Analysis of differential microRNA expression in patient with gallbladder stones through high-throughput sequencing technologies

doi:10.11958/j.issn.0253-9896.2015.04.004

Abstract

Abstract: Abstract: Objective To detect the differential expression profile of microRNAs between patients with or without gall⁃ bladder stone. Methods Samples from 30 patients with gallbladder stones (GS) and 30 without gallbladder stones (GP) were collected, in which microRNAs expression profiles were examined using high-throughput sequencing instrument Illumi⁃ na HiSeq 2500. MicroRNA sequences were obtained and compared to Genebank and Rfam database for classification. Differ⁃ entially expressed microRNAs were screened, and their target genes were predicted. Significant enrichment analysis of GO and KEGG were performed. Real-time quantitative PCR was performed on selected miRNAs in order to validate their expres⁃ sion. Results Clean tags were obtained from both GS group (n=2 215 832) and GP group (n=1 424 770). A total of 17 mi⁃ croRNAs were differentially expressed between GS and GP groups with statistical significance, among which 9 were up-regu⁃ lated and 8 were down-regulated in GS group compared to those in GP group. GO (Gene ocology) analysis showed that target genes were enriched in ion binding and transport, apolipoprotein binding, calcium channel activity, protein kinase activity, steroid hormone biosynthesis and metabolism. KEGG（Kyoto Encyclopedia of Genes and Genomes）analysis is shown for the target genes enriched in cancer related pathways, including WNT, HIPPO pathways. qRT-PCR validation of some differen⁃ tially expressed miRNAs confirmed the result of high-throughput data analysis. Conclusion The differential expression levels of microRNAs may play an important role in occurrence and development of gallbladder stones.

Key words: microRNA, gene expression profiling, sequence analysis, cholecystolithiasis, differential expression, highthrough sequencing, bioinformation

References

[1] Liu J, Zhang H. MicroRNA in developments of sugar metabolism[J]. Tianjin Med J, 2013, 41(1): 83-86. [刘佳, 张宏. MicroRNAs 与糖代谢的研究进展[J]. 天津医药, 2013, 41(1): 83-86]. [2] Zhou N, Mo Y. Roles of microRNAs in cancer stem cells[J]. Frontiers in bioscience (Scholar edition), 2011, 4: 810-818.
[3] Sreekumar R, Sayan BS, Mirnezami AH, et al. MicroRNA control of invasion and metastasis pathways[J]. Front Genet, 2011, 2: 58. http://dx.doi.org/10.3389/fgene.2011.00058
[4] Zhang LQ, Sun GL. Research and clinical application of miRNAs in cancer stem cells and as tumor markers [J]. Tianjin Med J, 2014, 42 (10): 1048-1050. [张娄强, 孙庚林. 肿瘤干细胞miRNA 及miRNA 作为肿瘤标志物的研究和临床应用进展[J]. 天津医药, 2014, 42(10):1048-1050].
[5] Lammert F, Carey MC, Paigen B. Chromosomal organization of can⁃ didate genes involved in cholesterol gallstone formation: a murine gallstone map[J]. Gastroenterology, 2001, 120(1): 221-238.
[6] Brabletz S, Brabletz T. The ZEB/miR-200 feedback loop-a motor of cellular plasticity in development and cancer[J]. EMBO Rep, 2010, 11(9): 670-677. doi: 10.1038/embor.2010.117
[7] Srivastava K, Srivastava A, Mittal B. Common genetic variants in pre-microRNAs and risk of gallbladder cancer in North Indian pop⁃ ulation[J].J Hum Genet, 2010, 55(8): 495-499. [8] Wang J, Bi J, Liu X, et al. Has- miR- 146a polymorphism (rs2910164) and cancer risk: a meta-analysis of 19 case–control studies[J]. Mol Biol Rep, 2012, 39(4): 4571- 4579. doi: 10.1007/ s11033-011-1247-7.
[9] Jin K, Xiang Y, Tang J, et al. miR-34 is associated with poor prog⁃ nosis of patients with gallbladder cancer through regulating telo⁃ mere length in tumor stem cells[J].Tumour Biol, 2014, 35(2):1503- 1510.
[10] Sachdeva M, Mo YY. MicroRNA-145 suppresses cell invasion and metastasis by directly targeting mucin 1[J]. Cancer Res, 2010, 70 (1): 378-387. doi: 10.1158/0008-5472.CAN-09-2021.
[11] Inyawilert W, Fu TY, Lin CT, et al. MicroRNA-199a mediates mu⁃ cin 1 expression in mouse uterus during implantation[J]. Reprod Fertil Dev, 2014, 26(5):653-664. doi: 10.1071/RD12097.
[12] Srivastava SK, Bhardwaj A, Singh S, et al. MicroRNA-150 directly targets MUC4 and suppresses growth and malignant behavior of pancreatic cancercells[J]. Carcinogenesis, 2011, 32(12): 1832- 1839. doi: 10.1093/carcin/bgr223.
[13] Wang HH, Portincasa P, Bari O, et al. Prevention of cholesterol gall⁃ stones by inhibiting hepatic biosynthesis and intestinal absorption of cholesterol[J]. Eur J Clin Invest, 2013, 43(4): 413- 426. doi: 10.1111/eci.12058.
[14] Yu LH, Yin XG, Wu WX, et al. Expression and clinical significance of gallbladder Hedgehog signaling pathway effector proteins[J]. Chinese Journal of General Surgery, 2013, 28(12): 968-969. [虞玲华, 殷新光, 邬万新, 等. 胆囊癌中Hedgehog 信号通路效应蛋白的表达及临床意义[J]. 中华普通外科杂志, 2013, 28(12):968-969].

[1]	XIAO Xiaoli, XIE Yao, LONG Zhi. Changes and clinical significance of serum miR-155 and miR-205-5p expression levels in patients with hepatitis C virus infection [J]. Tianjin Medical Journal, 2024, 52(9): 967-970.
[2]	ZHANG Chunhong, HUANG Hongchao, LIU Yue, DU Lilong, XU Haiwei, LI Ning, LI Yongjin. Identification of key ferroptosis genes in paraspinal muscle degeneration based on RNA sequencing and bioinformatics analysis [J]. Tianjin Medical Journal, 2024, 52(9): 991-995.
[3]	YAN Haifeng, WU Xiaohong, LIN Yuqing, HUO Kaiming, WANG Yingying. Effect of miR-582-5p targeting regulation of FOXO1 on neuronal damage in neonatal rats with hypoxic ischemic encephalopathy [J]. Tianjin Medical Journal, 2024, 52(4): 356-361.
[4]	XUE Wenping, QIN Wei, LIU Tingting, ZHANG Aiwen, SHI Fei. Correlation between serum miR-34a and miR-182 levels before PCI and postoperative contrast-induced nephropathy occurrence in elderly patients with acute coronary syndrome [J]. Tianjin Medical Journal, 2024, 52(4): 422-426.
[5]	MAN Jun, GAO Yanyan, SONG Longfei, GAO Fusheng. The effect of lncRNA FEZF1-AS1 targeting regulation of miR-200c-3p on biological behaviors of human lung fibroblasts [J]. Tianjin Medical Journal, 2024, 52(3): 231-236.
[6]	MIAO Chunbo, XU Yingchun, CHANG Yifang. Phlorizin allevistes oxidative stress and apoptosis of rat cardiac myocytes H9C2 induced by hypoxia/reoxygenation by down-regulating miR-125a-5p [J]. Tianjin Medical Journal, 2024, 52(12): 1233-1238.
[7]	WU Meina, DAI Weizheng, PAN Yudun, FU Maolin, CHEN Xiaoyu. Clinical value of routine electroencephalogram combined with serum miR-146a and miR-129-5p levels in diagnosis of drug-resistant epilepsy patients [J]. Tianjin Medical Journal, 2024, 52(11): 1207-1210.
[8]	DENG Qianbao, ZHANG Zhongxia, WANG Ru, XU Lin, LUO Shu. Efficacy analysis of a preeclampsia risk prediction model based on exosomal multiple miRNA expression levels [J]. Tianjin Medical Journal, 2024, 52(1): 91-96.
[9]	HOU Yongbo, YU Junma, ZHU Haijuan. New research progress of exosomes in the treatment of myocardial infarction [J]. Tianjin Medical Journal, 2023, 51(9): 1016-1019.
[10]	ZHAO Dandan, ZHANG Sue, MIAO Liye, WANG Yan. Effects of aconitine regulating miR-181d-5p/DDX3 axis on proliferation and apoptosis of HeLa cells of cervical cancer [J]. Tianjin Medical Journal, 2023, 51(9): 922-927.
[11]	ZHANG Liqun, WURI Jimusi, ZHENG Xiaoming, WANG Lin, HAN Yuxiu, ZHANG Wei, YAN Tao. The mechanisms of circFAT1 on the biological process of GBM cells [J]. Tianjin Medical Journal, 2023, 51(8): 797-802.
[12]	WANG Yuning, SONG Juxing, TIAN Zhigang, HAO Guorong, SHEN Hao. The effect of piceatannol on the migration and invasion of cervical cancer cells by regulating miR-106b-5p/RUNX3 axis [J]. Tianjin Medical Journal, 2023, 51(8): 814-819.
[13]	LI Shaoru, LI Yan, LIU Shan, HU Ruili. Influences of lncRNA SNHG11 on proliferation, apoptosis, migration and invasion of ovarian cancer cells by regulating miR-184/CARM1 signaling axis [J]. Tianjin Medical Journal, 2023, 51(6): 561-567.
[14]	ZHAO Yuanyuan, WU Xiaohua. The effect of exosomal miR-1260a derived from human umbilical mesenchymal stem cells on apoptosis of granulosa cells in PCOS patients [J]. Tianjin Medical Journal, 2023, 51(4): 337-343.
[15]	JIANG Hua, SHEN Yanmei, MA Xunkai. The effects of down-regulation of miR-106a-5p on hydrogen peroxide-induced cardiomyocyte damage and JAK1/STAT3 pathway [J]. Tianjin Medical Journal, 2023, 51(2): 113-117.