10
Research Article Long Noncoding RNA Expression Profile in BV2 Microglial Cells Exposed to Lipopolysaccharide Yajuan Li, 1,2 Qingmin Li, 3 Cunjuan Wang , 4 Shengde Li , 2 and Lingzhi Yu 1 Department of Pain Management, Jinan Central Hospital, Shandong University, Jinan , China Department of Anesthesiology, Taian City Central Hospital, Taian , China Department of Neurosurgery, Taian City Central Hospital, Taian , China Department of Children Rehabilitation, W. F. Maternal and Child Health Hospital, Weifang , China Correspondence should be addressed to Lingzhi Yu; [email protected] Received 13 March 2019; Accepted 26 May 2019; Published 11 June 2019 Academic Editor: Maria C. De Rosa Copyright © 2019 Yajuan Li et al. is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Neuropathic pain, which is one of the most common forms of chronic pain, seriously increases healthcare costs and impairs patients’ quality of life with an incidence of 7–10% worldwide. Microglia cell activation plays a key role in the progression of neuropathic pain. Better understanding of novel molecules modulating microglia cell activation and these underlying functions will extremely benefit the exploration of new treatment. Recent studies suggested long noncoding RNAs may be involved in neuropathic pain. However, its underlying functions and mechanisms in microglia cell activation remain unclear. To identify the differentially expressed lncRNAs and predict their functions in the progression of microglia cell activation, GSE103156 was analyzed using integrated bioinformatics methods. e expression levels of selected lncRNAs and mRNAs were determined by real-time PCR. In the present study, a total of 56 lncRNAs and 298 mRNAs were significantly differentially expressed. e differentially expressed mRNAs were mainly enriched in NF-kappa B signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and NOD-like receptor signaling pathway. e top 10 hub genes were Tnf, Il6, Stat1, Cxcl10, Il1b, Tlr2, Irf1, Ccl2, Irf7, and Ccl5 in the PPI network. Our results showed that Gm8989, Gm8979, and AV051173 may be involved in the progression of microglia cell activation. Taken together, our findings suggest that lots of lncRNAs may be involved in BV2 microglia cell activation in vitro. e findings may provide relevant information for the development of promising targets for the microglial cells activation of neuropathic pain in vivo in the future. 1. Introduction Neuropathic pain, which is one of the most common forms of chronic pain [1, 2], seriously increased healthcare costs and impairs patients’ quality of life with an incidence of 7–10% worldwide [3, 4]. Moreover, there are no effective treatments for patients with neuropathic pain. To design new prophylactic and therapeutic strategies, more studies are needed to explore the pathogenesis of neuropathic pain. Neuropathic pain oſten results from traumatic, infectious, chemical, metabolic, or cancerous impairments [3–5], in which significant features are hyperalgesia, allodynia, and spontaneous burning pain. Although the pathogenesis of neuropathic pain is obscure, microglia cell activation has been shown to be essential for neuropathic pain [6, 7]. A recent study has shown that spinal microglia activation was induced by peripheral nerve injury and contributed to central sensitization [8]. Considerable advances have been made in high- throughput technology for identifying microglial factors in neuropathic pain [9–11] in the past decade. However, the mechanisms of microglia activation-induced neuropathic pain are still poorly understood. In general, ncRNAs do not encode functional proteins. It has shown that lncRNAs participate in most essential biological processes at the levels of posttranscription, tran- scription, and epigenetics [12–15]. Recent research has shown that some lncRNAs may be involved in the pathophysiology of neuropathic pain. Xiuli Zhao et al. reported that Kcna2 antisense RNA was an endogenous trigger in the progression of neuropathic pain [16]. Differentially expressed lncRNAs were identified in SNI-induced neuropathic pain using Hindawi BioMed Research International Volume 2019, Article ID 5387407, 9 pages https://doi.org/10.1155/2019/5387407

Long Noncoding RNA Expression Profile in BV2 Microglial ...Long Noncoding RNA Expression Profile in BV2 Microglial Cells Exposed to Lipopolysaccharide YajuanLi,1,2 QingminLi,3 CunjuanWang

  • Upload
    others

  • View
    5

  • Download
    0

Embed Size (px)

Citation preview

  • Research ArticleLong Noncoding RNA Expression Profile in BV2 Microglial CellsExposed to Lipopolysaccharide

    Yajuan Li,1,2 Qingmin Li,3 CunjuanWang ,4 Shengde Li ,2 and Lingzhi Yu 1

    1Department of Pain Management, Jinan Central Hospital, Shandong University, Jinan 250013, China2Department of Anesthesiology, Taian City Central Hospital, Taian 271000, China3Department of Neurosurgery, Taian City Central Hospital, Taian 271000, China4Department of Children Rehabilitation, W. F. Maternal and Child Health Hospital, Weifang 261011, China

    Correspondence should be addressed to Lingzhi Yu; [email protected]

    Received 13 March 2019; Accepted 26 May 2019; Published 11 June 2019

    Academic Editor: Maria C. De Rosa

    Copyright © 2019 Yajuan Li et al.This is an open access article distributed under the Creative Commons Attribution License, whichpermits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Neuropathic pain, which is one of themost common forms of chronic pain, seriously increases healthcare costs and impairs patients’quality of life with an incidence of 7–10%worldwide.Microglia cell activation plays a key role in the progression of neuropathic pain.Better understanding of novel molecules modulatingmicroglia cell activation and these underlying functions will extremely benefitthe exploration of new treatment. Recent studies suggested long noncodingRNAsmay be involved in neuropathic pain.However, itsunderlying functions and mechanisms in microglia cell activation remain unclear. To identify the differentially expressed lncRNAsand predict their functions in the progression of microglia cell activation, GSE103156 was analyzed using integrated bioinformaticsmethods.The expression levels of selected lncRNAs and mRNAs were determined by real-time PCR. In the present study, a total of56 lncRNAs and 298 mRNAs were significantly differentially expressed.The differentially expressed mRNAs were mainly enrichedin NF-kappa B signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and NOD-like receptor signalingpathway. The top 10 hub genes were Tnf, Il6, Stat1, Cxcl10, Il1b, Tlr2, Irf1, Ccl2, Irf7, and Ccl5 in the PPI network. Our resultsshowed that Gm8989, Gm8979, and AV051173 may be involved in the progression of microglia cell activation. Taken together, ourfindings suggest that lots of lncRNAs may be involved in BV2 microglia cell activation in vitro. The findings may provide relevantinformation for the development of promising targets for the microglial cells activation of neuropathic pain in vivo in the future.

    1. Introduction

    Neuropathic pain, which is one of the most common formsof chronic pain [1, 2], seriously increased healthcare costsand impairs patients’ quality of life with an incidence of7–10% worldwide [3, 4]. Moreover, there are no effectivetreatments for patients with neuropathic pain. To designnew prophylactic and therapeutic strategies, more studiesare needed to explore the pathogenesis of neuropathic pain.Neuropathic pain often results from traumatic, infectious,chemical, metabolic, or cancerous impairments [3–5], inwhich significant features are hyperalgesia, allodynia, andspontaneous burning pain. Although the pathogenesis ofneuropathic pain is obscure, microglia cell activation hasbeen shown to be essential for neuropathic pain [6, 7]. Arecent study has shown that spinal microglia activation was

    induced by peripheral nerve injury and contributed to centralsensitization [8].

    Considerable advances have been made in high-throughput technology for identifying microglial factors inneuropathic pain [9–11] in the past decade. However, themechanisms of microglia activation-induced neuropathicpain are still poorly understood.

    In general, ncRNAs do not encode functional proteins.It has shown that lncRNAs participate in most essentialbiological processes at the levels of posttranscription, tran-scription, and epigenetics [12–15]. Recent research has shownthat some lncRNAs may be involved in the pathophysiologyof neuropathic pain. Xiuli Zhao et al. reported that Kcna2antisense RNA was an endogenous trigger in the progressionof neuropathic pain [16]. Differentially expressed lncRNAswere identified in SNI-induced neuropathic pain using

    HindawiBioMed Research InternationalVolume 2019, Article ID 5387407, 9 pageshttps://doi.org/10.1155/2019/5387407

    http://orcid.org/0000-0001-9163-6335http://orcid.org/0000-0001-8591-8766http://orcid.org/0000-0001-8206-3694https://creativecommons.org/licenses/by/4.0/https://doi.org/10.1155/2019/5387407

  • 2 BioMed Research International

    high-throughput sequencing techniques, identifying a seriesof potential therapeutic targets of neuropathic pain [17].However, the potential functions and mechanisms of lncR-NAs in microglia cell activation remain incompletely under-stood.

    In this study, we investigated the expression profile oflncRNAs andmRNAs in BV2microglial cells stimulated withLPS and predicted the potential functions and mechanismsof differentially expressed lncRNAs. Due to opportunitiesto identify novel promising targets of BV2 microglial cellsactivation, our results may provide relevant information forfuture study of microglial cells activation of neuropathic painin vivo.

    2. Materials and Methods

    2.1. Cell Culture, LPS Treatment, and RNA Isolation. BV2microglial cells were purchased from ATCC (Manassas,VA, USA) and cultured according to the manufacturer’sinstructions. BV2 microglial cells were stimulated for 24 hwith LPS (1 𝜇g/ml) or vehicle control (HBSS) in DMEM highglucose media containing 2.5% FBS. Total RNA was isolatedand identified as previously described.

    2.2. Microarray Data. Raw data of GSE103156 (AffymetrixMouse Gene 2.1 ST Array) were downloaded from the GEOdata repository [18, 19]. In the present study, three BV2control samples and three BV2 LPS samples were used forbioinformatic analysis.

    2.3. Identification of Differentially Expressed lncRNAs andmRNAs. Using Transcriptome Analysis Console (TAC) 4.01(Affymetrix, Santa Clara, CA, USA), differentially expressedlncRNAs and differentially expressed genes (DEGs) wereidentified. 2.0-fold or greater and an adjusted p value < 0.01were selected as a threshold.

    2.4. Gene Ontology (GO) and Pathway Enrichment Analyses.The Database for Annotation, Visualization and IntegratedDiscovery (DAVID; http://david.ncifcrf.gov) (version 6.8)was used to analyze the biological function of differentiallyexpressed genes [20–24]. p value < 0.05 was selected as athreshold.

    2.5. Protein-Protein Interactions (PPI) Network and Mod-ule Analysis. The interactions of DEGs were predicted bySTRING online database (http://string-db.org, version 10.5)[25]. PPI networkwas drawn byCytoscape (version 3.7.1) [26]and its plugin (MCODE [27] and CytoNCA [28]).

    2.6. Transcription Factor (TF) Regulatory Network Analysis.IRegulon plugin in Cytoscape was used to predict TFs ofselected DEGs [29]. Normalized enrichment score (NES) >10 was used as the thresholds.

    2.7. LncRNA-mRNACoexpression Network. LncRNA-mRNAcoexpression network was constructed to analyze theinteractions between lncRNA and mRNA by weighted

    correlation network analysis (WGCNA) as describedpreviously [30].

    2.8. Real-Time PCR. SuperReal PreMix Plus (Tiangen, Bei-jing, China) was used to perform real-time PCR in the Ari-aMx Real-time PCR System (Agilent Technologies, Palo Alto,CA). The reaction conditions were as follows: incubation at95∘C for 10 min, followed by 40 cycles of 95∘C for 15 s, 61∘Cfor 20 s, and 72∘C for 30 s. The 2-ΔΔCt method was usedto calculate the relative expression levels of selected lncRNAsand mRNA normalizing to GAPDH levels.

    2.9. Statistical Analysis. All data were expressed as the mean± SEM. Unpaired Student’s t-test for parametric data andMann-Whitney’s U-test for nonparametric data were utilizedfor comparisons between 2 groups. GraphPad Prism 7.04(GraphPad Software, San Diego, CA, USA) was used for allstatistical analyses. p value < 0.05 was considered statisticallysignificant.

    3. Results

    3.1. Identification of Differentially Expressed lncRNAs andmRNAs. In total, 56 lncRNAs and 298 mRNAs were signifi-cantly differentially expressed in BV2microglial cells exposedto LPS. The top 30 most significantly differentially expressedlncRNAs (Figure 1(a)) and mRNAs (Figure 1(b)) were shownon heat map.

    3.2. GO and Pathway Enrichment Analyses. DEGs weremainly enriched in the following functions: immune systemprocess, innate immune response, inflammatory response,and response to lipopolysaccharide (Figures 2(a)–2(c)). Ourresults also suggested that DEGs were mainly enriched in thefollowing pathways: Herpes simplex infection, NF-kappa Bsignaling pathway, TNF signaling pathway, Toll-like receptorsignaling pathway, and NOD-like receptor signaling pathway(Figure 2(d)).

    3.3. PPI Network Analysis. To identify hub genes of microgliacell activation, we used STRING to look for interactions ofDEGs in BV2 microglial cells stimulated with LPS. In thepresent study, we constructed a PPI network of 210 nodes and1842 interaction pairs (Figure 3). In the PPI network, the top10 most significantly hub genes were Tnf, Il6, Stat1, Cxcl10,Il1b, Tlr2, Irf1, Ccl2, Irf7, and Ccl5.

    3.4. TF Regulatory Network Analysis. The TFs of the top 30hub genes in the PPI network were predicted.With NES > 10,nine TFs (Irf1, Irf2, Irf4, Irf5, Irf8, Irf9, Stat1, Nfkb1, and Rela)were predicted in the TF regulatory network (Figure 4).

    3.5. LncRNA-mRNA Coexpression Network. We constructedthe lncRNA-mRNA coexpression network of 26 differentiallyexpressed lncRNAs and 127 interacting DEGs to predictthe functions and mechanisms of differentially expressedlncRNAs in BV2 microglial cells treated with LPS (Figure 5).

    http://david.ncifcrf.govhttp://string-db.org

  • BioMed Research International 3

    Gm3170H2-Q5Gm69046530402F18RikGm13822Mir221LOC100041057Gm16181Mir147Gm21188Gm26527Rnf213Gm38718Gm10719Gm6665Gm23722Gm23442Gm8989Gm10719Gm8979Gm8995Gm41656Pstpip2Gm23514Gm18853Gm17757Gm7609Gm7592Ms4a14Mir155

    3.5

    1.75

    0

    CtrlLPS

    lncRNA

    (a)

    SpicZfp811Cxcl10Gbp7Slamf7MarcoCcrl2Cxcl2I16Clec4a1SlpiBcl3Vnn3FasRtp4Clec4eTxnrd1Saa3Zc3h12cCalcrlSlIfn2AoahNfkbiaC3SIc7a11ll1all1bLcn2Rsad2Irg1

    4

    2.28

    0.55

    mRNA

    CtrlLPS

    (b)

    Figure 1: Hierarchical clustering of differentially expressed lncRNAs (a) andmRNAs (b). Red and blue columns refer to high and low relativeexpression, respectively.

    The top 5 hub lncRNAs were Gm8989, Gm8979, Gm8995,AV051173, and Gm7609 in the coexpression network.

    3.6. Real-TimePCR. Five lncRNAs (6530402F18Rik,AV051173,Gm8979, Gm8989, and Gm18853) and IL6 mRNA wereselected to determine their relative expression levels by real-time PCR (Figure 6). Our results showed that Gm8979,Gm8989, AV051173, 6530402F18Rik, and IL6 were upreg-ulated. The expression of Gm18853 showed no significantchange.

    4. Discussion

    Neuropathic pain seriously increases healthcare costs andimpairs patients’ quality of life with an incidence of 7–10%worldwide [3, 4]. Microglia cell activation is essential to theprogression of neuropathic pain in vivo [6, 7].The research ofmicroglia cell activation provides opportunities to reveal themolecular and cellular basis of neuropathic pain [6–8].

    It has shown that lncRNAs participate in most essentialbiological processes at the levels of posttranscription, tran-scription, and epigenetics [12–15, 31]. Over the past decade,there have been several lncRNA transcriptome researchesin chronic pain. Differentially expressed lncRNAs wereidentified in SNI-induced neuropathic pain using high-throughput sequencing techniques, revealing a series ofpotential therapeutic targets of neuropathic pain [17]. Unlikethe previous study, which made the spinal cord as a whole,we downloaded and analysed raw data of GSE103156, whichestablished microglia cell activation model by stimulating

    BV2 microglial cells with LPS. In addition to common prop-erties of immortalized cell lines (e.g., increased proliferationand adherence), BV2 cells retain most crucial functions ofmicroglia in immune response and inflammation [32, 33].BV2 cells stimulatedwith LPS in vitro resemble themicroglialresponse in vivo to some extent.

    In the present study, we identified 56 differentiallyexpressed lncRNAs and 298 DEGs in BV2 microglialcells stimulated with LPS. DEGs were mainly enriched inthe following functions: immune system process, innateimmune response, inflammatory response, and response tolipopolysaccharide. Pathway analysis results showed thatDEGs mainly involved in Herpes simplex infection, NF-kappa B signaling pathway, TNF signaling pathway, Toll-likereceptor signaling pathway, and NOD-like receptor signalingpathway.The experimentalmodel was successfully developedsince the mRNA expression levels of Il6, Il1a, Il1b, Tnf, andCxcl10 increased in BV2 microglial cells stimulated withLPS [34, 35]. The expression levels of IL6 mRNAs in themicroarray were similar to those detected by real-time PCR.

    PPI network analysis results showed that many differ-entially expressed genes, such as Irf1, Irf7, Stat1, and Tlr2,acted as hub genes in microglia cell activation. Recent studieshave revealed a crosstalk between Tlr2 and microglia cellactivation [6, 36]. Although further experimental validationwas needed, our results suggested new directions for futureexperimental research. We predicted 9 TFs (Irf1, Irf2, Irf4,Irf5, Irf8, Irf9, Stat1, Nfkb1, andRela)mapping to 32 hug genesin PPI network. Notably, IRF1, IRF9, Stat1, and Nfkb1 weresignificantly upregulated in BV2 microglial cells exposed toLPS in the microarray analysis results.

  • 4 BioMed Research International

    BP

    intrinsic apoptotic signaling pathwaypositive regulation of interleukin−6 production

    lipopolysaccharide−mediated signaling pathwaynegative regulation of viral genome replicationdefense response to Gram−positive bacterium

    cellular response to interleukin−1cellular response to interferon−gamma

    transcription factor activitypositive regulation of NF−kappaB

    positive regulation of ERK1 and ERK2 cascaderegulation of cell proliferation

    regulation of apoptotic processpositive regulation of apoptotic process

    response to lipopolysaccharideimmune responseresponse to virus

    cellular response to lipopolysaccharidedefense response to virus

    inflammatory responseinnate immune responseimmune system process

    1020

    3040

    Count

    10152025

    -log(p value)

    Gene ratio0.025 0.050 0.075 0.100 0.125

    (a)

    Gene ratio

    CC

    semaphorin receptor complexsymbiont-containing vacuole membrane

    MHC class I protein complex

    extrinsic component of cytoplasmic sideof plasma membrane

    phagocytic vesicle membranelysosome

    external side of plasma membraneprotein complex

    cytoplasmic vesicleperinuclear region of cytoplasm

    integral component of plasma membranecell surface

    endoplasmic reticulumGolgi apparatus

    extracellular spaceextracellular region

    cytosolextracellular exosome

    membranecytoplasm

    0.0 0.1 0.2 0.3

    23456

    -log(p value)

    Count255075

    100125

    (b)

    MF

    Gene ratio

    hydrolase activity, acting on acid anhydridesCCR5 chemokine receptor binding

    tumor necrosis factor-activated receptor activitychannel activity

    BH domain bindingsemaphorin receptor activity

    chemokine activitymanganese ion binding

    non-membrane spanning proteintyrosine kinase activity

    peptide antigen binding2'-5'-oligoadenylate synthetase activity

    ubiquitin protein ligase bindingdouble-stranded RNA binding

    cytokine activityprotein heterodimerization activity

    receptor bindingoxidoreductase activity

    hydrolase activityATP binding

    protein binding

    0.00 0.05 0.10 0.15 0.20

    234567

    -log(p value)

    Count2040

    6080

    (c)

    KEGG

    Gene ratio

    Cytosolic DNA-sensing pathwayLeishmaniasis

    Allograft rejectionType I diabetes mellitus

    PertussisNOD-like receptor signaling pathway

    Graft-versus-host diseaseHepatitis BHepatitis C

    Osteoclast differentiationToll-like receptor signaling pathway

    Transcriptional misregulation in cancerEpstein-Barr virus infection

    Viral carcinogenesisTuberculosis

    MeaslesTNF signaling pathway

    NF-kappa B signaling pathwayInfluenza A

    Herpes simplex infection

    0.04 0.06 0.08

    7.510.012.515.017.5

    -log(p value)

    Count101520

    2530

    (d)

    Figure 2: GO and KEGG enrichment analyses of differentially expressed mRNAs (Top 20, p < 0.05). GO functional analysis includes threecategories: biological process (BP) (a), cellular component (CC), (b) and molecular function (MF) (c). Red to green colors indicate high tolow -log (p value) levels. Point size indicates the number of differentially expressed genes in the corresponding pathway.

    Many studies have indicated that interferon regulatoryfactor (IRF) family was involved in the pathophysiology ofmicroglial activation and neuropathic pain [37–39]. IRF8,interacted with IRF1 and IRF5, played an important regu-latory role in the progression of neuropathic pain [40–42].Recent studies have shown that Stat1 and Nfkb1 were closelyrelated to neuropathic pain [43–46]. However, the regulatorymechanisms of the IRF family and other transcriptionalfactors in microglia cell activation should be further studiedto determine their therapeutic effects in neuropathic pain invivo.

    Based on fold change and degree in the lncRNA-mRNAcoexpression network, five lncRNAs (AV051173, Gm8979,Gm8989, 6530402F18Rik, and Gm18853) were selected toevaluate the expression levels using real-time PCR. Therelative expression levels of selected lncRNAs, except forGm18853,were consistentwith these trends in themicroarray.The variation between real-time PCR and microarray mayrelate to differences between the methods [47].

    LncRNAs often transcribed together with their adjacentor overlapping target genes and regulate their expressionthrough cis-regulation. Integrated bioinformatics analysis

  • BioMed Research International 5

    Rtn2

    Dtx2Cd40

    Ifi205

    Cd52Sgms2

    C1qc

    Acp5

    Rab11fip1Bik

    Il1b

    Saa3Cxcr4 Ebi3Irf7 Ddx58Gpr84

    Cd14

    Fut8

    Parp14

    Wdtc1Mina

    Hp

    Rhou

    Il1rnCcdc88a

    Thbs1

    Id3Fosl1

    Tlr3

    Pilrb1Tnfrsf8Ifih1

    HckTnfaip3

    H2-M2

    Abcc5 Plxna1

    Rgs11

    Traf1

    Cysltr1Ampd3

    Lrrc25Mef2cPlk2

    Oasl2

    Syk

    Clec4eLamc1 Nos2Sqrdl Cd274Ccrl2

    Sqstm1

    Lcn2

    Zc3h12a

    Casp4 Sepp1

    Mx2

    Slfn2

    Cfb

    Sod2Plau Il1a

    Srxn1 Ifit2Stat1

    Birc3

    Il6Epsti1

    Slc2a6Me1

    St3gal1Tlr2

    Clec4d

    Mpeg1

    Stx11Tnf

    BC006779

    Gbp5

    Gclm

    Ccl2Src Irf1

    Cp F13a1

    Aqp9

    Cxcl10

    Ifi44

    Ccdc41

    Ppap2b

    Serp1

    Cfl2Ehd1Bcl2a1a

    Calcrl Rsad2

    Bcl2a1d

    Pou2f2

    Malt1

    Ms4a6d

    Cxcl2

    Zbp1

    Ripk2

    PilraMycIrak3

    Isg15

    Gch1

    Creb5

    Ptgs1

    Plxnd1

    Rab20

    Rtp4

    Apol9a

    Pim1Hdc

    H2-Q4

    Osbp2Prdx1

    Ikbke

    Herc6

    Jak2

    Dtx4

    Nfkb2 Nlrp3Slc11a2

    Tnfrsf1b

    Met

    Plxna2

    Ms4a7Ccl4

    Nrp2Tnip1

    Ppp2r5bTm9sf4

    Serpinb1a

    Smurf1

    Hdac9 Usp18

    Hspa4l

    Xaf1Ppp3cc

    H2-T23Isg20

    Gbp7Gbp2

    Ifitm3Cybb

    Plagl2

    Ddx60

    Adora2a

    Itga5Lilrb3

    Prdm1Cd80

    Gpd2

    Cmpk2

    Nod2

    EsdNol10

    Cd69

    Ifit1

    Irak2 Tnfaip2

    Traf2

    Gsr

    FasNfkbiz

    Ttpal

    Uchl1

    Pde4b

    Txnrd1

    Ccl9

    Bcl3

    Ptgir

    Oas1g

    Oas1a

    Sp100

    Ets2Parp12

    Rel

    Gadd45g

    Oas3

    Gbp3

    Grap

    Irgm1

    Prkar2b

    Ccl5

    Bcl2a1cPhf11b

    Procr

    Ptgs2

    Oasl1

    Tnip3

    Oas2

    Gadd45a

    C3

    Dhx58Agrn

    Skil

    Irg1

    Nfkbia

    Slc15a3Mmp9

    Mrc1

    Gtpbp2

    Nfkbie

    Slpi

    Tyk2

    Figure 3: PPI network of 210 differentially expressed mRNAs with 1842 interaction pairs. Blue dots and red dots indicate downregulated andupregulated mRNAs, respectively. Circle size indicates the node degree.

    Ifit1

    Ifit2

    Nos2Ifih1

    Ifi44SrcStat1

    Tnf

    RelaNfkb1

    Ccl2

    Nfkbia

    Irf9

    Irf8

    Irf7

    Oasl2

    Irf5

    Irf2

    Irf1

    Mx2

    Irf4Rsad2

    Ddx58Il1b

    Tlr3

    Usp18Myc

    Tlr2

    Cxcl10

    Ccl5Zbp1

    Il6

    Cd40 Jak2

    Oas2

    Isg15

    Oasl1

    Rel

    Figure 4: TF regulatory network of the top 30 hub genes in the PPI network. Green octagons represent TFs, and purple circles represent theircorrelated mRNAs.

  • 6 BioMed Research International

    Helz2

    Apol9a Gm13213

    Gbp5

    Ms4a7Gm21188

    Oas1a

    Gm14636

    Zbp1

    Epsti1

    Tlr3

    LOC100041903

    Ifi44

    D130040H23Rik

    Ifi205

    Usp18

    Myc

    Oas1g

    Gm7592

    Gm15433Ifitm3

    Sp100

    Oasl2

    Gm18853

    Cd302

    Gm17757

    Abcc5Procr

    Src

    Ifit1

    Prdx1Plxna1

    Clec4d

    H2-M2

    Ebi3

    Tm9sf4

    Mx2

    H2-Q4Gm38718

    Xaf1Slc11a2

    Ms4a6d

    Gm7609

    Ifit2Oas2

    Casp4

    Met

    Herc6Pilrb1

    Srxn1

    Itga5

    Sqrdl

    Ddx60Gdf15

    LOC102633783

    Mcoln2Irf1

    Eid3

    Phf11d

    Isg20

    Cd274Pirb

    Isg15

    Gm5424Tnfaip3

    Car13

    Gm3170

    Plk2

    H2-T23

    Gm4070

    Gm8979Irgm1

    Gm23514Gm8995

    Blvrb

    Rtp4 Stx11

    Gm8989Acp5

    Rnf213Slc22a4

    Ifih1Oas3

    Stat1

    Ddx58

    Ppt2

    Dhx58

    Gsap

    Slc15a3

    Susd6

    Parp14Adora2aAim1

    Clec4e

    Snora44 Tma16 Oasl1

    Rasa4Slamf7 Traf2

    Phf11b

    Gbp2Plpp1St5

    Gm25160

    AV051173

    Lrrc25Cfb

    Cmpk2

    Gbp7

    Gbp3

    Mir221Plpp3Nfkbie

    Cyb561a3

    C3Creb5

    Gclm

    Ddhd1

    Ms4a14Tnfrsf1b St3gal1Traf1

    Ccl5

    Fam20c

    Mapkbp1

    Aoah

    RhouGm6665

    Gm39969

    Ampd3 Bcl2a1a

    Ralgps1

    Ccl4

    Cd40

    Plagl2

    Irf7Slfn2Zcchc2

    Parp12

    Sqstm1

    Zc3h12a

    Trim12a

    Zscan29

    Cd52

    Tnip1

    Gtpbp2

    Gadd45g

    Mpeg1 Ehd1

    Slc2a6

    H2-T22

    Tnfaip2

    Figure 5: Coexpression network of 26 differentially expressed lncRNAs and 127 interacting differentially expressed mRNAs. The diamondswith blue represent lncRNAs; the circles with red represent their correlated mRNAs. Circle size indicates the node degree.

    showed that AV051173 was coexpressed with Prdx1, with itslocation next to the Prdx1 gene on the same chromosome.Notably, Prdx1 was upregulated in BV2 microglial cellsexposed to LPS. Prdx 1 regulated NF-𝜅B-mediated microglialactivation as an antioxidant [48]. AV051173might be involvedin microglia cell activation by cis-regulatory role in theexpression of Prdx1.

    In contrast to cis-regulating lncRNAs, trans-regulatinglncRNAs regulate gene expression far away from the siteof primary locus of transcription [49, 50]. Gm8979 andGm8989 are Gvin1 pseudogene, located on Chromosome 7.In the lncRNA-mRNA coexpression network, Gm8979 andGm8989 were significantly coexpressed with mRNAs (Stat1and Tlr3) via trans-acting mechanism. Stat1 and TLR3 playedan important regulatory role in BV2 cell activation [44, 51].Gm8979 and Gm8989 might be involved in microglial cellactivation by regulating the expression of Stat1 and Tlr3through a trans-acting mechanism.

    Despite the results obtained above, there were somelimitations in this study. Firstly, even with the similarity toprimary microglia, BV2 microglial cells contain oncogeneswhich render them different from primarymicroglia in someways, such as proliferation, adhesion, and the variance of

    morphologies. Secondary, the vitro model of microglia cellactivation has limitations because the condition is encom-passed bymultiple cell types and responses in vivo.Therefore,it needs to be considered with caution about the associationbetween the findings and the microglial cells activation ofneuropathic pain in vivo.

    5. Conclusions

    In conclusion, we downloaded raw data of GSE103156from the GEO data repository and identified differentiallyexpressed lncRNAs and DEGs in BV2 microglia cell acti-vation. The findings suggested that differentially expressedlncRNAs may regulate the expression of target genes actingas cis-acting or trans-acting factors. The findings may pro-vide relevant information for the development of promisingtargets for the microglial cells activation of neuropathic painin vivo in the future.

    Data Availability

    The data used to support the findings of this study areavailable from the corresponding author upon request.

  • BioMed Research International 7

    0

    8

    6

    4

    2Rela

    tive e

    xpre

    ssio

    n

    Gm8979

    Ctrl LP

    S0

    3

    2

    1

    Rela

    tive e

    xpre

    ssio

    n

    Gm8989

    Ctrl

    LPS

    0.0

    2.0

    1.5

    1.0

    0.5Rela

    tive e

    xpre

    ssio

    n

    AV051173

    Ctrl LP

    S

    0

    8

    6

    4

    2Relat

    ive e

    xpre

    ssio

    n

    6530402F18Rik

    Ctrl LP

    S

    Relat

    ive e

    xpre

    ssio

    nGm18853

    Ctrl LP

    S0

    20

    15

    10

    5Rel

    ativ

    e exp

    ress

    ion

    IL6

    Ctrl LP

    S

    ∗∗

    ∗∗∗

    0.0

    2.0

    1.5

    1.0

    0.5

    NS

    25∗∗

    Figure 6: Real-time PCR of five lncRNAs and IL6 mRNA in BV2 microglial cells exposed to LPS. All data are means ± SEM (n=3), Student’st-test. ∗ P < 0.05; ∗∗ P < 0.01; ∗ ∗ ∗ P < 0.001; NS, not significant.

    Conflicts of Interest

    The authors declare that there is no conflict of interestregarding the publication of this paper.

    References

    [1] A. I. Basbaum, D. M. Bautista, G. Scherrer, and D. Julius,“Cellular and molecular mechanisms of pain,” Cell, vol. 139, no.2, pp. 267–284, 2009.

    [2] G. Descalzi, D. Ikegami, T. Ushijima, E. J. Nestler, V. Zachariou,andM.Narita, “Epigeneticmechanisms of chronic pain,”Trendsin Neurosciences, vol. 38, no. 4, pp. 237–246, 2015.

    [3] L. Colloca, T. Ludman, D. Bouhassira et al., “Neuropathic pain,”Nature Reviews Disease Primers, vol. 3, Article ID 17002, 2017.

    [4] S. R. A. Alles and P. A. Smith, “Etiology and pharmacology ofneuropathic pain,” Pharmacological Reviews, vol. 70, no. 2, pp.315–347, 2018.

    [5] P. M. Grace, M. R. Hutchinson, S. F. Maier, and L. R. Watkins,“Pathological pain and the neuroimmune interface,” NatureReviews Immunology, vol. 14, no. 4, pp. 217–231, 2014.

    [6] K. Inoue andM.Tsuda, “Microglia in neuropathic pain: Cellularand molecular mechanisms and therapeutic potential,” NatureReviews Neuroscience, vol. 19, no. 3, pp. 138–152, 2018.

    [7] C. J. Woolf, “Central sensitization: implications for the diagno-sis and treatment of pain,” PAIN, vol. 152, no. 3, pp. S2–S15, 2011.

    [8] M. Calvo and D. L. H. Bennett, “Themechanisms of microglio-sis and pain following peripheral nerve injury,” ExperimentalNeurology, vol. 234, no. 2, pp. 271–282, 2012.

    [9] H. Jeong, Y.-J. Na, K. Lee et al., “High-resolution transcriptomeanalysis reveals neuropathic pain gene-expression signatures inspinal microglia after nerve injury,” PAIN, vol. 157, no. 4, pp.964–976, 2016.

    [10] F. Denk, M. Crow, A. Didangelos, D. M. Lopes, and S. B.McMahon, “Persistent alterations in microglial enhancers in amodel of chronic pain,”Cell Reports, vol. 15, no. 8, pp. 1771–1781,2016.

    [11] J. Peng, N. Gu, L. Zhou et al., “Microglia and monocytessynergistically promote the transition from acute to chronicpain after nerve injury,” Nature Communications, vol. 7, no. 1,Article ID 12029, 2016.

    [12] J. S. Mattick and I. V. Makunin, “Non-coding RNA,” HumanMolecular Genetics, vol. 15, no. Spec No 1, pp. R17–R29, 2006.

    [13] K. C. Wang and H. Y. Chang, “Molecular mechanisms of longnoncoding RNAs,” Molecular Cell, vol. 43, no. 6, pp. 904–914,2011.

    [14] Q. Yang, K. Yang, and A. Li, “microRNA-21 protects againstischemia-reperfusion and hypoxia-reperfusion-induced car-diocyte apoptosis via the phosphatase and tensin homolog/Akt-dependent mechanism,”Molecular Medicine Reports, vol. 9, no.6, pp. 2213–2220, 2014.

    [15] H. Li, Z. He, Y. Gu, L. Fang, and X. Lv, “Prioritization of non-coding disease-causing variants and long non-coding RNAs inliver cancer,”Oncology Letters, vol. 12, no. 5, pp. 3987–3994, 2016.

    [16] X. Zhao, Z. Tang, H. Zhang et al., “A long noncoding RNAcontributes to neuropathic pain by silencing Kcna2 in primaryafferent neurons,” Nature Neuroscience, vol. 16, no. 8, pp. 1024–1031, 2013.

  • 8 BioMed Research International

    [17] J. Zhou, Q. Xiong, H. Chen, C. Yang, and Y. Fan, “Identificationof the spinal expression profile of non-coding rnas involved inneuropathic pain following spared nerve injury by sequenceanalysis,” Frontiers in Molecular Neuroscience, vol. 10, p. 91, 2017.

    [18] R. Edgar, M. Domrachev, and A. E. Lash, “Gene ExpressionOmnibus: NCBI gene expression and hybridization array datarepository,” Nucleic Acids Research, vol. 30, no. 1, pp. 207–210,2002.

    [19] T. Barrett, S. E.Wilhite, P. Ledoux et al., “NCBIGEO: archive forfunctional genomics data sets—update,”Nucleic Acids Research,vol. 41, no. 1, pp. D991–D995, 2013.

    [20] D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Systematicand integrative analysis of large gene lists using DAVID bioin-formatics resources,” Nature Protocols, vol. 4, no. 1, pp. 44–57,2009.

    [21] M. Ashburner, C. A. Ball, J. A. Blake et al., “Gene ontology: toolfor the unification of biology,”Nature Genetics, vol. 25, no. 1, pp.25–29, 2000.

    [22] The Gene Ontology Consortium, “Expansion of the GeneOntology knowledgebase and resources,” Nucleic AcidsResearch, vol. 45, no. D1, pp. D331–D338, 2017.

    [23] M. Kanehisa and S. Goto, “KEGG: kyoto encyclopedia of genesand genomes,” Nucleic Acids Research, vol. 28, no. 1, pp. 27–30,2000.

    [24] D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Bioin-formatics enrichment tools: paths toward the comprehensivefunctional analysis of large gene lists,” Nucleic Acids Research,vol. 37, no. 1, pp. 1–13, 2009.

    [25] A. Franceschini, D. Szklarczyk, S. Frankild et al., “STRING v9.1:protein-protein interaction networks, with increased coverageand integration,”Nucleic Acids Research, vol. 41, no. 1, pp. D808–D815, 2013.

    [26] M. E. Smoot, K. Ono, J. Ruscheinski, P. L. Wang, and T. Ideker,“Cytoscape 2.8: new features for data integration and networkvisualization,” Bioinformatics, vol. 27, no. 3, pp. 431-432, 2011.

    [27] W. P. Bandettini, P. Kellman, C. Mancini et al., “MultiContrastDelayed Enhancement (MCODE) improves detection of suben-docardial myocardial infarction by late gadolinium enhance-ment cardiovascular magnetic resonance: a clinical validationstudy,” Journal of Cardiovascular Magnetic Resonance, vol. 14,no. 1, article no. 83, 2012.

    [28] Y. Tang, M. Li, J. Wang, Y. Pan, and F.-X. Wu, “CytoNCA:a cytoscape plugin for centrality analysis and evaluation ofprotein interaction networks,” BioSystems, vol. 127, pp. 67–72,2015.

    [29] R. Janky, A. Verfaillie, H. Imrichová et al., “iRegulon: from agene list to a gene regulatory network using large motif andtrack collections,” PLoS Computational Biology, vol. 10, no. 7,Article ID e1003731, 2014.

    [30] P. Langfelder and S. Horvath, “WGCNA: an R package forweighted correlation network analysis,” BMC Bioinformatics,vol. 9, article no. 559, 2008.

    [31] S. Wu, J. Bono, and Y. Tao, “Long noncoding RNA (lncRNA):a target in neuropathic pain,” Expert Opinion on �erapeuticTargets, vol. 23, no. 1, pp. 15–20, 2019.

    [32] Y. He, X. Yao, N. Taylor, Y. Bai, T. Lovenberg, and A. Bhat-tacharya, “RNA sequencing analysis reveals quiescentmicrogliaisolation methods from postnatal mouse brains and limitationsof BV2 cells,” Journal of Neuroinflammation, vol. 15, no. 1, p. 153,2018.

    [33] A. Henn, S. Lund, M. Hedtjärn, A. Schrattenholz, P. Pörzgen,and M. Leist, “The suitability of BV2 cells as alternativemodel system for primary microglia cultures or for animalexperiments examining brain inflammation,” ALTEX, vol. 26,no. 2, pp. 83–94, 2009.

    [34] J. Guedes, A. L. C. Cardoso, and M. C. Pedroso de Lima,“Involvement of microRNA in microglia-mediated immuneresponse,” Clinical and Developmental Immunology, vol. 2013,Article ID 186872, 11 pages, 2013.

    [35] R. Ji, T. Berta, and M. Nedergaard, “Glia and pain: is chronicpain a gliopathy?” PAIN, vol. 154, supplement 1, pp. S10–S28,2013.

    [36] M. J. Lacagnina, L. R. Watkins, and P. M. Grace, “Toll-likereceptors and their role in persistent pain,” Pharmacology &�erapeutics, vol. 184, pp. 145–158, 2018.

    [37] K. Kierdorf, D. Erny, T. Goldmann et al., “Microglia emergefrom erythromyeloid precursors via Pu.1-and Irf8-dependentpathways,”Nature Neuroscience, vol. 16, no. 3, pp. 273–280, 2013.

    [38] T. Masuda, M. Tsuda, R. Yoshinaga et al., “IRF8 is a criticaltranscription factor for transforming microglia into a reactivephenotype,” Cell Reports, vol. 1, no. 4, pp. 334–340, 2012.

    [39] M.Horiuchi, K.Wakayama, A. Itoh et al., “Interferon regulatoryfactor 8/interferon consensus sequence binding protein is acritical transcription factor for the physiological phenotype ofmicroglia,” Journal of Neuroinflammation, vol. 9, p. 227, 2012.

    [40] T.Masuda, S. Iwamoto, R. Yoshinaga et al., “Transcription factorIRF5 drives P2X4R+-reactive microglia gating neuropathicpain,” Nature Communications, vol. 5, article 3771, 2014.

    [41] T. Akagi, Y. Matsumura, M. Yasui et al., “Interferon regulatoryfactor 8 expressed in microglia contributes to tactile allodyniainduced by repeated cold stress in rodents,” Journal of Pharma-cological Sciences, vol. 126, no. 2, pp. 172–176, 2014.

    [42] T. Masuda, S. Iwamoto, S. Mikuriya et al., “Transcription factorIRF1 is responsible for IRF8-mediated IL-1𝛽 expression inreactivemicroglia,” Journal of Pharmacological Sciences, vol. 128,no. 4, pp. 216–220, 2015.

    [43] T. Tanaka, K. Murakami, Y. Bando, and S. Yoshida, “Interferonregulatory factor 7 participates in the M1-like microglial polar-ization switch,” Glia, vol. 63, no. 4, pp. 595–610, 2015.

    [44] I. R. Holtman, D. Skola, and C. K. Glass, “Transcriptionalcontrol of microglia phenotypes in health and disease,” �eJournal of Clinical Investigation, vol. 127, no. 9, pp. 3220–3229,2017.

    [45] D. Bhatt and S. Ghosh, “Regulation of theNF-kappaB-mediatedtranscription of inflammatory genes,” Front Immunol, vol. 5, p.71, 2014.

    [46] R. Von Bernhardi, J. E. Tichauer, and J. Eugenı́n, “Aging-dependent changes of microglial cells and their relevance forneurodegenerative disorders,” Journal of Neurochemistry, vol.112, no. 5, pp. 1099–1114, 2010.

    [47] J. S. Morey, J. C. Ryan, and F. M. Van Dolah, “Microarray vali-dation: factors influencing correlation between oligonucleotidemicroarrays and real-time PCR,” Biological Procedures Online,vol. 8, no. 1, pp. 175–193, 2006.

    [48] S. Kim, Y. Park, J. Min et al., “Peroxiredoxin I is a ROS/p38MAPK-dependent inducible antioxidant that regulates NF-𝜅B-mediated iNOS induction and microglial activation,” Journal ofNeuroimmunology, vol. 259, no. 1-2, pp. 26–36, 2013.

    [49] C. P. Ponting, P. L. Oliver, andW.Reik, “Evolution and functionsof longnoncodingRNAs,”Cell, vol. 136, no. 4, pp. 629–641, 2009.

  • BioMed Research International 9

    [50] T. R. Mercer, M. E. Dinger, and J. S. Mattick, “Long non-codingRNAs: insights into functions,”Nature Reviews Genetics, vol. 10,no. 3, pp. 155–159, 2009.

    [51] J. A. Stokes, J. Cheung, K. Eddinger, M. Corr, and T. L. Yaksh,“Toll-like receptor signaling adapter proteins govern spread ofneuropathic pain and recovery following nerve injury in malemice,” Journal of Neuroinflammation, vol. 10, p. 148, 2013.

  • Hindawiwww.hindawi.com

    International Journal of

    Volume 2018

    Zoology

    Hindawiwww.hindawi.com Volume 2018

    Anatomy Research International

    PeptidesInternational Journal of

    Hindawiwww.hindawi.com Volume 2018

    Hindawiwww.hindawi.com Volume 2018

    Journal of Parasitology Research

    GenomicsInternational Journal of

    Hindawiwww.hindawi.com Volume 2018

    Hindawi Publishing Corporation http://www.hindawi.com Volume 2013Hindawiwww.hindawi.com

    The Scientific World Journal

    Volume 2018

    Hindawiwww.hindawi.com Volume 2018

    BioinformaticsAdvances in

    Marine BiologyJournal of

    Hindawiwww.hindawi.com Volume 2018

    Hindawiwww.hindawi.com Volume 2018

    Neuroscience Journal

    Hindawiwww.hindawi.com Volume 2018

    BioMed Research International

    Cell BiologyInternational Journal of

    Hindawiwww.hindawi.com Volume 2018

    Hindawiwww.hindawi.com Volume 2018

    Biochemistry Research International

    ArchaeaHindawiwww.hindawi.com Volume 2018

    Hindawiwww.hindawi.com Volume 2018

    Genetics Research International

    Hindawiwww.hindawi.com Volume 2018

    Advances in

    Virolog y Stem Cells InternationalHindawiwww.hindawi.com Volume 2018

    Hindawiwww.hindawi.com Volume 2018

    Enzyme Research

    Hindawiwww.hindawi.com Volume 2018

    International Journal of

    MicrobiologyHindawiwww.hindawi.com

    Nucleic AcidsJournal of

    Volume 2018

    Submit your manuscripts atwww.hindawi.com

    https://www.hindawi.com/journals/ijz/https://www.hindawi.com/journals/ari/https://www.hindawi.com/journals/ijpep/https://www.hindawi.com/journals/jpr/https://www.hindawi.com/journals/ijg/https://www.hindawi.com/journals/tswj/https://www.hindawi.com/journals/abi/https://www.hindawi.com/journals/jmb/https://www.hindawi.com/journals/neuroscience/https://www.hindawi.com/journals/bmri/https://www.hindawi.com/journals/ijcb/https://www.hindawi.com/journals/bri/https://www.hindawi.com/journals/archaea/https://www.hindawi.com/journals/gri/https://www.hindawi.com/journals/av/https://www.hindawi.com/journals/sci/https://www.hindawi.com/journals/er/https://www.hindawi.com/journals/ijmicro/https://www.hindawi.com/journals/jna/https://www.hindawi.com/https://www.hindawi.com/