/j.issn.1671-7554.0.2019.813

   

Comparison of DNA methylation levels between three-dimensional and two-dimensional cultured umbilical cord mesenchymal stem cells

HUANG Jinxian1, LI Dong2, LI Cong1, SHI Qing2, JU Xiuli1   

  1. 1. Department of Pediatrics, Qilu Hospital of Shandong University, Jinan 250012, Shandong, China;
    2. Stem Cell and Regenerative Medicine Research Center, Shandong University, Jinan 250012, Shandong, China
  • Published:2022-09-27

PDF (PC)

16

Abstract: Objective To explore the effects of three-dimensional(3D)culture on the whole genome DNA methylation profile of umbilical cord mesenchymal stem cells(UC-MSCs). Methods UC-MSCs were isolated from umbilical cords using tissue adherent culture. Their phenotypes were identified with flow cytometry. Then UC-MSCs were cultured in 3D polyvinyl fluoride nested scaffolds and 2D conventional culture flask, respectively. Acridine orange was used to observe UC-MSCs on the scaffold. Methylated DNA immunoprecipitation(MeDIP-Seq)method was used to detect the whole genome DNA methylation of UC-MSCs. Results UC-MSCs were successfully isolated from umbilical cords and able to grow on the 3D scaffold. The genomic DNA methylation level of UC-MSCs increased after 3D culture. Gene ontology analysis showed that the up-regulated differential methylation genes were involved in protein metabolism, membrane-related organelle composition, and enzyme activity regulation. Down-regulated differential methylation genes were involved in vesicle trafficking and cGMP metabolic processes regulating. According to pathway analyses, differential methylation genes were involved in RNA transport, neuroactive ligand-receptor interaction, cellular communication, and 山 东 大 学 学 报 (医 学 版)57卷11期 -黄金献,等.三维和二维培养的脐带间充质干细胞DNA甲基化水平比较 \=-vesicle secretion-related pathways. Conclusion 3D culture changes the DNA methylation profile of UC-MSCs. The up-regulated methylation levels will alter the function of cell migration and proliferation. 3D culture reduces the methylation level of immune regulation and secretion of vesicle-related genes in UC-MSCs.

Key words: Mesenchymal stromal cells, Three-dimensional culture, DNA methylation, methylated DNA immunoprecipitation sequencing

CLC Number: 

  • R574
[1] Arutyunyan I, Elchaninov A, Makarov A, et al. Umbilical cord as prospective source for mesenchymal stem cell-based therapy[J]. Stem Cells Int, 2016, 2016: 17. doi: 10.1155/2016/6901286.
[2] Cosgrove BD, Mui KL, Driscoll TP, et al. N-cadherin adhesive interactions modulate matrix mechanosensing and fate commitment of mesenchymal stem cells[J]. Nat Mater, 2016, 15(12): 1297-1306.
[3] Qazi TH, Mooney DJ, Duda GN, et al. Biomaterials that promote cell-cell interactions enhance the paracrine function of MSCs[J]. Biomaterials, 2017, 140: 103-114. doi: 10.1016/j.biomaterials.2017.06.019.
[4] Li Y, Wu Q, Wang Y, et al. Immunogenicity of hepatic differentiated human umbilical cord mesenchymal stem cells promoted by porcine decellularized liver scaffolds[J]. Xenotransplantation, 2017, 24(1): e12287.
[5] Moore LD, Le T, Fan G. DNA methylation and its basic function[J]. Neuropsychopharmacology, 2013, 38(1): 23-38.
[6] Jeltsch A, Jurkowska RZ. New concepts in DNA methylation[J]. Trends Biochem Sci, 2014, 39(7): 310-318.
[7] Fouse SD, Nagarajan RP, Costello JF. Genome-scale DNA methylation analysis[J]. Epigenomics, 2010, 2(1): 105-117.
[8] Dominici M, Le Blanc K, Mueller I, et al. Minimal criteria for defining multipotent mesenchymal stromal cells. The International Society for Cellular Therapy position statement[J]. Cytotherapy, 2006, 8(4): 315-317.
[9] 宁雪, 李栋, 汪大琨, 等. 脐带间充质干细胞体外衰老过程中生物学特性及基因表达谱的变化[J]. 中国实验血液学杂志, 2012, 20(2): 458-465. NING Xue, LI Dong, WANG Dakun, et al. Changes of biological characteristics and gene expression profile of umbilical cord mesenchymal stem cells during senescence in culture[J]. Journal of Experimental Hematology, 2012, 20(2):458-465.
[10] Goldberg MW. Nuclear pore complex tethers to the cytoskeleton[J]. Semin Cell Dev Biol, 2017, 68: 52-58. doi: 10.1016/j.semcdb.2017.06.017.
[11] Holzer K, Ori A, Cooke A, et al. Nucleoporin Nup155 is part of the p53 network in liver cancer[J]. Nat Commun, 2019, 10(1): 2147. doi: 10.1038/s41467-019-10133-z.
[12] Jin LZ, Lu JS, Gao JW. Silencing SUMO2 promotes protection against degradation and apoptosis of nucleus pulposus cells through p53 signaling pathway in intervertebral disc degeneration[J]. Biosci Rep, 2018, 38(3). pii: BSR20171523. doi: 10.1042/BSR20171523.
[13] Gomes-Duarte A, Lacerda R, Menezes J, et al. eIF3: a factor for human health and disease[J]. RNA Biol, 2018, 15(1): 26-34.
[14] Wang Z, Murigneux V, Le Hir H. Transcriptome-wide modulation of splicing by the exon junction complex[J]. Genome Biol, 2014, 15(12): 551.
[15] Silver DL, Leeds KE, Hwang HW, et al. The EJC component Magoh regulates proliferation and expansion of neural crest-derived melanocytes[J]. Dev Biol, 2013, 375(2): 172-181.
[16] Kim YD, Lee J, Kim HS, et al. The unique spliceosome signature of human pluripotent stem cells is mediated by SNRPA1, SNRPD1, and PNN[J]. Stem Cell Res, 2017, 22: 43-53. doi: 10.1016/j.scr.2017.05.010.
[17] Shi Y, Simmons MN, Seki T, et al. Change in gene expression subsequent to induction of Pnn/DRS/memA: increase in p21(cip1/waf1)[J]. Oncogene, 2001, 20(30): 4007-4018.
[18] Yuan X, Zhang T, Yao F, et al. THO complex-dependent posttranscriptional control contributes to vascular smooth muscle cell fate decision[J]. Circ Res, 2018, 123(5): 538-549.
[19] Siebel C, Lendahl U. Notch signaling in development, tissue homeostasis, and disease[J]. Physiol Rev, 2017, 97(4): 1235-1294.
[20] Hans CP, Sharma N, Sen S, et al. Transcriptomics analysis reveals new insights into the roles of Notch1 signaling on macrophage polarization[J]. Sci Rep, 2019, 9(1): 7999. doi: 10.1038/s41598-019-44266-4.
[21] Choi BY, Choi Y, Park JS, et al. Inhibition of Notch1 induces population and suppressive activity of regulatory T cell in inflammatory arthritis[J]. Theranostics, 2018, 8(17): 4795-4804.
[22] Sandel DA, Liu M, Ogbonnaya N, et al. Notch3 is involved in adipogenesis of human adipose-derived stromal/stem cells[J]. Biochimie, 2018, 150: 31-36. doi: 10.1016/j.biochi.2018.04.020.
[23] Kim C, Park JM, Song Y, et al. HIF1α-mediated AIMP3 suppression delays stem cell aging via the induction of autophagy[J]. Aging Cell, 2019, 18(2): e12909. doi: 10.1111/acel.12909.
[24] García-Heredia JM, Carnero A. NUMB and NUMBL differences in gene regulation[J]. Oncotarget, 2018, 9(10): 9219-9234.
[25] Nan J, Guan S, Jin X, et al. Down-regulation of C-terminal binding protein 2(CtBP2)inhibits proliferation, migration, and invasion of human SHSY5Y cells in vitro[J]. Neurosci Lett, 2017, 647: 104-109. doi: 10.1016/j.neulet.2017.02.006.
[26] Phinney DG, Pittenger MF. Concise review: MSC-derived exosomes for cell-free therapy[J]. Stem Cells, 2017, 35(4): 851-858.
[27] Andreeva AV, Kutuzov MA, Voyno-Yasenetskaya TA. A ubiquitous membrane fusion protein alpha SNAP: a potential therapeutic target for cancer, diabetes and neurological disorders?[J]. Expert Opin Ther Targets, 2006, 10(5): 723-733.
[28] Miot S, Voituron N, Sterlin A, et al. The vesicular glutamate transporter VGLUT3 contributes to protection against neonatal hypoxic stress[J]. J Physiol, 2012, 590(20): 5183-5198.
[29] Abonyo BO, Wang P, Narasaraju TA, et al. Characterization of alpha-soluble N-ethylmaleimide-sensitive fusion attachment protein in alveolar type II cells: implications in lung surfactant secretion[J]. Am J Respir Cell Mol Biol, 2003, 29(3 Pt 1): 273-282. doi: 10.1165/rcmb.2002-0189OC.
[1] WANG Jing, XIE Yan, LI Peilong, DU Lutao, WANG Chuanxin. Value of abnormal methylation of cg16212145 on GZMB gene in early screening of gastric cancer [J]. Journal of Shandong University (Health Sciences), 2022, 60(6): 26-34.
[2] ZHENG Haotian, WANG Guanghui, ZHAO Xiaogang, WANG Yadong, ZENG Yukai, DU Jiajun. A prognostic risk model for LKB1 mutant lung adenocarcinoma based on aberrant DNA methylation sites [J]. Journal of Shandong University (Health Sciences), 2022, 60(3): 51-58.
[3] Bing LUO. Impact of EBV on the epigenetics of gastric carcinoma [J]. Journal of Shandong University (Health Sciences), 2021, 59(5): 30-39.
[4] ZHOU Xue, WANG Yanrong, TIAN Long, MA Lianghong, YAN Bei, TIAN Jia, ZHANG Fan, ZHOU Yue, WANG Hongyan. DNA methylation and expression of SNRPN and GRB10 imprinted genes in human semen freezing-thawing process [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2017, 55(1): 54-59.
[5] XU Jia, SONG Qiang. Deletion of the RASSF1A gene and promoter methylation in the bone marrow of patients with myelodysplastic syndromes [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2013, 51(2): 65-69.
[6] CHEN Hai-yan, YAO Shu-zhe, ZHANG Xiao-ying, ZHANG Jian-ping, ZHANG Cui-juan, ZHANG Ting-guo. Effect of the methylation of SOCS-3 and 3-OST-2 genes in endometrial cancer and its clinical pathological significances [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2013, 51(06): 75-80.
[7] GUO Xiao-yu1, JIANG Yan2, XING Zhao-quan3, GUO Zhao-xin3, FANG Zhi-qing3, LIU Zhao-xu1,3. The effect of methyltransferase inhibitor on the expression of
XAF1 mRNA in prostate cancer [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2012, 50(12): 94-.
[8] LU Fei, LIU Chuanfang, MA Daoxin, LIU Yanping，KONG Haili, ZHANG Jingjing. Effect of 5-Aza-2′-deoxycytidine on SOCS-1 gene expression, proliferation and apoptosis in RPMI8226 cells [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2010, 48(4): 45-.
[9] . Expression and methylation of p16 in carcinoma ex pleomorphic adenoma of the parotid gland [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2009, 47(11): 108-110.
[10] . Deletion of the p15 Gene and Promoter Methylation in the Bone Marrow 
of patients with Myelodysplastic Syndromes [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2009, 47(10): 106-109.
[11] YANG Xi1, GAO Peng2, XUE Yuwen1, WANG Yan2, LIU Wenjun2, ZHANG Xiaofang2
. Expression of DNA methyltransferase 1（DNMT1）in lung adenocarcinoma and its prognosis significance [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2009, 47(01): 30-33.
[12] LI Qi-rong,LIU Pei-shu,ZHANG Yan. Aberrant methylation of the RASSF1A gene in tissues and serums of ovarian cancer patients and its clinical significance [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2007, 45(10): 1046-1049.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Copyright 2018 © Editorial office of Journal of Shandong University (Health Sciences)
Supported by Beijing Magtech Co.Ltd