Einav Lab Research Interests
Our basic research program focuses on understanding the roles of virus-host interactions in viral infection and pathogenesis. This program is combined with translational efforts to apply this knowledge for the development of broad-spectrum host-centered antiviral approaches to combat emerging viral infections, including dengue, encephalitic alphaviruses, and Ebola, and means to predict disease progression.
One of our major goals is to better understand the roles of virus-host interactions in viral infection and pathogenesis and identify host functions required by multiple unrelated viruses. This program is combined with translational efforts to apply this knowledge for the development of broad-spectrum host-centered antiviral approaches to combat emerging viral infections. Our work has recently provided a proof of concept that effective host-centered broad-spectrum antivirals can be discovered and developed via repurposing. One such approach that emerged from our lab is advancing into clinic for the treatment of dengue.
Another major goal of our lab is to discover critical protective and pathogenic elements of the host response to dengue virus (DENV) and identify biomarkers that are predictive of progression to severe dengue. We have recently discovered such candidate biomarkers and are currently validating them on a larger scale and advancing the development of a prognostic assay to predict severe dengue early in the course of infection.
Our work combines systems virology approaches, such as novel proteomic and single cell transcriptomic approaches, with molecular virology, biochemistry, genomic, cell biology, bioinformatics, immunology, medicinal chemistry and molecular pharmacology approaches to achieve these goals. We focus on several acute emerging viruses including DENV, Zika virus, Ebola virus (EBOV), and encephalitic alphaviruses as well as hepatitis C virus (HCV). We utilize both in vitro and in vivo infection models of these viral pathogens either at Stanford or via collaborations.
The advantages of the host-targeted broad-spectrum
Global health is threatened by emerging viruses, such as dengue (DENV) and Ebola (EBOV), which largely lack effective vaccines or therapies. Most antiviral strategies targeting viral factors by “one drug, one bug” approaches are associated with the emergence of viral resistance and are developed slowly and expensively and therefore not easily scalable. Our goal is to overcome these challenges by developing host-targeted antiviral approaches.
1. Deciphering the mechanisms by which RNA viruses hijack various intracellular membrane trafficking pathways for mediating key steps in the viral life cycle. These include the roles of adaptor protein complexes in viral trafficking during viral entry, assembly, release, and direct cell-to-cell spread, the role of the ESCRT machinery in intracellular viral budding, and the roles of ubiquitin pathways in the regulation of viral assembly and release.
2. Mapping an atlas of DENV immune cellular targets and profiling the host response to natural dengue infection to better understand the pathogenesis of severe dengue. We integrate single-cell transcriptomics (see project #3) and innovative bioinformatics approaches with advanced immune monitoring technologies (e.g. CyTOF) to comprehensively analyze samples derived from a cohort of dengue patients that we have established in Colombia. The translational goals of this project are to identify candidate biomarkers of dengue severity and novel targets for host-targeted anti-DENV agents.
3. Developing and applying genome-wide single cell transcriptomic approaches to better understand viral infections. In collaboration with the Quake lab we have developed a novel virus-inclusive, single-cell transcriptomic (viscRNA-seq) platform that enables monitoring host gene expression dynamics with virus abundance in thousands of individual cells. We have reported its capability to monitor host response to DENV and ZIKV infection and identify pro- and antiviral factors with an unprecedented resolution in cultured cells. Recently, we furthered this platform and applied it to study gene expression dynamics in PBMC samples from our Colombia cohort. Our pilot study demonstrates that viscRNA-seq transforms our ability to monitor differential host responses to DENV infection in distinct cell populations and identify biomarkers of severity. We are currently advancing this and other single cell transcriptomic approaches and utilizing them to study the virus-host interplay in cultured cells infected with various viruses and in clinical samples.
4. Determining the feasibility and biological rationale for predicting severe dengue by a novel prognostic 20-gene set. In collaboration with the Khatri lab, we have used a novel multi-cohort analysis of the publicly available gene expression data sets to identify and in silico validate a 20-gene set predictive of severe dengue and have started to prospectively validate it in the Colombia cohort. This discovery is groundbreaking since the 20-gene set is predictive of severe dengue prior to its onset, and is generalizable across a wide variety of countries, ages, and samples. We are currently validating the predictive power of this gene set at a larger scale and are deciphering the roles of these genes in the pathogenesis of severe dengue.
5. Mapping the signaling pathways of cellular kinases essential for viral replication. We have discovered AAK1 and GAK, two host cell kinases, as novel targets for broad-spectrum antivirals. To better characterize the signal transduction that these poorly characterized kinases mediate, we have conducted high-throughput proteomic screens for identification of novel cellular phosphorylation targets of these kinases. We are currently validating these hits and defining their roles in cell biology and viral infection.
6. Advancing the development of repurposed and novel, selective AAK1 and GAK inhibitors as broad-spectrum antivirals. We discovered that the combination of erlotinib and sunitinib, anticancer drugs with potent anti-AAK1 and GAK activity, has antiviral activity against multiple RNA viruses both in vitro and in mouse models. We are currently advancing this strategy into the clinic and studying its mechanism of action. In parallel, we have been developing chemically distinct, selective inhibitors of AAK1 and GAK and are currently optimizing these compounds to combat DENV, encephalitic alphaviruses and EBOV.