HIV-1 Nef-induced lncRNA AK006025 regulates CXCL9/10/11 cluster gene expression in astrocytes through interaction with CBP/P300

Abstract

BackgroundHIV-associated neurocognitive disorder (HAND) is a neurodegenerative disease associated with persistent neuroinflammation and subsequent neuron damage. Pro-inflammatory factors and neurotoxins from activated astrocytes by HIV-1 itself and its encoded proteins, including the negative factor (Nef), are involved in the pathogenesis of HAND. This study was designed to find potential lncRNAs that regulate astrocyte functions and inflammation process.MethodsWe performed microarray analysis of lncRNAs from primary mouse astrocytes treated with Nef protein. Top ten lncRNAs were validated through real-time PCR analysis. Gene ontology (GO) and KEGG pathway analysis were applied to explore the potential functions of lncRNAs. RIP and ChIP assays were performed to demonstrate the mechanism of lncRNA regulating gene expression.ResultsThere were 638 co-upregulated lncRNAs and 372 co-downregulated lncRNAs in primary astrocytes treated with Nef protein for both 6 h and 12 h. GO and KEGG pathway analysis showed that the biological functions of top differential-expressed mRNAs were associated with inflammatory cytokines and chemokine. Knockdown of lncRNA AK006025, not AK138360, inhibited significantly CXCL9, CXCL10 (IP-10), and CXCL11 expression in astrocytes treated with Nef protein. Mechanism study showed that AK006025 associated with CBP/P300 was enriched in the promoter of CXCL9, CXCL10, and CXCL11 genes.ConclusionsOur findings uncovered the expression profiles of lncRNAs and mRNAs in vitro, which might help to understand the pathways that regulate astrocyte activation during the process of HAND.Electronic supplementary materialThe online version of this article (10.1186/s12974-018-1343-x) contains supplementary material, which is available to authorized users.

Long Non-coding RNAs Mechanisms of Action in HIV-1 Modulation and the Identification of Novel Therapeutic Targets

“…Further, they suggested that these effects occurred through an lncRNA-protein interaction with the transcription factor CREB (cAMP response element-binding protein) binding protein (CBP/P300) and the nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) p65 isoform. This association/and or interaction of AK006025 with CBP/P300 and NFκB p65, resulted in an enrichment of CBP/P300 and NFκB p65, as well as an increase in acetylation (H3K27ac), a marker for an active promoter, at the promoter sites of CXCL9, CXCL10, and CXCL11 genes [82]. However, the authors did not elucidate the full mechanism of this lncRNA.…”

“…However, due to the poor conservation of lncRNAs between species, it would be beneficial to determine the effect in human astrocytes. Nevertheless, the paper demonstrates the effects of HIV-1 accessory proteins, such as Nef [82] on the non-coding transcriptome, and how this could contribute towards secondary disease outcomes associated with HIV-1 disease progression.…”

“…The authors identified two lncRNAs in modulating smooth muscle cell proliferation (ncRNA ENST00000495536 associated the HOXB13 gene expression and lncRNA ENST00000585387, a ceRNA for miRNAs, miR-491 and miR-185) [46] and found that, when these lncRNAs were silenced using siRNA, the effects of cocaine and Tat treatment on cell proliferation were lost, suggesting that these lncRNAs may play a role in the development of PAH in HIV-1-positive individuals [46]. Zhou et al (2018) investigated the role of acute exposure of the viral protein Nef in regulating lncRNAs in mouse astrocytes, as a proxy to the development of HIV-1-associated neurological disorder (HAND) [82]. HAND is associated with persistent inflammation in the brain.…”

“…In particular, the authors were able to screen lncRNAs for their relevancy in their bioinformatic approaches. This aided in the identification of lncRNAs with the most pronounced effects in their disease models [46,82]. Further, Chinnappan et al (2018) identified lncRNAs with potential direct effects on their mRNA targets, by screening for lncRNA-mRNA and lncRNA-mRNA-miRNA associations [46].…”

Current approaches for RNA-labelling to identify RNA-binding proteins

“…Although these RBPs have been known to play important cellular roles by interacting with mRNAs (Gerstberger et al 2014;Dixit and Lukeš 2018;Moore and von Lindern 2018), recent work has demonstrated the importance of RBPs and their interactions with various types of noncoding RNA such as microRNAs, small nucleolar RNAs, long-noncoding RNA, piRNA, and viral RNA (Bagni and Lapeyre 1998;Jiang and Coller 2012;Ciafrè and Galardi 2013;Falaleeva et al 2016;Zealy et al 2017;Grzechnik et al 2018;Lei et al 2018;Tedeschi et al 2018;Baou et al 2011;Zhou et al 2018;Qiao et al 2019;Yang et al 2019). The formation of RNP complexes acts to regulate essential cellular functions from cell division to cell death, transcription to post-translational gene regulation, and downstream functions (Clayton and Shapira 2007;Glisovic et al 2008;Kishore et al 2010;Brinegar and Cooper 2016).…”