Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice

Shaogen Wu, Brianna Marie Lutz, Xuerong Miao, Lingli Liang, Kai Mo, Yun Juan Chang, Peicheng Du, Patricia Soteropoulos, Bin Tian, Andrew G. Kaufman, Alex Bekker, Yali Hu, Yuanxiang Tao

Research output: Contribution to journalArticle

22 Citations (Scopus)

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. Conclusion: 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.

Original languageEnglish (US)
JournalMolecular Pain
Volume12
DOIs
StatePublished - Mar 4 2016

Fingerprint

Peripheral Nerve Injuries
Spinal Nerves
Spinal Ganglia
Gene Expression Profiling
Ligation
RNA Sequence Analysis
Long Noncoding RNA
Untranslated RNA
Neuralgia
Gene Expression
Messenger RNA
Real-Time Polymerase Chain Reaction
Antisense RNA
Pseudogenes
Wounds and Injuries
Sensory Receptor Cells
Reverse Transcriptase Polymerase Chain Reaction
Transcriptome
Genes
Down-Regulation

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Cellular and Molecular Neuroscience
  • Anesthesiology and Pain Medicine

Keywords

  • Dorsal root ganglion
  • neuropathic pain
  • next generation sequencing
  • transcriptomes

Cite this

Wu, Shaogen ; Marie Lutz, Brianna ; Miao, Xuerong ; Liang, Lingli ; Mo, Kai ; Chang, Yun Juan ; Du, Peicheng ; Soteropoulos, Patricia ; Tian, Bin ; Kaufman, Andrew G. ; Bekker, Alex ; Hu, Yali ; Tao, Yuanxiang. / Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice. In: Molecular Pain. 2016 ; Vol. 12.
@article{6f96e2ac90bb4e7f8d2bb3345c77860d,
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. Conclusion: 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.",
keywords = "Dorsal root ganglion, neuropathic pain, next generation sequencing, transcriptomes",
author = "Shaogen Wu and {Marie Lutz}, Brianna and Xuerong Miao and Lingli Liang and Kai Mo and Chang, {Yun Juan} and Peicheng Du and Patricia Soteropoulos and Bin Tian and Kaufman, {Andrew G.} and Alex Bekker and Yali Hu and Yuanxiang Tao",
year = "2016",
month = "3",
day = "4",
doi = "10.1177/1744806916629048",
language = "English (US)",
volume = "12",
journal = "Molecular Pain",
issn = "1744-8069",
publisher = "BioMed Central",

}

Wu, S, Marie Lutz, B, Miao, X, Liang, L, Mo, K, Chang, YJ, Du, P, Soteropoulos, P, Tian, B, Kaufman, AG, Bekker, A, Hu, Y & Tao, Y 2016, 'Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice', Molecular Pain, vol. 12. https://doi.org/10.1177/1744806916629048

Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice. / Wu, Shaogen; Marie Lutz, Brianna; Miao, Xuerong; Liang, Lingli; Mo, Kai; Chang, Yun Juan; Du, Peicheng; Soteropoulos, Patricia; Tian, Bin; Kaufman, Andrew G.; Bekker, Alex; Hu, Yali; Tao, Yuanxiang.

In: Molecular Pain, Vol. 12, 04.03.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice

AU - Wu, Shaogen

AU - Marie Lutz, Brianna

AU - Miao, Xuerong

AU - Liang, Lingli

AU - Mo, Kai

AU - Chang, Yun Juan

AU - Du, Peicheng

AU - Soteropoulos, Patricia

AU - Tian, Bin

AU - Kaufman, Andrew G.

AU - Bekker, Alex

AU - Hu, Yali

AU - Tao, Yuanxiang

PY - 2016/3/4

Y1 - 2016/3/4

N2 - 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. Conclusion: 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.

AB - 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. Conclusion: 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.

KW - Dorsal root ganglion

KW - neuropathic pain

KW - next generation sequencing

KW - transcriptomes

UR - http://www.scopus.com/inward/record.url?scp=84980394727&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84980394727&partnerID=8YFLogxK

U2 - 10.1177/1744806916629048

DO - 10.1177/1744806916629048

M3 - Article

VL - 12

JO - Molecular Pain

JF - Molecular Pain

SN - 1744-8069

ER -