Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4 ⁺ T Cell Line

Abstract

Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4+ T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes.

Deep Transcriptional Sequencing of Mucosal Challenge Compartment from Rhesus Macaques Acutely Infected with Simian Immunodeficiency Virus Implicates Loss of Cell Adhesion Preceding Immune Activation

“…This scenario suggests that if the downregulated expression of claudins and other tight junction proteins could be prevented, the host would stand a better chance of restricting the virus to the primary infection compartment (and adjacent tissues) for a longer period of time. The potential benefit of delaying SIV infection is supported by previous studies that implicated slow CD8 ϩ lymphocyte (6) and type I interferon (20,49) responses in the loss of HIV/SIV control by failing to manifest itself when the virus is the most vulnerable. Maintenance of mucosal integrity would provide additional opportunity for these antiviral mechanisms to come into play and increase the chance that the virus would be eliminated before it could infect enough host cells to spread systemically (Fig.…”

“…Likewise, knockdown of particular long ncRNA can affect HIV replication (19), similar to the knockdown of coding genes known as HIV dependency factors. In addition, RNA sequencing of HIV-infected SUP-T1 cells has shown the differential regulation of several classes of ncRNA (20). Whereas these previous studies were carried out in vitro, the design of the present study allowed us to examine ncRNA expression in vivo on a genomic scale.…”

Not so Pseudo Anymore: Pseudogenes as Therapeutic Targets

“…Similarly, pseudogene-derived transcripts are upregulated in laryngeal cancer [51] and neuroblastoma [52]. Differential expression of pseudogene transcripts has also been implicated in the context of asthma [53] and HIV infection [54]. …”

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

“…Despite this, many studies have used various mapping tools to analyze sequence reads in ways similar to that which RAMICS was designed for (55–58) and, thus, we present comparisons of RAMICS to a number of commonly used mapping tools on the basis of alignment quality and speed.…”