title: Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice.
abstract: BACKGROUND
  Peripheral nerve injury leads to changes in gene expression in primary sensory neurons of the injured dorsal root ganglia. These changes are believed to be involved in neuropathic pain genesis. Previously, these changes have been identified using gene microarrays or next generation RNA sequencing with poly-A tail selection, but these approaches cannot provide a more thorough analysis of gene expression alterations after nerve injury.
  
  
  METHODS
  The present study chose to eliminate mRNA poly-A tail selection and perform strand-specific next generation RNA sequencing to analyze whole transcriptomes in the injured dorsal root ganglia following spinal nerve ligation. Quantitative real-time reverse transcriptase polymerase chain reaction assay was carried out to verify the changes of some differentially expressed RNAs in the injured dorsal root ganglia after spinal nerve ligation.
  
  
  RESULTS
  Our results showed that more than 50 million (M) paired mapped sequences with strand information were yielded in each group (51.87 M-56.12 M in sham vs. 51.08 M-57.99 M in spinal nerve ligation). Six days after spinal nerve ligation, expression levels of 11,163 out of a total of 27,463 identified genes in the injured dorsal root ganglia significantly changed, of which 52.14% were upregulated and 47.86% downregulated. The largest transcriptional changes were observed in protein-coding genes (91.5%) followed by noncoding RNAs. Within 944 differentially expressed noncoding RNAs, the most significant changes were seen in long interspersed noncoding RNAs followed by antisense RNAs, processed transcripts, and pseudogenes. We observed a notable proportion of reads aligning to intronic regions in both groups (44.0% in sham vs. 49.6% in spinal nerve ligation). Using quantitative real-time polymerase chain reaction, we confirmed consistent differential expression of selected genes including Kcna2, Oprm1 as well as lncRNAs Gm21781 and 4732491K20Rik following spinal nerve ligation.
  
  
  CONCLUSIONS
  Our findings suggest that next generation RNA sequencing can be used as a promising approach to analyze the changes of whole transcriptomes in dorsal root ganglia following nerve injury and to possibly identify new targets for prevention and treatment of neuropathic pain.
authors.affiliation: Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Jiangsu, China Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Shaogen
authors.initials: S
authors.lastname: Wu
authors.affiliation: Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Brianna
authors.initials: B
authors.lastname: Marie Lutz
authors.affiliation: Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA Department of Anesthesiology and Intensive Care, Eastern Hepatobiliary Surgical Hospital, The Second Military Medical University, Shanghai, China.
authors.forename: Xuerong
authors.initials: X
authors.lastname: Miao
authors.affiliation: Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Lingli
authors.initials: L
authors.lastname: Liang
authors.affiliation: Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA Department of Anesthesiology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Mo
authors.affiliation: High Performance and Research Computing, Office of Information Technology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Yun-Juan
authors.initials: YJ
authors.lastname: Chang
authors.affiliation: High Performance and Research Computing, Office of Information Technology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Peicheng
authors.initials: P
authors.lastname: Du
authors.affiliation: Departments of Biochemistry & Microbiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Soteropoulos
authors.affiliation: Departments of Biochemistry & Microbiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
authors.affiliation: Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Kaufman
authors.affiliation: Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Bekker
authors.affiliation: Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Jiangsu, China.
authors.forename: Yali
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA Departments of Cell Biology & Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA Department of Pharmacology & Physiology and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA yuanxiang.tao@njms.rutgers.edu.
authors.forename: Yuan-Xiang
authors.initials: YX
authors.lastname: Tao
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D005727:Ganglia, Spinal / Q000378:metabolism* / Q000473:pathology; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D006930:Hyperalgesia / Q000150:complications / Q000235:genetics; D008026:Ligation; D008159:Lumbar Vertebrae / Q000473:pathology; D008297:Male; D008810:Mice, Inbred C57BL; D059348:Peripheral Nerve Injuries / Q000150:complications / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D013127:Spinal Nerves / Q000473:pathology
keywords: Dorsal root ganglion; neuropathic pain; next generation sequencing; transcriptomes