Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing

BMC Genomics

Volumn 18, Issue 1, 2017, Pages

  Shi, Ling Ling ^a   Zhang, Nan ^a   Xie, Xiu Mei ^a   Chen, Yue Juan ^a   Wang, Rui ^a   Shen, Lin ^a   Zhou, Jian Sheng ^a   Hu, Jian Guo ^a   Lü, He Zuo ^a  

^a BENGBU MEDICAL COLLEGE   (China)

Author keywords

GO enrichment; Pathway analysis; RNA Seq; Spinal cord injury; Sprague Dawley rats (RRID:RGD_70508)

Indexed keywords

B LYMPHOCYTE RECEPTOR; CALCIUM; CHEMOKINE; CYCLIC AMP; GUANOSINE TRIPHOSPHATASE; HYPOXIA INDUCIBLE FACTOR 1; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MAJOR HISTOCOMPATIBILITY ANTIGEN; NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN LIKE RECEPTOR; OXYTOCIN; RAP1 PROTEIN; TOLL LIKE RECEPTOR; TUMOR NECROSIS FACTOR;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ANTIGEN PRESENTATION; ARTICLE; CONTROLLED STUDY; DISEASE COURSE; DOPAMINERGIC SYSTEM; DOWN REGULATION; FEMALE; GABAERGIC SYSTEM; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE ONTOLOGY; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GLUTAMATERGIC SYNAPSE; IMMUNE RESPONSE; NERVE GROWTH; NONHUMAN; QUANTITATIVE ANALYSIS; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SIGNAL TRANSDUCTION; SPINAL CORD INJURY; SYNAPTIC TRANSMISSION; TISSUE INJURY; TISSUE REPAIR; TRANSLATION INITIATION; UPREGULATION; ANIMAL; GENE EXPRESSION PROFILING; GENETICS; SEQUENCE ANALYSIS; SPRAGUE DAWLEY RAT;

ANIMALS; FEMALE; GENE EXPRESSION PROFILING; GENE ONTOLOGY; RATS; RATS, SPRAGUE-DAWLEY; SEQUENCE ANALYSIS, RNA; SPINAL CORD INJURIES;

EID: 85012949927     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-017-3532-x     Document Type: Article

References (66)

1. Devivo MJ. Epidemiology of traumatic spinal cord injury: trends and future implications. Spinal Cord. 2012;50(5):365-72.
2. Qiu J. China Spinal Cord Injury Network: changes from within. Lancet Neurol. 2009;8(7):606-7.
3. Liu NK, Wang XF, Lu QB, Xu XM. Altered microRNA expression following traumatic spinal cord injury. Exp Neurol. 2009;219(2):424-9.
4. Aimone JB, Leasure JL, Perreau VM, Thallmair M, Christopher Reeve Paralysis Foundation Research C. Spatial and temporal gene expression profiling of the contused rat spinal cord. Exp Neurol. 2004;189(2):204-21.
5. Nesic O, Svrakic NM, Xu GY, McAdoo D, Westlund KN, Hulsebosch CE, Ye Z, Galante A, Soteropoulos P, Tolias P, et al. DNA microarray analysis of the contused spinal cord: effect of NMDA receptor inhibition. J Neurosci Res. 2002;68(4):406-23.
6. Tachibana T, Noguchi K, Ruda MA. Analysis of gene expression following spinal cord injury in rat using complementary DNA microarray. Neurosci Lett. 2002;327(2):133-7.
7. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008;18(9):1509-17.
8. Gamsiz ED, Ouyang Q, Schmidt M, Nagpal S, Morrow EM. Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing. Genomics. 2012;99(1):44-51.
9. Lu HZ, Xu L, Zou J, Wang YX, Ma ZW, Xu XM, Lu PH. Effects of autoimmunity on recovery of function in adult rats following spinal cord injury. Brain Behav Immun. 2008;22(8):1217-30.
10. Basso DM, Beattie MS, Bresnahan JC. A sensitive and reliable locomotor rating scale for open field testing in rats. J Neurotrauma. 1995;12(1):1-21.
11. Basso DM, Beattie MS, Bresnahan JC, Anderson DK, Faden AI, Gruner JA, Holford TR, Hsu CY, Noble LJ, Nockels R, et al. MASCIS evaluation of open field locomotor scores: effects of experience and teamwork on reliability. Multicenter Animal Spinal Cord Injury Study. J Neurotrauma. 1996;13(7):343-59.
12. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511-5.
13. Hu JG, Shen L, Wang R, Wang QY, Zhang C, Xi J, Ma SF, Zhou JS, Lu HZ. Effects of Olig2-overexpressing neural stem cells and myelin basic protein-activated T cells on recovery from spinal cord injury. Neurotherapeutics. 2012;9(2):422-45.
14. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29(9), e45.
15. Ma SF, Chen YJ, Zhang JX, Shen L, Wang R, Zhou JS, Hu JG, Lu HZ. Adoptive transfer of M2 macrophages promotes locomotor recovery in adult rats after spinal cord injury. Brain Behav Immun. 2015;45:157-70.
16. Chen K, Deng S, Lu H, Zheng Y, Yang G, Kim D, Cao Q, Wu JQ. RNA-seq characterization of spinal cord injury transcriptome in acute/subacute phases: a resource for understanding the pathology at the systems level. PLoS One. 2013;8(8), e72567.
17. Areschoug T, Gordon S. Pattern recognition receptors and their role in innate immunity: focus on microbial protein ligands. Contrib Microbiol. 2008;15:45-60.
18. Kawai T, Akira S. The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors. Nat Immunol. 2010;11(5):373-84.
19. Byrnes KR, Fricke ST, Faden AI. Neuropathological differences between rats and mice after spinal cord injury. J Magn Reson Imaging. 2010;32(4):836-46.
20. Sroga JM, Jones TB, Kigerl KA, McGaughy VM, Popovich PG. Rats and mice exhibit distinct inflammatory reactions after spinal cord injury. J Comp Neurol. 2003;462(2):223-40.
21. Jin L, Wu Z, Xu W, Hu X, Zhang J, Xue Z, Cheng L. Identifying gene expression profile of spinal cord injury in rat by bioinformatics strategy. Mol Biol Rep. 2014;41(5):3169-77.
22. Wen T, Hou J, Wang F, Zhang Y, Zhang T, Sun T. Comparative analysis of molecular mechanism of spinal cord injury with time based on bioinformatics data. Spinal Cord. 2016;54(6):431-8.
23. Chamankhah M, Eftekharpour E, Karimi-Abdolrezaee S, Boutros PC, San-Marina S, Fehlings MG. Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. BMC Genomics. 2013;14:583.
24. Fortune RD, Grill RJ, Jr., Beeton C, Tanner M, Huq R, Loose DS. Changes in gene expression and metabolism in the testes of the rat following spinal cord injury. J Neurotrauma 2016. [Epub ahead of print].
25. Park KW, Lin CY, Lee YS. Expression of suppressor of cytokine signaling-3 (SOCS3) and its role in neuronal death after complete spinal cord injury. Exp Neurol. 2014;261:65-75.
26. Zong S, Zeng G, Fang Y, Peng J, Tao Y, Li K, Zhao J. The role of IL-17 promotes spinal cord neuroinflammation via activation of the transcription factor STAT3 after spinal cord injury in the rat. Mediat Inflamm. 2014;2014:786947.
27. Wang CX, Nuttin B, Heremans H, Dom R, Gybels J. Production of tumor necrosis factor in spinal cord following traumatic injury in rats. J Neuroimmunol. 1996;69(1-2):151-6.
28. Hayashi M, Ueyama T, Tamaki T, Senba E. Expression of neurotrophin and IL-1 beta mRNAs following spinal cord injury and the effects of methylprednisolone treatment. Kaibogaku zasshi J Anatomy. 1997;72(3):209-13.
29. Moon C, Heo S, Sim KB, Shin T. Upregulation of CD44 expression in the spinal cords of rats with clip compression injury. Neurosci Lett. 2004;367(1):133-6.
30. Mocchetti I, Rabin SJ, Colangelo AM, Whittemore SR, Wrathall JR. Increased basic fibroblast growth factor expression following contusive spinal cord injury. Exp Neurol. 1996;141(1):154-64.
31. Liu N, Han S, Lu PH, Xu XM. Upregulation of annexins I, II, and V after traumatic spinal cord injury in adult rats. J Neurosci Res. 2004;77(3):391-401.
32. Hansen CN, Fisher LC, Deibert RJ, Jakeman LB, Zhang H, Noble-Haeusslein L, White S, Basso DM. Elevated MMP-9 in the lumbar cord early after thoracic spinal cord injury impedes motor relearning in mice. J Neurosci. 2013;33(32):13101-11.
33. Antonsson B, Conti F, Ciavatta A, Montessuit S, Lewis S, Martinou I, Bernasconi L, Bernard A, Mermod JJ, Mazzei G, et al. Inhibition of Bax channel-forming activity by Bcl-2. Science. 1997;277(5324):370-2.
34. Woodcock JM, Zacharakis B, Plaetinck G, Bagley CJ, Qiyu S, Hercus TR, Tavernier J, Lopez AF. Three residues in the common beta chain of the human GM-CSF, IL-3 and IL-5 receptors are essential for GM-CSF and IL-5 but not IL-3 high affinity binding and interact with Glu21 of GM-CSF. EMBO J. 1994;13(21):5176-85.
35. Huang X, Kim JM, Kong TH, Park SR, Ha Y, Kim MH, Park H, Yoon SH, Park HC, Park JO, et al. GM-CSF inhibits glial scar formation and shows long-term protective effect after spinal cord injury. J Neurol Sci. 2009;277(1-2):87-97.
36. van Leeuwen BH, Martinson ME, Webb GC, Young IG. Molecular organization of the cytokine gene cluster, involving the human IL-3, IL-4, IL-5, and GM-CSF genes, on human chromosome 5. Blood. 1989;73(5):1142-8.
37. Kiss-Toth E, Bagstaff SM, Sung HY, Jozsa V, Dempsey C, Caunt JC, Oxley KM, Wyllie DH, Polgar T, Harte M, et al. Human tribbles, a protein family controlling mitogen-activated protein kinase cascades. J Biol Chem. 2004;279(41):42703-8.
38. Sung HY, Guan H, Czibula A, King AR, Eder K, Heath E, Suvarna SK, Dower SK, Wilson AG, Francis SE, et al. Human tribbles-1 controls proliferation and chemotaxis of smooth muscle cells via MAPK signaling pathways. J Biol Chem. 2007;282(25):18379-87.
39. Satoh T, Kidoya H, Naito H, Yamamoto M, Takemura N, Nakagawa K, Yoshioka Y, Morii E, Takakura N, Takeuchi O, et al. Critical role of Trib1 in differentiation of tissue-resident M2-like macrophages. Nature. 2013;495(7442):524-8.
40. Chen YJ, Zhu H, Zhang N, Shen L, Wang R, Zhou JS, Hu JG, Lu HZ. Temporal kinetics of macrophage polarization in the injured rat spinal cord. J Neurosci Res. 2015;93(10):1526-33.
41. Liebermann DA, Hoffman B. Gadd45 in the response of hematopoietic cells to genotoxic stress. Blood Cells Mol Dis. 2007;39(3):329-35.
42. Grill M, Syme TE, Nocon AL, Lu AZ, Hancock D, Rose-John S, Campbell IL. Strawberry notch homolog 2 is a novel inflammatory response factor predominantly but not exclusively expressed by astrocytes in the central nervous system. Glia. 2015;63(10):1738-52.
43. Bosma M, Hesselink MK, Sparks LM, Timmers S, Ferraz MJ, Mattijssen F, van Beurden D, Schaart G, de Baets MH, Verheyen FK, et al. Perilipin 2 improves insulin sensitivity in skeletal muscle despite elevated intramuscular lipid levels. Diabetes. 2012;61(11):2679-90.
44. van der Flier A, Sonnenberg A. Structural and functional aspects of filamins. Biochim Biophys Acta. 2001;1538(2-3):99-117.
45. Richard M, Louahed J, Demoulin JB, Renauld JC. Interleukin-9 regulates NF-kappaB activity through BCL3 gene induction. Blood. 1999;93(12):4318-27.
46. Hunter RB, Kandarian SC. Disruption of either the Nfkb1 or the Bcl3 gene inhibits skeletal muscle atrophy. J Clin Invest. 2004;114(10):1504-11.
47. van Galen J, Olrichs NK, Schouten A, Serrano RL, Nolte-'t Hoen EN, Eerland R, Kaloyanova D, Gros P, Helms JB. Interaction of GAPR-1 with lipid bilayers is regulated by alternative homodimerization. Biochim Biophys Acta. 2012;1818(9):2175-83.
48. Liotta LA, Goldfarb RH, Brundage R, Siegal GP, Terranova V, Garbisa S. Effect of plasminogen activator (urokinase), plasmin, and thrombin on glycoprotein and collagenous components of basement membrane. Cancer Res. 1981;41(11 Pt 1):4629-36.
49. Wyatt E, Wu R, Rabeh W, Park HW, Ghanefar M, Ardehali H. Regulation and cytoprotective role of hexokinase III. PLoS One. 2010;5(11), e13823.
50. Sessa G, Podini P, Mariani M, Meroni A, Spreafico R, Sinigaglia F, Colonna M, Panina P, Meldolesi J. Distribution and signaling of TREM2/DAP12, the receptor system mutated in human polycystic lipomembraneous osteodysplasia with sclerosing leukoencephalopathy dementia. Eur J Neurosci. 2004;20(10):2617-28.
51. Takahashi K, Rochford CD, Neumann H. Clearance of apoptotic neurons without inflammation by microglial triggering receptor expressed on myeloid cells-2. J Exp Med. 2005;201(4):647-57.
52. Holmdahl R, Sareila O, Olsson LM, Backdahl L, Wing K. Ncf1 polymorphism reveals oxidative regulation of autoimmune chronic inflammation. Immunol Rev. 2016;269(1):228-47.
53. Bardos T, Kamath RV, Mikecz K, Glant TT. Anti-inflammatory and chondroprotective effect of TSG-6 (tumor necrosis factor-alpha-stimulated gene-6) in murine models of experimental arthritis. Am J Pathol. 2001;159(5):1711-21.
54. McDaneld TG, Spurlock DM. Ankyrin repeat and suppressor of cytokine signaling (SOCS) box-containing protein (ASB) 15 alters differentiation of mouse C2C12 myoblasts and phosphorylation of mitogen-activated protein kinase and Akt. J Anim Sci. 2008;86(11):2897-902.
55. Roger M, Biaso F, Castelle CJ, Bauzan M, Chaspoul F, Lojou E, Sciara G, Caffarri S, Giudici-Orticoni MT, Ilbert M. Spectroscopic characterization of a green copper site in a single-domain cupredoxin. PLoS One. 2014;9(6), e98941.
56. Xia L, Huang W, Tian D, Chen Z, Zhang L, Li Y, Hu H, Liu J, Chen Z, Tang G, et al. ACP5, a direct transcriptional target of FoxM1, promotes tumor metastasis and indicates poor prognosis in hepatocellular carcinoma. Oncogene. 2014;33(11):1395-406.
57. Lindblom RP, Aeinehband S, Parsa R, Strom M, Al Nimer F, Zhang XM, Dominguez CA, Flytzani S, Diez M, Piehl F. Genetic variability in the rat Aplec C-type lectin gene cluster regulates lymphocyte trafficking and motor neuron survival after traumatic nerve root injury. J Neuroinflammation. 2013;10:60.
58. Lee YB, Yune TY, Baik SY, Shin YH, Du S, Rhim H, Lee EB, Kim YC, Shin ML, Markelonis GJ, et al. Role of tumor necrosis factor-alpha in neuronal and glial apoptosis after spinal cord injury. Exp Neurol. 2000;166(1):190-5.
59. Esposito E, Cuzzocrea S. Anti-TNF therapy in the injured spinal cord. Trends Pharmacol Sci. 2011;32(2):107-15.
60. Impellizzeri D, Ahmad A, Di Paola R, Campolo M, Navarra M, Esposito E, Cuzzocrea S. Role of Toll like receptor 4 signaling pathway in the secondary damage induced by experimental spinal cord injury. Immunobiology. 2015;220(9):1039-49.
61. Brambilla R, Bracchi-Ricard V, Hu WH, Frydel B, Bramwell A, Karmally S, Green EJ, Bethea JR. Inhibition of astroglial nuclear factor kappaB reduces inflammation and improves functional recovery after spinal cord injury. J Exp Med. 2005;202(1):145-56.
62. Kigerl KA, de Rivero Vaccari JP, Dietrich WD, Popovich PG, Keane RW. Pattern recognition receptors and central nervous system repair. Exp Neurol. 2014;258:5-16.
63. Jacobi A, Loy K, Schmalz AM, Hellsten M, Umemori H, Kerschensteiner M, Bareyre FM. FGF22 signaling regulates synapse formation during post-injury remodeling of the spinal cord. EMBO J. 2015;34(9):1231-43.
64. Pallier PN, Poddighe L, Zbarsky V, Kostusiak M, Choudhury R, Hart T, Burguillos MA, Musbahi O, Groenendijk M, Sijben JW, et al. A nutrient combination designed to enhance synapse formation and function improves outcome in experimental spinal cord injury. Neurobiol Dis. 2015;82:504-15.
65. Korostelev A, Trakhanov S, Laurberg M, Noller HF. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell. 2006;126(6):1065-77.
66. Hetman M, Pietrzak M. Emerging roles of the neuronal nucleolus. Trends Neurosci. 2012;35(5):305-14.