Identification of key candidate genes in neuropathic pain by integrated bioinformatic analysis

Tang, Simin; Jing, Huan; Huang, Zhenxing; Huang, Teng; Shi, Lin; Liao, Mengyang; Zhou, Jun

doi:10.1002/jcb.29398

Cited by 53 publications

(43 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Additionally, the potential co-expression genes of TMEM206 were extracted from Gene Expression Omnibus (GEO; ) datasets GSE36376 and GSE76427, separately, which have previously been used to analyze gene expression for tumor and adjacent non-tumor tissues in HCC ( 24 , 25 ). To identify the genes co-expressed with TMEM206, a Spearman's correlation test was used by the R platform (|Spearman's correlation coefficient|>0.4) ( 26 ). Finally, using online Venn software ( ), the intersection of these gene lists was determined as the co-expression genes of TMEM206 in HCC.…”

Section: Methodsmentioning

confidence: 99%

TMEM206 is a potential prognostic marker of hepatocellular carcinoma

et al. 2020

View full text Add to dashboard Cite

Transmembrane proteins are involved in the transportation of materials into and out of cells. The transmembrane protein (TMEM) family is a collection of poorly described transmembrane proteins that serve important roles in tumor development and progression. A number of TMEM proteins have been discovered. A newly discovered TMEM protein, TMEM206, transports ions across the membrane under physiological and pathological conditions, generating an acidic environment, which serves an important role in the microenvironment. However, the prognostic value and regulatory mechanisms of action of TMEM206 in tumors is unclear. The aim of the present study was to evaluate the prognostic value and regulation mechanisms of TMEM206 in tumors. Firstly, the expression of TMEM206 in tumors and normal tissues was assessed using the GEPIA and Oncomine databases and the results revealed that TMEM206 expression increased or decreased depending on the type of tumor. Subsequently, using the Human Protein Atlas and the Kaplan-Meier plotter, the findings of the present study revealed that TMEM206 is related to the prognosis of hepatocellular carcinoma. In order to explore the mechanism of TMEM206 in promoting tumor progression, GEO and cBioPortal were used to determine genes that may be co-expressed with TMEM206. MetaScape was used to identify the signaling pathways that TMEM206 may participate in. Finally, miRWalk, miRDB and TargetScan were used to identify miRNAs that may regulate the expression of TMEM206 and the findings revealed that 2 miRNA (hsa-miR-325 and hsa-miR-510-5p) were involved. In conclusion, upregulation of TMEM206 is associated with poor prognosis in patients with hepatocellular carcinoma.

show abstract

Section: Methodsmentioning

confidence: 99%

TMEM206 is a potential prognostic marker of hepatocellular carcinoma

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Gene sequencing and bioinformatics analysis are widely used in the study of the molecular mechanism of diseases. Tang found several DEGs upon analysis of the transcriptional data of DRG in spared nerve injury (SNI) model mice and determined that mir-16-5p may be involved in the pathogenesis of neuropathic pain (NP) [ 13 ]. Following an analysis of the transcriptional data of patients with fibromyalgia, Qiu found evidence that CD38 and GATM are involved in the occurrence and development of this disease through regulation of ion channels and inflammatory pathways, which provides new insights into the molecular mechanisms [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatics Analysis of Genes and Mechanisms in Postherpetic Neuralgia

Qiu

Hao

Cheng

et al. 2020

Pain Research and Management

View full text Add to dashboard Cite

Objective. Elderly patients are prone to postherpetic neuralgia (PHN), which may cause anxiety, depression, and sleep disorders and reduce quality of life. As a result, the life quality of patients was seriously reduced. However, the pathogenesis of PHN has not been fully elucidated, and current treatments remain inadequate. Therefore, it is important to explore the molecular mechanism of PHN. Methods. We analyzed the GSE64345 dataset, which includes gene expression from the ipsilateral dorsal root ganglia (DRG) of PHN model rats. Differentially expressed genes (DEGs) were identified and analyzed by Gene Ontology. Protein-protein interaction (PPI) network was constructed. The miRNA associated with neuropathic pain and inflammation was found in miRNet. Hub genes were identified and analyzed in Comparative Toxicogenomics Database (CTD). miRNA-mRNA networks associated with PHN were constructed. Results. A total of 116 genes were up-regulated in the DRG of PHN rats, and 135 genes were down-regulated. Functional analysis revealed that variations were predominantly enriched for genes involved in neuroactive ligand-receptor interactions, the Jak-STAT signaling pathway, and calcium channel activity. Eleven and thirty-one miRNAs associated with neuropathic pain and inflammation, respectively, were found. Eight hub genes (S1PR1, OPRM1, PDYN, CXCL3, S1PR5, TBX5, TNNI3, MYL7, PTGDR2, and FBXW2) associated with PHN were identified. Conclusions. Bioinformatics analysis is a useful tool to explore the mechanism and pathogenesis of PHN. The identified hub genes may participate in the onset and development of PHN and serve as therapeutic targets.

show abstract

“…Preoperative VSTM2B positively correlated with MDAS scores on both postoperative day 1 (correlation coefficient r = 0.869, p = 0.005) and day 2 (correlation coefficient r = 0.928, p = 0.008). A previous study investigated differentially expressed genes in the dorsal root ganglia in a neuropathic pain from spared nerve injury model; they reported that VSTM2B was downregulated, which indicates that reduced VSTM2B is related to neuropathic pain (27). Another recent study used proteomics to identify CSF biomarkers in genetic frontotemporal dementia, and found that symptomatic granulin mutation carriers had significantly lower levels of VSTM2B than both non-carriers and presymptomatic carriers (28).…”

Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of Preoperative CSF Reveals Risk Biomarkers of Postoperative Delirium

et al. 2020

View full text Add to dashboard Cite

Objective: To analyze the proteome of preoperative cerebrospinal fluid (CSF) in older orthopedic patients with or without postoperative delirium (POD) using untargeted proteomics.Methods: A prospective cohort study was conducted. Eighty hip fracture patients aged ≥65 years were recruited. After successful spinal anesthesia, CSF was collected. The patients were divided into POD and No-POD groups based on the Confusion Assessment Method, and patients with POD were graded using the Memorial Delirium Assessment Scale (MDAS). Thirty No-POD patients were matched to 10 POD patients by age (±2 years) and Mini-Mental State Examination score (±2 scores). Label-free proteomic analysis was performed using a liquid chromatography coupled to mass spectrometry (LC-MS) workflow. Validation was performed using mass-spectrometry-based parallel reaction monitoring (PRM) for the 30 No-POD and 10 POD patients, as well as for an additional 5 POD patients. Bioinformatics were used to investigate possible relevant pathological mechanisms.Results: The incidence of POD in older orthopedic patients was 18.8% in our cohort of 80 patients. Proteomics results revealed 63 dysregulated CSF proteins, and PRM analysis validated these results. The preoperative CSF levels of both V-set and transmembrane domain-containing protein 2B (VSTM2B) and coagulation factor V (FA5) were positively correlated with MDAS scores on postoperative day 1 (r > 0.8, p < 0.05). Bioinformatic analysis revealed that several nervous-system-related pathways are relevant to POD development. Conclusion:We identified and validated several novel CSF proteins that are dysregulated in POD, and revealed several pathways that are relevant to POD development. Our results not only provide risk biomarkers for POD, but also give clues for further investigations into the pathological mechanisms of delirium. Clinical trial registration: This study was registered in the Chinese Clinical Trial Registry (ChiCTR1900021533).

show abstract

Identification of key candidate genes in neuropathic pain by integrated bioinformatic analysis

Cited by 53 publications

References 46 publications

TMEM206 is a potential prognostic marker of hepatocellular carcinoma

TMEM206 is a potential prognostic marker of hepatocellular carcinoma

Bioinformatics Analysis of Genes and Mechanisms in Postherpetic Neuralgia

Proteomic Analysis of Preoperative CSF Reveals Risk Biomarkers of Postoperative Delirium

Contact Info

Product

Resources

About