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Volume 12, Issue 3 (May-Jun 2018)
mljgoums 2018, 12(3): 6-11 |
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Kheiri S, Aliarab A, Haghighatfard H, Sadeghi H. Prioritization of rs187728237 and rs80320514 as miRNA-related Variants of Human AEG-1 Gene. mljgoums 2018; 12 (3) :6-11
URL: http://mlj.goums.ac.ir/article-1-1076-en.html
URL: http://mlj.goums.ac.ir/article-1-1076-en.html
1- Laboratory Sciences Research Center, Golestan University of Medical Science, Gorgan, Iran
2- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
3- Cellular & Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
4- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran Medical Cellular & Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran ,Hsadeqi86@gmail.com
2- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
3- Cellular & Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
4- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran Medical Cellular & Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran ,
Abstract: (11231 Views)
ABSTRACT
Background and objectives: 3' untranslated region (3'UTR) single nucleotide polymorphisms (SNPs) represent genetic variations that may potentially affect binding of miRNA to coding genes, potentially leading to complex disorders. We aimed to perform in silico analysis of the potential phenotypic effect of 3'UTR SNPs on human astrocyte elevated gene-1 (AEG-1), a newly identified candidate cancer gene.
Methods: We gathered a list of all 3'UTR SNPs located in the human AEG-1 gene from the SNP database. Analysis of the potential effects was done using MirSNP and MicroSNiper.
Results: Analysis by the MirSNP estimated that rs187728237 might increase the affinity of two miRNAs and decrease the affinity of 10 other miRNAs to the AEG-1 transcript. Moreover, MicroSNiPer showed that rs80320514 might affect 24 putative miRNA binding sites in the 3'UTR of AEG-1.
Conclusion: Based on our findings, it can be concluded that the 3'UTR SNPs located in the human AEG-1 gene may be within the miRNA targets of the transcript, therefore affecting the stability of putative miRNA-target interactions.
Keywords: AEG-1, miRNA, SNPs, 3' Untranslated Region.
Background and objectives: 3' untranslated region (3'UTR) single nucleotide polymorphisms (SNPs) represent genetic variations that may potentially affect binding of miRNA to coding genes, potentially leading to complex disorders. We aimed to perform in silico analysis of the potential phenotypic effect of 3'UTR SNPs on human astrocyte elevated gene-1 (AEG-1), a newly identified candidate cancer gene.
Methods: We gathered a list of all 3'UTR SNPs located in the human AEG-1 gene from the SNP database. Analysis of the potential effects was done using MirSNP and MicroSNiper.
Results: Analysis by the MirSNP estimated that rs187728237 might increase the affinity of two miRNAs and decrease the affinity of 10 other miRNAs to the AEG-1 transcript. Moreover, MicroSNiPer showed that rs80320514 might affect 24 putative miRNA binding sites in the 3'UTR of AEG-1.
Conclusion: Based on our findings, it can be concluded that the 3'UTR SNPs located in the human AEG-1 gene may be within the miRNA targets of the transcript, therefore affecting the stability of putative miRNA-target interactions.
Keywords: AEG-1, miRNA, SNPs, 3' Untranslated Region.
Research Article: Original Paper |
Received: 2018/04/30 | Accepted: 2018/04/30 | Published: 2018/04/30 | ePublished: 2018/04/30
Received: 2018/04/30 | Accepted: 2018/04/30 | Published: 2018/04/30 | ePublished: 2018/04/30
References
1. Yoo BK, Chen D, Su Z-z, Gredler R, Yoo J, Shah K, et al. Molecular mechanism of chemoresistance by astrocyte elevated gene-1. Cancer research. 2010; 70(8): 3249-58. doi: 10.1158/0008-5472.CAN-09-4009. [DOI:10.1158/0008-5472.CAN-09-4009]
2. Yoo BK, Emdad L, Su Z-z, Villanueva A, Chiang DY, Mukhopadhyay ND, et al. Astrocyte elevated gene-1 regulates hepatocellular carcinoma development and progression. The Journal of clinical investigation. 2009; 119(3): 465-77. doi: 10.1172/JCI36460. [DOI:10.1172/JCI36460]
3. Emdad L, Lee S-G, Su ZZ, Jeon HY, Boukerche H, Sarkar D, et al. Astrocyte elevated gene-1 (AEG-1) functions as an oncogene and regulates angiogenesis. Proceedings of the National Academy of Sciences. 2009; 106(50): 21300-5. doi: 10.1073/pnas.0910936106. [DOI:10.1073/pnas.0910936106]
4. Yu C, Chen K, Zheng H, Guo X, Jia W, Li M, et al. Overexpression of astrocyte elevated gene-1(AEG-1) is associated with esophageal squamous cell carcinoma (ESCC) progression and pathogenesis.Carcinogenesis. 2009; 30(5): 894-901. doi: 10.1093/carcin/bgp064. [DOI:10.1093/carcin/bgp064]
5. Yoo BK, Emdad L, Lee S-G, Su Z-z, Santhekadur P, Chen D, et al. Astrocyte elevated gene-1 (AEG-1): A multifunctional regulator of normal and abnormal physiology. Pharmacology & therapeutics. 2011; 130(1): 1-8. [DOI:10.1016/j.pharmthera.2011.01.008]
6. Lee SG, Su ZZ, Emdad L, Sarkar D, Fisher PB. Astrocyte elevated gene-1 (AEG-1) is a target gene of oncogenic Ha-ras requiring phosphatidylinositol 3-kinase and c-Myc. Proceedings of the National Academy of Sciences. 2006; 103(46): 17390-5. DOI:10.1073/pnas.0608386103. [DOI:10.1073/pnas.0608386103]
7. Emdad L, Sarkar D, Su Z-z, Randolph A, Boukerche H, Valerie K, et al. Activation of the nuclear factor κB pathway by astrocyte elevated gene-1: implications for tumor progression and metastasis. Cancer research. 2006; 66(3): 1509-16. DOI:10.1158/0008-5472.CAN-05-3029. [DOI:10.1158/0008-5472.CAN-05-3029]
8. Ramensky V, Bork P, Sunyaev S. Human non‐synonymous SNPs: server and survey. Nucleic acids research. 2002; 30(17): 3894-900. [DOI:10.1093/nar/gkf493]
9. Liu H, Song X, Liu C, Xie L, Wei L, Sun R. Knockdown of astrocyte elevated gene-1 inhibits proliferation and enhancing chemo-sensitivity to cisplatin or doxorubicin in neuroblastoma cells. Journal of Experimental & Clinical Cancer Research. 2009; 28(1): 19. doi: 10.1186/1756-9966-28-19. [DOI:10.1186/1756-9966-28-19]
10. Li J, Zhang N, Song L-B, Liao W-T, Jiang L-L, Gong L-Y, et al. Astrocyte elevated gene-1 is a novel prognostic marker for breast cancer progression and overall patient survival. Clinical Cancer Research. 2008; 14(11): 3319-26. [DOI:10.1158/1078-0432.CCR-07-4054]
11. Sutherland HG, Lam YW, Briers S, Lamond AI, Bickmore WA. 3D3/lyric: a novel transmembrane protein of the endoplasmic reticulum and nuclear envelope, which is also present in the nucleolus. Experimental cell research. 2004; 294(1): 94-105. [DOI:10.1016/j.yexcr.2003.11.020]
12. Ying Z, Li J, Li M. Astrocyte elevated gene 1: biological functions and molecular mechanism in cancer and beyond. Cell & bioscience. 2011;1(1): 36. doi: 10.1186/2045-3701-1-36. [DOI:10.1186/2045-3701-1-36]
13. Lee S-G, Kang D-C, DeSalle R, Sarkar D, Fisher PB. AEG-1/MTDH/LYRIC, the beginning: initial cloning, structure, expression profile, and regulation of expression. Advances in cancer research. 2013;120: :1-38. doi: 10.1016/B978-0-12-401676-7.00001-2. [DOI:10.1016/B978-0-12-401676-7.00001-2]
14. Lin P, Yu S, Yang P. MicroRNA in lung cancer. British journal of cancer. 2010; 103(8): 1144-8. doi:10.1038/sj.bjc.6605901. [DOI:10.1038/sj.bjc.6605901]
15. Hsu S-D, Lin F-M, Wu W-Y, Liang C, Huang W-C, Chan W-L, et al. miRTarBase: a database curates experimentally validated microRNA–target interactions. Nucleic acids research. 2010 39(Database issue): D163-9. doi: 10.1093/nar/gkq1107. [DOI:10.1093/nar/gkq1107]
16. Barenboim M, Zoltick BJ, Guo Y, Weinberger DR. MicroSNiPer: a web tool for prediction of SNP
17. effects on putative microRNA targets. Human mutation. 2010; 31(11):1223-32. doi: 10.1002/humu.21349. [DOI:10.1002/humu.21349]
18. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009; 136(2): 215-33. doi: 10.1016/j.cell.2009.01.002. [DOI:10.1016/j.cell.2009.01.002]
19. genes. Cancer journal (Sudbury, Mass). 2012;18(3):223-31. doi: 10.1097/PPO.0b013e318258b771. [DOI:10.1097/PPO.0b013e318258b771]
20. Eder M, Scherr M. MicroRNA and lung cancer. N Engl J Med. 2005; 352(23): 2446-8. DOI:10.1056/NEJMcibr051201. [DOI:10.1056/NEJMcibr051201]
21. Jevsinek Skok D, Godnic I, Zorc M, Horvat S, Dovc P, Kovac M, et al. Genome‐wide in silico screening for microRNA genetic variability in livestock species. Animal genetics. 2013; 44(6): 669-77. doi: 10.1111/age.12072. [DOI:10.1111/age.12072]
22. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005; 120(1): 15-20. [DOI:10.1016/j.cell.2004.12.035]
23. Nahvi A, Shoemaker CJ, Green R. An expanded seed sequence definition accounts for full regulation of the hid 3′ UTR by bantam miRNA. RNA. 2009; 15(5): 814-22. [DOI:10.1261/rna.1565109]
24. Sun G, Yan J, Noltner K, Feng J, Li H, Sarkis DA, et al. SNPs in human miRNA genes affect biogenesis and function. Rna. 2009; 15(9):1640-51. doi: 10.1261/rna.1560209. [DOI:10.1261/rna.1560209]
25. Wang C, Yang Q. Astrocyte elevated gene-1 and breast cancer (Review). Oncology letters. 2011; 2(3): 399-405. [DOI:10.3892/ol.2011.268]
26. Nicoloso MS, Sun H, Spizzo R, Kim H, Wickramasinghe P, Shimizu M, et al. Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Cancer research. 2010; 70(7): 2789-98. [DOI:10.1158/0008-5472.CAN-09-3541]
27. Naderi M, Gharaei R, Soleymani-Nejadian E, Samadian E. In Silico survey of functional coding variants in human AEG-1 gene. Egyptian Journal of Medical Human Genetics. 2013; 14(4): 419-22. [DOI:10.1016/j.ejmhg.2013.08.002]
28. Liu C, Zhang F, Li T, Lu M, Wang L, Yue W, et al. MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs. BMC genomics.2012;13(1): 661. doi: 10.1186/1471-2164-13-661. [DOI:10.1186/1471-2164-13-661]
29. Hajjari M, Mowla SJ, Faghihi MA. Editorial: Molecular Function and Regulation of Non-coding RNAs in Multifactorial Diseases. Frontiers in genetics. 2016;7. Fang Z, Rajewsky N. The impact of miRNA target sites in coding sequences and in 3′ UTRs. PloS one. 2011; 6(3): e18067.
30. Trisilowati, Mallet DG. In silico experimental modeling of cancer treatment. ISRN oncology. 2012;2012:828701. doi: 10.5402/2012/828701. [DOI:10.5402/2012/828701]
31. Kang D-c, Su Z-z, Sarkar D, Emdad L, Volsky DJ, Fisher PB. Cloning and characterization of HIV-1-inducible astrocyte elevated gene-1, AEG-1. Gene. 2005; 353(1): 8-15. [DOI:10.1016/j.gene.2005.04.006]
32. Dai L, Huang C, Chen L, Shan G, Li Z. Altered expression of microRNAs in the response to ER stress. Science Bulletin. 2015; 60(2): 202-9. [DOI:10.1007/s11434-014-0657-z]
33. Ma J, Mannoor K, Gao L, Tan A, Guarnera MA, Zhan M, et al. Characterization of microRNA transcriptome in lung cancer by next-generation deep sequencing. Molecular oncology. 2014; 8(7): 1208-19. doi: 10.1016/j.molonc.2014.03.019. [DOI:10.1016/j.molonc.2014.03.019]
34. Liang T, Guo L, Liu C. Genome-wide analysis of mir-548 gene family reveals evolutionary and functional implications. BioMed Research International. 2012; 2012 :679563. doi: 10.1155/2012/679563. [DOI:10.1155/2012/679563]
35. Rentoft M, Fahlén J, Coates P, Laurell G, Sjöström B, Rydén P, et al. miRNA analysis of formalinfixed squamous cell carcinomas of the tongue is affected by age of the samples. International journal of oncology. 2011; 38(1): 61-9.
36. Chen H, guo Sun J, Cao X-w, Ma X-g, Xu J-p, Luo F-k, et al. Preliminary validation of ERBB2 expression regulated by miR-548d-3p and miR-559. Biochemical and biophysical research communications. 2009; 385(4): 596-600. doi: 10.1016/j.bbrc.2009.05.113. [DOI:10.1016/j.bbrc.2009.05.113]
37. Keller A, Leidinger P, Lange J, Borries A, Schroers H, Scheffler M, et al. Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PloS one. 2009; 4(10): e7440. doi: 10.1371/journal.pone.0007440. [DOI:10.1371/journal.pone.0007440]
38. Ali S, Almhanna K, Chen W, Philip PA, Sarkar FH. Differentially expressed miRNAs in the plasma may provide a molecular signature for aggressive pancreatic cancer. Am J Transl Res. 2010; 3(1): 28-47.
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