The gene and microRNA networks of stem cells and reprogramming

Shihori Tanabe; Ryuichi Ono

doi:10.3934/celltissue.2018.4.238

AIMS Cell and Tissue Engineering, 2018, 2(4): 238-245. doi: 10.3934/celltissue.2018.4.238. Review Special Issues

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The gene and microRNA networks of stem cells and reprogramming

Shihori Tanabe, Ryuichi Ono

1 Division of Risk Assessment, Biological Safety Research Center, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Japan
2 Division of Toxicology, Biological Safety Research Center, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Japan

Received: , Accepted: , Published:

Special Issues: Cellular Reprogramming

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The molecular interactions and regulations are dynamically changed in stem cells and reprogramming. This review article mainly focuses on the networks of molecules and epigenetic regulations including microRNA. The stem cells have molecular networks related to the stemness and the reprogramming of differentiated cells include the signaling networks consist of the transcriptional and post-transcriptional regulation of the genes and the protein modification. The gene expression is regulated by the binding of microRNAs towards the regulating regions of the coding genes. The molecular network pathways in stem cells include Wnt/β-catenin signaling and MAPK signaling, Shh signaling and Hippo signaling pathway. The epigenetic regulation of the genes included in the signaling pathways related to stem cells is mediated by the transcription factors and microRNAs consist of 18–25 nucleotides. Molecular interactions of the signaling proteins in stem cells is at least three factors including the quantity of the molecules partly regulated by the gene transcription and protein synthesis, the modification of the proteins such as phosphorylation, and localization of the molecules. In the epigenetic regulation level, the methylation and acetylation of genomes are critical for the regulation of the transcription. The binding sites and the combination of microRNAs, and regulated genes related to the stem cells and reprogramming are discussed in this review.

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Keywords: network; stem cell; reprogramming; microRNA; molecular interaction; epigenetic regulation

Citation: Shihori Tanabe, Ryuichi Ono. The gene and microRNA networks of stem cells and reprogramming. AIMS Cell and Tissue Engineering, 2018, 2(4): 238-245. doi: 10.3934/celltissue.2018.4.238

References:

1. Salim A, Amjesh R, Chandra SS (2017) An approach to forecast human cancer by profiling microRNA expression from NGS data. BMC Cancer 17: 77.
2. Bartel DP (2009) microRNAs: target recognition and regulatory functions. Cell 136: 215–233.
3. Bartel DP (2004) microRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297.
4. Agarwal V, Bell GW, Nam JW, et al. (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife 4: e05005.
5. Siciliano V, Garzilli I, Fracassi C, et al. (2013) miRNAs confer phenotypic robustness to gene networks by suppressing biological noise. Nat Commun 4: 2364.
6. Cuccato G, Polynikis A, Siciliano V, et al. (2011) Modeling RNA interference in mammalian cells. BMC Syst Biol 5: 19.
7. Santpere G, Lopez-Valenzuela M, Petit-Marty N, et al. (2016) Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes. BMC Genomics 17: 528.
8. Beg F, Wang R, Saeed Z, et al. (2017) Inflammation-associated microRNA changes in circulating exosomes of heart failure patients. BMC Res Notes 10: 751.
9. Hannafon BN, Trigoso YD, Calloway CL, et al. (2016) Plasma exosome microRNAs are indicative of breast cancer. Breast Cancer Res 18: 90.
10. Bengoa-Vergniory N, Gorroño-Etxebarria I, González-Salazar I, et al. (2014) A switch from canonical to noncanonical Wnt signaling mediates early differentiation of human neural stem cells. Stem Cells 32: 3196–3208.
11. Zhou R, Yuan Z, Liu J, et al. (2016) Calcitonin gene-related peptide promotes the expression of osteoblastic genes and activates the WNT signal transduction pathway in bone marrow stromal stem cells. Mol Med Rep 13: 4689–4696.
12. Dokanehiifard S, Yasari A, Najafi H, et al. (2017) A novel microRNA located in the TrkC gene regulates the Wnt signaling pathway and is differentially expressed in colorectal cancer specimens. J Biol Chem 292: 7566–7577.
13. Cheleschi S, De Palma A, Pecorelli A, et al. (2017) Hydrostatic pressure regulates microRNA expression levels in osteoarthritic chondrocyte cultures via the Wnt/b-catenin pathway. Int J Mol Sci 18: 133.
14. Liang J, Huang W, Cai W, et al. (2017) Inhibition of microRNA-495 enhances therapeutic angiogenesis of human induced pluripotent stem cells. Stem Cells 35: 337–350.
15. Yata K, Beder LB, Tamagawa S, et al. (2015) microRNA expression profiles of cancer stem cells in head and neck squamous cell carcinoma. Int J Oncol 47:1249–1256.
16. Hodges WM, O'Brien F, Fulzele S, et al. (2017) Function of microRNAs in the osteogenic differentiation and therapeutic application of adipose-derived stem cells (ASCs). Int J Mol Sci 18: 2597.
17. Yang CL, Zheng XL, Ye K, et al. (2018) microRNA-183 acts as a tumor suppressor in human non-small cell lung cancer by down-regulating MTA1. Cell Physiol Biochem 46: 93–106.
18. Zheng J, Wang W, Yu F, et al. (2018) microRNA-30a suppresses the activation of hepatic stellate cells by inhibiting epithelial-to-mesenchymal transition. Cell Physiol Biochem 46: 82–92.
19. Liu W, Li M, Chen X, et al. (2018) microRNA-1 suppresses proliferation, migration and invasion by targeting Notch2 in esophageal squamous cell carcinoma. Sci Rep 8: 5183.
20. Yu T, Wang LN, Li W, et al. (2018) Downregulation of miR-491-5p promotes gastric cancer metastasis by regulating SNAIL and FGFR4. Cancer Sci 109: 1393–1403.
21. Li Y, Huo J, Pan X, et al. (2018) microRNA 302b-3p/302c-3p/302d-3p inhibits epithelial-mesenchymal transition and promotes apoptosis in human endometrial carcinoma cells. Onco Targets Ther 11: 1275–1284.
22. Xu R, Zhu X, Chen F, et al. (2018) LncRNA XIST/miR-200c regulates the stemness properties and tumourigenicity of human bladder cancer stem cell-like cells. Cancer Cell Int 18: 41.
23. Liu X, Wang S, Xu J, et al. (2018) Extract of Stellerachamaejasme L(ESC) inhibits growth and metastasis of human hepatocellular carcinoma via regulating microRNA expression. BMC Complement Altern Med 18: 99.
24. Zhang J, Chen D, Liang S, et al. (2018) miR-106b promotes cell invasion and metastasis via PTEN mediated EMT in ESCC. Oncol Lett 15: 4619–4626.
25. Ma J, Zhang L, Hao J, et al. (2018) Up-regulation of microRNA-93 inhibits TGF-β1-induced EMT and renal fibrogenesis by down-regulation of Orai1. J Pharmacol Sci 136: 218–227.
26. Yin C, Mou Q, Pan X, et al. (2018) miR-577 suppresses epithelial-mesenchymal transition and metastasis of breast cancer by targeting Rab25. Thorac Cancer 9: 472–479.
27. Miyazaki H, Takahashi RU, Prieto-Vila M, et al. (2018) CD44 exerts a functional role during EMT induction in cisplatin-resistant head and neck cancer cells. Oncotarget 9: 10029–10041.
28. Li D, Zhang Y, Zhang H, et al. (2018) CADM2, as a new target of miR-10b, promotes tumor metastasis through FAK/AKT pathway in hepatocellular carcinoma. J Exp Clin Cancer Res 37: 46.
29. Li J, Zou K, Yu L, et al. (2018) microRNA-140 inhibits the epithelial-mesenchymal transition and metastasis in colorectal cancer. Mol Ther Nucleic Acids 10: 426–437.
30. Clark RJ, Craig MP, Agrawal S, et al. (2018) microRNA involvement in the onset and progression of Barrett's esophagus: a systematic review. Oncotarget 9: 8179–8196.
31. Gao Y, Ma H, Gao C, et al. (2018) Tumor-promoting properties of miR-8084 in breast cancer through enhancing proliferation, suppressing apoptosis and inducing epithelial-mesenchymal transition. J Transl Med 16: 38.
32. Chen J, Gao F, Liu N (2018) L1CAM promotes epithelial to mesenchymal transition and formation of cancer initiating cells in human endometrial cancer. Exp Ther Med 15: 2792–2797.
33. Xu M, Li J, Wang X, et al. (2018) miR-22 suppresses epithelial-mesenchymal transition in bladder cancer by inhibiting Snail and MAPK1/Slug/vimentin feedback loop. Cell Death Dis 9: 209.
34. Guo H, Zhang X, Chen Q, et al. (2018) miR-132 suppresses the migration and invasion of lung cancer cells by blocking USP9X-induced epithelial-mesenchymal transition. Am J Transl Res 10: 224–234.
35. Li J, Huang Y, Deng X, et al. (2018) Long noncoding RNA H19 promotes transforming growth factor-β-induced epithelial-mesenchymal transition by acting as a competing endogenous RNA of miR-370-3p in ovarian cancer cells. Onco Targets Ther 11: 427–440.
36. Yáñez-Mó M, Siljander PR, Andreu Z,et al. (2015) Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles 4: 27066.
37. de Jong OG, Verhaar MC, Chen Y, et al. (2012) Cellular stress conditions are reflected in the protein and RNA content of endothelial cell-derived exosomes. J Extracell Vesicles 1.
38. Raposo G, Nijman HW, Stoorvogel W, et al. (1996) B lymphocytes secrete antigen-presenting vesicles. J Exp Med 183: 1161–1172.
39. Raposo G, Stoorvogel W (2013) Extracellular vesicles: exosomes, microvesicles, and friends. J Cell Biol 200: 373–383.
40. Colombo M, Raposo G, Théry C (2014) Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. Annu Rev Cell Dev Biol 30: 255–289.
41. Yoshioka Y, Konishi Y, Kosaka N, et al. (2013) Comparative marker analysis of extracellular vesicles in different human cancer types. J Extracell Vesicles 2.
42. Valadi H, Ekstrom K, Bossios A, et al. (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9: 654–659.
43. Kosaka N, Iguchi H, Yoshioka Y, et al. (2010) Secretory mechanisms and intercellular transfer of microRNAs in living cells. J Biol Chem 285: 17442–17452.
44. Pegtel DM, Cosmopoulos K, Thorley-Lawson DA, et al. (2010) Functional delivery of viral miRNAs via exosomes. Proc Natl Acad Sci U S A 107: 6328–6333.
45. Zhang Y, Liu D, Chen X, et al. (2010) Secreted monocytic miR-150 enhances targeted endothelial cell migration. Mol Cell 39: 133–144.
46. Kalluri R, Zeisberg M (2006) Fibroblasts in cancer. Nat Rev Cancer 6: 392–401.
47. Fang T, Lv H, Lv G, et al. (2018) Tumor-derived exosomal miR-1247-3p induces cancer-associated fibroblast activation to foster lung metastasis of liver cancer. Nat Commun 9: 191.
48. Tominaga N, Kosaka N, Ono M, et al. (2015) Brain metastatic cancer cells release microRNA-181c-containing extracellular vesicles capable of destructing blood-brain barrier. Nat Commun 6: 6716.
49. Sieuwerts AM, Mostert B, Bolt-de Vries J, et al. (2011) mRNA and microRNA expression profiles in circulating tumor cells and primary tumors of metastatic breast cancer patients. Clin Cancer Res 17: 3600–3618.
50. Ohshima K, Inoue K, Fujiwara A, et al. (2010) Let-7 microRNA family is selectively secreted into the extracellular environment via exosomes in a metastatic gastric cancer cell line. PLoS One 5: e13247.
51. Taylor DD, Gercel-Taylor C (2008) microRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer. Gynecol Oncol 110: 13–21.
52. Jones CI, Zabolotskaya MV, King AJ, et al. (2012) Identification of circulating microRNAs as diagnostic biomarkers for use in multiple myeloma. Br J Cancer 107: 1987–1996.
53. Tanaka M, Oikawa K, Takanashi M, et al. (2009) Down-regulation of miR-92 in human plasma is a novel marker for acute leukemia patients. PLoS One 4: e5532.
54. Hu Z, Chen X, Zhao Y, et al. (2010) Serum microRNA signatures identified in a genome-wide serum microRNA expression profiling predict survival of non-small-cell lung cancer. J Clin Oncol 28: 1721–1726.
55. Aushev VN, Zborovskaya IB, Laktionov KK, et al. (2013) Comparisons of microRNA patterns in plasma before and after tumor removal reveal new biomarkers of lung squamous cell carcinoma. PLoS One 8: e78649.
56. Ho AS, Huang X, Cao H, et al. (2010) Circulating miR-210 as a novel hypoxia marker in pancreatic cancer. Transl Oncol 3: 109–113.
57. Wang J, Chen J, Chang P, et al. (2009) microRNAs in plasma of pancreatic ductal adenocarcinoma patients as novel blood-based biomarkers of disease. Cancer Prev Res (Phila) 2: 807–813.
58. Camacho L, Guerrero P, Marchetti D (2013) microRNA and protein profiling of brain metastasis competent cell-derived exosomes. PLoS One 8: e73790.
59. Cheng HH, Mitchell PS, Kroh EM, et al. (2013) Circulating microRNA profiling identifies a subset of metastatic prostate cancer patients with evidence of cancer-associated hypoxia. PLoS One 8: e69239.
60. Jones K, Nourse JP, Keane C, et al. (2014) Plasma microRNA are disease response biomarkers in classical Hodgkin lymphoma. Clin Cancer Res 20: 253–264.
61. Shimomura A, Shiino S, Kawauchi J, et al. (2016) Novel combination of serum microRNA for detecting breast cancer in the early stage. Cancer Sci 107: 326–334.
62. Carter JV, Roberts HL, Pan J, et al. (2016) A highly predictive model for diagnosis of colorectal neoplasms using plasma microRNA: improving specificity and sensitivity. Ann Surg 264: 575–584.

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