(274) RNA-seq based transcriptome profiling of human and mouse dorsal root ganglia provides insight into potential new pain targets

AbstractMolecular neurobiological insight into human nervous tissues is needed to generate next generation therapeutics for neurological disorders like chronic pain. We obtained human Dorsal Root Ganglia (DRG) samples from organ donors and performed RNA-sequencing (RNA-seq) to study the human DRG (hDRG) transcriptional landscape, systematically comparing it with publicly available data from a variety of human and orthologous mouse tissues, including mouse DRG (mDRG). We characterized the hDRG transcriptional profile in terms of tissue-restricted gene co-expression patterns and putative transcriptional regulators, and formulated an information-theoretic framework to quantify DRG enrichment. Our analyses reveal an hDRG-enriched protein-coding gene set (~140), some of which have not been described in the context of DRG or pain signaling. A majority of these show conserved enrichment in mDRG, and were mined for known drug - gene product interactions. Comparison of hDRG and tibial nerve transcriptomes suggest pervasive mRNA transport of sensory neuronal genes to axons in adult hDRG, with potential implications for mechanistic insight into chronic pain in patients. Relevant gene families and pathways were also analyzed, including transcription factors (TFs), g-protein coupled receptors (GCPRs) and ion channels. We present our work as an online, searchable repository (http://www.utdallas.edu/bbs/painneurosciencelab/DRGtranscriptome), creating a valuable resource for the community. Our analyses provide insight into DRG biology for guiding development of novel therapeutics, and a blueprint for cross-species transcriptomic analyses.SummaryWe generated RNA sequencing data from human DRG samples and comprehensively compared this transcriptome to other human tissues and a matching panel of mouse tissues. Our analysis uncovered functionally enriched genes in the human and mouse DRG with important implications for understanding sensory biology and pain drug discovery.

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Comparative transcriptome profiling of the human and mouse dorsal root ganglia

Pain ◽

10.1097/j.pain.0000000000001217 ◽

2018 ◽

Vol 159 (7) ◽

pp. 1325-1345 ◽

Cited By ~ 80

Author(s):

Pradipta Ray ◽

Andrew Torck ◽

Lilyana Quigley ◽

Andi Wangzhou ◽

Matthew Neiman ◽

...

Keyword(s):

Dorsal Root Ganglia ◽

Dorsal Root ◽

Transcriptome Profiling ◽

Comparative Transcriptome ◽

Human And Mouse

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Sex-specific Transcriptomic Differences From Human Dorsal Root Ganglia Associated With Painful Radiculopathy

Neurosurgery ◽

10.1093/neuros/nyz310_189 ◽

2019 ◽

Vol 66 (Supplement_1) ◽

Author(s):

Robert Y North ◽

Yan Li ◽

Pradipta Ray ◽

Laurence D Rhines ◽

Claudio E Tatsui ◽

...

Keyword(s):

Dorsal Root Ganglia ◽

Dorsal Root ◽

Differential Expression Analysis ◽

Enrichment Analysis ◽

Epidemiological Studies ◽

Gene Set Enrichment Analysis ◽

Afferent Neurons ◽

Rna Seq ◽

Cord Injury ◽

Medical Histories

Abstract INTRODUCTION Women are at greater risk to suffer from many chronic pain conditions, more often report painful symptoms in epidemiological studies, and demonstrate greater pain sensitivity to experimentally measured pain responses. There is growing evidence from animal models for sex-specific biological differences in nociception, particularly involving primary afferent neurons, that may contribute to these differences. However, the details and extent of sex-specific differences associated with pain in human afferent neurons has not been previously investigated. METHODS Human dorsal root ganglia (DRG) and medical histories were obtained from patients undergoing spinal surgery that necessitated sacrifice of spinal nerve roots as part of standard of care. Clinical data for presence of painful radiculopathy was obtained through retrospective review of medical records or collected at study enrollment. RNA sequencing (RNA-seq) was performed on 21 DRG from 15 patients with variable presence of radicular pain reported in a corresponding dermatome. Differential expression analysis for male w/pain (MP) vs female w/pain (FP) samples was performed with thresholds for robustly expressed autosomal genes (TPM >3.0), fold change of 2.0 or higher, with false discovery rate (FDR) <0.05. RESULTS Comparison of the MP and FP cohorts yielded 575 differentially expressed genes with 426 upregulated in MP and 149 upregulated in FP. Gene set enrichment analysis demonstrated significant differences in genes related to inflammation and immune regulation (increased MAPK and BDNF signaling in MP, increased Rhodopsin-like GPCR in FP) and differing clusters of spinal cord injury-associated genes (TLR4, AIF1, OMG, C1QB increased in FP, EGR1, NR4A1, ZFP36, BTG2, MYC in MP). CONCLUSION Utilizing RNA-seq of human DRG innervating regions of pain, this study provides the first demonstration of sex-specific differences for the biology of pain within the dorsal root ganglion in humans and implicates the immune system as a critical influence in these differences.

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Transcriptome Profiling Analyses in Psoriasis: A Dynamic Contribution of Keratinocytes to the Pathogenesis

Genes ◽

10.3390/genes11101155 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1155 ◽

Cited By ~ 1

Author(s):

Geneviève Rioux ◽

Zainab Ridha ◽

Mélissa Simard ◽

Florence Turgeon ◽

Sylvain L. Guérin ◽

...

Keyword(s):

Disease Onset ◽

Transcriptome Profiling ◽

Relevant Information ◽

Genomic Alteration ◽

Psoriatic Skin ◽

Rna Seq ◽

Altered Expression ◽

Immune Mediated ◽

New Biomarkers ◽

Insight Into

Psoriasis is an immune-mediated inflammatory skin disease with a complex etiology involving environmental and genetic factors. A better insight into related genomic alteration helps design precise therapies leading to better treatment outcome. Gene expression in psoriasis can provide relevant information about the altered expression of mRNA transcripts, thus giving new insights into the disease onset. Techniques for transcriptome analyses, such as microarray and RNA sequencing (RNA-seq), are relevant tools for the discovery of new biomarkers as well as new therapeutic targets. This review summarizes the findings related to the contribution of keratinocytes in the pathogenesis of psoriasis by an in-depth review of studies that have examined psoriatic transcriptomes in the past years. It also provides valuable information on reconstructed 3D psoriatic skin models using cells isolated from psoriatic patients for transcriptomic studies.

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Spared Nerve Injury Causes Sexually Dimorphic Mechanical Allodynia and Differential Gene Expression in Spinal Cords and Dorsal Root Ganglia in Rats

Molecular Neurobiology ◽

10.1007/s12035-021-02447-1 ◽

2021 ◽

Author(s):

F.H.G. Ahlström ◽

K. Mätlik ◽

H. Viisanen ◽

K.J. Blomqvist ◽

X. Liu ◽

...

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Nerve Injury ◽

Dorsal Root Ganglia ◽

Dorsal Root ◽

Mechanical Allodynia ◽

Female Rats ◽

Sexually Dimorphic ◽

Spared Nerve Injury ◽

Rna Seq

AbstractNeuropathic pain is more prevalent in women. However, females are under-represented in animal experiments, and the mechanisms of sex differences remain inadequately understood. We used the spared nerve injury (SNI) model in rats to characterize sex differences in pain behaviour, unbiased RNA-Seq and proteomics to study the mechanisms. Male and female rats were subjected to SNI- and sham-surgery. Mechanical and cold allodynia were assessed. Ipsilateral lumbar dorsal root ganglia (DRG) and spinal cord (SC) segments were collected for RNA-seq analysis with DESeq2 on Day 7. Cerebrospinal fluid (CSF) samples for proteomic analysis and DRGs and SCs for analysis of IB-4 and CGRP, and IBA1 and GFAP, respectively, were collected on Day 21. Females developed stronger mechanical allodynia. There were no differences between the sexes in CGRP and IB-4 in the DRG or glial cell markers in the SC. No CSF protein showed change following SNI. DRG and SC showed abundant changes in gene expression. Sexually dimorphic responses were found in genes related to T-cells (cd28, ctla4, cd274, cd4, prf1), other immunological responses (dpp4, c5a, cxcr2 and il1b), neuronal transmission (hrh3, thbs4, chrna4 and pdyn), plasticity (atf3, c1qc and reg3b), and others (bhlhe22, mcpt1l, trpv6). We observed significantly stronger mechanical allodynia in females and numerous sexually dimorphic changes in gene expression following SNI in rats. Several genes have previously been linked to NP, while some are novel. Our results suggest gene targets for further studies in the development of new, possibly sex-specific, therapies for NP.

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Pharmacological target-focused transcriptomic analysis of native vs cultured human and mouse dorsal root ganglia

Pain ◽

10.1097/j.pain.0000000000001866 ◽

2020 ◽

Vol 161 (7) ◽

pp. 1497-1517 ◽

Cited By ~ 2

Author(s):

Andi Wangzhou ◽

Lisa A. McIlvried ◽

Candler Paige ◽

Paulino Barragan-Iglesias ◽

Stephanie Shiers ◽

...

Keyword(s):

Dorsal Root Ganglia ◽

Dorsal Root ◽

Transcriptomic Analysis ◽

Pharmacological Target ◽

Human And Mouse

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Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction

10.1101/474031 ◽

2018 ◽

Author(s):

Hengyi Xu ◽

Jun Yao ◽

Douglas C. Wu ◽

Alan M. Lambowitz

Keyword(s):

Rna Structure ◽

Transcriptome Profiling ◽

Rna Seq ◽

Structure Mapping ◽

Dimer Formation ◽

Biochemical Basis ◽

Reverse Transcriptases ◽

Small Ncrnas ◽

Rna Structure Mapping ◽

Insight Into

ABSTRACTThermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by (i) rationally designing RNA-seq adapters that minimize adapter dimer formation, and (ii) developing biochemical and computational methods that remediate 5’- and 3’-end biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5’- and 3’-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.

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Expression Profiling of Contralateral Dorsal Root Ganglia of a Rat Model of Complex Regional Pain Syndrome Type-i Uncovers Potential Mechanisms Involved in Mirror-image Painexpression Profiling of Contralateral Dorsal Root Ganglia of a Rat Model of Complex Regional Pain Syndrome Type-i Uncovers Potential Mechanisms Involved in Mirror-image Pain

10.21203/rs.3.rs-532136/v1 ◽

2021 ◽

Author(s):

Huimin Nie ◽

Boyu Liu ◽

Chengyu Yin ◽

Ruixiang Chen ◽

Jie Wang ◽

...

Keyword(s):

Complex Regional Pain Syndrome ◽

Dorsal Root Ganglia ◽

Expression Profiling ◽

Dorsal Root ◽

Pain Syndrome ◽

Mirror Image ◽

Type I ◽

Syndrome Type ◽

Rna Seq ◽

Pain Mechanisms

Abstract Background: Mirror-image pain (MIP), which develops from the healthy body region contralateral to the actual injured site, is a mysterious pain phenomenon accompanying many chronic pain conditions, including complex regional pain syndrome (CRPS). However, the pathogenesis of MIP still remained largely unknown. The purpose of this study is to perform an expression profiling to identify genes related with MIP in an animal model of CRPS-I. Methods: We established a rat chronic post-ischemic pain (CPIP) model to mimic human CRPS-I. RNA-sequencing (RNA-Seq), bioinformatics, qPCR, immunostaining and animal behavioral assays were used to screen potential genes in contralateral dorsal root ganglia (DRG) that may be involved in MIP. Results: The CPIP model rats developed robust and persistent MIP in contralateral hind paws. Bilateral DRG neurons did not exhibit obvious neuronal damage. RNA-Seq of contralateral DRG from CPIP model rats identified a total 527 differentially expressed genes (DEGs) vs. control rats. The expression changes of several representative DEGs were verified by qPCR. Bioinformatics analysis indicated that immune system process, innate immune response and cell adhesion were among the mostly enriched biological processes, which are all important processes involved in pain sensitization, neuroinflammation and chronic pain. We further identified DEGs potentially involved in pain mechanisms or enriched in small- to medium-sized sensory neurons or TRPV1-lineage nociceptors. By comparing with published datasets summarizing genes enriched in pain mechanisms, we sorted out a core set of genes which might contribute to nociception and pain mechanism in MIP. Conclusions: We provided by far the first study to profile gene expression changes and pathway analysis of contralateral DRG for investigating MIP mechanisms. This work may provide novel insights into understanding the mysterious mechanisms underlying MIP.

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Molecular profiling of murine sensory neurons in the nodose and dorsal root ganglia labeled from the peritoneal cavity

Physiological Genomics ◽

10.1152/physiolgenomics.00169.2005 ◽

2006 ◽

Vol 24 (3) ◽

pp. 252-263 ◽

Cited By ~ 33

Author(s):

Pieter J. Peeters ◽

Jeroen Aerssens ◽

Ronald de Hoogt ◽

Andrzej Stanisz ◽

Hinrich W. Göhlmann ◽

...

Keyword(s):

Gene Expression ◽

Sensory Neurons ◽

Dorsal Root Ganglia ◽

Peritoneal Cavity ◽

Dorsal Root ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Afferent Neurons ◽

Spinal Afferents ◽

Insight Into

Vagal afferent neurons are thought to convey primarily physiological information, whereas spinal afferents transmit noxious signals from the viscera to the central nervous system. To elucidate molecular identities for these different properties, we compared gene expression profiles of neurons located in nodose ganglia (NG) and dorsal root ganglia (DRG) in mice. Intraperitoneal administration of Alexa Fluor-488-conjugated cholera toxin B allowed enrichment for neurons projecting to the viscera. Fluorescent neurons in DRG (from T10 to T13) and NG were isolated using laser-capture microdissection. Gene expression profiles of these afferent neurons, obtained by microarray hybridization, were analyzed using multivariate spectral map analysis, significance analysis of microarrays (SAM) algorithm, and fold-difference filtering. A total of 1,996 genes were differentially expressed in DRG vs. NG, including 41 G protein-coupled receptors and 60 ion channels. Expression profiles obtained on laser-captured neurons were contrasted to those obtained on whole ganglia, demonstrating striking differences and the need for microdissection when studying visceral sensory neurons because of dilution of the signal by somatic sensory neurons. Furthermore, we provide a detailed catalog of all adrenergic and cholinergic, GABA, glutamate, serotonin, and dopamine receptors; voltage-gated potassium, sodium, and calcium channels; and transient receptor potential cation channels present in afferents projecting to the peritoneal cavity. Our genome-wide expression profiling data provide novel insight into molecular signatures that underlie both functional differences and similarities between NG and DRG sensory neurons. Moreover, these findings will offer novel insight into mode of action of pharmacological agents modulating visceral sensation.

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