Int J Hum Genet, 18(2): 188-200 (2018) © Kamla-Raj 2018 DOI: 10.31901/24566330.2018/18.2.702 The Identification of Sub-pathways in Juvenile Idiopathic Arthritis by Integrating Expression Profiles between lncRNA-mRNA and Pathway Topologies Wen-Hua Wang1, Bin Wang2, Jian Song1, Hai-Yue Yu1, Tao Wu1 and Rong-Bin Li1* 1Department of Rheumatism, The First Hospital of Qiqihar, Qiqihar 161005, China 2Department of Emergency, The First Hospital of Qiqihar, Qiqihar 161005, China KEYWORDS Functional Role. Biomarker. Bioinformatics. Interactions. Networks ABSTRACT Juvenile Idiopathic Arthritis (JIA) is a systemic disorder with autoimmune chronic joint inflammation. The pathogenic mechanisms of JIA are still unclear. It has been reported that lncRNA can regulate the mRNA by competitively binding to miRNAs. Analysis of pathway underlying certain disease is a valuable strategy for exploring the functional roles of these transcripts. Therefore, identification of competitively regulated subpathways can not only contribute to understand the occurrence and development of diseases, but also further help to gain the functional roles of lncRNAs. In this work, an effective method was proposed to identify the subpathways that competitively regulated by lncRNAs in JIA, which integrated the lncRNA-mRNA expression profile and pathway topologies. Eventually, based on the expression profile of JIA, 38 subpathways involved in 31 complete pathways were confirmed. Some key lncRNAs associated with JIA may be detected by identification of lncRNA competitively regulated subpathways. INTRODUCTION NAs can share identical miRNA binding sites with mRNAs to competitively regulate the ex- Juvenile Idiopathic Arthritis (JIA) and Rheu- pression levels of mRNAs, which is a signifi- matoid Arthritis (RA) are systemic disorders, cant universal layer of RNA regulation (Wang et characterized by autoimmune chronic joint in- al. 2016; Wang et al. 2015). Interestingly, a new flammation, and have some similar clinical and regulatory circuitry identified by Lin et al. (2016) pathological features, such as an intense pro- revealed that large intergenic non-coding RNAs inflammatory response to joints and tissue de- (lincRNAs) can act as a competing endogenous struction (Kobus et al. 2016; Wang et al. 2017). It RNA (ceRNA) to regulate the concentration and has been reported that the occurrence of JIA is a biological functions of miRNAs, since such ceR- complex genetic trait affected by multiple genes NAs can mediate the expression levels of miR- that associated with immunity and inflammation NA molecules on their targets, and thereby caus- (Hinks et al. 2017). However, up till now, the ing a supplemental level of post-transcriptional pathogenic mechanisms of JIA are still unclear. regulation was imposed. Fu et al. (2017) found Therefore, identifying the function of genes in that lincRNA-RoR can act as a competing en- JIA is useful to understand effectively the oc- dogenous RNA (ceRNA) to regulate several tu- currence and development of JIA. mor inhibitor miRNAs. The proliferative and in- Long non-coding RNA (lncRNA) is a heter- vasive abilities of cells in pancreatic ductal ade- ogeneous class of ncRNA which plays an im- nocarcinoma can be inhibited by lincRNA-RoR. portant role in the occurrence and progression Additionally, it has been proposed by Sumazin of diseases by regulating various biological func- et al. (2011) that the oncogenic pathways in glio- tions (Pradeepa et al. 2017; Sun et al. 2017). A blastoma can be regulated by the competing in- large number of reports demonstrated that lncR- teraction networks between RNA-RNA. Since the mechanisms by which lncRNAs impact the *Address for correspondence: activation of aberrant pathway associated with Rong-Bin Li diseases are not fully understood, and the com- Department of Rheumatism, petitive interaction of RNA can affect signifi- The First Hospital of Qiqihar, cant functions of disease, thus the identifica- 30 Park Road, Longsha District, Qiqihar 161005, Heilongjiang Province, China tion of lncRNA competitive regulatory pathways E-mail: [email protected] not only can insight into the potential mecha- SUB-PATHWAYS IDENTIFICATION AND LNCRNA-MRNA INTERACTIONS 189 nism and also contribute to investigate the func- itively regulated signaling subpathway of lncR- tional roles of lncRNAs in disease. NAs under certain conditions. In this process, Although it has been demonstrated that the the researchers integrated transcriptional expres- competitive regulatory function of lncRNAs sion, lncRNAs- mRNAs association network and plays an important role in the occurrence and pathway topologies to identify the subpathway development of diseases. However, very few of lncRNAs competitive regulatory and predict methods are provided to systematically predict the function of lncRNAs in disease states. aberrant pathways competitively regulated by lncRNAs in disease. Recently, several methods MATERIAL AND METHODS are proposed to explore the functional roles of lncRNAs in diseases (Wang et al. 2017). For ex- Juvenile Idiopathic Arthritis Datasets ample, Cabili et al. (2011) used chromatin-state maps to identify putative functions of numer- In this work, datasets associated with JIA ous lincRNA. He et al. (2017) developed a lncR- were obtained from ArrayExpress (https:// NA-protein coding gene co-expression network www.ebi.ac.uk/arrayexpress/experiments/E- and applied it to predict the functions of lncR- GEOD-26554/) that is recognized database of NAs. Although the methods that have been pro- microarray gene expression data. The expres- posed are significant in identification of lncR- sion data of JIA that were analyzed in this paper NAs functions and regulation, the functional from a genome-wide association study (GWAS), roles of lncRNAs that contribute to disease which was constructed by 814 Caucasian JIA states cannot be investigated by these meth- cases and 3058 Caucasian controls. In this study, ods. Additionally, most of these methods can expression sets of 91 samples were selected for identify functions only for a single lncRNA. further analysis, including 23 healthy samples Since the occurrence and progression of the dis- (control group) and 68 JIA samples (disease ease are hardly determined by a single factor group). Consequently, after pretreatment, expres- alone, it is more informative for the evaluation of sion profile data of 20514 genes were detected lncRNAs functions by identifying sets of risk by mapping between the genes and the probes. lncRNAs. Some studies have reported that the different, but related pathways under different Obtaining the Interaction Data between situations may be collectively affected by multi- lncRNA-mRNA ple risk-associated lncRNAs. Therefore, novel detection strategies and methods are required Firstly, the interaction data of lncRNA-miR- for analyzing the function of lncRNAs. Some NA were extracted from starBase v2.0 whereas studies have shown that abnormalities of lncR- the TarBase, mirTarBase, mir2Disease and mi- NAs in “subpathway regions” play a crucial role Records (V4.0) tools were used to collect the in etiology of disease (Xu et al. 2017; Zhang et experimentally validated mRNA-miRNA interac- al. 2017), and the destabilization of signaling tions. Because miRNA was shared by lncRNA pathways that contribute to human disease may and mRNA, thereby the researchers could con- be caused not only by dysfunctional nodes, but struct a competing triplet related to lncRNA (ln- also by the interactions of dysfunctional molec- cRNA-miRNA-mRNA relationships), and then ular outside of those nodes (Sun and Zhang obtained candidate competitively regulated re- 2017). lationship between lncRNA-mRNA. To ensure the reliability of the data, in the screening pro- Objectives cess of lncRNA-mRNA competitively regulated relationship, the following two criteria should A possible inference is that dysregulation of be satisfied; (i) The hypergeometric test was lncRNAs may affect the development of disease used to evaluate the enrichment significance of by regulating subpathway regions. And found- the shared miRNAs that were interacted with ing subpathway regions related to dysregulat- lncRNA and mRNA, and PDR correction was ed lncRNAs may contribute to explore the mech- performed for the obtained p values, eventually, anisms by which lncRNAs act on disease states. screened out lncRNA-mRNA interactions that In this work, an effective computational tech- have p values less than 0.05 after adjustment; nique was proposed for evaluating the compet- (ii) Ranking of Jaccard coefficient of lncRNA- 190 WEN-HUA WANG, BIN WANG, JIAN SONG ET AL. mRNA intersections at top twenty percent was new networks that retained the original path- selected. Based on lncRNA and mRNA shared way topologies. Based on Fisher’s Z transfor- miRNAs, the hypergeometric test formula used mation, the pathways of gene enrichment in in this paper was as follows: mRNAs expression profile were identified. Then ⎛n⎞⎛ N − K ⎞ ⎜ ⎟⎜ ⎟ the pathways with p value less than 0.01 after m ⎜k ⎟⎜ M − K ⎟ P =1− ∑ ⎝ ⎠⎝ ⎠ correction were selected, and were called candi- k =0 ⎛ N ⎞ (1) ⎜ ⎟ date differential pathways. ⎝ M ⎠ Where N represents all of miRNAs interact- Embedding lncRNAs Pathways ing with lncRNA or mRNA, M represents the number of miRNAs interacting with the given mRNAs, n represents the number of miRNAs Based on the obtained LncGenePairs results, interacting with the given mRNA, m represents these lncRNAs were inset into candidate differ- the total number of