In this study, we compared the expression profiles of lncRNAs before and after AIDS treatment and further analyzed their potential function. A total of 974 lncRNAs and 619 associated genes, whose expression levels became abnormal after HIV infection and restored to normal after treatment, were identified. We believe that these lncRNAs, along with their associated genes, may have a potential impact on HIV replication.
LncRNAs have many functions in vivo, participating in the epigenetic, transcriptional, posttranscriptional, and translational regulation of genes and acting as vectors in biological processes. Studies have found that the expression or functional abnormalities of lncRNAs are closely related to the occurrence of human diseases, including cancer[23, 24], neurodegenerative diseases and diabetes. LncRNAs also play an important role in viral infection, and some studies have shown that lncRNAs are involved in the regulation of many biological processes during HIV infection. RNA-seq is a quantitative and extremely sensitive technique for genome-wide transcriptome analysis based on sequencing. This technique and its derivative methods have been widely used to identify potential lncRNAs in several species. In this study, we analyzed the expression changes of lncRNAs in PBMCs of healthy people and HIV-infected patients before and after HAART treatment by RNA-seq.
Many genes showed significant abnormal expression patterns during HIV infection, and some of these genes were restored to normal expression after treatment. The upregulated genes were enriched in immune/inflammatory processes, while the downregulated genes were enriched in cell-cell/cell-matrix processes. Although the expression of inflammation-related genes decreased after treatment, there was still widespread inflammation in the infected patients. The expression levels of genes in cell-cell/cell-matrix processes decreased after treatment, which may be related to the persistence of the consequences of HIV-1 infection.
The PCA clustering results of identified lncRNAs showed significant expression differences during HIV infection and treatment. We found that a total of 974 abnormally expressed lncRNAs (268 upregulated lncRNAs and 706 downregulated lncRNAs) were restored to normal expression levels after treatment. Homeopathic regulation target gene analysis of the lncRNAs showed that RP11–685M7.3, AC002550.5, RP 11–290F5.1, RP 11–96D1.3, RP 5–1057120.4, and RP 11–972P1.10 have cis-regulation target genes. These lncRNAs may have a potential role in HIV infection and pathogenesis. For example, interferon regulatory factor 2 (IRF2), a cis-regulatory target gene of lncRNA RP 11–290F5.1, has been reported to be associated with HIV infection. As the most representative members of the IRF family, IRF1 and IRF2 can be involved in a variety of biological processes, including inflammation, immune response, cell proliferation, and differentiation. Previous studies have shown that a sequence homologous to ISRE, which is the binding site of IRF1 and IRF2, is in the 5' LTR downstream of HIV-1. Deletion of the LTR-ISRE sequence leads to impaired LTR promoter activity and decreased synthesis of viral RNA and proteins. In the absence of viral transactivator (Tat), IRF2 can bind to the LTR-ISRE sequence and drive LTR transcription. The IRF2 gene is a cis-regulatory target of lncRNA RP11–290F5.1, suggesting that this lncRNA may play a regulatory role in the process of HIV-1 infection.
By coexpression analysis of differentially expressed lncRNAs and genes, transregulatory targets of lncRNAs were identified. The results indicated that the target genes participate in multiple biological processes, including the immune inflammatory response, angiogenesis, cell proliferation, and mitotic cell cycle, and these genes could be involved in the complications caused by HIV-1 infection[32–35]. For example, IL-1α, IL-10, CCL2, LMNA and VCAM1, the target genes identified in this study, have been reported to be associated with HIV-1 infection and pathogenesis[36–38]. It is worthwhile to further explore the regulatory relationship between the lncRNAs and their target genes identified in this study. The lncRNA CTB-119C2.1, with the most significant differential expression pattern and the most coexpression-associated genes, was selected for qRT–PCR verification. Its qRT–PCR results were consistent with those of RNA-sEq. The results indicated that the abnormally downregulated expression level of lncRNA CTB-119C2.1 during HIV infection increased after treatment. The following coexpression analysis showed that its associated genes were mainly involved in the p53 pathway and the signaling pathways responsible for the cell cycle and DNA replication, suggesting that lncRNA CTB-119C2.1 may play an important role during HIV infection and treatment. The detailed mechanism needs to be clarified in further studies[39–41].
There are also some limitations in this study. First, only total PBMCs were investigated in this study, and further studies are needed to clarify the role of lncRNAs in specific cell types. Second, although the regulatory network of lncRNA-related genes has been obtained, more experiments are still needed to confirm the results. Third, the number of patients investigated in this study may be small, and more samples should be included in the future to confirm the universality of the results.