Viruses exploit host factors to replicate. However, each of these interactions also represents a viral weakness that may be targeted to combat infection. Functional genomics represents a powerful methodology for uncovering such viral dependency factors. By combining the human genome sequencing project and the technology of RNAi, we can specifically deplete each human gene product, and subsequently test if loss of that factor impacts viral replication. Combined with proteomics, as well as conventional molecular genetic and biochemical approaches, functional genomics promises to greatly increase our knowledge of host-viral interactions, and further our goal of alleviating human suffering by defeating these pathogens.
We are currently applying these strategies to studying the pathogenesis of human immunodeficiency virus (HIV-1), hepatitis C virus (HCV), and most recently influenza A virus, revealing not only key host components which are co-opted by invading viruses, but also native host genes (e.g., the IFITM family) which confer a baseline level of resistance to influenza, as well as other devastating viruses.
The IFITMs inhibit influenza A virus (IAV) replication in vitro and in vivo. In this study, we establish that amphotericin B (AmphoB), an antifungal heptaen, disrupts IFITM3-mediated restriction of IAV consequently improving IAV replication. Mechanistic studies determined that IFITM1 decreases membrane fluidity and may underlie the mechanism of IFITM-mediated restriction as well as its abolishment by AmphoB. Mice treated with AmBisome, a clinical preparation of AmphoB, had an increased mortality rate when infected with IAV compared to controls. Therefore, patients receiving treatment with AmBisome may be immunocompromised and more vulnerable to IFITM3-restricted viruses.
Schematic representation of the screen. Arrayed pools of siRNAs were transfected into TZM-bl cells in a 384-well format. After 72 hours, HIV-IIIB virus was added, and 48 hours after infection, cultured supernatant was removed and added to fresh TZM-bl cells. In part one, 48 hours after infection, the siRNA transfected cells were fixed, permeabilized, stained, and imaged for HIV p24 protein and DNA. In part two, cells were cultured for 24 hours after the addition of supernatant, then analysed, exposed to a luminescent b-Gal substrate, and relative light units (RLU) recorded. From Fig. 1A, Brass et al. Science, 2008.
The results of the screen are shown with the siRNA SMARTpools ranked in order of average Z score, from lowest (decreased infection) to highest (increased infection). The position of known influenza A virus-host factors and several newly identified genes from the screen are indicated. From Fig. 1C, Brass et al. Cell, 2009.
Immunofluorescence images showing the block to HIV infection with loss of TNPO3. Cells were treated as described in (B), with either the luciferase (Luc), negative control siRNA; or TNPO3, siRNA #8 targeting TNPO3. “Merge” denotes the combined image for nuclei (blue) and HIV p24 (green). From Fig. 3H, Brass et al. Science, 2008..
A549 or U2OS cells stably overexpressing IFITM3 protein or vector alone were infected with influenza A H1N1 WSN/33. Twelve hours later, cells were fixed and stained for surface HA expression. Values represent the mean ± SD, n = 3 (green: HA, blue: nuclei; 43). From Fig. 4C, Brass et al. Cell, 2009.
Localization of IFITM3 in A549 cells stably overexpressing IFITM3 protein, by confocal microscopy