Identification of HIV-1-specific cascaded microRNA-mRNA regulatory relationships by parallel mRNA and microRNA expression profiling with AIDS patients after antiviral treatment

BACKGROUND: The pathogenesis of human immunodeficiency virus 1 (HIV-1) infection is so complex that have not been clearly defined, despite intensive efforts have been made by many researchers. MicroRNA (miRNA) as regulation factor in various human diseases may influence the course of HIV-1 infection by targeting mRNAs. Thus, studies combining transcription of posttranscriptional miRNA regulation are required. METHODS: With the purpose of identifying cascaded miRNA-mRNA regulatory relationships related to HIV infection in gene level, the parallel miRNA, and mRNA expression profiles were analyzed to select differential expressed miRNAs and mRNAs. Then, miRNA-mRNA interactions were predicted using 3 data sources and Pearson correlation coefficient was calculated based on the gene expression level for accuracy improvement. Furthermore, the calculation of the regulatory impact factors was conducted to reveal crucial regulators in HIV-1 infection. To give further insight into these transcription factor (TF) regulators, the differentially co-expression analysis was conducted to identify differentially co-expressed links and differential co-expressed genes and the co-expression gene modules were identified using a threshold-based hierarchical clustering method, then modules were combined into a miRNA-TF-mRNA network. RESULTS: A total of 69,126 differentially co-expressed links and 626 differential co-expressed genes were identified. Functional enrichment analysis indicated that these co-expressed genes were significantly involved in immune response and apoptosis. Moreover, according to regulatory impact factors, 5 most influential TFs and miRNA in HIV-1 infection were identified and miRNA-TF-mRNA regulatory networks were built during the computing process. CONCLUSIONS: In our study, a set of integrated methods was generated to identify important regulators and miRNA-TF-mRNA interactions. Parallel profiling analysis of the miRNAs and mRNAs expression of HIV/acquired immunodeficiency syndrome (AIDS) patients after antiretroviral therapy indicated that some regulators have wide impact on gene regulation and that these regulatory elements may bear significant implications on the underlying molecular mechanism and pathogenesis of AIDS occurrence.