Identification of hub genes, miRNAs and regulatory factors relevant for Duchenne muscular dystrophy by bioinformatics analysis

References

• Hoffman EP, Brown RH Jr, Kunkel LM. Dystrophin: the protein product of the Duchenne muscular dystrophy locus. Cell. 1987;51(6):919–928.
   PubMed Web of Science ®Google Scholar
• Bulfield G, Siller WG, Wight PA, et al. X chromosome-linked muscular dystrophy (mdx) in the mouse. Proc Natl Acad Sci USA. 1984;81(4):1189–1192.
   PubMed Web of Science ®Google Scholar
• Campbell KP, Kahl SD. Association of dystrophin and an integral membrane glycoprotein. Nature. 1989;338(6212):259–262.
   PubMed Web of Science ®Google Scholar
• Yiu EM, Kornberg AJ. Duchenne muscular dystrophy. Neurol India. 2008;56(3):236–247.
   PubMed Web of Science ®Google Scholar
• Judge DP, Kass DA, Thompson WR, et al. Pathophysiology and therapy of cardiac dysfunction in Duchenne muscular dystrophy. Am J Cardiovasc Drugs. 2011;11(5):287–294.
   PubMed Web of Science ®Google Scholar
• Szigyarto CA, Spitali P. Biomarkers of Duchenne muscular dystrophy: current findings. Degener Neurol Neuromuscul Dis. 2018;8:1–13.
   PubMed Web of Science ®Google Scholar
• Hrach HC, Mangone M. miRNA profiling for early detection and treatment of Duchenne muscular dystrophy. IJMS. 2019;20(18):4638.
   Google Scholar
• Coenen-Stass AML, Wood MJA, Roberts TC. Biomarker potential of extracellular miRNAs in Duchenne muscular dystrophy. Trends Mol Med. 2017;23(11):989–1001.
   PubMed Web of Science ®Google Scholar
• Parolo S, Marchetti L, Lauria M, et al. Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy. PLoS One. 2018;13(3):e0194225.
   PubMed Web of Science ®Google Scholar
• Iannotti FA, Pagano E, Guardiola O, et al. Genetic and pharmacological regulation of the endocannabinoid CB1 receptor in Duchenne muscular dystrophy. Nat Commun. 2018;9(1):3950.
   PubMedGoogle Scholar
• Tian LJ, Cao JH, Deng XQ, et al. Gene expression profiling of Duchenne muscular dystrophy reveals characteristics along disease progression. Genet Mol Res. 2014;13(1):1402–1411.
   PubMed Web of Science ®Google Scholar
• Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets – update. Nucleic Acids Res. 2013;41(Database issue):D991–D995.
   PubMed Web of Science ®Google Scholar
• Gene Ontology C. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006;34:D322–D326.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Sato Y, Kawashima M, et al. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44(D1):D457–D462.
   PubMed Web of Science ®Google Scholar
• Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D613.
   PubMed Web of Science ®Google Scholar
• Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003;4:2.
   PubMed Web of Science ®Google Scholar
• Assenov Y, Ramirez F, Schelhorn SE, et al. Computing topological parameters of biological networks. Bioinformatics. 2008;24(2):282–284.
   PubMed Web of Science ®Google Scholar
• Janky R, Verfaillie A, Imrichova H, et al. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PLoS Comput Biol. 2014;10(7):e1003731.
   PubMed Web of Science ®Google Scholar
• Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005;33(Web Server issue):W741–W748.
   PubMed Web of Science ®Google Scholar
• Zanotti S, Saredi S, Ruggieri A, et al. Altered extracellular matrix transcript expression and protein modulation in primary Duchenne muscular dystrophy myotubes. Matrix Biol. 2007;26(8):615–624.
   PubMed Web of Science ®Google Scholar
• Heydemann A. Skeletal muscle metabolism in Duchenne and Becker muscular dystrophy-implications for therapies. Nutrients. 2018;10(6):796.
   PubMed Web of Science ®Google Scholar
• Sandri M, Coletto L, Grumati P, et al. Misregulation of autophagy and protein degradation systems in myopathies and muscular dystrophies. J Cell Sci. 2013;126(Pt 23):5325–5333.
   PubMed Web of Science ®Google Scholar
• Salajegheh M, Kong SW, Pinkus JL, et al. Interferon-stimulated gene 15 (ISG15) conjugates proteins in dermatomyositis muscle with perifascicular atrophy. Ann Neurol. 2010;67(1):53–63.
   PubMed Web of Science ®Google Scholar
• Werner A, Disanza A, Reifenberger N, et al. SCFFbxw5 mediates transient degradation of actin remodeller Eps8 to allow proper mitotic progression. Nat Cell Biol. 2013;15(2):179–188.
   PubMed Web of Science ®Google Scholar
• Puklowski A, Homsi Y, Keller D, et al. The SCF-FBXW5 E3-ubiquitin ligase is regulated by PLK4 and targets HsSAS-6 to control centrosome duplication. Nat Cell Biol. 2011;13(8):1004–1009.
   PubMed Web of Science ®Google Scholar
• Bond M, Wu YJ. Proliferation unleashed: the role of Skp2 in vascular smooth muscle cell proliferation. Front Biosci (Landmark Ed). 2011;16:1517–1535.
   PubMed Web of Science ®Google Scholar
• Li C, Yu L, Xue H, et al. Nuclear AMPK regulated CARM1 stabilization impacts autophagy in aged heart. Biochem Biophys Res Commun. 2017;486(2):398–405.
   PubMed Web of Science ®Google Scholar
• Ha JY, Kim JS, Kang YH, et al. Tnfaip8l1/Oxi-beta binds to FBXW5, increasing autophagy through activation of TSC2 in a Parkinson's disease model. J Neurochem. 2014;129(3):527–538.
   PubMed Web of Science ®Google Scholar
• Lynch SA, McLeod MA, Orsech HC, Cirelli AM, et al. Zinc finger protein 593 is upregulated during skeletal muscle atrophy and modulates muscle cell differentiation. Exp Cell Res. 2019;383(2):111563.
   PubMed Web of Science ®Google Scholar
• Ninfali C, Siles L, Darling DS, et al. Regulation of muscle atrophy-related genes by the opposing transcriptional activities of ZEB1/CtBP and FOXO3. Nucleic Acids Res. 2018;46(20):10697–10708.
   PubMed Web of Science ®Google Scholar
• Li L, Yang XJ. Tubulin acetylation: responsible enzymes, biological functions and human diseases. Cell Mol Life Sci. 2015;72(22):4237–4255.
   PubMed Web of Science ®Google Scholar
• Nekooki-Machida Y, Nakakura T, Nishijima Y, et al. Dynamic localization of α-tubulin acetyltransferase ATAT1 through the cell cycle in human fibroblastic KD cells. Med Mol Morphol. 2018;51(4):217–226.
   PubMed Web of Science ®Google Scholar
• Delestre L, Cui H, Esposito M, et al. Senescence is a Spi1-induced anti-proliferative mechanism in primary hematopoietic cells. Haematologica. 2017;102(11):1850–1860.
   PubMed Web of Science ®Google Scholar
• Oikawa T, Yamada T, Kihara-Negishi F, et al. The role of Ets family transcription factor PU.1 in hematopoietic cell differentiation, proliferation and apoptosis. Cell Death Differ. 1999;6(7):599–608.
   PubMed Web of Science ®Google Scholar
• Parker MH, Perry RL, Fauteux MC, et al. MyoD synergizes with the E-protein HEB beta to induce myogenic differentiation. Mol Cell Biol. 2006;26(15):5771–5783.
   PubMed Web of Science ®Google Scholar
• Fu L, Wang H, Liao Y, et al. miR-208b modulating skeletal muscle development and energy homoeostasis through targeting distinct targets. RNA Biol. 2020;17(5):743–712.
   PubMed Web of Science ®Google Scholar
• Gao J, Dai C, Yu X, et al. Circ-TCF4.85 silencing inhibits cancer progression through microRNA-486-5p-targeted inhibition of ABCF2 in hepatocellular carcinoma. Mol Oncol. 2020;14(2):447–461.
   PubMed Web of Science ®Google Scholar
• Bao L, Wu J, Dodson M, et al. ABCF2, an Nrf2 target gene, contributes to cisplatin resistance in ovarian cancer cells. Mol Carcinog. 2017;56(6):1543–1553.
   PubMed Web of Science ®Google Scholar
• Qadir AS, Woo KM, Ryoo HM, et al. MiR-124 inhibits myogenic differentiation of mesenchymal stem cells via targeting Dlx5. J Cell Biochem. 2014;115(9):1572–1581.
   PubMed Web of Science ®Google Scholar
• D'Agostino M, Torcinaro A, Madaro L, et al. Role of miR-200c in myogenic differentiation impairment via p66Shc: implication in skeletal muscle regeneration of dystrophic mdx mice. Oxid Med Cell Longev. 2018;2018:4814696.
   PubMed Web of Science ®Google Scholar
• Kong D, He M, Yang L, et al. MiR-17 and miR-19 cooperatively promote skeletal muscle cell differentiation. Cell Mol Life Sci. 2019;76(24):5041–5054.
   PubMed Web of Science ®Google Scholar
• Pinto SK, Lamon S, Stephenson EJ, et al. Expression of microRNAs and target proteins in skeletal muscle of rats selectively bred for high and low running capacity. Am J Physiol Endocrinol Metabol. 2017;313(3):E335–E343.
   PubMed Web of Science ®Google Scholar
• Hudson MB, Woodworth-Hobbs ME, Zheng B, et al. miR-23a is decreased during muscle atrophy by a mechanism that includes calcineurin signaling and exosome-mediated export. Am J Physiol, Cell Physiol. 2014;306(6):C551–C558.
   PubMed Web of Science ®Google Scholar
• Murata M, Nonaka H, Komatsu S, et al. Delphinidin prevents muscle atrophy and upregulates miR-23a expression. J Agric Food Chem. 2017;65(1):45–50.
   PubMed Web of Science ®Google Scholar
• Wada S, Kato Y, Okutsu M, et al. Translational suppression of atrophic regulators by microRNA-23a integrates resistance to skeletal muscle atrophy. J Biol Chem. 2011;286(44):38456–38465.
   PubMed Web of Science ®Google Scholar
• Zhang A, Li M, Wang B, et al. miRNA-23a/27a attenuates muscle atrophy and renal fibrosis through muscle–kidney crosstalk. J Cachexia Sarcopenia Muscle. 2018;9(4):755–770.
   PubMed Web of Science ®Google Scholar
• Wang B, Zhang C, Zhang A, et al. MicroRNA-23a and microRNA-27a mimic exercise by ameliorating CKD-induced muscle atrophy. J Am Soc Nephrol. 2017;28(9):2631–2640.
   PubMed Web of Science ®Google Scholar
• Hudson MB, Rahnert JA, Zheng B, et al. miR-182 attenuates atrophy-related gene expression by targeting FoxO3 in skeletal muscle. Am J Physiol Cell Physiol. 2014;307(4):C314–C319.
   PubMed Web of Science ®Google Scholar
• Zhang D, Li Y, Yao X, et al. miR-182 regulates metabolic homeostasis by modulating glucose utilization in muscle. Cell Rep. 2016;16(3):757–768.
   PubMed Web of Science ®Google Scholar
• Chu W, Zhang F, Song R, et al. Proteomic and microRNA transcriptome analysis revealed the microRNA-SmyD1 network regulation in skeletal muscle fibers performance of Chinese perch. Sci Rep. 2017;7(1):16498.
   PubMedGoogle Scholar
• Mercatelli N, Fittipaldi S, De Paola E, et al. MiR-23–TrxR1 as a novel molecular axis in skeletal muscle differentiation. Sci Rep. 2017;7(1):7219.
   PubMedGoogle Scholar
• Wang L, Chen X, Zheng Y, et al. MiR-23a inhibits myogenic differentiation through down regulation of fast myosin heavy chain isoforms. Exp Cell Res. 2012;318(18):2324–2334.
   PubMed Web of Science ®Google Scholar