Browsing by Author "Garcia-Blanco, Mariano A"

Our ability to convert basic knowledge into robust anti-viral therapeutics requires discovery of novel host-virus interactions as well as an informed anti-viral discovery pipeline. We used a genome-scale RNAi-based screen followed by a chemical screen of FDA-approved therapeutics to identify scores of novel dengue virus (DENV) human host dependency factors (HDF) and identified more than 20 potential anti-Zika virus (ZIKV) therapeutics.

Two genes in particular, TTC35 and TMEM111, strongly inhibited DENV infection and, based on comparisons with published literature, implicated a larger protein, the ER Membrane Protein Complex (EMC), as a pan-flavivirus HDF. The EMC is a poorly characterized multiprotein complex that may function in ER-associated protein biogenesis and/or lipid metabolism. Based on our screen data, we hypothesized that the EMC is an uncharacterized HDF that functions through a common mechanism to promote replication of flaviviruses. We report that DENV, ZIKV, and yellow fever virus (YFV) infections were impressively inhibited, while West Nile Virus (WNV) infection was unchanged, in cell lines engineered to lack EMC subunit 4 (EMC4). Furthermore, targeted depletion of EMC subunits in live mosquitos significantly reduced DENV-2 propagation in vivo. In addition, the accumulation of DENV proteins shortly after infection in EMC4 knockout cells was significantly reduced, suggesting that the EMC promotes viral protein biogenesis.

We interrogated a library of FDA-approved drugs for their ability to block infection of human HuH-7 cells by a newly isolated ZIKV strain. Selected compounds were further validated for inhibition of ZIKV infection in human cervical, placental, and neural stem cell lines, as well as primary human amnion cells. Established anti-flaviviral drugs (e.g., bortezomib and mycophenolic acid) and others that had no previously known antiviral activity (e.g., daptomycin) were identified as inhibitors of ZIKV infection. Several drugs reduced ZIKV infection across multiple cell types.

We propose that the EMC may be exploited as a novel therapeutic target for multiple flaviviruses in the future. Also we identified drugs that could be tested in clinical studies of ZIKV infection and provides a resource of small molecules to study ZIKV pathogenesis.

Dengue fever and dengue hemorrhagic fever are estimated to afflict 50-100 million people annually and are caused by one of the four serotypes of dengue virus. Dengue virus is carried and transmitted to humans by mosquitoes of the Aedes genus. Given the broad geographic distribution of Aedes mosquitoes, it has been estimated that nearly half the world's population is at risk of contracting the disease. Currently, no vaccine or specific antiviral treatment is available to combat this emerging menace.

A greater understanding of how dengue virus interacts with its insect and human hosts will facilitate the intelligent design of specific antivirals to combat the disease and enable the selective breeding of mosquitoes resistant to the virus. Although the genomes of the two primary mosquito vectors have been sequenced, the molecular tools necessary for conducting a systematic genetic analysis of host factors required for DEN infection are not yet available. These tools do however exist in the closely related fruit fly, Drosophila melanogaster. By using a strain of dengue virus that was adapted to propagate in fruit fly cells, we completed a full genetic screen for host factors required for efficient dengue virus propagation. When homologues of these host factors were assayed in a human cell line, over half were also shown to be required for efficient viral propagation. This indicates that while the virus is utilizing many of the same pathways in both of its hosts, the interaction with the insect vector has unique features that may contribute to the observed lack of pathogenesis in mosquitoes.

Alternative mRNA processing can result in the generation of multiple, qualitatively different RNA transcripts from the same gene and is a powerful engine of complexity in higher organisms. Recent deep sequencing studies have indicated that essentially all human genes containing more than a single exon generate multiple RNA transcripts. Functional roles of alternative processing have been established in virtually all areas of biological regulation, particularly in development and cancer. Changes in alternative mRNA processing can now be detected from over a billion dollars' worth of conventional gene expression microarray data archived over the past 20 years using a program we created called SplicerAV. Application of SplicerAV to publicly available microarray data has granted new insights into previously existing studies of oncogene over-expression and clinical cancer prognosis.

Adaptation of SplicerAV to the new Affymetrix Human Exon arrays has resulted in the creation of SplicerEX, the first program that can automatically categorize microarray detected changes in alternative processing into biologically pertinent categories. We use SplicerEX's automatic event categorization to identify changes in global mRNA processing during B cell transformation and show that the conventional U133 platform is able to detect 3' located changes in mRNA processing five times more frequently than the Human Exon array.

HIV-1 relies on both viral and cellular host factors for expression of its genome. Tat specific factor 1 (Tat-SF1) was identified as a cellular cofactor required for enhanced transcription of HIV-1 in vitro. Insight into the role of Tat-SF1 in the HIV-1 lifecycle has previously been limited to immunodepletions and in vitro analyses or transient overexpression experiments. Here, we present studies that utilize RNA interference (RNAi) to reevaluate Tat-SF1's role in Tat transactivation and HIV-1 replication in vivo. We report that although Tat-SF1 depletion reduces HIV-1 infectivity, it does not affect Tat transactivation in vivo. However, Tat-SF1 depletion changes the levels of unspliced and spliced RNAs. We propose that Tat-SF1 has a novel role of post-transcriptionally regulating HIV-1 gene expression, possibly through alternative splicing.

The functions of Tat-SF1 in cellular gene expression are not well understood, so we utilized the stable cell lines constructed for our HIV-1 studies to investigate the cellular functions of Tat-SF1. To identify target genes of Tat-SF1, we employed a combination of RNAi and human exon arrays. These arrays, which survey both transcript-level and exon-level changes genome-wide, revealed approximately 1,400 genes with alternative exon usage after Tat-SF1 depletion (p≤0.01). In contrast, 500 genes showed significant transcript-level changes (p≤0.01), all with minimal fold changes. Computational analyses showed that genes with alternative exon usage after Tat-SF1 depletion were over-represented in the insulin signaling and ubiquitin mediated proteolysis biological pathways. Furthermore, there was approximately 2-fold enrichment of Tat-SF1 target genes among previously reported HIV-1 dependency factors. The type of exon choice affected by Tat-SF1 depletion exhibited a strong 5’ bias. Finally, a novel Tat-SF1 binding motif, GACGGG, was found to be over-represented among target genes and may play a functional role in first exon choice. Together, these data are the strongest evidence to date of Tat-SF1 functioning in both transcription and splicing of cellular genes.

The Flavivirus genus contains several arthropod-borne viruses that pose global health threats, including dengue virus (DENV). We identified two ribosomal proteins, RPLP1 and RPLP2 (RPLP1/2), that are crucial host factors required for translation of flaviviruses and efficient flavivirus infection of human cell lines and Aedes aegypti mosquitoes, which are natural vectors for these viruses. We hypothesized that RPLP1/2 are accessory ribosomal proteins that function to promote translation of specific cellular mRNAs sharing undefined features with the DENV genome. We found that these proteins are not broadly required for cellular translation and but are necessary for efficient accumulation of DENV proteins early in infection and ectopically expressed DENV structural proteins. The ribosome profiling technique allowed us to quantitative map ribosomes across the transcriptome during early DENV infection in human cell lines depleted for RPLP1/2. We observed that local ribosome occupancy is altered in the viral open reading frame with RPLP1/2 knockdown, consistent with a role for RPLP1/2 in promoting translation elongation. The most prominent ribosome pausing site in the DENV RNA was in the 5’ end of the E protein coding sequence which is located 210 nts downstream of two adjacent TMs. We also observed that RPLP1/2 depletion resulted in altered ribosome density in mRNAs encoding two or more transmembrane domains. This work increases our knowledge on DENV translation regulation and sheds light on the function of RPLP1/2 in translation of specific cellular RNAs.