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Peng C, Huang J, Li M, Liu G, Liu L, Lin J, Sun W, Liu H, Huang Y, Chen X. Uncovering periodontitis-associated markers through the aggregation of transcriptomics information from diverse sources. Front Genet 2024; 15:1398582. [PMID: 38919957 PMCID: PMC11196414 DOI: 10.3389/fgene.2024.1398582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/10/2024] [Indexed: 06/27/2024] Open
Abstract
Introduction Periodontitis, a common chronic inflammatory disease, significantly impacted oral health. To provide novel biological indicators for the diagnosis and treatment of periodontitis, we analyzed public microarray datasets to identify biomarkers associated with periodontitis. Method The Gene Expression Omnibus (GEO) datasets GSE16134 and GSE106090 were downloaded. We performed differential analysis and robust rank aggregation (RRA) to obtain a list of differential genes. To obtain the core modules and core genes related to periodontitis, we evaluated differential genes through enrichment analysis, correlation analysis, protein-protein interaction (PPI) network and competing endogenous RNA (ceRNA) network analysis. Potential biomarkers for periodontitis were identified through comparative analysis of dual networks (PPI network and ceRNA network). PPI network analysis was performed in STRING. The ceRNA network consisted of RRA differentially expressed messenger RNAs (RRA_DEmRNAs) and RRA differentially expressed long non-coding RNAs (RRA_DElncRNAs), which regulated each other's expression by sharing microRNA (miRNA) target sites. Results RRA_DEmRNAs were significantly enriched in inflammation-related biological processes, osteoblast differentiation, inflammatory response pathways and immunomodulatory pathways. Comparing the core ceRNA module and the core PPI module, C1QA, CENPK, CENPU and BST2 were found to be the common genes of the two core modules, and C1QA was highly correlated with inflammatory functionality. C1QA and BST2 were significantly enriched in immune-regulatory pathways. Meanwhile, LINC01133 played a significant role in regulating the expression of the core genes during the pathogenesis of periodontitis. Conclusion The identified biomarkers C1QA, CENPK, CENPU, BST2 and LINC01133 provided valuable insight into periodontitis pathology.
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Affiliation(s)
- Chujun Peng
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou, China
| | - Jinhang Huang
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou, China
| | - Mingyue Li
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Guanru Liu
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Lingxian Liu
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Jiechun Lin
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Weijun Sun
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Hongtao Liu
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Yonghui Huang
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Xin Chen
- School of Automation, Guangdong University of Technology, Guangzhou, China
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Chen X, Liu Q, Chen N, Ma J, Wu X, Zhang H, Yu L, Huang H. Diagnostic biomarker for type 2 diabetic peripheral neuropathy via comprehensive bioinformatics analysis. J Diabetes 2024; 16:e13506. [PMID: 38018513 PMCID: PMC10925884 DOI: 10.1111/1753-0407.13506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 09/12/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Diabetic peripheral neuropathy (DPN) is a common complication of Type 2 diabetes mellitus (T2DM), which frequently results in disabling neuropathic pain and lower-limb amputation. The identification of noninvasive biomarkers for DPN may help early detection and individualized treatment of DPN. METHODS In this study, we identified differentially expressed genes (DEGs) between DPN and the control based on blood-source (GSE95849) and tissue-source gene expression profiles (GSE143979) from the Gene Expression Omnibus (GEO) database using limma, edgeR, and DESeq2 approaches. KEGGG and GO functional enrichments were performed. Hub genes and their correlation with infiltrating immune cells were analyzed. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to quantify hub gene expression. RESULTS In total, 144 DEGs between DPN and the control were identified. Functional enrichment revealed that the DEGs were mainly enriched in immune-related pathways like the Fc epsilon receptor Ig signaling pathway. By protein-protein interaction (PPI) network analysis, FCER1G, SYK, ITGA4, F13A1, MS4A2, and PTK2B were screened as hub genes with higher expression in DPN patients, among which half were immune genes (FCER1G, PTK2B, and SYK). RT-qPCR demonstrated that mRNA expression of FCER1G, PTK2B, and SYK was significantly increased in patients with DPN compared with both diabetic nonperipheral neuropathy (DNN) and normal subjects. The area under the receiver operating characteristic (ROC) curve of FCER1G, PTK2B, and SYK was 0.84, 0.81, and 0.73, respectively, suggesting their great advantages as diagnostic biomarkers to predict the progression of neuropathy in T2DM. Further analysis indicated that the expression of FCER1G, PTK2B, and SYK was negatively correlated with the cell proportion of significantly altered resting natural killer cells, T follicular helper cells, and activated mast cells, but positively correlated with monocytes. CONCLUSIONS Our findings demonstrated FCER1G, PTK2B, and SYK are potential diagnostic biomarkers and therapeutic targets for DPN, which provides new insight into DPN pathogenesis and therapies.
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Affiliation(s)
- Xiaoyu Chen
- Department of EndocrinologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Qingquan Liu
- Department of CardiologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Niyao Chen
- Department of EndocrinologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Jiangxin Ma
- Department of EndocrinologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Xiaohong Wu
- Department of EndocrinologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Haibin Zhang
- Department of EndocrinologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Liying Yu
- Central LaboratoryThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
| | - Huibin Huang
- Department of EndocrinologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
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3
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Zhang Z, Zhu Z, Wang X, Liu D, Liu X, Mi Z, Tao H, Fan H. Comprehensive landscape of immune-based classifier related to early diagnosis and macrophage M1 in spinal cord injury. Aging (Albany NY) 2023; 15:1158-1176. [PMID: 36842142 PMCID: PMC10008498 DOI: 10.18632/aging.204548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Numerous studies have documented that immune responses are crucial in the pathophysiology of spinal cord injury (SCI). Our study aimed to uncover the function of immune-related genes (IRGs) in SCI. Here, we comprehensively evaluated the transcriptome data of SCI and healthy controls (HC) obtained from the GEO Database integrating bioinformatics and experiments. First, a total of 2067 DEGs were identified between the SCI and HC groups. Functional enrichment analysis revealed substantial immune-related pathways and functions that were abnormally activated in the SCI group. Immune analysis revealed that myeloid immune cells were predominantly upregulated in SCI patients, while a large number of lymphoid immune cells were dramatically downregulated. Subsequently, 51 major IRGs were screened as key genes involved in SCI based on the intersection of the results of WGCNA analysis, DEGs, and IRGs. Based on the expression profiles of these genes, two distinct immune modulation patterns were recognized exhibiting opposite immune characteristics. Moreover, 2 core IRGs (FCER1G and NFATC2) were determined to accurately predict the occurrence of SCI via machine learning. qPCR analysis was used to validate the expression of core IRGs in an external independent cohort. Finally, the expression of these core IRGs was validated by sequencing, WB, and IF analysis in vivo. We found that these two core IRGs were closely associated with immune cells and verified the co-localization of FCER1G with macrophage M1 via IF analysis. Our study revealed the key role of immune-related genes in SCI and contributed to a fresh perspective for early diagnosis and treatment of SCI.
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Affiliation(s)
- Zhao Zhang
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an 710032, China
| | - Zhijie Zhu
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an 710032, China
| | - Xuankang Wang
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an 710032, China
| | - Dong Liu
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an 710032, China
| | - Xincheng Liu
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an 710032, China
| | - Zhenzhou Mi
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an 710032, China
| | - Huiren Tao
- Department of Orthopaedics, Shenzhen University General Hospital, Shenzhen 518052, China
| | - Hongbin Fan
- Department of Orthopaedics, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an 710032, China
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An M, Qiu Y, Wang C, Ma P, Ding Y. Rac2 enhances activation of microglia and astrocytes, inflammatory response, and apoptosis via activating JNK signaling pathway and suppressing SIRT1 expression in chronic constriction injury-induced neuropathic pain. J Neuropathol Exp Neurol 2023; 82:419-426. [PMID: 36779914 DOI: 10.1093/jnen/nlad006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Neuropathic pain (NP) is pain caused by injury or dysfunction of the somatosensory system. The role of Rac2, a member of the Rac family, which is expressed in neutrophils, macrophages, and adult T cells, in NP remains unclear. Using a chronic constriction injury (CCI)-induced NP model in rats, we found that Rac2 expression was elevated in rats with CCI-induced NP and that overexpression of Rac2 aggravated the NP. Rac2 overexpression also aggravated the inflammatory response, induced activation of microglia and astrocytes, and enhanced apoptosis whereas knockdown of Rac2 had the opposite effects. Rac2 suppressed SIRT1 expression via activating the c-Jun N-terminal kinase (JNK) signaling pathway. In rescue experiments, SRT1720, an activator of SIRT1, reversed the effect of Rac2 on glial activation, inflammatory response, and apoptosis. These findings indicate that Rac2 enhances the activation of microglia and astrocytes, inflammatory response, and apoptosis via activating the JNK signaling pathway and suppressing SIRT1 expression in CCI-induced NP.
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Affiliation(s)
- Min An
- Department of Anesthesiology, The Second Affiliated Hospital of Inner Mongolia Medical College, Hohhot, China
| | - Yi Qiu
- Department of Anesthesiology, The Second Affiliated Hospital of Inner Mongolia Medical College, Hohhot, China
| | - Caixia Wang
- Department of Anesthesiology, The Second Affiliated Hospital of Inner Mongolia Medical College, Hohhot, China
| | - Penglei Ma
- Department of Anesthesiology, The Second Affiliated Hospital of Inner Mongolia Medical College, Hohhot, China
| | - Yumei Ding
- Department of Anesthesiology, The Second Affiliated Hospital of Inner Mongolia Medical College, Hohhot, China
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Analysis of Potential Hub Genes for Neuropathic Pain Based on Differential Expression in Rat Models. Pain Res Manag 2022; 2022:6571987. [PMID: 35281346 PMCID: PMC8913144 DOI: 10.1155/2022/6571987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/03/2022] [Accepted: 01/21/2022] [Indexed: 11/30/2022]
Abstract
Objective Neuropathic pain (NP) is a type of intractable chronic pain with complicated etiology. The exact molecular mechanism underlying NP remains unclear. In this study, we searched for molecular biomarkers of NP. Methods Differentially expressed genes (DEGs) were predicted by analyzing three NP-related microarray datasets in Gene Expression Omnibus with robust rank aggregation. A weighted gene coexpression network analysis was conducted to construct a network of differentially expressed genes, followed by the evaluation of correlations between gene sets and the determination of hub genes. The candidate genes from the key module were identified using a gene set enrichment analysis. Results In total, 353 upregulated and 383 downregulated genes were obtained, among which five hub genes were determined to be related to pain phenotypes. Reverse transcription-quantitative polymerase chain reaction was performed to verify the expression of these hub genes in the dorsal root ganglia of rats with spared nerve injury, which revealed the decreased expression of EMC4. Hence, EMC4 was defined as a biomarker for NP development. Conclusions The results of this study form a basis for further research into the mechanism of NP development and are expected to aid in the development of novel therapeutic strategies.
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Zhang Y, Jiang S, Liao F, Huang Z, Yang X, Zou Y, He X, Guo Q, Huang C. A transcriptomic analysis of neuropathic pain in the anterior cingulate cortex after nerve injury. Bioengineered 2022; 13:2058-2075. [PMID: 35030976 PMCID: PMC8973654 DOI: 10.1080/21655979.2021.2021710] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The anterior cingulate cortex (ACC) is a core brain region processing pain emotion. In this study, we performed RNA sequencing analysis to reveal transcriptomic profiles of the ACC in a rat chronic constriction injury (CCI) model. A total of 1628 differentially expressed genes (DEGs) were identified by comparing sham-operated rats with rats of 12 hours, 1, 3, 7, and 14 days after surgery, respectively. Although these inflammatory-related DEGs were generally increased after CCI, different kinetics of time-series expression were observed with the development of neuropathic pain affection. Specifically, the expression of Ccl5, Cxcl9 and Cxcl13 continued to increase following CCI. The expression of Ccl2, Ccl3, Ccl4, Ccl6, and Ccl7 were initially upregulated after CCI and subsequently decreased after 12 hours. Similarly, the expression of Rac2, Cd68, Icam-1, Ptprc, Itgb2, and Fcgr2b increased after 12 hours but reduced after 1 day. However, the expression of the above genes increased again 7 days after CCI, when the neuropathic pain affection had developed. Furthermore, gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment and interaction network analyses further showed a high connectivity degree among these chemokine targeting genes. Similar expressional changes in these genes were found in the rat spinal dorsal horn responsible for nociception processing. Taken together, our results indicated chemokines and their targeting genes in the ACC may be differentially involved in the initiation and maintenance of neuropathic pain affection. These genes may be a target for not only the nociception but also the pain affection following nerve injury.
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Affiliation(s)
- Yu Zhang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Shiwei Jiang
- Medical College of Xiangya, Central South University, Changsha, China
| | - Fei Liao
- Department of Anesthesiology, People's Hospital of Yuxi City, Yuxi, China
| | - Zhifeng Huang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Yang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Yu Zou
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin He
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Qulian Guo
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Changsheng Huang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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7
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Li L, Du X, Ling H, Li Y, Wu X, Jin A, Yang M. Gene correlation network analysis to identify regulatory factors in sciatic nerve injury. J Orthop Surg Res 2021; 16:622. [PMID: 34663380 PMCID: PMC8522103 DOI: 10.1186/s13018-021-02756-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sciatic nerve injury (SNI), which frequently occurs under the traumatic hip and hip fracture dislocation, induces serious complications such as motor and sensory loss, muscle atrophy, or even disabling. The present work aimed to determine the regulating factors and gene network related to the SNI pathology. METHODS Sciatic nerve injury dataset GSE18803 with 24 samples was divided into adult group and neonate group. Weighted gene co-expression network analysis (WGCNA) was carried out to identify modules associated with SNI in the two groups. Moreover, differentially expressed genes (DEGs) were determined from every group, separately. Subsequently, co-expression network and protein-protein interaction (PPI) network were overlapped to identify hub genes, while functional enrichment and Reactome analysis were used for a comprehensive analysis of potential pathways. GSE30165 was used as the test set for investigating the hub gene involvement within SNI. Gene set enrichment analysis (GSEA) was performed separately using difference between samples and gene expression level as phenotype label to further prove SNI-related signaling pathways. In addition, immune infiltration analysis was accomplished by CIBERSORT. Finally, Drug-Gene Interaction database (DGIdb) was employed for predicting the possible therapeutic agents. RESULTS 14 SNI status modules and 97 DEGs were identified in adult group, while 15 modules and 21 DEGs in neonate group. A total of 12 hub genes was overlapping from co-expression and PPI network. After the results from both test and training sets were overlapped, we verified that the ten real hub genes showed remarkably up-regulation within SNI. According to functional enrichment of hub genes, the above genes participated in the immune effector process, inflammatory responses, the antigen processing and presentation, and the phagocytosis. GSEA also supported that gene sets with the highest significance were mostly related to the cytokine-cytokine receptor interaction. Analysis of hub genes possible related signaling pathways using gene expression level as phenotype label revealed an enrichment involved in Lysosome, Chemokine signaling pathway, and Neurotrophin signaling pathway. Immune infiltration analysis showed that Macrophages M2 and Regulatory T cells may participate in the development of SNI. At last, 25 drugs were screened from DGIdb to improve SNI treatment. CONCLUSIONS The gene expression network is determined in the present work based on the related regulating factors within SNI, which sheds more light on SNI pathology and offers the possible biomarkers and therapeutic targets in subsequent research.
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Affiliation(s)
- Liuxun Li
- Department of Spine Surgery, the First Affiliated Hospital, Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Xiaokang Du
- Department of Spine Surgery, the First Affiliated Hospital, Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Haiqian Ling
- Department of Spine Surgery, the First Affiliated Hospital, Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Yuhang Li
- Department of Joint and Trauma Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xuemin Wu
- Department of Endocrinology, Shenzhen Hospital of Guangzhou University of Chinese Medicine (Futian), Shenzhen, Guangdong, China
| | - Anmin Jin
- Department of Spine Surgery, ZhuJiang Hospital of Southern Medical University, Southern Medical University, Guangzhou, Guangdong, China
| | - Meiling Yang
- Department of Oncology, Shenzhen Hospital of Guangzhou University of Chinese Medicine (Futian), Shenzhen, 518034, Guangdong, China.
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Analysis of Crucial Genes and Pathways Associated with Spared Nerve Injury-Induced Neuropathic Pain. Neural Plast 2020. [DOI: 10.1155/2020/8822001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Purpose. The study was aimed at elucidating the molecular mechanism underlying neuropathic pain induced by spared nerve injury (SNI). Methods. The microarray data of GSE30691 were downloaded from the Gene Expression Omnibus database, including sciatic nerve lesion samples at 3, 7, 21, and 40 days after SNI and sham control samples at 3, 7, and 21 days. Differential analysis along with Mfuzz clustering analysis was performed to screen crucial clusters and cluster genes. Subsequently, comprehensive bioinformatic analyses were performed, including functional enrichment analysis, protein-protein interaction (PPI) network and module analysis, and transcription factor- (TF-) gene and miRNA-target interaction predictions. Moreover, the screened differentially expressed genes (DEGs) were corroborated using two other microarray datasets. Results. Three clusters with different change trends over time after SNI were obtained. Protein kinase CAMP-activated catalytic subunit beta (Prkacb), complement C3 (C3), and activating transcription factor 3 (Atf3) were hub nodes in the PPI network, and fibroblast growth factor 9 (Fgf9) was found to interact with more TFs. Prkacb and Fgf9 were significantly enriched in the MAPK signaling pathway. Moreover, rno-miR-3583-5p was targeted by Fgf9, and rno-miR-1912-3p was targeted by neuregulin 1 (Nrg1). Key genes like Nrg1 and Fgf9 in cluster 1, Timp1 in cluster 2, and Atf3 and C3 in cluster 3 were screened out after corroborating microarray data with other microarray data. Conclusions. Key pathways like the MAPK signaling pathway and crucial genes like Prkacb, Nrg1, Fgf9, Timp1, C3, and Atf3 may contribute to SNI-induced neuropathic pain development in rats.
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9
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Du Z, Yin S, Song X, Zhang L, Yue S, Jia X, Zhang Y. Identification of Differentially Expressed Genes and Key Pathways in the Dorsal Root Ganglion After Chronic Compression. Front Mol Neurosci 2020; 13:71. [PMID: 32431596 PMCID: PMC7214750 DOI: 10.3389/fnmol.2020.00071] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/14/2020] [Indexed: 12/31/2022] Open
Abstract
Neuropathic pain (NP) is caused by primary or secondary impairment of the peripheral or central nervous systems. Its etiology is complex and involves abnormal patterns of gene expression and pathway activation. Using bioinformatics analysis, we aimed to identify NP-associated changes in genes and pathways in L4 and L5 dorsal root ganglia (DRG) in a rat model of NP induced by chronic compression of the DRG (CCD). Genome-wide transcriptional analyses were used to elucidate the molecular mechanisms underlying NP. We screened differentially expressed genes (DEGs) 7 days after CCD in comparison with sham-operated controls. Quantitative real-time polymerase chain reaction (RT-qPCR) and western blotting were used to confirm the presence of key DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG)-pathway analysis of DEGs and global signal transduction network analysis of DEGs were also conducted. The CCD group developed clear mechanical and thermal allodynia in the ipsilateral hind paw compared with the sham group. This comparison identified 1,887 DEGs, with 1156 upregulated and 731 downregulated DEGs, and 123 DEG-enriched pathways. We identified the key candidate genes that might play a role in the development of NP, namely syndecan 1 (Sdc1), phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma (Pi3k), Janus kinase 2 (Jak2), jun proto-oncogene, AP-1 transcription factor subunit (Jun), and interleukin 6 (IL-6) by analyzing the global signal transduction network. RT-qPCR and western blot analysis confirmed the microarray results. The DEGs Sdc1, Pi3k, Jak2, Jun, and IL-6, and the cytokine signaling pathway, the neuroactive ligand-receptor interaction, the toll-like receptor signaling pathway, and the PI3K-Akt signaling pathway may have decisive modulatory roles in both nerve regeneration and NP. These results provide deeper insight into the mechanism underlying NP and promising therapeutic targets for its treatment.
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Affiliation(s)
- Zhanhui Du
- Department of Physical Medicine & Rehabilitation, Qilu Hospital, Shandong University, Jinan, China.,Heart Center, Qingdao Women and Children's Hospital, Qingdao, China
| | - Sen Yin
- Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Xiuhui Song
- Department of Neurosurgery, The People's Hospital of Jimo City, Qingdao, China
| | - Lechi Zhang
- Department of Physical Medicine & Rehabilitation, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou, China
| | - Shouwei Yue
- Department of Physical Medicine & Rehabilitation, Qilu Hospital, Shandong University, Jinan, China
| | - Xiaofeng Jia
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Orthopaedics, Anatomy & Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States.,Departments of Biomedical Engineering, Anesthesiology and Critical Care Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yang Zhang
- Department of Physical Medicine & Rehabilitation, Qilu Hospital, Shandong University, Jinan, China.,Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, United States
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10
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Gu Y, Qiu Z, Cheng N, Chen C, Hei Z, Li X. Identification of potential mechanism and hub genes for neuropathic pain by expression-based genome-wide association study. J Cell Biochem 2018; 120:4912-4923. [PMID: 30269359 DOI: 10.1002/jcb.27766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/06/2018] [Indexed: 01/07/2023]
Abstract
Neuropathic pain (NP) is a common pathological pain state with limited effective treatments. This study was designed to identify potential mechanisms and candidate genes using gene expression-based genome-wide association study (eGWAS). All NP-related microarray experiments were obtained from Gene Expression Omnibus and ArrayExpress. Significantly dysregulated genes were identified between experimental and untreated groups, and the number of microarray experiments in which each gene was dysregulated was calculated. Significantly dysregulated genes were ranked according to P values of the chi-square test. Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database, we performed functional and pathway enrichment analysis. Protein-protein interaction (PPI) network and module analysis was performed using Cytoscape software. A total of 115 candidate genes were identified from 19 independent microarray experiments by eGWAS based on the Bonferroni threshold ( P < 2.97 × 10 -6 ). Immune and inflammatory responses, and complement and coagulation cascades, were respectively the most enriched biological process and pathways for candidate genes. The hub genes with highest connectivity in PPI network and two modules Ccl2 and Jun, and Ctss application of the eGWAS methodology can identify mechanisms and candidate genes associated with NP. Our results support the validity and prevalence of inflammatory and immune mechanisms across different NP models, and Ccl2, Jun, and Ctss may be the hub genes for NP.
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Affiliation(s)
- Yu Gu
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhuolin Qiu
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Nan Cheng
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chaojin Chen
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ziqing Hei
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiang Li
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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11
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Du H, Shi J, Wang M, An S, Guo X, Wang Z. Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats. J Neuroinflammation 2018; 15:280. [PMID: 30253787 PMCID: PMC6156955 DOI: 10.1186/s12974-018-1316-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/18/2018] [Indexed: 12/29/2022] Open
Abstract
Background Neuropathic pain is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. Methods Wistar rats were employed for the establishment of the chronic constriction injury (CCI) models. Using the Illumina HiSeq 4000 platform, we examined differentially expressed genes (DEGs) in the rat dorsal horn by RNA sequencing (RNA-seq) between CCI and control groups. Then, enrichment analyses were performed for these DEGs using Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Hierarchical Cluster, and protein-protein interaction (PPI) network. Results A total of 63 DEGs were found significantly changed with 56 upregulated (e.g., Cxcl13, C1qc, Fcgr3a) and 7 downregulated (e.g., Dusp1) at 14 days after CCI. Quantitative reverse-transcribed PCR (qRT-PCR) verified changes in 13 randomly selected DEGs. GO and KEGG biological pathway analyses showed that the upregulated DEGs were mostly enriched in immune response-related biological processes, as well as 14 immune- and inflammation-related pathways. The downregulated DEGs were enriched in inactivation of mitogen-activated protein kinase (MAPK) activity. PPI network analysis showed that Cd68, C1qc, C1qa, Laptm5, and Fcgr3a were crucial nodes with high connectivity degrees. Most of these genes which have previously been linked to immune and inflammation-related pathways have not been reported in neuropathic pain (e.g., Laptm5, Fcgr3a). Conclusions Our results revealed that immune and defense pathways may contribute to the generation of neuropathic pain after CCI. These mRNAs may represent new therapeutic targets for the treatment of neuropathic pain. Electronic supplementary material The online version of this article (10.1186/s12974-018-1316-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Du
- Department of Histology and Embryology, Taishan Medical University, Taian, 271000, China
| | - Juan Shi
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China
| | - Ming Wang
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China
| | - Shuhong An
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China
| | - Xingjing Guo
- Department of Physiology, Taishan Medical University, Taian, 271000, China
| | - Zhaojin Wang
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China.
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12
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Gu Y, Qiu ZL, Liu DZ, Sun GL, Guan YC, Hei ZQ, Li X. Differential gene expression profiling of the sciatic nerve in type 1 and type 2 diabetic mice. Biomed Rep 2018; 9:291-304. [PMID: 30233781 PMCID: PMC6142038 DOI: 10.3892/br.2018.1135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/17/2018] [Indexed: 12/21/2022] Open
Abstract
Diabetic peripheral neuropathy (DPN) is a common complication of diabetes mellitus (DM). The pathogenic mechanisms of DPN and the therapeutic interventions required may be distinct between type 1 (T1) and type 2 (T2) DM. However, the molecular mechanisms underlying the pathogenesis of DPN in both types of diabetes remain unclear. The aim of the current study was to identify the changes in genes and pathways associated with DPN in sciatic nerves of T1- and T2DM mice using bioinformatics analysis. The microarray profiles of sciatic nerves of T1DM (GSE11343) and T2DM (GSE27382) mouse models were downloaded from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) in each. DEGs in the two types of DM (with fold change ≥2 and P<0.05) were identified with BRB-ArrayTools. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins and visualized using Cytoscape. Compared with control samples, 623 and 1,890 DEGs were identified in sciatic nerves of T1- and T2DM mice, respectively. Of these, 75 genes were coordinately dysregulated in the sciatic nerves of both models. Many DEGs unique to T1DM mice were localized to the nucleoplasm and were associated with regulation of transcription processes, while many unique to T2DM mice were localized at cell junctions and were associated with ion transport. In addition, certain DEGs may be associated with the different treatment strategies used for the two types of DM. This analysis provides insight into the functional gene sets and pathways operating in sciatic nerves in T1- and T2DM. The results should improve understanding of the molecular mechanisms underlying the pathophysiology of DPN, and provide information for the development of therapeutic strategies for DPN specific to each type of DM.
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Affiliation(s)
- Yu Gu
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Zhuo-Lin Qiu
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - De-Zhao Liu
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Guo-Liang Sun
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Ying-Chao Guan
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Zi-Qing Hei
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Xiang Li
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
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13
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Young A, Kalladka M, Viswanath A, Zusman T, Khan J. Consomic rats parental strains differ in sensory perception, pain developed following nerve injury and in IL-1 beta and IL-6 levels. ACTA ACUST UNITED AC 2018; 25:137-141. [PMID: 29580677 DOI: 10.1016/j.pathophys.2018.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Andrew Young
- Orofacial Disorders Clinic, Department of Diagnostic Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, 155 Fifth Street, San Francisco, CA, 94103, USA.
| | - Mythili Kalladka
- Orofacial Pain and TMJ Disorders, Eastman Institute for Oral Health, 625 Elmwood Ave, Rochester, NY, 14620, USA.
| | - Archana Viswanath
- Department of Oral and Maxillofacial Surgery, Tufts University School of Dental Medicine, USA.
| | - Tal Zusman
- Graduate School of Biomedical Sciences, Rutgers University, Newark, NJ, USA.
| | - Junad Khan
- Orofacial Pain and TMJ Disorders, Eastman Institute for Oral Health, 625 Elmwood Ave, Rochester, NY, 14620, USA.
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Starobova H, S. W. A. H, Lewis RJ, Vetter I. Transcriptomics in pain research: insights from new and old technologies. Mol Omics 2018; 14:389-404. [DOI: 10.1039/c8mo00181b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Physiological and pathological pain involves a complex interplay of multiple cell types and signaling pathways.
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Affiliation(s)
- H. Starobova
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
| | - Himaya S. W. A.
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
| | - R. J. Lewis
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
| | - I. Vetter
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
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15
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Chen CJ, Liu DZ, Yao WF, Gu Y, Huang F, Hei ZQ, Li X. Identification of key genes and pathways associated with neuropathic pain in uninjured dorsal root ganglion by using bioinformatic analysis. J Pain Res 2017; 10:2665-2674. [PMID: 29180893 PMCID: PMC5694199 DOI: 10.2147/jpr.s143431] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Purpose Neuropathic pain is a complex chronic condition occurring post-nervous system damage. The transcriptional reprogramming of injured dorsal root ganglia (DRGs) drives neuropathic pain. However, few comparative analyses using high-throughput platforms have investigated uninjured DRG in neuropathic pain, and potential interactions among differentially expressed genes (DEGs) and pathways were not taken into consideration. The aim of this study was to identify changes in genes and pathways associated with neuropathic pain in uninjured L4 DRG after L5 spinal nerve ligation (SNL) by using bioinformatic analysis. Materials and methods The microarray profile GSE24982 was downloaded from the Gene Expression Omnibus database to identify DEGs between DRGs in SNL and sham rats. The prioritization for these DEGs was performed using the Toppgene database followed by gene ontology and pathway enrichment analyses. The relationships among DEGs from the protein interactive perspective were analyzed using protein–protein interaction (PPI) network and module analysis. Real-time polymerase chain reaction (PCR) and Western blotting were used to confirm the expression of DEGs in the rodent neuropathic pain model. Results A total of 206 DEGs that might play a role in neuropathic pain were identified in L4 DRG, of which 75 were upregulated and 131 were downregulated. The upregulated DEGs were enriched in biological processes related to transcription regulation and molecular functions such as DNA binding, cell cycle, and the FoxO signaling pathway. Ctnnb1 protein had the highest connectivity degrees in the PPI network. The in vivo studies also validated that mRNA and protein levels of Ctnnb1 were upregulated in both L4 and L5 DRGs. Conclusion This study provides insight into the functional gene sets and pathways associated with neuropathic pain in L4 uninjured DRG after L5 SNL, which might promote our understanding of the molecular mechanisms underlying the development of neuropathic pain.
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Affiliation(s)
- Chao-Jin Chen
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - De-Zhao Liu
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wei-Feng Yao
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yu Gu
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Fei Huang
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zi-Qing Hei
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiang Li
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
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