Analyses of long non-coding RNA and mRNA profiles in the spinal cord of rats using RNA sequencing during the progression of neuropathic pain in an SNI model

References

• Backonja MiM. Defining Neuropathic Pain. Anesth Analg. 2003;97(3):785–90. doi:10.1213/01.ANE.0000062826.70846.8D.
   PubMed Web of Science ®Google Scholar
• Backonja MM, Galer BS. Pain assessment and evaluation of patients who have neuropathic pain. Neurol Clin. 1998;16(4):775–90. doi:10.1016/S0733-8619(05)70097-9.
   PubMed Web of Science ®Google Scholar
• Ossipov MH, Lai J, Malan TP Jr, Porreca F. Spinal and supraspinal mechanisms of neuropathic pain. Ann N Y Acad Sci. 2000;909:12–24. doi:10.1111/j.1749-6632.2000.tb06673.x.
   PubMed Web of Science ®Google Scholar
• Taylor BK. Pathophysiologic mechanisms of neuropathic pain. Curr Pain Headache Rep. 2001;5(2):151–61. doi:10.1007/s11916-001-0083-1.
   PubMedGoogle Scholar
• Cummins TR, Sheets PL, Waxman SG. The roles of sodium channels in nociception: Implications for mechanisms of pain. Pain. 2007;131(3):243–57. doi:10.1016/j.pain.2007.07.026.
   PubMed Web of Science ®Google Scholar
• Zhuo M, Wu G, Wu LJ. Neuronal and microglial mechanisms of neuropathic pain. Mol Brain. 2011;4:31. doi:10.1186/1756-6606-4-31.
   PubMed Web of Science ®Google Scholar
• Da Sacco L, Baldassarre A, Masotti A. Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis. Int J Mol Sci. 2012;13(1):97–114.
   PubMed Web of Science ®Google Scholar
• Huarte M. The emerging role of lncRNAs in cancer. Nat Med. 2015;21(11):1253–61. doi:10.1038/nm.3981.
   PubMed Web of Science ®Google Scholar
• Sun M, Kraus WL. From Discovery to Function: The Expanding Roles of Long Non-Coding RNAs in Physiology and Disease. Endocr Rev. 2015;36(1):25–64. doi:10.1210/er.2014-1034.
   PubMed Web of Science ®Google Scholar
• Pefanis E, Wang J, Rothschild G, Lim J, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu ZP, et al. RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity. Cell. 2015;161(4):774–89. doi:10.1016/j.cell.2015.04.034.
   PubMed Web of Science ®Google Scholar
• Gong C, Maquat LE. LncRNA stransactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature. 2011;470 (7333):284–8. doi:10.1038/nature09701.
   PubMed Web of Science ®Google Scholar
• Guo L, Zhao Y, Yang S, Zhang H, Chen F. An integrated analysis of miRNA, lncRNA, and mRNA expression profiles. Biomed Res Int. 2014:345605.
   PubMedGoogle Scholar
• Paraskevopoulou MD, Hatzigeorgiou AG. Analyzing MiRNA-LncRNA Interactions. Methods Mol Biol. 2016;1402:271–86. doi:10.1007/978-1-4939-3378-5_21.
   PubMedGoogle Scholar
• Yalcin I, Megat S, Barthas F, Waltisperger E, Kremer M, Salvat E, Barrot M. The sciatic nerve cuffing model of neuropathic pain in mice. J Vis Exp. 2014;(89):e51608. doi:10.3791/51608.
   Web of Science ®Google Scholar
• Lau WK, Lau YM, Zhang HQ, Wong SC, Bian ZX. Electroacupuncture versus celecoxib for neuropathic pain in rat SNL model. Neuroscience. 2010;170(2):655–61. doi:10.1016/j.neuroscience.2010.07.031.
   PubMed Web of Science ®Google Scholar
• Jiang BC, Sun WX, He LN4, Cao DL, Zhang ZJ, Gao YJ. Identification of lncRNA expression profile in the spinal cord of mice following spinal nerve ligation-induced neuropathic pain. Mol Pain. 2015;11:43. doi:10.1186/s12990-015-0047-9.
   PubMed Web of Science ®Google Scholar
• E Park, D Youn. Rat Models of Neuropathic Pain: CCI, PSNL, SNL and SNI. Laboratory Animal Research. 2009;25(2):87–94.
   Google Scholar
• Bourquin AF, Süveges M, Pertin M, Gilliard N, Sardy S, Davison AC, Spahn DR, Decosterd I. Assessment and analysis of mechanical allodynia-like behavior induced by spared nerve injury (SNI) in the mouse. Pain. 2006;122(1–2):14.e1–14. doi:10.1016/j.pain.2005.10.036.
   PubMed Web of Science ®Google Scholar
• 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. doi:10.1038/nbt.1621.
   PubMed Web of Science ®Google Scholar
• Woolf CJ, Mannion RJ. Neuropathic pain: aetiology, symptoms, mechanisms, and management. Lancet. 1999;353(9168):1959–64. doi:10.1016/S0140-6736(99)01307-0.
   PubMed Web of Science ®Google Scholar
• Bouhassira D, Attal N. Translational neuropathic pain research: A clinical perspective. Neuroscience. 2016;338:27–35. doi:10.1016/j.neuroscience.2016.03.029.
   PubMed Web of Science ®Google Scholar
• Gilron I, Baron R, Jensen T. Neuropathic pain: Principles of diagnosis and treatment. Mayo Clin Proc. 2015;90(4):532–45. doi:10.1016/j.mayocp.2015.01.018.
   PubMed Web of Science ®Google Scholar
• Li J, Meng H, Bai Y, Wang K. Regulation of lncRNA and Its Role in Cancer Metastasis. Oncol Res. 2016;23(5):205–17. doi:10.3727/096504016X14549667334007.
   PubMed Web of Science ®Google Scholar
• Ballantyne MD, McDonald RA, Baker AH. LncRNA/microRNA interactions in the vasculature. Clin Pharmacol Ther. 2016;99(5):494–501. doi:10.1002/cpt.355.
   PubMed Web of Science ®Google Scholar
• LaCroix-Fralish ML, Austin JS, Zheng FY, Levitin DJ, Mogil JS. Patterns of pain: meta-analysis of microarray studies of pain. Pain. 2011;152(8):1888–98. doi:10.1016/j.pain.2011.04.014.
   PubMed Web of Science ®Google Scholar
• Sorge RE, Mapplebeck JC, Rosen S, Beggs S, Taves S, Alexander JK, Martin LJ, Austin JS, Sotocinal SG, Chen D, et al. Different immune cells mediate mechanical pain hypersensitivity in male and female mice. Nat Neurosci. 2015;18(8):1081–3. doi:10.1038/nn.4053.
   PubMed Web of Science ®Google Scholar
• Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet. 2016;17(1):47–62. doi:10.1038/nrg.2015.10.
   PubMed Web of Science ®Google Scholar
• Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA. 2008;105(2):716–21. doi:10.1073/pnas.0706729105.
   PubMed Web of Science ®Google Scholar
• Zhang B1, Arun G, Mao YS, Lazar Z, Hung G, Bhattacharjee G, Xiao X, Booth CJ, Wu J, Zhang C, Spector DL. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep. 2012;2(1):111–23. doi:10.1016/j.celrep.2012.06.003.
   PubMed Web of Science ®Google Scholar
• Yu B, Zhou S, Hu W, Qian T, Gao R, Ding G, Ding F, Gu X. Altered long noncoding RNA expressions in dorsal root ganglion after rat sciatic nerve injury. Neurosci Lett. 2013;534:117–22. doi:10.1016/j.neulet.2012.12.014.
   PubMed Web of Science ®Google Scholar
• Zhao X, Tang Z, Zhang H, Atianjoh FE, Zhao JY, Liang L, Wang W, Guan X, Kao SC, Tiwari V, et al. A long noncoding RNA contributes to neuropathic pain by silencing Kcna2 in primary afferent neurons. Nat Neurosci. 2013;16(8):1024–31. doi:10.1038/nn.3438.
   PubMed Web of Science ®Google Scholar
• Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell. 2013;154(1):26–46. doi:10.1016/j.cell.2013.06.020.
   PubMed Web of Science ®Google Scholar
• Chakrabarti KS, Agafonov RV, Pontiggia F, Otten R, Higgins MK, Schertler GF, Oprian DD, Kern D. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis. Cell Reports. 2015;14(1):32–42. doi:10.1016/j.celrep.2015.12.010.
   PubMed Web of Science ®Google Scholar
• D'Mello R, Dickenson AH. Spinal cord mechanisms of pain. Br J Anaesth. 2008;101(1): 8–16. doi:10.1093/bja/aen088.
   PubMed Web of Science ®Google Scholar
• Bee LA, Dickenson AH. Rostral ventromedial medulla control of spinal sensory processing in normal and pathophysiological states. Neuroscience. 2007;147:786–93. doi:10.1016/j.neuroscience.2007.05.004.
   PubMed Web of Science ®Google Scholar
• Raju HB, Englander Z, Capobianco E, Tsinoremas NF, Lerch JK. Identification of potential therapeutic targets in a model of neuropathic pain. Front Genet. 2014;5:131. doi:10.3389/fgene.2014.00131.
   PubMed Web of Science ®Google Scholar
• Hori N, Narita M, Yamashita A, Horiuchi H, Hamada Y, Kondo T, Watanabe M, Igarashi K, Kawata M, Shibasaki M, et al. Changes in the expression of IL-6-Mediated MicroRNAs in the dorsal root ganglion under neuropathic pain in mice. Synapse. 2016;70(8):317–24. doi:10.1002/syn.21902.
   PubMed Web of Science ®Google Scholar
• Wang W, Zhuang Q, Ji K, Wen B, Lin P, Zhao Y, Li W, Yan C. Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation. Sci Rep. 2017;7:41639.
   PubMed Web of Science ®Google Scholar
• Schomberg D, Ahmed M, Miranpuri G, Olson J, Resnick DK. Neuropathic pain: Role of inflammation, immune response, and ion channel activity in central injury mechanisms. Ann Neurosci. 2012;19(3):125–132.
   PubMedGoogle Scholar
• Decosterd I, Woolf CJ. Spared nerve injury: an animal model of persistent peripheral neuropathic pain. Pain. 2000;87(2):149–58. doi:10.1016/S0304-3959(00)00276-1.
   PubMed Web of Science ®Google Scholar
• Chaplan SR, Bach FW, Pogrel JW, Chung JM, Yaksh TL. Quantitative assessment of tactile allodynia in the rat paw. J Neurosci Methods. 1994;53(1):55–63. doi:10.1016/0165-0270(94)90144-9.
   PubMed Web of Science ®Google Scholar
• Hargreaves K, Dubner R, Brown F, Flores C, Joris J. A new and sensitive method for measuring thermal nociception in cutaneous hyperalgesia. Pain. 1988;32(1):77–88. doi:10.1016/0304-3959(88)90026-7.
   PubMed Web of Science ®Google Scholar
• Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012;40(1):37–52. doi:10.1093/nar/gkr688.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014;15(12):550. doi:10.1186/s13059-014-0550-8.
   PubMed Web of Science ®Google Scholar