A Genome-Wide RNA Interference Screen Identifies a Role for Wnt/ß-Catenin Signaling during Rift Valley Fever Virus Infection.

UNLABELLED: Rift Valley fever virus (RVFV) is an arbovirus within the Bunyaviridae family capable of causing serious morbidity and mortality in humans and livestock. To identify host factors involved in bunyavirus replication, we employed genome-wide RNA interference (RNAi) screening and identified 381 genes whose knockdown reduced infection. The Wnt pathway was the most represented pathway when gene hits were functionally clustered. With further investigation, we found that RVFV infection activated Wnt signaling, was enhanced when Wnt signaling was preactivated, was reduced with knockdown of ß-catenin, and was blocked using Wnt signaling inhibitors. Similar results were found using distantly related bunyaviruses La Crosse virus and California encephalitis virus, suggesting a conserved role for Wnt signaling in bunyaviral infection. We propose a model where bunyaviruses activate Wnt-responsive genes to regulate optimal cell cycle conditions needed to promote efficient viral replication. The findings in this study should aid in the design of efficacious host-directed antiviral therapeutics. IMPORTANCE: RVFV is a mosquito-borne bunyavirus that is endemic to Africa but has demonstrated a capacity for emergence in new territories (e.g., the Arabian Peninsula). As a zoonotic pathogen that primarily affects livestock, RVFV can also cause lethal hemorrhagic fever and encephalitis in humans. Currently, there are no treatments or fully licensed vaccines for this virus. Using high-throughput RNAi screening, we identified canonical Wnt signaling as an important host pathway regulating RVFV infection. The beneficial role of Wnt signaling was observed for RVFV, along with other disparate bunyaviruses, indicating a conserved bunyaviral replication mechanism involving Wnt signaling. These studies supplement our knowledge of the fundamental mechanisms of bunyavirus infection and provide new avenues for countermeasure development against pathogenic bunyaviruses.

Rift Valley fever virus strain MP-12 enters mammalian host cells via caveola-mediated endocytosis.

Rift Valley fever virus (RVFV) is a zoonotic pathogen capable of causing serious morbidity and mortality in both humans and livestock. The lack of efficient countermeasure strategies, the potential for dispersion into new regions, and the pathogenesis in humans and livestock make RVFV a serious public health concern. The receptors, cellular factors, and entry pathways used by RVFV and other members of the family Bunyaviridae remain largely uncharacterized. Here we provide evidence that RVFV strain MP-12 uses dynamin-dependent caveola-mediated endocytosis for cell entry. Caveolae are lipid raft domains composed of caveolin (the main structural component), cholesterol, and sphingolipids. Caveola-mediated endocytosis is responsible for the uptake of a wide variety of host ligands, as well as bacteria, bacterial toxins, and a number of viruses. To determine the cellular entry mechanism of RVFV, we used small-molecule inhibitors, RNA interference (RNAi), and dominant negative (DN) protein expression to inhibit the major mammalian cell endocytic pathways. Inhibitors and RNAi specific for macropinocytosis and clathrin-mediated endocytosis had no effect on RVFV infection. In contrast, inhibitors of caveola-mediated endocytosis, and RNAi targeted to caveolin-1 and dynamin, drastically reduced RVFV infection in multiple cell lines. Expression of DN caveolin-1 also reduced RVFV infection significantly, while expression of DN EPS15, a protein required for the assembly of clathrin-coated pits, and DN PAK-1, an obligate mediator of macropinocytosis, had no significant impact on RVFV infection. These results together suggest that the primary mechanism of RVFV MP-12 uptake is dynamin-dependent, caveolin-1-mediated endocytosis.

Microfluidic chip for combinatorial mixing and screening of assays.

This paper reports the design, fabrication and validation of a microfluidic well plate for combinatorial screening applications. Each well within the array is comprised of two 200 picoliter compartments that each contain a photonic crystal biosensor to enable the on-chip, in situ detection of (bio-) molecular binding events. This microfluidic chip utilizes arrays of Actuate-to-Open valves to isolate all compartments, which allows the chip to be decoupled from pneumatic control lines and thus to be transported freely between filling, sensing and characterization platforms. A proof-of-principle 4 x 4 protein/antibody binding assay was performed to demonstrate the discrete mixing and on-chip sensing capabilities.

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation.

The high-affinity receptor for IgE expressed on the surface of mast cells and basophils interacts with antigens, via bound IgE antibody, and triggers secretion of inflammatory mediators that contribute to allergic reactions. To understand how past inputs (memory) influence future inflammatory responses in mast cells, a microfluidic device was used to precisely control exposure of cells to alternating stimulatory and non-stimulatory inputs. We determined that the response to subsequent stimulation depends on the interval of signaling quiescence. For shorter intervals of signaling quiescence, the second response is blunted relative to the first response, whereas longer intervals of quiescence induce an enhanced second response. Through an iterative process of computational modeling and experimental tests, we found that these memory-like phenomena arise from a confluence of rapid, short-lived positive signals driven by the protein tyrosine kinase Syk; slow, long-lived negative signals driven by the lipid phosphatase Ship1; and slower degradation of Ship1 co-factors. This work advances our understanding of mast cell signaling and represents a generalizable approach for investigating the dynamics of signaling systems.

Microfluidic platforms for RNA interference screening of virus-host interactions.

RNA interference (RNAi) is a powerful tool for functional genomics with the capacity to comprehensively analyze host-pathogen interactions. High-throughput RNAi screening is used to systematically perturb cellular pathways and discover therapeutic targets, but the method can be tedious and requires extensive capital equipment and expensive reagents. To aid in the development of an inexpensive miniaturized RNAi screening platform, we have developed a two part microfluidic system for patterning and screening gene targets on-chip to examine cellular pathways involved in virus entry and infection. First, a multilayer polydimethylsiloxane (PDMS)-based spotting device was used to array siRNA molecules into 96 microwells targeting markers of endocytosis, along with siRNA controls. By using a PDMS-based spotting device, we remove the need for a microarray printer necessary to perform previously described small scale (e.g. cellular microarrays) and microchip-based RNAi screening, while still minimizing reagent usage tenfold compared to conventional screening. Second, the siRNA spotted array was transferred to a reversibly sealed PDMS-based screening platform containing microchannels designed to enable efficient cell loading and transfection of mammalian cells while preventing cross-contamination between experimental conditions. Validation of the screening platform was examined using Vesicular stomatitis virus and emerging pathogen Rift Valley fever virus, which demonstrated virus entry pathways of clathrin-mediated endocytosis and caveolae-mediated endocytosis, respectively. The techniques here are adaptable to other well-characterized infection pathways with a potential for large scale screening in high containment biosafety laboratories.

Multiplexed detection of nucleic acids in a combinatorial screening chip.

Multiplexed diagnostic testing has the potential to dramatically improve the quality of healthcare. Simultaneous measurement of health indicators and/or disease markers reduces turnaround time and analysis cost and speeds up the decision making process for diagnosis and treatment. At present, however, most diagnostic tests only provide information on a single indicator or marker. Development of efficient diagnostic tests capable of parallel screening of infectious disease markers could significantly advance clinical and diagnostic testing in both developed and developing parts of the world. Here, we report the multiplexed detection of nucleic acids as disease markers within discrete wells of a microfluidic chip using molecular beacons and total internal reflection fluorescence microscopy (TIRFM). Using a 4 × 4 array of 200 pL wells, we screened for the presence of four target single stranded oligonucleotides encoding for conserved regions of the genomes of four common viruses: human immunodeficiency virus-1 (HIV-1), human papillomavirus (HPV), Hepatitis A (Hep A) and Hepatitis B (Hep B). Target oligonucleotides are accurately detected and discriminated against alternative oligonucleotides with different sequences. This combinatorial chip represents a versatile platform for the development of clinical diagnostic tests for simultaneous screening, detection and monitoring of a wide range of biological markers of disease and health using minimal sample size.

A microfluidic platform for pharmaceutical salt screening.

We describe a microfluidic platform comprised of 48 wells to screen for pharmaceutical salts. Solutions of pharmaceutical parent compounds (PCs) and salt formers (SFs) are mixed on-chip in a combinatorial fashion in arrays of 87.5-nanolitre wells, which constitutes a drastic reduction of the volume of PC solution needed per condition screened compared to typical high throughput pharmaceutical screening approaches. Nucleation and growth of salt crystals is induced by diffusive and/or convective mixing of solutions containing, respectively, PCs and SFs in a variety of solvents. To enable long term experiments, solvent loss was minimized by reducing the thickness of the absorptive polymeric material, polydimethylsiloxane (PDMS), and by using solvent impermeable top and bottom layers. Additionally, well isolation was enhanced via the incorporation of pneumatic valves that are closed at rest. Brightfield and polarized light microscopy and Raman spectroscopy were used for on-chip analysis and crystal identification. Using a gold-coated glass substrate and minimizing the thickness of the PDMS control layer drastically improved the signal-to-noise ratio for Raman spectra. Two drugs, naproxen (acid) and ephedrine (base), were used for validation of the platform's ability to screen for salts. Each PC was mixed combinatorially with potential SFs in a variety of solvents. Crystals were visualized using brightfield polarized light microscopy. Subsequent on-chip analyses of the crystals with Raman spectroscopy identified four different naproxen salts and five different ephedrine salts.