Systematic analysis of co-expression network and gene expression profile of differentially expressed lncRNA-mRNA one week after spinal cord injury

References

• Ahuja CS, Wilson JR, Nori S, Kotter MRN, Druschel C, Curt A, Fehlings MG. 2017. Traumatic spinal cord injury. Nat Rev Dis Primers. 3:17018–17039. doi:10.1038/nrdp.2017.18.
   PubMed Web of Science ®Google Scholar
• Ban DX, Kong XH, Feng SQ, Ning GZ, Chen JT, Guo SF. 2009. Intraspinal cord graft of autologous activated Schwann cells efficiently promotes axonal regeneration and functional recovery after rat's spinal cord injury. Brain Res. 1256:149–161. doi:10.1016/j.brainres.2008.11.098.
   PubMed Web of Science ®Google Scholar
• Ban Y, Cui C. 2020. Silencing of long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) protects PC-12 cells from LPS-induced injury via targeting miR-29a. Med Sci Monit. 26:e923914.
   PubMed Web of Science ®Google Scholar
• Bano D, Young K, Guerin C, Lefeuvre R, Rothwell N, Naldini L, Rizzuto R, Carafoli E, Nicotera P. 2005. Cleavage of the plasma membrane Na+/Ca2 + exchanger in excitotoxicity. Cell. 120(2):275–285. doi:10.1016/j.cell.2004.11.049.
   PubMed Web of Science ®Google Scholar
• Barnabé-Heider F, Göritz C, Sabelström H, Takebayashi H, Pfrieger F, Meletis K, Frisén J. 2010. Origin of new glial cells in intact and injured adult spinal cord. Cell Stem Cell. 7(4):470–482. doi:10.1016/j.stem.2010.07.014.
   PubMed Web of Science ®Google Scholar
• Calì T, Ottolini D, Brini M. 2011. Mitochondria, calcium, and endoplasmic reticulum stress in Parkinson's disease. BioFactors (Oxford, England). 37(3):228–240. doi:10.1002/biof.159.
   PubMed Web of Science ®Google Scholar
• Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. 2011. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 44(4):667–678. doi:10.1016/j.molcel.2011.08.027.
   PubMed Web of Science ®Google Scholar
• David S, Kroner A. 2011. Repertoire of microglial and macrophage responses after spinal cord injury. Nat Rev Neurosci. 12(7):388–399. doi:10.1038/nrn3053.
   PubMed Web of Science ®Google Scholar
• Dong X, Cong S. 2021. DNM3OS regulates GAPDH expression and influences the molecular pathogenesis of Huntington's disease. J Cell Mol Med. 25(18):9066–9071. doi:10.1111/jcmm.16838.
   PubMed Web of Science ®Google Scholar
• Fan B, Wei Z, Yao X, Shi G, Cheng X, Zhou X, Zhou H, Ning G, Kong X, Feng S. 2018. Microenvironment imbalance of spinal cord injury. Cell Transplant. 27(6):853–866. doi:10.1177/0963689718755778.
   PubMed Web of Science ®Google Scholar
• Fan B, Wei Z, Yao X, Shi G, Cheng X, Zhou X, Zhou H, Ning G, Kong X, Feng S. 2018. Microenvironment imbalance of spinal cord injury. Cell Transplant. 27(6):853–866. doi:10.1177/0963689718755778.
   PubMed Web of Science ®Google Scholar
• Figley S, Liu Y, Karadimas S, Satkunendrarajah K, Fettes P, Spratt S, Lee G, Ando D, Surosky R, Giedlin M, Fehlings M. 2014. Delayed administration of a bio-engineered zinc-finger VEGF-A gene therapy is neuroprotective and attenuates allodynia following traumatic spinal cord injury. PLoS One. 9(5):e96137. doi:10.1371/journal.pone.0096137.
   PubMed Web of Science ®Google Scholar
• Garcia E, Aguilar-Cevallos J, Silva-Garcia R, Ibarra A. 2016. Cytokine and growth factor activation in vivo and in vitro after spinal cord injury. Mediat Inflamm. 2016:9476020–9476041. doi:10.1155/2016/9476020.
   PubMed Web of Science ®Google Scholar
• Greenhalgh A, David S. 2014. Differences in the phagocytic response of microglia and peripheral macrophages after spinal cord injury and its effects on cell death. J Neurosci. 34(18):6316–6322. doi:10.1523/JNEUROSCI.4912-13.2014.
   PubMed Web of Science ®Google Scholar
• Gu S, Xie R, Liu X, Shou J, Gu W, Che X. 2017. Long coding RNA XIST contributes to neuronal apoptosis through the downregulation of AKT phosphorylation and is negatively regulated by miR-494 in Rat spinal cord injury. Int J Mol Sci. 18(4):732–749. doi:10.3390/ijms18040732.
   PubMed Web of Science ®Google Scholar
• Hagg T, Oudega M. 2006. Degenerative and spontaneous regenerative processes after spinal cord injury. J Neurotrauma. 23:264–280.
   PubMed Web of Science ®Google Scholar
• Hu X, Li R, Wu Y, Li Y, Zhong X, Zhang G, Kang Y, Liu S, Xie L, Ye J, Xiao J. 2020. Thermosensitive heparin-poloxamer hydrogel encapsulated bFGF and NGF to treat spinal cord injury. J Cell Mol Med. 24(14):8166–8178. doi:10.1111/jcmm.15478.
   PubMed Web of Science ®Google Scholar
• Jain NB, Ayers GD, Peterson EN, Harris MB, Morse L, O'Connor KC, Garshick E. 2015. Traumatic spinal cord injury in the United States, 1993-2012. JAMA. 313(22):2236–2243. doi:10.1001/jama.2015.6250.
   PubMed Web of Science ®Google Scholar
• James SL, Theadom A, Ellenbogen RG, Bannick MS, Montjoy-Venning W, Lucchesi LR, Abbasi N, Abdulkader R, Abraha HN, Adsuar JC, Afarideh M. 2019. Global, regional, and national burden of traumatic brain injury and spinal cord injury, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Neurol. 18(1):56–87. doi:10.1016/S1474-4422(18)30415-0.
   PubMed Web of Science ®Google Scholar
• Kang Y, Ding H, Zhou H, Wei Z, Liu L, Pan D, Feng S. 2018. Epidemiology of worldwide spinal cord injury: a literature review. J Neurorestor. 6:1–9. doi:10.2147/JN.S143236.
   Google Scholar
• Keefe K, Sheikh I, Smith G. 2017. Targeting neurotrophins to specific populations of neurons: NGF, BDNF, and NT-3 and their relevance for treatment of spinal cord injury. Int J Mol Sci. 18(3):548–565. doi:10.3390/ijms18030548.
   PubMed Web of Science ®Google Scholar
• Kim K, Nam J, Mukouyama Y, Kawamoto S. 2013. Rbfox3-regulated alternative splicing of numb promotes neuronal differentiation during development. J Cell Biol. 200(4):443–458. doi:10.1083/jcb.201206146.
   PubMed Web of Science ®Google Scholar
• Lin Y, Kuo K, Chen S, Huang H. 2018. RBFOX3/NeuN is dispensable for visual function. PLoS One. 13(2):e0192355.
   PubMed Web of Science ®Google Scholar
• Ling L, Hu H, Liu K, Ram Y, Gao J, Cao Y. 2019. Long noncoding RNA MIRG induces osteoclastogenesis and bone resorption in osteoporosis through negative regulation of miR-1897. Eur Rev Med Pharmacol Sci. 23(23):10195–10203.
   PubMed Web of Science ®Google Scholar
• Liu Y, Figley S, Spratt S, Lee G, Ando D, Surosky R, Fehlings M. 2010. An engineered transcription factor which activates VEGF-A enhances recovery after spinal cord injury. Neurobiol Dis. 37(2):384–393. doi:10.1016/j.nbd.2009.10.018.
   PubMed Web of Science ®Google Scholar
• Loy D, Crawford C, Darnall J, Burke D, Onifer S, Whittemore S. 2002. Temporal progression of angiogenesis and basal lamina deposition after contusive spinal cord injury in the adult rat. J Comp Neurol. 445(4):308–324. doi:10.1002/cne.10168.
   PubMed Web of Science ®Google Scholar
• Lu J, Ashwell K, Waite P. 2000. Advances in secondary spinal cord injury: role of apoptosis. Spine. 25(14):1859–1866. doi:10.1097/00007632-200007150-00022.
   PubMed Web of Science ®Google Scholar
• Miller LE, Herbert WG. 2016. Health and economic benefits of physical activity for patients with spinal cord injury. ClinicoEcon Outcomes Res. 8:551–558. doi:10.2147/CEOR.S115103.
   PubMed Web of Science ®Google Scholar
• Mitra R, Chen X, Greenawalt E, Maulik U, Jiang W, Zhao Z, Eischen C. 2017. Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition. Nat Commun. 8(1):1604–1616. doi:10.1038/s41467-017-01781-0.
   PubMed Web of Science ®Google Scholar
• Ng M, Stammers A, Kwon B. 2011. Vascular disruption and the role of angiogenic proteins after spinal cord injury. Transl Stroke Res. 2(4):474–491. doi:10.1007/s12975-011-0109-x.
   PubMed Web of Science ®Google Scholar
• Nicholls D. 2004. Mitochondrial dysfunction and glutamate excitotoxicity studied in primary neuronal cultures. Curr Mol Med. 4(2):149–177. doi:10.2174/1566524043479239.
   PubMed Web of Science ®Google Scholar
• Osuka K, Watanabe Y, Usuda N, Atsuzawa K, Aoshima C, Yamauchi K, Takayasu M, Yoshida J. 2007. Phosphorylation of neuronal nitric oxide synthase at Ser847 in the nucleus intermediolateralis after spinal cord injury in mice. Neuroscience. 145(1):241–247. doi:10.1016/j.neuroscience.2006.10.034.
   PubMed Web of Science ®Google Scholar
• Pineau I, Lacroix S. 2007. Proinflammatory cytokine synthesis in the injured mouse spinal cord: multiphasic expression pattern and identification of the cell types involved. J Comp Neurol. 500(2):267–285. doi:10.1002/cne.21149.
   PubMed Web of Science ®Google Scholar
• Quarles R. 2009. A hypothesis about the relationship of myelin-associated glycoprotein's function in myelinated axons to its capacity to inhibit neurite outgrowth. Neurochem Res. 34(1):79–86. doi:10.1007/s11064-008-9668-y.
   PubMed Web of Science ®Google Scholar
• Rinn JL, Chang HY. 2012. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 81:145–166. doi:10.1146/annurev-biochem-051410-092902.
   PubMed Web of Science ®Google Scholar
• Ruddy M, Wong G, Liu X, Yamamoto H, Kasayama S, Kirkwood K, Gaffen S. 2004. Functional cooperation between interleukin-17 and tumor necrosis factor-alpha is mediated by CCAAT/enhancer-binding protein family members. J Biol Chem. 279(4):2559–2567. doi:10.1074/jbc.M308809200.
   PubMed Web of Science ®Google Scholar
• Ruschel J, Hellal F, Flynn K, Dupraz S, Elliott D, Tedeschi A, Bates M, Sliwinski C, Brook G, Dobrindt K, et al. 2015. Axonal regeneration. Systemic administration of epothilone B promotes axon regeneration after spinal cord injury. Science (New York, NY). 348(6232):347–352. doi:10.1126/science.aaa2958.
   Google Scholar
• Schacker M, Cheng Y, Eckersley-Maslin M, Snaith R, Colledge W. 2020. Hypermethylation and reduced expression of Gtl2, Rian and Mirg at the Dlk1-Dio3 imprinted locus as a marker for poor developmental potential of mouse embryonic stem cells. Stem Cell Res. 48:101931–101943. doi:10.1016/j.scr.2020.101931.
   PubMed Web of Science ®Google Scholar
• Sekita Y, Wagatsuma H, Irie M, Kobayashi S, Kohda T, Matsuda J, Yokoyama M, Ogura A, Schuster-Gossler K, Gossler A, et al. 2006. Aberrant regulation of imprinted gene expression in Gtl2lacZ mice. Cytogenet Genome Res. 113:223–229. doi:10.1159/000090836.
   PubMed Web of Science ®Google Scholar
• Shi G, Zhou X, Wang X, Zhang X, Zhang P, Feng S. 2020. Signatures of altered DNA methylation gene expression after central and peripheral nerve injury. J Cell Physiol. 235(6):5171–5181. doi:10.1002/jcp.29393.
   PubMed Web of Science ®Google Scholar
• Shi Z, Pan B, Feng S. 2018. The emerging role of long non-coding RNA in spinal cord injury. J Cell Mol Med. 22(4):2055–2061. doi:10.1111/jcmm.13515.
   PubMed Web of Science ®Google Scholar
• Silva NA, Sousa N, Reis RL, Salgado AJ. 2014. From basics to clinical: a comprehensive review on spinal cord injury. Prog Neurobiol. 114:25–57. doi:10.1016/j.pneurobio.2013.11.002.
   PubMed Web of Science ®Google Scholar
• Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 27(3):431–432. doi:10.1093/bioinformatics/btq675.
   PubMed Web of Science ®Google Scholar
• Springer J, Azbill R, Knapp P. 1999. Activation of the caspase-3 apoptotic cascade in traumatic spinal cord injury. Nat Med. 5(8):943–946. doi:10.1038/11387.
   PubMed Web of Science ®Google Scholar
• Sun X, Wang X, Chen T, Li T, Cao K, Lu A, Chen Y, Sun D, Luo J, Fan J, et al. 2010. Myelin activates FAK/Akt/NF-kappaB pathways and provokes CR3-dependent inflammatory response in murine system. PLoS One. 5(2):e9380. doi:10.1371/journal.pone.0009380.
   PubMed Web of Science ®Google Scholar
• Tao F, Li Q, Liu S, Wu H, Skinner J, Hurtado A, Belegu V, Furmanski O, Yang Y, McDonald J, Johns R. 2013. Role of neuregulin-1/ErbB signaling in stem cell therapy for spinal cord injury-induced chronic neuropathic pain. Stem Cells (Dayton, Ohio). 31(1):83–91. doi:10.1002/stem.1258.
   PubMed Web of Science ®Google Scholar
• Tran AP, Warren PM, Silver J. 2018. The biology of regeneration failure and success after spinal cord injury. Physiol Rev. 98(2):881–917. doi:10.1152/physrev.00017.2017.
   PubMed Web of Science ®Google Scholar
• Wang KC, Chang HY. 2011. Molecular mechanisms of long noncoding RNAs. Mol Cell. 43(6):904–914. doi:10.1016/j.molcel.2011.08.018.
   PubMed Web of Science ®Google Scholar
• Wang P, Qi X, Xu G, Liu J, Guo J, Li X, Ma X, Sun H. 2019. CCL28 promotes locomotor recovery after spinal cord injury via recruiting regulatory T cells. Aging. 11(18):7402–7415. doi:10.18632/aging.102239.
   PubMedGoogle Scholar
• Wang S, Deng J, Fu H, Guo Z, Zhang L, Tang P. 2020. Astrocytes directly clear myelin debris through endocytosis pathways and followed by excessive gliosis after spinal cord injury. Biochem Biophys Res Commun. S0006-291X(20):30337–5.
   Google Scholar
• Xue W, Zhao W, Meng X, Shen H, Huang P. 2019. Spinal cord injury induced neuregulin 1 signaling changes in mouse prefrontal cortex and hippocampus. Brain Res Bull. 144:180–186. doi:10.1016/j.brainresbull.2018.12.002.
   PubMed Web of Science ®Google Scholar
• You T, Bi Y, Li J, Zhang M, Chen X, Zhang K, Li J. 2017. IL-17 induces reactive astrocytes and up-regulation of vascular endothelial growth factor (VEGF) through JAK/STAT signaling. Sci Rep. 7:41779–41794. doi:10.1038/srep41779.
   PubMed Web of Science ®Google Scholar
• Yu B, Zhou S, Yi S, Gu X. 2015. The regulatory roles of non-coding RNAs in nerve injury and regeneration. Prog Neurobiol. 134:122–139. doi:10.1016/j.pneurobio.2015.09.006.
   PubMed Web of Science ®Google Scholar
• Yuan S, Shi Z, Cao F, Li J, Feng S. 2018. Epidemiological features of spinal cord injury in China: A systematic review. Front Neurol. 9:683–695. doi:10.3389/fneur.2018.00683.
   PubMed Web of Science ®Google Scholar
• Zhang L, Lu X, Gong L, Cui L, Zhang H, Zhao W, Jiang P, Hou G, Hou Y. 2021. Tetramethylpyrazine protects blood-spinal cord barrier integrity by modulating microglia polarization through activation of STAT3/SOCS3 and inhibition of NF-kB signaling pathways in experimental autoimmune encephalomyelitis mice. Cell Mol Neurobiol. 41(4):717–731. doi:10.1007/s10571-020-00878-3.
   PubMed Web of Science ®Google Scholar
• Zhao Q, Lu F, Su Q, Liu Z, Xia X, Yan Z, Zhou F, Qin R. 2020. Knockdown of long noncoding RNA XIST mitigates the apoptosis and inflammatory injury of microglia cells after spinal cord injury through miR-27a/Smurf1 axis. Neurosci Lett. 715:134649. doi:10.1016/j.neulet.2019.134649
   PubMed Web of Science ®Google Scholar