Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-Infected Brain: Novel Analysis of Retrospective Cases

Abstract

HIV infection disturbs the central nervous system (CNS) through inflammation and glial activation. Evidence suggests roles for microRNA (miRNA) in host defense and neuronal homeostasis, though little is known about miRNAs' role in HIV CNS infection. MiRNAs are non-coding RNAs that regulate gene translation through post-transcriptional mechanisms. Messenger-RNA profiling alone is insufficient to elucidate the dynamic dance of molecular expression of the genome. We sought to clarify RNA alterations in the frontal cortex (FC) of HIV-infected individuals and those concurrently infected and diagnosed with major depressive disorder (MDD). This report is the first published study of large-scale miRNA profiling from human HIV-infected FC. The goals of this study were to: 1. Identify changes in miRNA expression that occurred in the frontal cortex (FC) of HIV individuals, 2. Determine whether miRNA expression profiles of the FC could differentiate HIV from HIV/MDD, and 3. Adapt a method to meaningfully integrate gene expression data and miRNA expression data in clinical samples. We isolated RNA from the FC (n = 3) of three separate groups (uninfected controls, HIV, and HIV/MDD) and then pooled the RNA within each group for use in large-scale miRNA profiling. RNA from HIV and HIV/MDD patients (n = 4 per group) were also used for non-pooled mRNA analysis on Affymetrix U133 Plus 2.0 arrays. We then utilized a method for integrating the two datasets in a Target Bias Analysis. We found miRNAs of three types: A) Those with many dysregulated mRNA targets of less stringent statistical significance, B) Fewer dysregulated target-genes of highly stringent statistical significance, and C) unclear bias. In HIV/MDD, more miRNAs were downregulated than in HIV alone. Specific miRNA families at targeted chromosomal loci were dysregulated. The dysregulated miRNAs clustered on Chromosomes 14, 17, 19, and X. A small subset of dysregulated genes had many 3′ untranslated region (3′UTR) target-sites for dysregulated miRNAs. We provide evidence that certain miRNAs serve as key elements in gene regulatory networks in HIV-infected FC and may be implicated in neurobehavioral disorder. Finally, our data indicates that some genes may serve as hubs of miRNA activity.

Editorial NeuroAIDS review

“…Additional factors that may require attention include HAART resistance mutations, the particular mutational profile of the peripheral and CSF viruses that may influence HIV-1 neurovirulence, epigenetic mechanisms, and micro-(mi-) RNA expression. Factors including elevated plasma lipo-polysaccharide (LPS) as well as co-infections including HCV may be important in groups such as injection drug and alcohol abusers [91–96]. …”

“…In human astrocyte cultures, activation of indoleamine-2,3-dioxygenase (IDO) results in elevation of tryptophan catabolism and the production of neurotoxins including kynurenine due to Tat protein for HIV-1B and not C. The authors conclude from the latter experiment that the prevalence of HAD may correlate with epidemiological differences in HIV-1B vs. C [139,145–148]. Finally, microarray technology has been applied to NeuroAIDS to measure simultaneous expression of large numbers of genes including recently discovered micro-(mi)-RNAs, as reviewed in detail elsewhere (Table 3) [49,50,96,136,138,140,141,145–154]. …”

MicroRNAs function primarily in the pathogenesis of human anencephaly via the mitogen-activated protein kinase signaling pathway

“…Within mammalian cells, miRNAs associate with the RNA-induced silencing complex to hybridize 8-mer ''seed'' sequences in the 3'-untranslated regions of target mRNAs (Tatro et al, 2010). These regions are partially complementary to miRNAs that are directed for degradation and/or suppressed translation (Zhang et al, 2010).…”

MicroRNA: implications in HIV, a brief overview

“…Both miR-125a and miR-22 were found to be upregulated in HIV or HIV/major depressive disorder (MDD, Tatro et al 2010). Induction of these dysregulated miRNAs leads to decreased protein translation of interferon-induced transmembrane protein 3 (IFITM3), an intracellular membrane protein, and soluble tumor necrosis factor receptor (sTNFR1A), a secreted protein in primary human neuronal cultures.…”

“…IFITM protein is shown to inhibit HIV replication (Lu et al 2011), and sTNFR1A is involved in neuroinflammation. miR219, which was shown to modulate NMDA receptor-mediated neurobehavioral dysfunction in schizophrenia (Kocerha et al 2009), is also shown to be upregulated in HIV/MDD (Tatro et al 2010). …”