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Identification of Anoikis-Related Genes in Spinal Cord Injury: Bioinformatics and Experimental Validation

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Abstract

Spinal cord injury (SCI) is a serious disease without effective therapeutic strategies. To identify the potential treatments for SCI, it is extremely important to explore the underlying mechanism. Current studies demonstrate that anoikis might play an important role in SCI. In this study, we aimed to identify the key anoikis-related genes (ARGs) providing therapeutic targets for SCI. The mRNA expression matrix of GSE45006 was downloaded from the Gene Expression Omnibus (GEO) database, and the ARGs were downloaded from the Molecular Signatures Database (MSigDB database). Then, the potential differentially expressed ARGs were identified. Next, correlation analysis, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein–protein interaction (PPI) analysis were employed for the differentially expressed ARGs. Moreover, miRNA-gene networks were constructed by the hub ARGs. Finally, RNA expression of the top ten hub ARGs was validated in the SCI cell model and rat SCI model. A total of 27 common differentially expressed ARGs were identified at different time points (1, 3, 7, and 14 days) following SCI. The GO and KEGG enrichment analysis of these ARGs indicated several enriched terms related to proliferation, cell cycle, and apoptotic process. The PPI results revealed that most of the ARGs interacted with each other. Ten hub ARGs were further screened, and all the 10 genes were validated in the SCI cell model. In the rat model, only seven genes were validated eventually. We identified 27 differentially expressed ARGs of the SCI through bioinformatic analysis. Seven real hub ARGs (CCND1, FN1, IGF1, MYC, STAT3, TGFB1, and TP53) were identified eventually. These results may expand our understanding of SCI and contribute to the exploration of potential SCI targets.

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Data Availability

The datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.

References

  1. Mark AA, Jordan WS, Matthieu G, Thomas HH, Claudia K, Quentin B, Jocelyne B, Grégoire C (2022) Natural and targeted circuit reorganization after spinal cord injury[J]. Nat Neurosci 25(12):1584–1596

    Article  Google Scholar 

  2. Griffin JM, Bradke F (2020) Therapeutic repair for spinal cord injury: combinatory approaches to address a multifaceted problem[J]. EMBO Mol Med 12(3):e11505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ahuja CS, Wilson JR, Nori S, Mark RNK, Claudia D, Armin C, Michael GF (2017) Traumatic spinal cord injury[J]. Nat Rev Dis Primers 3:17018

    Article  PubMed  Google Scholar 

  4. Kwon BK, Tetzlaff W, Grauer JN et al (2004) Pathophysiology and pharmacologic treatment of acute spinal cord injury[J]. Spine J 4(4):451–464

    Article  PubMed  Google Scholar 

  5. Huang H, Young W, Skaper S, Lin C, Gustavo M, Hooshang S, Ziad AZ, Hari SS et al (2020) Clinical neurorestorative therapeutic guidelines for spinal cord injury (IANR/CANR version 2019)[J]. J Orthop Translat 20:14–24

    Article  PubMed  Google Scholar 

  6. Arnold PM, Anderson PA, Chi JH, Dailey TA, Dhall SS, Eichholz KM, Harrop JS, Hoh DJ et al (2019) Congress of Neurological surgeons systematic review and evidence-based guidelines on the evaluation and treatment of patients with thoracolumbar spine trauma: pharmacological treatment[J]. Neurosurgery 84(1):E36–E38

    Article  PubMed  Google Scholar 

  7. O’Toole JE, Kaiser MG, Anderson PA, Arnold PM, Chi JH, Dailey AT, Dhall SS, Eichholz KM, Harrop JS, Hoh DJ, Qureshi S et al (2019) Congress of neurological surgeons systematic review and evidence-based guidelines on the evaluation and treatment of patients with thoracolumbar spine trauma: executive summary[J]. Neurosurgery 84(1):2–6

    Article  PubMed  Google Scholar 

  8. Vacca V, Madaro L, De Angelis F, Proietti D, Cobianchi S, Orsini T, Puri PL, Luvisetto S et al (2020) Revealing the therapeutic potential of botulinum neurotoxin type A in counteracting paralysis and neuropathic pain in spinally injured mice[J]. Toxins (Basel) 12(8):491

    Article  CAS  PubMed  Google Scholar 

  9. Hausmann ON (2003) Post-traumatic inflammation following spinal cord injury[J]. Spinal Cord 41(7):369–378

    Article  CAS  PubMed  Google Scholar 

  10. Mothe AJ, Tam RY, Zahir T, Tator CH, Shoichet MS (2013) Repair of the injured spinal cord by transplantation of neural stem cells in a hyaluronan-based hydrogel[J]. Biomaterials 34(15):3775–3783

    Article  CAS  PubMed  Google Scholar 

  11. Chen Y, Liu S, Li J et al (2020) The latest view on the mechanism of ferroptosis and its research progress in spinal cord injury[J]. Oxid Med Cell Longev 2020:6375938

    Article  PubMed  PubMed Central  Google Scholar 

  12. Wang W, Huang X, Li J et al (2017) Methane suppresses microglial activation related to oxidative, inflammatory, and apoptotic injury during spinal cord injury in rats[J]. Oxid Med Cell Longev 2017:2190897

    Article  PubMed  PubMed Central  Google Scholar 

  13. Fan H, Tang HB, Shan LQ, Liu SC, Huang DG, Chen X, Chen Z, Yang M et al (2019) Quercetin prevents necroptosis of oligodendrocytes by inhibiting macrophages/microglia polarization to M1 phenotype after spinal cord injury in rats[J]. J Neuroinflammation 16(1):206

    Article  PubMed  PubMed Central  Google Scholar 

  14. Frisch SM, Francis H (1994) Disruption of epithelial cell-matrix interactions induces apoptosis[J]. J Cell Biol 124(4):619–626

    Article  CAS  PubMed  Google Scholar 

  15. Grossmann J (2002) Molecular mechanisms of “detachment-induced apoptosis–Anoikis”[J]. Apoptosis 7(3):247–260

    Article  CAS  PubMed  Google Scholar 

  16. Danial NN, Korsmeyer SJ (2004) Cell death: critical control points[J]. Cell 116(2):205–219

    Article  CAS  PubMed  Google Scholar 

  17. Gilmore AP (2005) Anoikis[J]. Cell Death Differ 12(Suppl 2):1473–1477

    Article  CAS  PubMed  Google Scholar 

  18. Paoli P, Giannoni E, Chiarugi P (2013) Anoikis molecular pathways and its role in cancer progression[J]. Biochim Biophys Acta 1833(12):3481–3498

    Article  CAS  PubMed  Google Scholar 

  19. Alvarez JI, Dodelet-Devillers A, Kebir H, Ifergan I, Fabre PJ, Terouz S, Sabbagh M, Wosik K et al (2011) The Hedgehog pathway promotes blood-brain barrier integrity and CNS immune quiescence[J]. Science 334(6063):1727–1731

    Article  CAS  PubMed  Google Scholar 

  20. Wang Y, Jin S, Sonobe Y et al (2014) Interleukin-1beta induces blood-brain barrier disruption by downregulating Sonic hedgehog in astrocytes[J]. PLoS ONE 9(10):e110024

    Article  PubMed  PubMed Central  Google Scholar 

  21. Kapadia R, Yi JH, Vemuganti R (2008) Mechanisms of anti-inflammatory and neuroprotective actions of PPAR-gamma agonists[J]. Front Biosci 13:1813–1826

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources[J]. Nat Protoc 4(1):44–57

    Article  CAS  PubMed  Google Scholar 

  23. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks[J]. Genome Res 13(11):2498–2504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Sticht C, De La Torre C, Parveen A et al (2018) miRWalk: an online resource for prediction of microRNA binding sites[J]. PLoS ONE 13(10):e0206239

    Article  PubMed  PubMed Central  Google Scholar 

  25. Zhou J, Li Z, Zhao Q, Wu T, Zhao Q, Cao Y (2021) Knockdown of SNHG1 alleviates autophagy and apoptosis by regulating miR-362-3p/Jak2/stat3 pathway in LPS-injured PC12 cells[J]. Neurochem Res 46(4):945–956

    Article  CAS  PubMed  Google Scholar 

  26. Boyd JG, Lee J, Skihar V, Doucette R, Kawaja MD (2004) LacZ-expressing olfactory ensheathing cells do not associate with myelinated axons after implantation into the compressed spinal cord[J]. Proc Natl Acad Sci U S A 101(7):2162–2166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Rossignol S, Frigon A (2011) Recovery of locomotion after spinal cord injury: some facts and mechanisms[J]. Annu Rev Neurosci 34:413–440

    Article  CAS  PubMed  Google Scholar 

  28. Ray SK, Samntaray S, Banik NL (2016) Future directions for using estrogen receptor agonists in the treatment of acute and chronic spinal cord injury[J]. Neural Regen Res 11(9):1418–1419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ahuja CS, Martin AR, Fehlings M (2016) Recent advances in managing a spinal cord injury secondary to trauma[J]. F1000Res 5:1017

    Article  Google Scholar 

  30. Sater AP, Rael LT, Tanner AH et al (2018) Cell death after traumatic brain injury: detrimental role of anoikis in healing[J]. Clin Chim Acta 482:149–154

    Article  CAS  PubMed  Google Scholar 

  31. Warren KM, Reeves TM, Phillips LL (2012) MT5-MMP, ADAM-10, and N-cadherin act in concert to facilitate synapse reorganization after traumatic brain injury[J]. J Neurotrauma 29(10):1922–1940

    Article  PubMed  PubMed Central  Google Scholar 

  32. Sandhir R, Gregory E, He YY et al (2011) Upregulation of inflammatory mediators in a model of chronic pain after spinal cord injury[J]. Neurochem Res 36(5):856–862

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Moon C, Heo S, Sim KB, Shin T (2004) Upregulation of CD44 expression in the spinal cords of rats with clip compression injury[J]. Neurosci Lett 367(1):133–136

    Article  CAS  PubMed  Google Scholar 

  34. Juan Z, Dake C, Tanaka K, Shuixiang H (2021) EGFL7 as a novel therapeutic candidate regulates cell invasion and anoikis in colorectal cancer through PI3K/AKT signaling pathway[J]. Int J Clin Oncol 26(6):1099–1108

    Article  PubMed  Google Scholar 

  35. Gan L, Liu P, Lu H, Chen S, Yang J, McCarthy JB, Knudsen KE, Huang H (2009) Cyclin D1 promotes anchorage-independent cell survival by inhibiting FOXO-mediated anoikis[J]. Cell Death Differ 16(10):1408–1417

    Article  CAS  PubMed  Google Scholar 

  36. Pinchi E, Frati A, Cantatore S, D’Errico S, Russa RL, Maiese A, Palmieri M, Pesce A et al (2019) Acute spinal cord injury: a systematic review investigating miRNA families involved[J]. Int J Mol Sci 20(8):1841. https://doi.org/10.3390/ijms20081841

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Zhang H, Wang D, Tong J et al (2022) MiR-30b-5p attenuates the inflammatory response and facilitates the functional recovery of spinal cord injury by targeting the NEFL/mTOR pathway[J]. Brain Behav 12(12):e2788

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Malvandi AM, Rastegar-Moghaddam SH, Ebrahimzadeh-Bideskan S, Lombardi G, Ebrahimzadeh-Bideskan A, Mohammadipour A (2022) Targeting miR-21 in spinal cord injuries: a game-changer?[J]. Mol Med 28(1):118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Zhang Z, Wan F, Zhuang Q, Zhang Y, Xu Z (2017) Suppression of miR-127 protects PC-12 cells from LPS-induced inflammatory injury by downregulation of PDCD4[J]. Biomed Pharmacother 96:1154–1162

    Article  CAS  PubMed  Google Scholar 

  40. Wakulik K, Wiatrak B, Szczukowski L, Bodetko D, Szandruk-Bender M, Dobosz A, Świątek P, Gąsiorowski K (2020) Effect of novel pyrrolo[3,4-d]pyridazinone derivatives on lipopolysaccharide-induced neuroinflammation[J]. Int J Mol Sci 21(7):2575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Wu J, Stoica BA, Faden AI (2011) Cell cycle activation and spinal cord injury[J]. Neurotherapeutics 8(2):221–228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Byrnes KR, Stoica BA, Fricke S et al (2007) Cell cycle activation contributes to post-mitotic cell death and secondary damage after spinal cord injury[J]. Brain 130(Pt 11):2977–2992

    Article  PubMed  Google Scholar 

  43. Wu J, Stoica BA, Dinizo M, Pajoohesh-Ganji A, Piao C, Faden AI (2012) Delayed cell cycle pathway modulation facilitates recovery after spinal cord injury[J]. Cell Cycle 11(9):1782–1795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Di Giovanni S, Knoblach SM, Brandoli C, Aden SA, Hoffman EP, Faden AI (2003) Gene profiling in spinal cord injury shows role of cell cycle in neuronal death[J]. Ann Neurol 53(4):454–468

    Article  PubMed  Google Scholar 

  45. Singh P, Carraher C, Schwarzbauer JE (2010) Assembly of fibronectin extracellular matrix[J]. Annu Rev Cell Dev Biol 26:397–419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Frisch SM, Ruoslahti E (1997) Integrins and anoikis[J]. Curr Opin Cell Biol 9(5):701–706

    Article  CAS  PubMed  Google Scholar 

  47. Gonzalez-Perez F, Hernandez J, Heimann C, Phillips JB, Udina E, Navarro X (2018) Schwann cells and mesenchymal stem cells in laminin- or fibronectin-aligned matrices and regeneration across a critical size defect of 15 mm in the rat sciatic nerve[J]. J Neurosurg Spine 28(1):109–118

    Article  PubMed  Google Scholar 

  48. Faber-Elman A, Solomon A, Abraham JA, Marikovsky M, Schwartz M (1996) Involvement of wound-associated factors in rat brain astrocyte migratory response to axonal injury: in vitro simulation[J]. J Clin Invest 97(1):162–171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Bellver-Landete V, Bretheau F, Mailhot B, Vallières N, Lessard M, Janelle ME, Vernoux N, Tremblay MÈ (2019) Microglia are an essential component of the neuroprotective scar that forms after spinal cord injury[J]. Nat Commun 10(1):518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Zaytseva O, Quinn LM (2017) Controlling the master: chromatin dynamics at the MYC promoter integrate developmental signaling[J]. Genes (Basel) 8(4):118

    Article  PubMed  Google Scholar 

  51. Li N, Yao M, Liu J, Zhu Z, Lam TL, Zhang P, Kiang KMY, Leung GKK (2022) Vitamin D promotes remyelination by suppressing c-Myc and Inducing oligodendrocyte precursor cell differentiation after traumatic spinal cord injury[J]. Int J Biol Sci 18(14):5391–5404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Dominguez E, Rivat C, Pommier B, Mauborgne A, Pohl M (2008) JAK/STAT3 pathway is activated in spinal cord microglia after peripheral nerve injury and contributes to neuropathic pain development in rat[J]. J Neurochem 107(1):50–60

    Article  CAS  PubMed  Google Scholar 

  53. Ramsauer M, Krause D, Dermietzel R (2002) Angiogenesis of the blood-brain barrier in vitro and the function of cerebral pericytes[J]. FASEB J 16(10):1274–1276

    Article  CAS  PubMed  Google Scholar 

  54. Ferbert T, Child C, Graeser V, Swing T, Akbar M, Heller R, Biglari B, Moghaddam A (2017) Tracking spinal cord injury: differences in cytokine expression of IGF-1, TGF- B1, and sCD95l can be measured in blood samples and correspond to neurological remission in a 12-week follow-up[J]. J Neurotrauma 34(3):607–614

    Article  PubMed  Google Scholar 

  55. Powell E, Piwnica-Worms D, Piwnica-Worms H (2014) Contribution of p53 to metastasis[J]. Cancer Discov 4(4):405–414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Babaei G, Aliarab A, AsghariVostakolaei M, Hotelchi M, Neisari R, Aziz SGG, Bazl MR (2021) Crosslink between p53 and metastasis: focus on epithelial-mesenchymal transition, cancer stem cell, angiogenesis, autophagy, and anoikis[J]. Mol Biol Rep 48(11):7545–7557

    Article  CAS  PubMed  Google Scholar 

  57. Joshi Y, Soria MG, Quadrato G et al (2015) The MDM4/MDM2-p53-IGF1 axis controls axonal regeneration, sprouting and functional recovery after CNS injury[J]. Brain 138(Pt 7):1843–1862

    Article  PubMed  Google Scholar 

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Acknowledgements

We thank everyone who provided support for this study. Thank the SangerBox website (http://sangerbox.com/Tool) for the helpful information on this manuscript.

Funding

This study was supported by the National Natural Science Foundation of China [Grant No. 81472355 (XJ)] and The Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16040601). We are sincerely grateful to those who created and maintained these public databases.

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Author notes

  1. Wen Yin and Zhipeng Jiang, and Youwei Guo contributed equally to this work.

Authors and Affiliations

  1. Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People’s Republic of China

    Wen Yin, Zhipeng Jiang, Youwei Guo, Yudong Cao, Zhaoping Wu, Yi Zhou, Quan Chen & Xingjun Jiang

  2. National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People’s Republic of China

    Wen Yin, Zhipeng Jiang, Youwei Guo, Yudong Cao, Zhaoping Wu, Yi Zhou, Quan Chen & Xingjun Jiang

  3. Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China

    Weidong Liu & Caiping Ren

  4. NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China

    Weidong Liu & Caiping Ren

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  1. Wen Yin
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Contributions

XJJ and CPR were responsible for experimental design. WY, ZPJ, and YWG were responsible for experimental analysis and thesis writing. HCZ, YDC, ZPW, YZ, QC, WDL, and MZ were responsible for data screening, and collection. All authors contributed to the article and approved the submitted version.

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Correspondence to Xingjun Jiang or Caiping Ren.

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Yin, W., Jiang, Z., Guo, Y. et al. Identification of Anoikis-Related Genes in Spinal Cord Injury: Bioinformatics and Experimental Validation. Mol Neurobiol (2024). https://doi.org/10.1007/s12035-024-04121-8

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