All Publications

  • M1 of Murine Gamma-Herpesvirus 68 Induces Endoplasmic Reticulum Chaperone Production SCIENTIFIC REPORTS Feng, J., Gong, D., Fu, X., Wu, T., Wang, J., Chang, J., Zhou, J., Lu, G., Wang, Y., Sun, R. 2015; 5


    Viruses rely on host chaperone network to support their infection. In particular, the endoplasmic reticulum (ER) resident chaperones play key roles in synthesizing and processing viral proteins. Influx of a large amount of foreign proteins exhausts the folding capacity in ER and triggers the unfolded protein response (UPR). A fully-executed UPR comprises signaling pathways that induce ER folding chaperones, increase protein degradation, block new protein synthesis and may eventually activate apoptosis, presenting both opportunities and threats to the virus. Here, we define a role of the MHV-68M1 gene in differential modulation of UPR pathways to enhance ER chaperone production. Ectopic expression of M1 markedly induces ER chaperone genes and expansion of ER. The M1 protein accumulates in ER during infection and this localization is indispensable for its function, suggesting M1 acts from the ER. We found that M1 protein selectively induces the chaperon-producing pathways (IRE1, ATF6) while, interestingly, sparing the translation-blocking arm (PERK). We identified, for the first time, a viral factor capable of selectively intervening the initiation of ER stress signaling to induce chaperon production. This finding provides a unique opportunity of using viral protein as a tool to define the activation mechanisms of individual UPR pathways.

    View details for DOI 10.1038/srep17228

    View details for Web of Science ID 000365424400001

    View details for PubMedID 26615759

    View details for PubMedCentralID PMC4663489

  • An application of a Hill-based response surface model for a drug combination experiment on lung cancer STATISTICS IN MEDICINE Ning, S., Xu, H., Al-Shyoukh, I., Feng, J., Sun, R. 2014; 33 (24): 4227-4236


    Combination chemotherapy with multiple drugs has been widely applied to cancer treatment owing to enhanced efficacy and reduced drug resistance. For drug combination experiment analysis, response surface modeling has been commonly adopted. In this paper, we introduce a Hill-based global response surface model and provide an application of the model to a 512-run drug combination experiment with three chemicals, namely AG490, U0126, and indirubin-3  ' -monoxime (I-3-M), on lung cancer cells. The results demonstrate generally improved goodness of fit of our model from the traditional polynomial model, as well as the original Hill model on the basis of fixed-ratio drug combinations. We identify different dose-effect patterns between normal and cancer cells on the basis of our model, which indicates the potential effectiveness of the drug combination in cancer treatment. Meanwhile, drug interactions are analyzed both qualitatively and quantitatively. The distinct interaction patterns between U0126 and I-3-M on two types of cells uncovered by the model could be a further indicator of the efficacy of the drug combination.

    View details for DOI 10.1002/sim.6229

    View details for Web of Science ID 000342897400006

    View details for PubMedID 24942112

    View details for PubMedCentralID PMC4230824

  • Control of Kaposi's Sarcoma-Associated Herpesvirus Reactivation Induced by Multiple Signals PLOS ONE Yu, F., Al-Shyoukh, I., Feng, J., Li, X., Liao, C. W., Ho, C., Shamma, J. S., Sun, R. 2011; 6 (6)


    The ability to control cellular functions can bring about many developments in basic biological research and its applications. The presence of multiple signals, internal as well as externally imposed, introduces several challenges for controlling cellular functions. Additionally the lack of clear understanding of the cellular signaling network limits our ability to infer the responses to a number of signals. This work investigates the control of Kaposi's sarcoma-associated herpesvirus reactivation upon treatment with a combination of multiple signals. We utilize mathematical model-based as well as experiment-based approaches to achieve the desired goals of maximizing virus reactivation. The results show that appropriately selected control signals can induce virus lytic gene expression about ten folds higher than a single drug; these results were validated by comparing the results of the two approaches, and experimentally using multiple assays. Additionally, we have quantitatively analyzed potential interactions between the used combinations of drugs. Some of these interactions were consistent with existing literature, and new interactions emerged and warrant further studies. The work presents a general method that can be used to quantitatively and systematically study multi-signal induced responses. It enables optimization of combinations to achieve desired responses. It also allows identifying critical nodes mediating the multi-signal induced responses. The concept and the approach used in this work will be directly applicable to other diseases such as AIDS and cancer.

    View details for DOI 10.1371/journal.pone.0020998

    View details for Web of Science ID 000292142800007

    View details for PubMedID 21904595

    View details for PubMedCentralID PMC3125160

  • Systematic quantitative characterization of cellular responses induced by multiple signals BMC SYSTEMS BIOLOGY Al-Shyoukh, I., Yu, F., Feng, J., Yan, K., Dubinett, S., Ho, C., Shamma, J. S., Sun, R. 2011; 5


    Cells constantly sense many internal and environmental signals and respond through their complex signaling network, leading to particular biological outcomes. However, a systematic characterization and optimization of multi-signal responses remains a pressing challenge to traditional experimental approaches due to the arising complexity associated with the increasing number of signals and their intensities.We established and validated a data-driven mathematical approach to systematically characterize signal-response relationships. Our results demonstrate how mathematical learning algorithms can enable systematic characterization of multi-signal induced biological activities. The proposed approach enables identification of input combinations that can result in desired biological responses. In retrospect, the results show that, unlike a single drug, a properly chosen combination of drugs can lead to a significant difference in the responses of different cell types, increasing the differential targeting of certain combinations. The successful validation of identified combinations demonstrates the power of this approach. Moreover, the approach enables examining the efficacy of all lower order mixtures of the tested signals. The approach also enables identification of system-level signaling interactions between the applied signals. Many of the signaling interactions identified were consistent with the literature, and other unknown interactions emerged.This approach can facilitate development of systems biology and optimal drug combination therapies for cancer and other diseases and for understanding key interactions within the cellular network upon treatment with multiple signals.

    View details for DOI 10.1186/1752-0509-5-88

    View details for Web of Science ID 000292637900001

    View details for PubMedID 21624115

    View details for PubMedCentralID PMC3138445

  • Oxidative Stress Induces Reactivation of Kaposi's Sarcoma-Associated Herpesvirus and Death of Primary Effusion Lymphoma Cells JOURNAL OF VIROLOGY Li, X., Feng, J., Sun, R. 2011; 85 (2): 715-724


    Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL) cells are predominantly infected with latent Kaposi's sarcoma-associated herpesvirus (KSHV), presenting a barrier to the destruction of tumor cells. Latent KSHV can be reactivated to undergo lytic replication. Here we report that in PEL cells, oxidative stress induced by upregulated reactive oxygen species (ROS) can lead to KSHV reactivation or cell death. ROS are upregulated by NF-κB inhibition and are required for subsequent KSHV reactivation. Disruption of the intracellular redox balance through depletion of the antioxidant glutathione or inhibition of the antioxidant enzyme catalase also induces KSHV reactivation, suggesting that hydrogen peroxide induces reactivation. In addition, p38 signaling is required for KSHV reactivation induced by ROS. Furthermore, treatment of PEL cells with a higher concentration of the NF-κB inhibitor than that used for inducing KSHV reactivation further upregulates ROS and induces massive cell death. ROS, but not p38 signaling, are required for PEL cell death induced by NF-κB inhibition as well as by glutathione depletion. Importantly, anticancer drugs, such as cisplatin and arsenic trioxide, also induce KSHV reactivation and PEL cell death in a ROS-dependent manner. Our study thus establishes a critical role for ROS and oxidative stress in the regulation of KSHV reactivation and PEL cell death. Disrupting the cellular redox balance may be a potential strategy for treating KSHV-associated lymphoma.

    View details for DOI 10.1128/JVI.01742-10

    View details for Web of Science ID 000285554300007

    View details for PubMedID 21068240

    View details for PubMedCentralID PMC3020037

  • MicroRNAs encoded by Kaposi's sarcoma-associated herpesvirus regulate viral life cycle EMBO REPORTS Lu, C., Li, Z., Chu, C., Feng, J., Feng, J., Sun, R., Rana, T. M. 2010; 11 (10): 784-790


    Kaposi's sarcoma-associated herpesvirus (KSHV) is linked with Kaposi's sarcoma and lymphomas. The pathogenesis of KSHV depends on the balance between two phases of the viral cycle: latency and lytic replication. In this study, we report that KSHV-encoded microRNAs (miRNAs) function as regulators by maintaining viral latency and inhibiting viral lytic replication. MiRNAs are short, noncoding, small RNAs that post-transcriptionally regulate the expression of messenger RNAs. Of the 12 viral miRNAs expressed in latent KSHV-infected cells, we observed that expression of miR-K3 can suppress both viral lytic replication and gene expression. Further experiments indicate that miR-K3 can regulate viral latency by targeting nuclear factor I/B. Nuclear factor I/B can activate the promoter of the viral immediate-early transactivator replication and transcription activator (RTA), and depletion of nuclear factor I/B by short hairpin RNAs had similar effects on the viral life cycle to those of miR-K3. Our results suggest a role for KSHV miRNAs in regulating the viral life cycle.

    View details for DOI 10.1038/embor.2010.132

    View details for Web of Science ID 000282210500017

    View details for PubMedID 20847741

    View details for PubMedCentralID PMC2948186

  • Inhibition of the phosphatidylinositol 3-kinase-Akt pathway enhances gamma-2 herpesvirus lytic replication and facilitates reactivation from latency JOURNAL OF GENERAL VIROLOGY Peng, L., Wu, T., Tchieu, J. H., Feng, J., Brown, H. J., Feng, J., Li, X., Qi, J., Deng, H., Vivanco, I., Mellinghoff, I. K., Jamieson, C., Sun, R. 2010; 91: 463-469


    Cellular signalling pathways are critical in regulating the balance between latency and lytic replication of herpesviruses. Here, we investigated the effect of the phosphatidylinositol 3-kinase (PI3K)-Akt pathway on replication of two gamma-2 herpesviruses, murine gammaherpesvirus-68 (MHV-68) and human herpesvirus-8/Kaposi's sarcoma-associated herpesvirus (HHV-8/KSHV). We found that de novo infection of MHV-68 induced PI3K-dependent Akt activation and the lytic replication of MHV-68 was enhanced by inhibiting the PI3K-Akt pathway with both chemical inhibitors and RNA interference technology. Inhibiting the activity of Akt using Akt inhibitor VIII also facilitated the reactivation of KSHV from latency. Both lytic replication and latency depend on the activity of viral transactivator RTA and we further show that the activity of RTA is increased by reducing Akt1 expression. The data suggest that the PI3K-Akt pathway suppresses the activity of RTA and thereby contributes to the maintenance of viral latency and promotes tumorigenesis.

    View details for DOI 10.1099/vir.0.015073-0

    View details for Web of Science ID 000274806600017

    View details for PubMedID 19864499

    View details for PubMedCentralID PMC2888311

  • B cell terminal differentiation factor XBP-1 induces reactivation of Kaposi's sarcoma-associated herpesvirus FEBS LETTERS Yu, F., Feng, J., Harada, J. N., Chanda, S. K., Kenney, S. C., Sun, R. 2007; 581 (18): 3485-3488


    The herpesvirus life cycle has two distinct phases: latency and lytic replication. The viral immediate early protein replication and transcription activator (RTA) plays a central role in mediating the balance between these two phases. Here, we demonstrate that a B cell terminal differentiation factor X-box binding protein 1 (XBP-1) can effectively initiates Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation by activating the RTA promoter, which results in the induction of other viral lytic transcripts. We also showed splicing of the XBP-1 mRNA which specifically occurs during B cell differentiation is critical in triggering KSHV reactivation. This work demonstrates the integration of KSHV reactivation mechanisms with host cell differentiation.

    View details for DOI 10.1016/j.febslet.2007.06.056

    View details for Web of Science ID 000248473200027

    View details for PubMedID 17617410