Honors & Awards

  • Early Career Award, Thrasher Research Fund (12/2016-12/2018)
  • Young Investigator Award, Institute for Immunity, Transplantation and Infection, Stanford University (10/2016-06/2018)
  • Walter V. and Idun Berry Postdoctoral Fellowship, Berry Foundation, Stanford University (09/2014-08/2017)
  • K99/R00 Pathway to Independence Award, National Institutes of Health/National Institute of Allergy and Infectious Diseases (07/2018-06/2019)
  • Summa Cum Laude Bachelor of Science, Fudan University (06/2009)
  • FDUROP Scholar, Fudan University (06/2008-05/2009)
  • Instructor Support Program, Stanford Maternal & Child Health Research Institute (02/2019-10/2019)

Current Research and Scholarly Interests

To explore interactions between rotavirus infection and the innate immune system

All Publications

  • Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication. The Journal of biological chemistry Ren, L., Ding, S., Song, Y., Li, B., Ramanathan, M., Co, J., Amieva, M. R., Khavari, P. A., Greenberg, H. B. 2019


    Genome replication and virion assembly of segmented RNA viruses are highly coordinated events, tightly regulated by sequence and structural elements in the UTRs of viral RNA. This process is poorly defined and likely requires the participation of host proteins in concert with viral proteins. In this study, we employed a proteomics-based approach, named RNA-protein interaction detection (RaPID), to comprehensively screen for host proteins that bind to a conserved motif within the rotavirus (RV) 3' terminus. Using this assay, we identified ATP5B, a core subunit of the mitochondrial ATP synthase, as having high affinity to the RV 3'UTR consensus sequences. During RV infection, ATP5B bound to the RV 3'UTR and co-localized with viral RNA and viroplasm. Functionally, siRNA-mediated genetic depletion of ATP5B or other ATP synthase subunits such as ATP5A1 and ATP5O reduced the production of infectious viral progeny without significant alteration of intracellular viral RNA levels or RNA translation. Chemical inhibition of ATP synthase diminished RV yield in both conventional cell culture and in human intestinal enteroids, indicating that ATP5B positively regulates late-stage RV maturation in primary intestinal epithelial cells. Collectively, our results shed light on the role of host proteins in RV genome assembly and particle formation and identify ATP5B as a novel pro-RV RNA-binding protein, contributing to our understanding of how host ATP synthases may galvanize virus growth and pathogenesis.

    View details for DOI 10.1074/jbc.RA118.006004

    View details for PubMedID 30770472

  • Rotavirus VP3 targets MAVS for degradation to inhibit type III interferon expression in intestinal epithelial cells. eLife Ding, S., Zhu, S., Ren, L., Feng, N., Song, Y., Ge, X., Li, B., Flavell, R. A., Greenberg, H. B. 2018; 7


    Rotaviruses (RVs), a leading cause of severe diarrhea in young children1 and many mammalian species, have evolved multiple strategies to counteract the host innate immunity, specifically interferon (IFN) signaling through RV non-structural protein 1 (NSP1)2. However, whether RV structural components also subvert antiviral response remains under-studied. Here, we found that MAVS, critical for the host RNA sensing pathway upstream of IFN induction3, is degraded by the RV RNA methyl- and guanylyl-transferase (VP3) in a host-range-restricted manner. Mechanistically, VP3 localizes to the mitochondria and mediates the phosphorylation of a previously unidentified SPLTSS motif within the MAVS proline-rich region, leading to its proteasomal degradation and blockade of IFN-lambda production in RV-infected intestinal epithelial cells. Importantly, VP3 inhibition of MAVS activity contributes to enhanced RV replication and to viral pathogenesis in vivo. Collectively, our findings establish RV VP3 as a viral antagonist of MAVS function in mammals and uncover a novel pathogen-mediated inhibitory mechanism of MAVS signaling.

    View details for DOI 10.7554/eLife.39494

    View details for PubMedID 30460894

  • New mitochondrial DNA synthesis enables NLRP3 inflammasome activation NATURE Zhong, Z., Liang, S., Sanchez-Lopez, E., He, F., Shalapour, S., Lin, X., Wong, J., Ding, S., Seki, E., Schnabl, B., Hevener, A. L., Greenberg, H. B., Kisseleva, T., Karin, M. 2018; 560 (7717): 198-+


    Dysregulated NLRP3 inflammasome activity results in uncontrolled inflammation, which underlies many chronic diseases. Although mitochondrial damage is needed for the assembly and activation of the NLRP3 inflammasome, it is unclear how macrophages are able to respond to structurally diverse inflammasome-activating stimuli. Here we show that the synthesis of mitochondrial DNA (mtDNA), induced after the engagement of Toll-like receptors, is crucial for NLRP3 signalling. Toll-like receptors signal via the MyD88 and TRIF adaptors to trigger IRF1-dependent transcription of CMPK2, a rate-limiting enzyme that supplies deoxyribonucleotides for mtDNA synthesis. CMPK2-dependent mtDNA synthesis is necessary for the production of oxidized mtDNA fragments after exposure to NLRP3 activators. Cytosolic oxidized mtDNA associates with the NLRP3 inflammasome complex and is required for its activation. The dependence on CMPK2 catalytic activity provides opportunities for more effective control of NLRP3 inflammasome-associated diseases.

    View details for DOI 10.1038/s41586-018-0372-z

    View details for Web of Science ID 000441115200041

    View details for PubMedID 30046112

  • STAG2 deficiency induces interferon responses via cGAS-STING pathway and restricts virus infection. Nature communications Ding, S., Diep, J., Feng, N., Ren, L., Li, B., Ooi, Y. S., Wang, X., Brulois, K. F., Yasukawa, L. L., Li, X., Kuo, C. J., Solomon, D. A., Carette, J. E., Greenberg, H. B. 2018; 9 (1): 1485


    Cohesin is a multi-subunit nuclear protein complex that coordinates sister chromatid separation during cell division. Highly frequent somatic mutations in genes encoding core cohesin subunits have been reported in multiple cancer types. Here, using a genome-wide CRISPR-Cas9 screening approach to identify host dependency factors and novel innate immune regulators of rotavirus (RV) infection, we demonstrate that the loss of STAG2, an important component of the cohesin complex, confers resistance to RV replication in cell culture and human intestinal enteroids. Mechanistically, STAG2 deficiency results in spontaneous genomic DNA damage and robust interferon (IFN) expression via the cGAS-STING cytosolic DNA-sensing pathway. The resultant activation of JAK-STAT signaling and IFN-stimulated gene (ISG) expression broadly protects against virus infections, including RVs. Our work highlights a previously undocumented role of the cohesin complex in regulating IFN homeostasis and identifies new therapeutic avenues for manipulating the innate immunity.

    View details for DOI 10.1038/s41467-018-03782-z

    View details for PubMedID 29662124

  • Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells NATURE Zhu, S., Ding, S., Wang, P., Wei, Z., Pan, W., Palm, N. W., Yang, Y., Yu, H., Li, H., Wang, G., Lei, X., de Zoete, M. R., Zhao, J., Zheng, Y., Chen, H., Zhao, Y., Jurado, K. A., Feng, N., Shan, L., Kluger, Y., Lu, J., Abraham, C., Fikrig, E., Greenberg, H. B., Flavell, R. A. 2017; 546 (7660): 667-+


    Rotavirus, a leading cause of severe gastroenteritis and diarrhoea in young children, accounts for around 215,000 deaths annually worldwide. Rotavirus specifically infects the intestinal epithelial cells in the host small intestine and has evolved strategies to antagonize interferon and NF-κB signalling, raising the question as to whether other host factors participate in antiviral responses in intestinal mucosa. The mechanism by which enteric viruses are sensed and restricted in vivo, especially by NOD-like receptor (NLR) inflammasomes, is largely unknown. Here we uncover and mechanistically characterize the NLR Nlrp9b that is specifically expressed in intestinal epithelial cells and restricts rotavirus infection. Our data show that, via RNA helicase Dhx9, Nlrp9b recognizes short double-stranded RNA stretches and forms inflammasome complexes with the adaptor proteins Asc and caspase-1 to promote the maturation of interleukin (Il)-18 and gasdermin D (Gsdmd)-induced pyroptosis. Conditional depletion of Nlrp9b or other inflammasome components in the intestine in vivo resulted in enhanced susceptibility of mice to rotavirus replication. Our study highlights an important innate immune signalling pathway that functions in intestinal epithelial cells and may present useful targets in the modulation of host defences against viral pathogens.

    View details for PubMedID 28636595

  • VP4-and VP7-specific antibodies mediate heterotypic immunity to rotavirus in humans SCIENCE TRANSLATIONAL MEDICINE Nair, N., Feng, N., Blum, L. K., Sanyal, M., Ding, S., Jiang, B., Sen, A., Morton, J. M., He, X., Robinson, W. H., Greenberg, H. B. 2017; 9 (395)


    Human rotaviruses (RVs) are the leading cause of severe diarrhea in young children worldwide. The molecular mechanisms underlying the rapid induction of heterotypic protective immunity to RV, which provides the basis for the efficacy of licensed monovalent RV vaccines, have remained unknown for more than 30 years. We used RV-specific single cell-sorted intestinal B cells from human adults, barcode-based deep sequencing of antibody repertoires, monoclonal antibody expression, and serologic and functional characterization to demonstrate that infection-induced heterotypic immunoglobulins (Igs) primarily directed to VP5*, the stalk region of the RV attachment protein, VP4, are able to mediate heterotypic protective immunity. Heterotypic protective Igs against VP7, the capsid glycoprotein, and VP8*, the cell-binding region of VP4, are also generated after infection; however, our data suggest that homotypic anti-VP7 and non-neutralizing VP8* responses occur more commonly in people. These results indicate that humans can circumvent the extensive serotypic diversity of circulating RV strains by generating frequent heterotypic neutralizing antibody responses to VP7, VP8*, and most often, to VP5* after natural infection. These findings further suggest that recombinant VP5* may represent a useful target for the development of an improved, third-generation, broadly effective RV vaccine and warrants more direct examination.

    View details for DOI 10.1126/scitranslmed.aam5434

    View details for Web of Science ID 000403788900004

    View details for PubMedID 28637924

  • Drebrin restricts rotavirus entry by inhibiting dynamin-mediated endocytosis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Li, B., Ding, S., Feng, N., Mooney, N., Ooi, Y. S., Ren, L., Diep, J., Kelly, M. R., Yasukawa, L. L., Patton, J. T., Yamazaki, H., Shirao, T., Jackson, P. K., Greenberg, H. B. 2017; 114 (18): E3642-E3651


    Despite the wide administration of several effective vaccines, rotavirus (RV) remains the single most important etiological agent of severe diarrhea in infants and young children worldwide, with an annual mortality of over 200,000 people. RV attachment and internalization into target cells is mediated by its outer capsid protein VP4. To better understand the molecular details of RV entry, we performed tandem affinity purification coupled with high-resolution mass spectrometry to map the host proteins that interact with VP4. We identified an actin-binding protein, drebrin (DBN1), that coprecipitates and colocalizes with VP4 during RV infection. Importantly, blocking DBN1 function by siRNA silencing, CRISPR knockout (KO), or chemical inhibition significantly increased host cell susceptibility to RV infection. Dbn1 KO mice exhibited higher incidence of diarrhea and more viral antigen shedding in their stool samples compared with the wild-type littermates. In addition, we found that uptake of other dynamin-dependent cargos, including transferrin, cholera toxin, and multiple viruses, was also enhanced in DBN1-deficient cells. Inhibition of cortactin or dynamin-2 abrogated the increased virus entry observed in DBN1-deficient cells, suggesting that DBN1 suppresses dynamin-mediated endocytosis via interaction with cortactin. Our study unveiled an unexpected role of DBN1 in restricting the entry of RV and other viruses into host cells and more broadly to function as a crucial negative regulator of diverse dynamin-dependent endocytic pathways.

    View details for DOI 10.1073/pnas.1619266114

    View details for PubMedID 28416666

  • DDX6 Represses Aberrant Activation of Interferon-Stimulated Genes. Cell reports Lumb, J. H., Li, Q., Popov, L. M., Ding, S., Keith, M. T., Merrill, B. D., Greenberg, H. B., Li, J. B., Carette, J. E. 2017; 20 (4): 819–31


    The innate immune system tightly regulates activation of interferon-stimulated genes (ISGs) to avoid inappropriate expression. Pathological ISG activation resulting from aberrant nucleic acid metabolism has been implicated in autoimmune disease; however, the mechanisms governing ISG suppression are unknown. Through a genome-wide genetic screen, we identified DEAD-box helicase 6 (DDX6) as a suppressor of ISGs. Genetic ablation of DDX6 induced global upregulation of ISGs and other immune genes. ISG upregulation proved cell intrinsic, imposing an antiviral state and making cells refractory to divergent families of RNA viruses. Epistatic analysis revealed that ISG activation could not be overcome by deletion of canonical RNA sensors. However, DDX6 deficiency was suppressed by disrupting LSM1, a core component of mRNA degradation machinery, suggesting that dysregulation of RNA processing underlies ISG activation in the DDX6 mutant. DDX6 is distinct among DExD/H helicases that regulate the antiviral response in its singular ability to negatively regulate immunity.

    View details for DOI 10.1016/j.celrep.2017.06.085

    View details for PubMedID 28746868

    View details for PubMedCentralID PMC5551412

  • Comparative Proteomics Reveals Strain-Specific ß-TrCP Degradation via Rotavirus NSP1 Hijacking a Host Cullin-3-Rbx1 Complex. PLoS pathogens Ding, S., Mooney, N., Li, B., Kelly, M. R., Feng, N., Loktev, A. V., Sen, A., Patton, J. T., Jackson, P. K., Greenberg, H. B. 2016; 12 (10)


    Rotaviruses (RVs) are the leading cause of severe gastroenteritis in young children, accounting for half a million deaths annually worldwide. RV encodes non-structural protein 1 (NSP1), a well-characterized interferon (IFN) antagonist, which facilitates virus replication by mediating the degradation of host antiviral factors including IRF3 and β-TrCP. Here, we utilized six human and animal RV NSP1s as baits and performed tandem-affinity purification coupled with high-resolution mass spectrometry to comprehensively characterize NSP1-host protein interaction network. Multiple Cullin-RING ubiquitin ligase (CRL) complexes were identified. Importantly, inhibition of cullin-3 (Cul3) or RING-box protein 1 (Rbx1), by siRNA silencing or chemical perturbation, significantly impairs strain-specific NSP1-mediated β-TrCP degradation. Mechanistically, we demonstrate that NSP1 localizes to the Golgi with the host Cul3-Rbx1 CRL complex, which targets β-TrCP and NSP1 for co-destruction at the proteasome. Our study uncovers a novel mechanism that RV employs to promote β-TrCP turnover and provides molecular insights into virus-mediated innate immunity inhibition.

    View details for DOI 10.1371/journal.ppat.1005929

    View details for PubMedID 27706223

  • Long-distance interferon signaling within the brain blocks virus spread. Journal of virology van den Pol, A. N., Ding, S., Robek, M. D. 2014; 88 (7): 3695–3704


    Serious permanent neurological or psychiatric dysfunction may result from virus infections in the central nervous system (CNS). Olfactory sensory neurons are in direct contact with the external environment, making them susceptible to infection by viruses that can enter the brain via the olfactory nerve. The rarity of full brain viral infections raises the important question of whether unique immune defense mechanisms protect the brain. Here we show that both RNA (vesicular stomatitis virus [VSV]) and DNA (cytomegalovirus [CMV]) virus inoculations of the nasal mucosa leading to olfactory bulb (OB) infection activate long-distance signaling that upregulates antiviral interferon (IFN)-stimulated gene (ISG) expression in uninfected remote regions of the brain. This signaling mechanism is dependent on IFN-α/β receptors deep within the brain, leading to the activation of a distant antiviral state that prevents infection of the caudal brain. In normal mice, VSV replication is limited to the OB, and these animals typically survive the infection. In contrast, mice lacking the IFN-α/β receptor succumbed to the infection, with VSV spreading throughout the brain. Chemical destruction of the olfactory sensory neurons blocked both virus trafficking into the OB and the IFN response in the caudal brain, indicating a direct signaling within the brain after intranasal infection. Most signaling within the brain occurs across the 20-nm synaptic cleft. The unique long-distance IFN signaling described here occurs across many millimeters within the brain and is critical for survival and normal brain function.The olfactory mucosa can serve as a conduit for a number of viruses to enter the brain. Yet infections in the CNS rarely occur. The mechanism responsible for protecting the brain from viruses that successfully invade the OB, the first site of infection subsequent to infection of the nasal mucosa, remains elusive. Here we demonstrate that the protection is mediated by a long-distance interferon signaling, particularly IFN-β released by infected neurons in the OB. Strikingly, in the absence of neurotropic virus infection, ISGs are induced in the posterior regions of the brain, activating an antiviral state and preventing further virus invasion.

    View details for DOI 10.1128/JVI.03509-13

    View details for PubMedID 24429359

  • Cytidine deamination and cccDNA degradation: A new approach for curing HBV? Hepatology (Baltimore, Md.) Ding, S., Robek, M. D. 2014

    View details for DOI 10.1002/hep.27386

    View details for PubMedID 25142126

  • Epigenetic reprogramming of the type III interferon response potentiates antiviral activity and suppresses tumor growth. PLoS biology Ding, S., Khoury-Hanold, W., Iwasaki, A., Robek, M. D. 2014; 12 (1): e1001758


    Type III interferon (IFN-λ) exhibits potent antiviral activity similar to IFN-α/β, but in contrast to the ubiquitous expression of the IFN-α/β receptor, the IFN-λ receptor is restricted to cells of epithelial origin. Despite the importance of IFN-λ in tissue-specific antiviral immunity, the molecular mechanisms responsible for this confined receptor expression remain elusive. Here, we demonstrate that the histone deacetylase (HDAC) repression machinery mediates transcriptional silencing of the unique IFN-λ receptor subunit (IFNLR1) in a cell-type-specific manner. Importantly, HDAC inhibitors elevate receptor expression and restore sensitivity to IFN-λ in previously nonresponsive cells, thereby enhancing protection against viral pathogens. In addition, blocking HDAC activity renders nonresponsive cell types susceptible to the pro-apoptotic activity of IFN-λ, revealing the combination of HDAC inhibitors and IFN-λ to be a potential antitumor strategy. These results demonstrate that the type III IFN response may be therapeutically harnessed by epigenetic rewiring of the IFN-λ receptor expression program.

    View details for DOI 10.1371/journal.pbio.1001758

    View details for PubMedID 24409098

    View details for PubMedCentralID PMC3883642

  • Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression. Hepatology (Baltimore, Md.) Bolen, C. R., Ding, S., Robek, M. D., Kleinstein, S. H. 2014; 59 (4): 1262–72


    Despite activating similar signaling cascades, the type I and type III interferons (IFNs) differ in their ability to antagonize virus replication. However, it is not clear whether these cytokines induce unique antiviral states, particularly in the liver, where the clinically important hepatitis B and C viruses cause persistent infection. Here, clustering and promoter analyses of microarray-based gene expression profiling were combined with mechanistic studies of signaling pathways to dynamically characterize the transcriptional responses induced by these cytokines in Huh7 hepatoma cells and primary human hepatocytes. Type I and III IFNs differed greatly in their level of interferon-stimulated gene (ISG) induction with a clearly detectable hierarchy (IFN-β > IFN-α > IFN-λ3 > IFN-λ1 > IFN-λ2). Notably, although the hierarchy identified varying numbers of differentially expressed genes when quantified using common statistical thresholds, further analysis of gene expression over multiple timepoints indicated that the individual IFNs do not in fact regulate unique sets of genes. The kinetic profiles of IFN-induced gene expression were also qualitatively similar with the important exception of IFN-α. While stimulation with either IFN-β or IFN-λs resulted in a similar long-lasting ISG induction, IFN-α signaling peaked early after stimulation then declined due to a negative feedback mechanism. The quantitative expression hierarchy and unique kinetics of IFN-α reveal potential specific roles for individual IFNs in the immune response, and elucidate the mechanism behind previously observed differences in IFN antiviral activity. While current clinical trials are focused on IFN-λ1 as a potential antiviral therapy, the finding that IFN-λ3 invariably possesses the highest activity among type III IFNs suggests that this cytokine may have superior clinical activity.

    View details for DOI 10.1002/hep.26657

    View details for PubMedID 23929627

  • TRIM15 is a focal adhesion protein that regulates focal adhesion disassembly. Journal of cell science Uchil, P. D., Pawliczek, T., Reynolds, T. D., Ding, S., Hinz, A., Munro, J., Huang, F., Floyd, R. W., Yang, H., Hamilton, W., Bewersdorf, J., Xiong, Y., Calderwood, D. A., Mothes, W. 2014


    Focal adhesions (FAs) are macromolecular complexes that connect the actin cytoskeleton to the extracellular matrix. Dynamic turnover of FAs is critical for cell migration. Paxillin is a multi-adaptor protein that plays an important role in regulating FA dynamics. Here, we identify TRIM15, a member of the TRIpartite Motif protein family, as a paxillin-interacting factor and a component of FAs. TRIM15 localizes to focal contacts in a myosin II-independent manner by an interaction between its coiled coil domain and the LD2 motif of paxillin. Unlike other FA proteins, TRIM15 is a stable FA component with restricted mobility due to its ability to form oligomers. TRIM15-depleted cells display impaired cell migration and FA disassembly rates in addition to enlarged FAs. Thus, our studies demonstrate a cellular function for TRIM15 as a regulatory component of FA turnover and cell migration.

    View details for DOI 10.1242/jcs.143537

    View details for PubMedID 25015296

  • Peroxisomal MAVS activates IRF1-mediated IFN-λ production. Nature immunology Ding, S., Robek, M. D. 2014; 15 (8): 700–701

    View details for DOI 10.1038/ni.2924

    View details for PubMedID 25045870

  • Chicken HS4 insulator significantly improves baculovirus-mediated foreign gene expression in insect cells by modifying the structure of neighbouring chromatin in virus minichromosome. Journal of biotechnology Wang, X., Li, L., Ding, S., Huang, X., Zhang, J., Yin, J., Zhong, J. 2009; 142 (3-4): 193–99


    The baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is widely used as a eukaryotic expression vector for protein production. In the current study, chicken beta-globin 5'-HS4 insulator (HS4) was placed downstream of the polyhedrin promoter-directed foreign gene expression cassette in AcMNPV, and found to markedly increase the expression of target gene. When enhanced green fluorescence protein gene (egfp) was used as the reporter gene, cells infected by the recombinant virus with HS4 (AcEGFP-HS4) showed 3.0 and 2.1-fold stronger fluorescence than that by the control virus without HS4 (AcEGFP) at 72 and 96 h post infection, respectively. The level of egfp mRNA was also much higher in cells infected by AcEGFP-HS4 than that by AcEGFP. An increase in gene expression was also seen when firefly luciferase gene or secreted alkaline phosphatase gene was used as a reporter. The insertion of HS4 in the polyhedrin locus has no significant effect on virus replication. The effect of HS4 was orientation-dependent, and sensitive to inhibitors of histone acetyltransferase. In DNase I sensitivity assay, HS4 significantly increased the sensitivity of neighbouring DNA to nuclease, but had little effect on DNA of a distal locus. These results suggested that HS4 insulator might affect baculovirus gene expression by modifying the structure of neighbouring chromatin in the virus minichromosome.

    View details for DOI 10.1016/j.jbiotec.2009.06.012

    View details for PubMedID 19539676