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Research Article

Identifying hub genes and dysregulated pathways in Duchenne muscular dystrophy

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Received 31 May 2022, Accepted 02 Jan 2024, Published online: 17 Jan 2024

References

  • Chadwick JA, Hauck JS, Lowe J, et al. Mineralocorticoid receptors are present in skeletal muscle and represent a potential therapeutic target. Faseb J. 2015;29(11):4544–4554. doi: 10.1096/fj.15-276782.
  • Falzarano MS, Scotton C, Passarelli C, et al. Duchenne muscular dystrophy: from diagnosis to therapy. Molecules. 2015;20(10):18168–18184. doi: 10.3390/molecules201018168.
  • Katharine Bushby RF, Birnkrant DJ, Case LE, et al. Diagnosis and management of Duchenne muscular dystrophy, part 1: diagnosis, and pharmacological and psychosocial management. Lancet Neurol. 2010;9(1):17.
  • Rosenberg AS, Puig M, Nagaraju K, et al. Immune-mediated pathology in Duchenne muscular dystrophy. Sci Transl Med. 2015;7(299):299rv4. doi: 10.1126/scitranslmed.aaa7322.
  • Kunkel E. Dystmphin: the protein product of the Duchenne muscular dystrophy locus. Cell. 1987;51(6):10.
  • Luce L, Carcione M, Mazzanti C, et al. Theragnosis for Duchenne muscular dystrophy. Front Pharmacol. 2021;12:648390. doi: 10.3389/fphar.2021.648390.
  • Diboun I, Wernisch L, Orengo CA, et al. Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics. 2006;7(1):252. doi: 10.1186/1471-2164-7-252.
  • Kanehisa M, Furumichi M, Tanabe M, et al. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45(D1):D353–D361. doi: 10.1093/nar/gkw1092.
  • Vila MCD. Effects of gene correction by exon skipping in a murine model of Duchenne muscular dystrophy. The George Washington University; 2016.
  • Wehling M, Spencer MJ, Tidball JG. A nitric oxide synthase transgene ameliorates muscular dystrophy in mdx mice. J Cell Biol. 2001;155(1):123–131. doi: 10.1083/jcb.200105110.
  • Spencer MJ, Montecino-Rodriguez E, Dorshkind K, et al. Helper (CD4(+)) and cytotoxic (CD8(+)) T cells promote the pathology of dystrophin-deficient muscle. Clin Immunol. 2001;98(2):235–243. doi: 10.1006/clim.2000.4966.
  • Radley HG, Davies MJ, Grounds MD. Reduced muscle necrosis and long-term benefits in dystrophic mdx mice after cV1q (blockade of TNF) treatment. Neuromuscul Disord. 2008;18(3):227–238. doi: 10.1016/j.nmd.2007.11.002.
  • Villalta SA, Rosenberg AS, Bluestone JA. The immune system in Duchenne muscular dystrophy: friend or foe. Rare Dis. 2015;3(1):e1010966. doi: 10.1080/21675511.2015.1010966.
  • Villalta SA, Deng B, Rinaldi C, et al. IFN-gamma promotes muscle damage in the mdx mouse model of Duchenne muscular dystrophy by suppressing M2 macrophage activation and inhibiting muscle cell proliferation. J Immunol. 2011;187(10):5419–5428. doi: 10.4049/jimmunol.1101267.
  • Hu X, Pickle NT, Grabowski AM, et al. Muscle eccentric contractions increase in downhill and high-grade uphill walking. Front Bioeng Biotechnol. 2020;8:573666. doi: 10.3389/fbioe.2020.573666.
  • Alderton JM, Steinhardt RA. Calcium influx through calcium leak channels is responsible for the elevated levels of calcium-dependent proteolysis in dystrophic myotubes. J Biol Chem. 2000;275(13):9452–9460. doi: 10.1074/jbc.275.13.9452.
  • Bao-Ting Zhang SSY, Allen DG, Qin L, et al. Role of the calcium-calpain pathway in cytoskeletal damage after eccentric contractions. J Appl Physiol. 2008;105:6.
  • Dadgar S, Wang Z, Johnston H, et al. Asynchronous remodeling is a driver of failed regeneration in Duchenne muscular dystrophy. J Cell Biol. 2014;207(1):139–158. doi: 10.1083/jcb.201402079.
  • Acharya PS, Majumdar S, Jacob M, et al. Fibroblast migration is mediated by CD44-dependent TGF beta activation. J Cell Sci. 2008;121(Pt 9):1393–1402. doi: 10.1242/jcs.021683.
  • Kawana H, Karaki H, Higashi M, et al. CD44 suppresses TLR-mediated inflammation. J Immunol. 2008;180(6):4235–4245. doi: 10.4049/jimmunol.180.6.4235.
  • Farini A, Villa C, Manescu A, et al. Novel insight into stem cell trafficking in dystrophic muscles. Int J Nanomed. 2012;7:3059–3067.
  • Xu X, Hao Y, Wu J, et al. Assessment of weighted gene co-expression network analysis to explore key pathways and novel biomarkers in muscular dystrophy. Pharmgenomics Pers Med. 2021;14:431–444. doi: 10.2147/PGPM.S301098.
  • Bai S, Chaurasiya AH, Banarjee R, et al. CD44, a predominant protein in methylglyoxal-induced secretome of muscle cells, is elevated in diabetic plasma. ACS Omega. 2020;5(39):25016–25028. doi: 10.1021/acsomega.0c01318.
  • Hassn Mesrati M, Syafruddin SE, Mohtar MA, et al. CD44: a multifunctional mediator of cancer progression. Biomolecules. 2021;11(12):1850. doi: 10.3390/biom11121850.
  • Dzobo K, Sinkala M. Cancer stem cell marker CD44 plays multiple key roles in human cancers: immune suppression/evasion, drug resistance, epithelial-mesenchymal transition, and metastasis. OMICS. 2021;25(5):313–332. doi: 10.1089/omi.2021.0025.
  • Schneid S, Wolff F, Buchner K, et al. The BRCT domains of ECT2 have distinct functions during cytokinesis. Cell Rep. 2021;34(9):108805. doi: 10.1016/j.celrep.2021.108805.
  • Chen Y-W, Nagaraju K, Bakay M, et al. Early onset of inflammation and later involvement of TGF in Duchenne muscular dystrophy. Neurology. 2005;65(6):826–834. doi: 10.1212/01.wnl.0000173836.09176.c4.
  • Kornegay JN, Bogan JR, Bogan DJ, et al. Canine models of Duchenne muscular dystrophy and their use in therapeutic strategies. Mamm Genome. 2012;23(1-2):85–108. doi: 10.1007/s00335-011-9382-y.
  • Klymiuk N, Blutke A, Graf A, et al. Dystrophin-deficient pigs provide new insights into the hierarchy of physiological derangements of dystrophic muscle. Hum Mol Genet. 2013;22(21):4368–4382. doi: 10.1093/hmg/ddt287.
  • Wang J, Fan Q, Yu T, et al. Identifying the hub genes for Duchenne muscular dystrophy and Becker muscular dystrophy by weighted correlation network analysis. BMC Genom Data. 2021;22(1):57. doi: 10.1186/s12863-021-01014-w.
  • Duarte BDP, Bonatto D. The heat shock protein 47 as a potential biomarker and a therapeutic agent in cancer research. J Cancer Res Clin Oncol. 2018;144(12):2319–2328. doi: 10.1007/s00432-018-2739-9.
  • Zhang R, Lv L, Ban W, et al. Identification of hub genes in Duchenne muscular dystrophy: evidence from bioinformatic analysis. J Comput Biol. 2020;27(1):1–8. doi: 10.1089/cmb.2019.0167.
  • Murphy S, Zweyer M, Henry M, et al. Subproteomic profiling of sarcolemma from dystrophic mdx-4cv skeletal muscle. Data Brief. 2018;17:980–993. doi: 10.1016/j.dib.2018.02.020.
  • Taguchi T, Razzaque MS. The collagen-specific molecular chaperone HSP47: is there a role in fibrosis? Trends Mol Med. 2007;13(2):45–53. doi: 10.1016/j.molmed.2006.12.001.
  • Wei B, Jin JP. TNNT1, TNNT2, and TNNT3: isoform genes, regulation, and structure-function relationships. Gene. 2016;582(1):1–13. doi: 10.1016/j.gene.2016.01.006.
  • Jin J-P. Alternative RNA splicing-generated cardiac troponin T isoform switching: a Non-Heart-Restricted genetic programming synchronized in developing cardiac and skeletal muscles. Biochem Biophys Res Commun. 1996;225(3):7.
  • Pescatori M, Broccolini A, Minetti C, et al. Gene expression profiling in the early phases of DMD: a constant molecular signature characterizes DMD muscle from early postnatal life throughout disease progression. Faseb J. 2007;21(4):1210–1226. doi: 10.1096/fj.06-7285com.
  • Lopomo A, Ricciardi R, De Rosa A, et al. The thymidylate synthase enhancer region (TSER) polymorphism increases the risk of thymic lymphoid hyperplasia in patients with myasthenia gravis. Gene. 2018;642:376–380. doi: 10.1016/j.gene.2017.11.055.
  • Jones JC. Reductions in expression of growth regulating genes are observed in skeletal muscle and organs with age [Doctoral dissertation]. Illinois Urbana-Champaign. 2012.
  • Sjöström A, Pellikaan K, Sjöström H, et al. Hyperprolactinemia in adults with Prader-Willi syndrome. J Clin Med. 2021;10(16):3163. doi: 10.3390/jcm10163613.
  • Zhang FW, Han ZB, Deng CY, et al. Conservation of genomic imprinting at the NDN, MAGEL2 and MEST loci in pigs. Genes Genet Syst. 2012;87(1):53–58. doi: 10.1266/ggs.87.53.
  • Barker PA, Salehi A. The MAGE proteins: emerging roles in cell cycle progression, apoptosis, and neurogenetic disease. J Neurosci Res. 2002;67(6):705–712. doi: 10.1002/jnr.10160.
  • Muscatelli I-D. The human MAGEL2 gene and its mouse homologue are paternally expressed and mapped to the Prader-Willi region. Hum Mol Genet. 1999;8(13):9.
  • Davey JR, Watt KI, Parker BL, et al. Integrated expression analysis of muscle hypertrophy identifies Asb2 as a negative regulator of muscle mass. JCI Insight. 2016;1(5):e85477. doi: 10.1172/jci.insight.85477.
  • Chen J, Ou Y, Luo R, et al. SAR1B senses leucine levels to regulate mTORC1 signalling. Nature. 2021;596(7871):281–284. doi: 10.1038/s41586-021-03768-w.
  • Marcil V, Seidman E, Sinnett D, et al. Tissue distribution and regulation of the small Sar1b GTPase in mice. Cell Physiol Biochem. 2014;33(6):1815–1826. doi: 10.1159/000362960.
  • Sané A, Ahmarani L, Delvin E, et al. SAR1B GTPase is necessary to protect intestinal cells from disorders of lipid homeostasis, oxidative stress, and inflammation. J Lipid Res. 2019;60(10):1755–1764. doi: 10.1194/jlr.RA119000119.
  • 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. doi: 10.1016/j.matbio.2007.06.004.

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