The Long Non-coding RNA Regulatory Mechanism To Early-onset Schizophrenia Based On The Co-expression Network Analysis

Objective:Schizophrenia is a common and severity mental illness whose pathogenesis remains unknown. Early-onset schizophrenia is one of important clinical subtypes of schizophrenia, with worse prognosis and higher incidence of adverse outcomes. Long non-coding RNA(Lnc RNA) is a kind of non-coding more than 200 nucleotides, with no or few protein-coding function and can participate in gene expression regulation in many ways, but the functions of lnc RNAs and their impacts on the disease is still not clear.Studies towards the lnc RNAs regulatory mechanism could elucidate the pathogenesis of schizophrenia. With the rapid development of microarray technology, it is now possible to high-throughput detect the lnc RNA, but the traditional differential expression analysis based on single gene level could no more satisfy the needs of research which accordingly propose the new challenge to data analysis strategy. Based on the system level, our research intend to explore the lnc RNAs expression changes in patients with early-onset schizophrenia, and to illustrate functions of related lnc RNAs on the basis of the m RNAs expression alteration in patients with early onset schizophrenia and their functional annotation.Methods:We collected 19 patients with early onset schizophrenia and 18 age and gender matched typically developed controls, and detected the lnc RNA and m RNAs expression levels in peripheral blood using the lnc RNA microarray. Based on the genetic statisticsand bioinformatics methods of Differentially Expressed Analysis, Weighted Gene Co-Expression Network Analysis(WGCNA), Canonical Correlation Analysis(CCA) and functional enrichment analysis, we carried out a comprehensive analysis.Results:(1) We carried out the differential expression analysis and screened the differentially expressed lnc RNAs and m RNAs. The results showed that compared with typically developed controls, 3416 lnc RNAs were differential expressed in patients with early-onset schizophrenia, with 1153 upregulated and 2263 downregulated. We also found a total of 3684 m RNAs were differential expressed in patients with early-onset schizophrenia, with 2778 upregulated and 906 downregulated. Our study revealed lnc RNAs expression alteration in early onset schizophrenia patients for the first time.(2) Using the differentially expressed lnc RNAs and m RNAs, we carried out the WGCNA to construct the lnc RNAs and m RNAs expression networks, respectively.Networks were constructed in two different ways: first, we constructed one network from control data and one network from case data, then identified modules in the control network and tested the preservation in case network. The results showed there were no global differences between two groups which indicated that the case modules had no obvious perturbations relative to the control group. Second, we constructed a network from the combined case and control data and identified modules within it. Nine lnc RNAs modules were constructed and module eigengenes were calculated subsequently. Using the correlation and regression analysis, we finally got two diseased related lnc RNAs Module(lnc RNAs Module Blue, lnc RNAs Module Brown) and identified six hub lnc RNAs in module Blue and 20 hub lnc RNAs in Module Brown. Next, we used to same way to identify 13 m RNAs modules, and three of which were related to schizophrenia(m RNAs Module Turquoise, m RNAs Module Brown, m RNAs Module Greenyellow), each module had two hub m RNAs with high connectivity. The functional enrichment analysis showed that diseased-related m RNAs were highly enriched for mitochondrion and related biological processes.(3) We detected the correlation between the hub lnc RNAs and hub m RNAs using the canonical correlation analysis(CCA). We identified 6 canonical correlatd variables totally, and the first, second and third canonical correlatd variables showed a cumulative contribution rate of 98.39%. Our findings showed that lnc RNAs were highly correlated with m RNAs in expression levels, which suggesting the similarity of their functions. The EOS associated lnc RNAs were associated with mitochondrion and related biological processes. Our study could provide evidence for the lnc RNAs may regulate specific m RNAs to induce the mitochondria dysfunction, which is involved in the pathophysiological process of schizophrenia.Conclusions:Two lnc RNAs coexpression modules were associated with Early-onset schizophrenia. Three m RNAs coexpression modules were associated with Early-onset schizophrenia, and the functions of which were significantly enriched in the mitochondria and related biological process.The hub lnc RNAs of Early-onset schizophrenia were significantly correlated with hub m RNAs. The Early onset schizophrenia related lnc RNAs function may be associated with mitochondrial and related biological process. Our research could provide evidences for the hypothesis of“The lnc RNAs could mediate m RNAs to cause the mitochondrial dysfunction which is involved in the pathogenesis of schizophrenia”. Our research suggested that the integrated research strategies(Differentially Expressed Analysis- Weighted Gene Co-Expression Network Analysis- Canonical Correlation Analysis) could effectively reveal the transcriptome change in Early-onset schizophrenia.