Genomics & Informatics

  • 제14권3호
  • /
  • Pages.112-124
  • /
  • 2016
  • /
  • 1598-866X(pISSN)
  • /
  • 2234-0742(eISSN)
한국유전체학회 (Korea Genome Organization)
권호 표지
DOI QR코드

DOI QR Code

In Silico Study of miRNA Based Gene Regulation, Involved in Solid Cancer, by the Assistance of Argonaute Protein

  • Rath, Surya Narayan (BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology) ;
  • Das, Debasrita (BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology) ;
  • Konkimalla, V Badireenath (School of Biological Sciences, National Institute of Science Education and Research) ;
  • Pradhan, Sukanta Kumar (BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology)
  • 투고 : 2016.06.13
  • 심사 : 2016.08.09
  • 발행 : 2016.09.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Solid tumor is generally observed in tissues of epithelial or endothelial cells of lung, breast, prostate, pancreases, colorectal, stomach, and bladder, where several genes transcription is regulated by the microRNAs (miRNAs). Argonaute (AGO) protein is a family of protein which assists in miRNAs to bind with mRNAs of the target genes. Hence, study of the binding mechanism between AGO protein and miRNAs, and also with miRNAs-mRNAs duplex is crucial for understanding the RNA silencing mechanism. In the current work, 64 genes and 23 miRNAs have been selected from literatures, whose deregulation is well established in seven types of solid cancer like lung, breast, prostate, pancreases, colorectal, stomach, and bladder cancer. In silico study reveals, miRNAs namely, miR-106a, miR-21, and miR-29b-2 have a strong binding affinity towards PTEN, TGFBR2, and VEGFA genes, respectively, suggested as important factors in RNA silencing mechanism. Furthermore, interaction between AGO protein (PDB ID-3F73, chain A) with selected miRNAs and with miRNAs-mRNAs duplex were studied computationally to understand their binding at molecular level. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding miRNAs based gene silencing mechanism in solid cancer.

키워드

참고문헌

  1. Alison RM. Encyclopedia of Life Sciences: Cancer. London: Nature Publishing Group, 2001.
  2. Lee YS, Dutta A. MicroRNAs in cancer. Annu Rev Pathol 2009;4:199-227. https://doi.org/10.1146/annurev.pathol.4.110807.092222
  3. Grammatikakis I, Gorospe M, Abdelmohsen K. Modulation of cancer traits by tumor suppressor microRNAs. Int J Mol Sci 2013;14:1822-1842. https://doi.org/10.3390/ijms14011822
  4. Zhang B, Pan X, Cobb GP, Anderson TA. microRNAs as oncogenes and tumor suppressors. Dev Biol 2007;302:1-12. https://doi.org/10.1016/j.ydbio.2006.08.028
  5. Esquela-Kerscher A, Slack FJ. Oncomirs-microRNAs with a role in cancer. Nat Rev Cancer 2006;6:259-269. https://doi.org/10.1038/nrc1840
  6. Lu Z, Liu M, Stribinskis V, Klinge CM, Ramos KS, Colburn NH, et al. MicroRNA-21 promotes cell transformation by targeting the programmed cell death 4 gene. Oncogene 2008;27:4373-4379. https://doi.org/10.1038/onc.2008.72
  7. Xu LF, Wu ZP, Chen Y, Zhu QS, Hamidi S, Navab R. MicroRNA-21 (miR-21) regulates cellular proliferation, invasion, migration, and apoptosis by targeting PTEN, RECK and Bcl-2 in lung squamous carcinoma, Gejiu City, China. PLoS One 2014;9:e103698. https://doi.org/10.1371/journal.pone.0103698
  8. Wang P, Zou F, Zhang X, Li H, Dulak A, Tomko RJ Jr, et al. microRNA-21 negatively regulates Cdc25A and cell cycle progression in colon cancer cells. Cancer Res 2009;69:8157-8165. https://doi.org/10.1158/0008-5472.CAN-09-1996
  9. Gong AY, Eischeid AN, Xiao J, Zhao J, Chen D, Wang ZY, et al. miR-17-5p targets the p300/CBP-associated factor and modulates androgen receptor transcriptional activity in cultured prostate cancer cells. BMC Cancer 2012;12:492. https://doi.org/10.1186/1471-2407-12-492
  10. Fang L, Li H, Wang L, Hu J, Jin T, Wang J, et al. Micro-RNA-17-5p promotes chemotherapeutic drug resistance and tumour metastasis of colorectal cancer by repressing PTEN expression. Oncotarget 2014;5:2974-2987. https://doi.org/10.18632/oncotarget.1614
  11. Yamada N, Kitamoto S, Yokoyama S, Hamada T, Goto M, Tsutsumida H, et al. Epigenetic regulation of mucin genes in human cancers. Clin Epigenetics 2011;2:85-96. https://doi.org/10.1007/s13148-011-0037-3
  12. Nagpal N, Kulshreshtha R. miR-191: an emerging player in disease biology. Front Genet 2014;5:99.
  13. Wang H, Guan X, Tu Y, Zheng S, Long J, Li S, et al. MicroRNA-29b attenuates non-small cell lung cancer metastasis by targeting matrix metalloproteinase 2 and PTEN. J Exp Clin Cancer Res 2015;34:59. https://doi.org/10.1186/s13046-015-0169-y
  14. Liu H, Wang B, Lin J, Zhao L. microRNA-29b: an emerging player in human cancer. Asian Pac J Cancer Prev 2014;15:9059-9064. https://doi.org/10.7314/APJCP.2014.15.21.9059
  15. Ru P, Steele R, Newhall P, Phillips NJ, Toth K, Ray RB. miRNA-29b suppresses prostate cancer metastasis by regulating epithelial-mesenchymal transition signaling. Mol Cancer Ther 2012;11:1166-1173. https://doi.org/10.1158/1535-7163.MCT-12-0100
  16. Wang Y, Li Y, Ma Z, Yang W, Ai C. Mechanism of micro-RNA-target interaction: molecular dynamics simulations and thermodynamics analysis. PLoS Comput Biol 2010;6:e1000866. https://doi.org/10.1371/journal.pcbi.1000866
  17. Gong J, Li J, Wang Y, Liu C, Jia H, Jiang C, et al. Characterization of microRNA-29 family expression and investigation of their mechanistic roles in gastric cancer. Carcinogenesis 2014;35:497-506. https://doi.org/10.1093/carcin/bgt337
  18. Wu LH, Cai QQ, Dong YW, Wang R, He BM, Qi B, et al. Decoy oligonucleotide rescues IGF1R expression from microRNA-223 suppression. PLoS One 2013;8:e82167. https://doi.org/10.1371/journal.pone.0082167
  19. Schickel R, Boyerinas B, Park SM, Peter ME. MicroRNAs: key players in the immune system, differentiation, tumorigenesis and cell death. Oncogene 2008;27:5959-5974. https://doi.org/10.1038/onc.2008.274
  20. Yin Y, Li J, Chen S, Zhou T, Si J. MicroRNAs as diagnostic biomarkers in gastric cancer. Int J Mol Sci 2012;13:12544-12555. https://doi.org/10.3390/ijms131012544
  21. Ding G, Huang G, Liu HD, Liang HX, Ni YF, Ding ZH, et al. MiR-199a suppresses the hypoxia-induced proliferation of non-small cell lung cancer cells through targeting $HIF1{\alpha}$. Mol Cell Biochem 2013;384:173-180. https://doi.org/10.1007/s11010-013-1795-3
  22. Zhang Y, Fan KJ, Sun Q, Chen AZ, Shen WL, Zhao ZH, et al. Functional screening for miRNAs targeting Smad4 identified miR-199a as a negative regulator of TGF-$\beta$ signalling pathway. Nucleic Acids Res 2012;40:9286-9297. https://doi.org/10.1093/nar/gks667
  23. Zhu X, Li H, Long L, Hui L, Chen H, Wang X, et al. miR-126 enhances the sensitivity of non-small cell lung cancer cells to anticancer agents by targeting vascular endothelial growth factor A. Acta Biochim Biophys Sin (Shanghai) 2012;44:519-526. https://doi.org/10.1093/abbs/gms026
  24. Zhou Y, Feng X, Liu YL, Ye SC, Wang H, Tan WK, et al. Down-regulation of miR-126 is associated with colorectal cancer cells proliferation, migration and invasion by targeting IRS-1 via the AKT and ERK1/2 signaling pathways. PLoS One 2013;8:e81203. https://doi.org/10.1371/journal.pone.0081203
  25. Liao YL, Tsai KW, Lin WC. miRNAs in gastric cancer. Rijeka: INTECH Open Access Publisher, 2011.
  26. Jia AY, Castillo-Martin M, Bonal DM, Sanchez-Carbayo M, Silva JM, Cordon-Cardo C. MicroRNA-126 inhibits invasion in bladder cancer via regulation of ADAM9. Br J Cancer 2014;110:2945-2954. https://doi.org/10.1038/bjc.2014.245
  27. Liu X, Sempere LF, Ouyang H, Memoli VA, Andrew AS, Luo Y, et al. MicroRNA-31 functions as an oncogenic microRNA in mouse and human lung cancer cells by repressing specific tumor suppressors. J Clin Invest 2010;120:1298-1309. https://doi.org/10.1172/JCI39566
  28. Zhang Q, Padi SK, Tindall DJ, Guo B. Polycomb protein EZH2 suppresses apoptosis by silencing the proapoptotic miR-31. Cell Death Dis 2014;5:e1486. https://doi.org/10.1038/cddis.2014.454
  29. Lin SL, Chiang A, Chang D, Ying SY. Loss of miR-146a function in hormone-refractory prostate cancer. RNA 2008;14:417-424. https://doi.org/10.1261/rna.874808
  30. Labbaye C, Testa U. The emerging role of miR-146A in the control of hematopoiesis, immune function and cancer. J Hematol Oncol 2012;5:13. https://doi.org/10.1186/1756-8722-5-13
  31. Zhang CM, Zhao J, Deng HY. MiR-155 promotes proliferation of human breast cancer MCF-7 cells through targeting tumor protein 53-induced nuclear protein 1. J Biomed Sci 2013;20:79. https://doi.org/10.1186/1423-0127-20-79
  32. Liu J, Huang W, Yang H, Luo Y. Expression and function of miR-155 in breast cancer. Biotechnol Biotechnol Equip 2015;29:840-843. https://doi.org/10.1080/13102818.2015.1043946
  33. Mansueto G, Forzati F, Ferraro A, Pallante P, Bianco M, Esposito F, et al. Identification of a new pathway for tumor progression: microRNA-181b up-regulation and CBX7 down-regulation by HMGA1 protein. Genes Cancer 2010;1:210-224. https://doi.org/10.1177/1947601910366860
  34. Iliopoulos D, Jaeger SA, Hirsch HA, Bulyk ML, Struhl K. STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell 2010;39:493-506. https://doi.org/10.1016/j.molcel.2010.07.023
  35. Aslam MI, Patel M, Singh B, Jameson JS, Pringle JH. MicroRNA manipulation in colorectal cancer cells: from laboratory to clinical application. J Transl Med 2012;10:128. https://doi.org/10.1186/1479-5876-10-128
  36. Lee KH, Lotterman C, Karikari C, Omura N, Feldmann G, Habbe N, et al. Epigenetic silencing of microRNA miR-107 regulates cyclin-dependent kinase 6 expression in pancreatic cancer. Pancreatology 2009;9:293-301. https://doi.org/10.1159/000186051
  37. Ambs S, Prueitt RL, Yi M, Hudson RS, Howe TM, Petrocca F, et al. Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. Cancer Res 2008;68:6162-6170. https://doi.org/10.1158/0008-5472.CAN-08-0144
  38. Wu W, Yang J, Feng X, Wang H, Ye S, Yang P, et al. Micro-RNA-32 (miR-32) regulates phosphatase and tensin homologue (PTEN) expression and promotes growth, migration, and invasion in colorectal carcinoma cells. Mol Cancer 2013;12:30. https://doi.org/10.1186/1476-4598-12-30
  39. Zhang XJ, Ye H, Zeng CW, He B, Zhang H, Chen YQ. Dysregulation of miR-15a and miR-214 in human pancreatic cancer. J Hematol Oncol 2010;3:46. https://doi.org/10.1186/1756-8722-3-46
  40. Azrak SS, Ginel-Picardo A, Drosten M, Barbacid M, Santos E. Reversible, interrelated mRNA and miRNA expression patterns in the transcriptome of Rasless fibroblasts: functional and mechanistic implications. BMC Genomics 2013;14:731. https://doi.org/10.1186/1471-2164-14-731
  41. Feng B, Dong TT, Wang LL, Zhou HM, Zhao HC, Dong F, et al. Colorectal cancer migration and invasion initiated by microRNA-106a. PLoS One 2012;7:e43452. https://doi.org/10.1371/journal.pone.0043452
  42. Li XM, Wang AM, Zhang J, Yi H. Down-regulation of miR-126 expression in colorectal cancer and its clinical significance. Med Oncol 2011;28:1054-1057. https://doi.org/10.1007/s12032-010-9637-6
  43. Yu J, Ohuchida K, Mizumoto K, Fujita H, Nakata K, Tanaka M. MicroRNA miR-17-5p is overexpressed in pancreatic cancer, associated with a poor prognosis, and involved in cancer cell proliferation and invasion. Cancer Biol Ther 2010;10:748-757. https://doi.org/10.4161/cbt.10.8.13083
  44. Wu W, Yang P, Feng X, Wang H, Qiu Y, Tian T, et al. The relationship between and clinical significance of microRNA-32 and phosphatase and tensin homologue expression in colorectal cancer. Genes Chromosomes Cancer 2013;52:1133-1140. https://doi.org/10.1002/gcc.22108
  45. Qin S, Zhu Y, Ai F, Li Y, Bai B, Yao W, et al. MicroRNA-191 correlates with poor prognosis of colorectal carcinoma and plays multiple roles by targeting tissue inhibitor of metalloprotease 3. Neoplasma 2014;61:27-34. https://doi.org/10.4149/neo_2014_005
  46. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 2006;103:2257-2261. https://doi.org/10.1073/pnas.0510565103
  47. Schaefer A, Jung M, Mollenkopf HJ, Wagner I, Stephan C, Jentzmik F, et al. Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma. Int J Cancer 2010;126:1166-1176.
  48. Baffa R, Fassan M, Volinia S, O'Hara B, Liu CG, Palazzo JP, et al. MicroRNA expression profiling of human metastatic cancers identifies cancer gene targets. J Pathol 2009;219:214-221. https://doi.org/10.1002/path.2586
  49. Bhaumik D, Scott GK, Schokrpur S, Patil CK, Campisi J, Benz CC. Expression of microRNA-146 suppresses NF-kappaB activity with reduction of metastatic potential in breast cancer cells. Oncogene 2008;27:5643-5647. https://doi.org/10.1038/onc.2008.171
  50. Zhu N, Zhang D, Xie H, Zhou Z, Chen H, Hu T, et al. Endothelial-specific intron-derived miR-126 is down-regulated in human breast cancer and targets both VEGFA and PIK3R2. Mol Cell Biochem 2011;351:157-164. https://doi.org/10.1007/s11010-011-0723-7
  51. Liu K, Li G, Fan C, Diao Y, Wu B, Li J. Increased expression of microRNA-221 in gastric cancer and its clinical significance. J Int Med Res 2012;40:467-474. https://doi.org/10.1177/147323001204000208
  52. Li X, Zhang Y, Zhang H, Liu X, Gong T, Li M, et al. miRNA-223 promotes gastric cancer invasion and metastasis by targeting tumor suppressor EPB41L3. Mol Cancer Res 2011;9:824-833. https://doi.org/10.1158/1541-7786.MCR-10-0529
  53. Li ZW, Yang YM, Du LT, Dong Z, Wang LL, Zhang X, et al. Overexpression of miR-223 correlates with tumor metastasis and poor prognosis in patients with colorectal cancer. Med Oncol 2014;31:256. https://doi.org/10.1007/s12032-014-0256-5
  54. Yabushita S, Fukamachi K, Tanaka H, Sumida K, Deguchi Y, Sukata T, et al. Circulating microRNAs in serum of human K-ras oncogene transgenic rats with pancreatic ductal adenocarcinomas. Pancreas 2012;41:1013-1018. https://doi.org/10.1097/MPA.0b013e31824ac3a5
  55. Wang Y, Yu Y, Tsuyada A, Ren X, Wu X, Stubblefield K, et al. Transforming growth factor-$\beta$ regulates the sphere-initiating stem cell-like feature in breast cancer through miRNA-181 and ATM. Oncogene 2011;30:1470-1480. https://doi.org/10.1038/onc.2010.531
  56. Li Y, Vandenboom TG 2nd, Wang Z, Kong D, Ali S, Philip PA, et al. miR-146a suppresses invasion of pancreatic cancer cells. Cancer Res 2010;70:1486-1495. https://doi.org/10.1158/0008-5472.CAN-09-2792
  57. Sun Q, Zhao X, Liu X, Wang Y, Huang J, Jiang B, et al. miR-146a functions as a tumor suppressor in prostate cancer by targeting Rac1. Prostate 2014;74:1613-1621. https://doi.org/10.1002/pros.22878
  58. Li BS, Zuo QF, Zhao YL, Xiao B, Zhuang Y, Mao XH, et al. MicroRNA-25 promotes gastric cancer migration, invasion and proliferation by directly targeting transducer of ERBB2, 1 and correlates with poor survival. Oncogene 2015;34:2556-2565. https://doi.org/10.1038/onc.2014.214
  59. Hamano R, Ishii H, Miyata H, Doki Y, Mori M. Role of microRNAs in solid tumors. J Nucleic Acids Investig 2011;2:e2. https://doi.org/10.4081/jnai.2011.2164
  60. Hutvagner G, Simard MJ. Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 2008;9:22-32. https://doi.org/10.1038/nrm2321
  61. Das RP, Konkimalla VB, Rath SN, Hansa J, Jagdeb M. Elucidation of the molecular interaction between miRNAs and the HOXA9 gene, involved in acute myeloid leukemia, by the assistance of Argonaute protein through a computational approach. Genomics Inform 2015;13:45-52. https://doi.org/10.5808/GI.2015.13.2.45
  62. Mascellani N, Tagliavini L, Gamberoni G, Rossi S, Marchesini J, Taccioli C, et al. Using miRNA expression data for the study of human cancer. Minerva Biotecnol 2008;20:23-30.
  63. Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, et al. Automated 3D structure composition for large RNAs. Nucleic Acids Res 2012;40:e112. https://doi.org/10.1093/nar/gks339
  64. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 2005;33:W363-W367. https://doi.org/10.1093/nar/gki481
  65. Junn E, Mouradian MM. MicroRNAs in neurodegenerative diseases and their therapeutic potential. Pharmacol Ther 2012;133:142-150. https://doi.org/10.1016/j.pharmthera.2011.10.002
  66. Chi SW, Zang JB, Mele A, Darnell RB. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009;460:479-486. https://doi.org/10.1038/nature08170

피인용 문헌

  1. Genomic Analysis of miR-21-3p and Expression Pattern with Target Gene in Olive Flounder vol.15, pp.3, 2017, https://doi.org/10.5808/GI.2017.15.3.98