Department of Microbiology
Training Program in Mechanisms of Virus-Host InteractionsWelcome to the virology training program of Mount Sinai School of Medicine (MSSM) and the NYU School of Medicine (NYUSOM). The goal of this program is to assist in the training of graduate and postdoctoral students in the broad discipline of Virology. The research training emphasis is directed toward teaching students the theory and experimental approaches required for independent scientific investigations. Students learn the molecular mechanisms involved in virus replication and host responses to viral infections. Additional research areas available for training include novel approaches for antiviral strategies and vaccine development. The specific aims of the program are (i) to recruit and provide rigorous training to high caliber students and fellows and (ii) to provide an administrative structure which will support and coordinate virology training between MSSM and NYUSOM. This program aids trainees in all phases of their development including understanding scientific method, interpretation of results, presentation of data and conclusions, research ethics, and career guidance. Resources for Trainees
Symposium on Virus - Host Interactions
Training FacultyA brief description of the research interests of the core training faculty and their current and future projects is presented below. Peter Palese, Ph.D.Peter Palese, Ph.D., Professor, Microbiology, MSSM Laboratory Research InterestsInfluenza viruses continue to be important pathogens with a potential to cause epidemics and pandemics in human and animal populations. The outbreaks of H5 avian influenza starting in Hong Kong in 1997/1998 are a reminder that we do not yet understand enough about the vagaries of this potentially devastating virus. In addition, work on influenza viruses is important because it serves as a paradigm for crucial biological phenomena. Specifically, the genetic variation of this virus represents one of the most rewarding evolutionary systems (and yes, I believe in evolution). Also, immunological questions have been successfully addressed by studying influenza viruses and the immune responses in animals or humans to the virus or to the viral components. Processes in the cell can also be better understood by using influenza viruses as biological probes; for example, the study of the fusion of lipid-containing membranes and the mechanisms of trafficking within the cell is greatly helped by insights gained with the influenza virus system. Our group is interested in fundamental questions concerning the genetic make-up and the biology of viruses. We are interested in training students and postdoctoral fellows who will become independent investigators in "molecular" areas of infectious diseases and infectious agents. We use molecular biological techniques to understand how viruses replicate and how they interact with cells to cause disease in their hosts. Emphasis is put on the study of RNA viruses, including influenza, paramyxo and SARS corona viruses. In summary, these projects are aimed at identifying the whole network of interactions between the host and different RNA viruses. Current and Future Research OpportunitiesA major emphasis of this laboratory is the study of the interactions between viral proteins and cellular proteins. One of the motivations for identifying such interactions is based on the fact that cellular proteins modulate viral gene expression and facilitate virus replication, thus affecting tissue specificity, host range and virulence. Specifically, we are interested in identifying cellular proteins which are involved in influenza virus replication. Another virus-host interaction project involves the identification of SARS virus proteins which function in the suppression of the antiviral (interferon) response of the host. A second major focus of interest is the development of improved viral vaccines and vaccine platforms. This effort involves the application of reverse genetics techniques to construct modified viral vaccine strains and subsequently study them in animal systems with respect to safety, efficacy and immune markers. A third theme is aimed at developing new antivirals which target viral or cellular genes. Small molecular weight compounds which are identified as antivirals via high-throughput assays are then studied in order to understand the mechanism of action of their biological activities. Finally, the laboratory continues to define the virulence and pathogenicity characteristics of pandemic influenza viruses (including the 1918 virus) using molecular biological and immunological techniques as well as complex animal models. Specifically, the guinea pig model has become a superb system for studying transmission of influenza viruses with different virulence characteristics under defined conditions of temperature and relative humidity. We are also interested in studying the effects of vaccination and the administration of antiviral compounds on transmission of influenza in the guinea pig model. Christopher F. Basler, Ph.D.Christopher F. Basler, Ph.D., Associate Professor, Microbiology, MSSM Laboratory Research InterestsHow viruses interact with host innate and adaptive immune responses is a major determinant of the outcome of infection. Our laboratory studies the interaction of emerging viruses with host defenses in the hopes of gaining insight into mechanisms of virulence and new therapeutic strategies. We have projects on several emerging viruses including pandemic influenza virus, Ebola virus, Nipah virus and Eastern equine encephalitis virus. Our current focus of the lab is the molecular characterization of the human humoral immune response to the 1918 pandemic influenza virus. We recently characterized neutralizing monoclonal antibodies derived from the B cells of 1918 influenza pandemic survivors. This study provided the first detailed molecular characterization of authentic human antibodies generated by natural infection with a pandemic influenza virus. The fact that we were able to recover memory B cells ninety years after the pandemic reveals the durability of human immunity. Future studies are expected to reveal in detail fundamental features underlying antibody neutralization of influenza viruses. It is hoped that this work cam lead to new, rationally-designed vaccine antigens that induce antibody responses characterized by high affinity, potency, and cross-reactivity. In the realm of innate immunity, we have identified proteins encoded by the highly lethal Ebola virus, Nipah virus and Eastern equine encephalitis virus that counteract the host interferon response. Interferons are cytokines that exert antiviral effects. The high virulence of these viruses most likely requires that they overcome the early antiviral interferon response. Thus, by defining virus-encoded factors that counteract interferon responses, we hope to elucidate mechanisms of virulence and to devise strategies to overcome the functions of these "interferon-antagonists." Forexample, we have identified the Ebola virus VP35 protein as an inhibitor of interferon alpha/beta production. We have also demonstrated that VP35 exerts this effect, at least in part, by preventing the activation of the cellular transcription factor, interferon regulatory factor 3. Recent experiments further demonstrate that mutations impairing the interferon-antagonist function of VP35 highly attenuate, in animal models, the otherwise deadly Ebola virus. Therefore, we predict that small molecules that inactivate this VP35 function will be effective anti-Ebola virus drugs. Current and Future Research OpportunitiesIt is anticipated that opportunities will be available for students interested in our work. Please e-mail Dr. Basler at chris.basler@mssm.edu for details. Constantin Bona, Ph.D.Constantin Bona, Ph.D., Professor, Microbiology, MSSM My laboratory's research on virus-host interactions was focused on two different areas: First, the genetics of immunization of neonates. The aim was to find out whether genetic immunization can overcome inability of neonates to respond to vaccines, particularly influenza virus vaccine. We demonstrated for the first time that the injection of a plasmid expressing NP gene is able to prime CTL precursors, enabling the animals to clear the virus from the lung. However, the rate of survival was only 40%. The ability of genetic immunization to induce an antibody response was studied by using a plasmid expressing HA gene. In contrast to the injection of neonates with virus that induced a long lasting unresponsiveness, the immunization with plasmid induced a weak humeral response that increased dramatically after challenge. The animals immunized with plasmid as neonates efficiently cleared the virus and e xhibited a high rate of survival. These findings demonstrate that the genetic immunization can be beneficial in vaccination of newborns and infants. Recently we are studying the role of T regulatory cells on persistence of memory T cells specific for HA of influenza virus. The second area is related to molecular studies of the regulation of collagen gene in fibroblasts by profibrogenic cytokine such as Il-4. IL13 and TGF-beta, In particular we are studying the cross talk between STAT6 and Smad3 signaling pathways and of ERK pathway on collagen gene expression in both murine and human dermal fibroblasts. This study is carried out by measuring the collagen promoter activity, the level of collagen gene transcript and collagen production. Current and Future Research Opportunities
James Borowiec, Ph.D.James Borowiec, Ph.D., Professor, Biochemistry, NYUSOM Genotoxic stresses that damage the chromosomal DNA or inhibit the progression of a DNA replication fork can lead to instability of the genetic information and hence cause cellular transformation. One key factor that both signals the presence of genotoxic stress and serves to minimize DNA damage is RPA, the eukaryotic single-stranded DNA-binding protein. A focus of our research is to understand the roles of RPA in enhancing genomic stability. A major line of investigation analyzes the functional significance of RPA phosphorylation by checkpoint (e.g., ATR, ATM) and cell-cycle (e.g., cyclin A-Cdk2) kinases under stress conditions. We have recently found that: 1) in interphase cells with DNA damage, RPA phosphorylation is required for efficient DNA repair; 2) under conditions of DNA replication stress, RPA phosphorylation by ATR stimulates repair DNA synthesis and prevents ssDNA accumulation; and 3) in cells experiencing mitotic DNA damage, mitotic RPA hyper-phosphorylation facilitates release of cells from a damaged mitosis into a 2N G1 phase, thereby increasing cell viability. Future work will pursue mechanistic understanding of these various effects. A second area of research interest is elucidating the roles of nucleolin in controlling cell cycle progression. The nucleolin protein is a key factor in ribosome biogenesis and is found over-expressed in many tumors. What is the significance of this over-expression? Recent work from my laboratory demonstrate that heightened nucleolin expression, mimicking that occurring under pathophysiological conditions, elevates the protein levels and activity of the tumor suppressor p53. These effects are caused by nucleolin binding to and inhibiting the p53-antagonist Hdm2, an E3 ubiquitin ligase, resulting in p53 stabilization. We and others have found that nucleolin physically interacts with the tumor suppressors p53 and p14ARF, as well as Hdm2. Future work will continue to investigate the synergistic interplay between nucleolin and factors in the p53 tumor suppression pathway, and how these interactions allow nucleolin to modulate the activity of p53 in the regulation of cell cycle progression and apoptosis. Current and Future Research Opportunities
Benjamin K. Chen, M.D., Ph.D.Benjamin K. Chen, M.D., Ph.D., Assistant Professor, Medicine / Infectious Diseases, Immunology Institute, MSSM Mechanisms of HIV cell-cell transmissionRecent studies have revealed that the efficiency of HIV dissemination is greatly facilitated by cell contact between infected and uninfected T cells. Infected T cells have been found to form adhesive contacts with uninfected CD4+ T cells. These contacts are called virological synapses (VS) because of some similarity to other adhesive structures in the immune system call immunological synapses. These structures require viral Env proteins to be expressed on the cell surface where they interact with CD4 on target cells. Using infectious fluorescent virus systems we are able to quantify and visualize the amount of viral transfer that occurs through VS. In vitro we find that these can be over 10,000-fold more efficient at transferring viral antigen from cell to cell. High resolution, real-time confocal microscopy allows us to directly visualize the changes in cellular distribution of viral protein that occur during VS formation. We find that the VS causes the massive transfer of viral particles into target T cells through an endocytic route that is still largely uncharacterized. The VS-mediated viral transfer can be resistant to patient antibodies that are capable of neutralizing homologous cell free virus. Our ongoing studies are directed at understanding the cellular mechanisms that regulate VS transfer. We are also working to understand how transfer may provide an important mechanism to evade humoral immune responses. The work will help us understand how this mode of efficient viral dissemination may allow HIV to spread efficiently in vivo. Matthew Evans, Ph.D.Matthew Evans, Ph.D., Assistant Professor, Microbiology, MSSM Our laboratory is interested in exploring how viruses interact with and enter host cells. Currently our focus is on hepatitis C virus (HCV) cell entry, but in the future we intend to pursue similar studies on the entry mechanisms of other viruses, such as the related Dengue and Yellow Fever viruses, or even more disparate viruses, including Ebola and HIV. HCV is a serious global public health problem, yet many aspects of the viral life cycle remain mysterious. In particular, only basic steps required for viral entry into a host cell have been defined. Historically, technical limitations have made this a difficult step in the HCV life cycle to study. However, systems including retroviral pseudotyped particles harboring functional HCV glycoproteins and cell culture produced infectious particles have recently been developed that enable the study of HCV infection of cultured cells. Through the use of these systems, HCV entry has been defined as a temperature and pH-dependent, clathrin-mediated process requiring at least several cellular molecules, including the tetraspanin CD81, scavenger receptor class B type I (SR-BI), and perhaps glycosaminoglycans (GAGs). We have recently identified claudin-1 (CLDN1), a component of tight junction complexes, as an essential HCV entry factor. This discovery suggests that the polarized nature of the hepatocyte cell may greatly influence the HCV entry process. Still, the list of HCV entry factors appears incomplete, as numerous cell lines express all of them yet remain uninfectable. Furthermore, at least one unknown HCV entry factor may be responsible for the narrow species-specific tropism of HCV, as only primate and human cells appear to support HCV entry and this restriction in murine cells is not even overcome by the expression of all the above human HCV entry factors. A greater understanding of the HCV entry process, including the definition of the complete set of entry factors and their specific roles, may be required for the development of therapies targeting HCV entry. In addition, such studies may lead to an understanding of why HCV selectively infects human hepatocytes with obvious implications for developing transgenic mouse models that support productive HCV infection. Current Research Opportunities
Future Research Opportunities
Ana Fernandez-Sesma, Ph.D.Ana Fernandez-Sesma, Ph.D., Assistant Professor, Microbiology, MSSM My laboratory focuses on the interactions between human viruses such as dengue (DenV) and influenza virus and human primary cells in order to analyze viral immune evasion. Both dengue and influenza viruses are human pathogens that cause devastating disease. While DenV is a blood pathogen that causes viremia in humans and can cause life threatening dengue hemorrhagic fever (DHF) in tropical areas, influenza virus causes significant respiratory disease world wide. There is little known about DenV pathogenesis and initiation of immunity in the host and to date there is no vaccine or treatment for dengue disease. We are trying to elucidate the main target cells for DenV in the host and the way DenV causes pathogenesis and evades immunity. We use human primary cells from blood to analyze the pattern of gene and protein expression induced in those cells after interaction with both viruses. Our ongoing collaboration with Dr. Jorge Munoz-Jordan at the Centers for Disease Control (CDC) in Puerto Rico (Dengue Branch) provides us with primary isolates of DenV and serum samples from dengue patients. Additionally, we are generating recombinant Newcastle disease virus (NDV) expressing DenV proteins in collaboration with Dr. Adolfo Garcia-Sastre's laboratory to analyze the contribution of different DenV proteins to the immune evasion by the virus. Our laboratory is also interested in understanding the ability of influenza virus to initiate or evade immunity using primary human cells as well. Using recombinant influenza viruses with specific mutations in several virulence genes (in collaboration with Dr. Palese's and Dr. Garcia-Sastre's laboratories) we are studying their ability to induce the activation of human dendritic cells and to induce or evade immune responses in human systems. The knowledge gained with these studies will help in the design better vaccines and antiviral drugs against influenza virus. Current Research Opportunities
Future Research Opportunities
Adolfo Garcia-Sastre, Ph.D.Adolfo Garcia-Sastre, Ph.D., Professor, Microbiology, MSSM Our laboratory is focused on exploring virus-host interactions with emphasis on virus regulation of innate and adaptive immune responses. The outcome of these interactions not only determines disease severity but also influences the development of protective immunity resulting from viral infection and/or vaccination. The team has developed several techniques (reverse genetics), which allow for the genetic manipulation of the genomes of several virus families including influenza virus and Newcastle disease virus. Other viruses being studied include Dengue virus, West Nile virus, and Crimean-Congo hemorrhagic fever virus. These techniques are currently being used in several research areas including: i) characterization of virus-encoded virulence factors, ii) identification of virus-encoded antagonists of the interferon system, iii) virus replication and gene expression, iv) immune regulation of influenza replication, and v) vaccine development. Reverse genetics are also being utilized to generate virus vectors based on influenza virus and Newcastle disease virus. These viruses are effective inducers of humoral and cellular immune responses. Live attenuated influenza virus vaccines are being generated by genetic modification of the influenza virus-encoded interferon antagonist that was originally identified by the laboratory. Also, recombinant viruses can be produced that express protective antigens of other pathogens for which no safe attenuated vaccine strains are available. Current and Future Research Opportunities
Mary Klotman, Ph.D.Mary Klotman, M.D., Professor, Microbiology, MSSM The primary focus of the work done in this laboratory is the molecular pathogenesis and molecular therapy of chronic viral diseases, particularly Human Immunodeficiency Virus 1 (HIV-1) infection. Ongoing molecular pathogenesis studies include establishing the role of virus and host factors in determining disease progression in HIV-1 infection. CD8+ cells from HIV-1 infected individuals have been shown to suppress HIV-1 replication both through an MHC-restricted cytolytic pathway as well as through a non-cytolytic pathway. It now appears that immune cells, particularly CD8+ cells, make a number of factors that have inhibitory effects against HIV-1, several of them through interactions with an increasing number of chemokine co-receptors. We have established a panel of herpesvirus saimiri (HVS)-transformed CD8+ cells in the laboratory, which have proven to provide a continuous source of supernatant with potent HIV-1 inhibitory activity. We have characterized this activity in HVS-transformed CD8+ cells from HIV-1 infected children with differing disease progression as well as CD8+ transformed cells from uninfected individuals. An isolated 6-8 kd protein appears to be unique from previously described CD8+ cell derived inhibitory factors with potent, broad HIV-1 inhibitory activity. Current Research OpportunitiesOngoing work in this laboratory is focused on the identification and cloning of the factor, the bacterial expression and subsequent purification of the protein, determination of the mechanism of inhibition by the recombinant protein and examining the role of the inhibitory protein in disease progression. In a multi-investigator program project grant, the laboratory is also studying both the host as well as viral factors that determine a unique outcome of HIV- infection, HIV-associated nephropathy or HIVAN. Future Research OpportunitiesA complementary project in the laboratory is the evaluation of viral vectors for delivery of therapeutic genes to cells, particularly renal cells. The viral vectors under study include the defective virus, adeno-associated virus as well as lentiviruses. Issues under investigation include elucidating optimum conditions for transduction using these vectors particularly the dependence on cell cycle and cell division. Therapeutic targets include the kidney as well as bone marrow stem cells. Nathaniel Landau, Ph.D.Nathaniel Landau, Ph.D., Professor, Microbiology, NYUSOM Intracellular restriction of HIV-1 and mechanisms of virus escapeMammalian cells resist viruses through a collection of mechanisms termed innate or intrinsic immunity. These differ from the adaptive immune response in which B and T cells recognize foreign antigens and clonally expand upon engagement of their antigen receptor. In contrast, intrinsic and innate mechanisms operate in a varieity of cell types and are not antigen-specific. Over the course of evolution, viruses have developed remarkable and diverse ways to escape both the adaptive and the innate response. Our research is focused on understanding the innate mechanisms that restrict HIV-1 and the related simian immunodeficiency virus, SIV. A primary focus is APOBEC3, a family of cytidine deaminases that has homology to RNA editing enzymes such as APOBEC1. In contrast to APOBEC1, APOBEC3 proteins are DNA mutators that target single-stranded DNA. One APOBEC3 family member, APOBEC3G, is particularly important because HIV-1 and related lentiviruses have a gene that encodes a protein dedicated to targeting APOBEC3G destruction. The gene encodes Vif (virion infectivity factor), a viral accessory protein that is required for the virus to replicate in T cells and macrophages. In the absence of Vif, HIV-1 packages APOBEC3G molecules as it assembles. When the virus infects a new target cell, the packaged APOBEC3G deaminates cytosines of the newly synthesized viral cDNA, resulting in a large number of mutations that incapacitate the virus. We are interested to understand how Vif binds to APOBEC3G and induces its degradation and want to develop small molecules that block Vif function, either by preventing the interaction of Vif with APOBEC3G or with the E3 ubiquitin ligase that mediates APOBEC3G degradation. We are also interested to define the transcriptional elements and factors that regulate expression of the APOBEC3 genes. We will then use this knowledge to develop methods to increase APOBEC3G expression in the cell. We are further interested to understand the role of the other APOBEC3 family members the function of which may be to inhibit other viruses. A second research focus is on another of the lentiviral accessory proteins, Vpr (viral protein R) and its relative, Vpx. These proteins are thought to induce the destruction of a yet unidentified anti-viral cellular protein. Vpr interacts with a specific E3 ubiquitin ligase and, we believe, with the unidentified protein. Interestingly, Vpr is present in the HIV-1 virion, suggesting that it acts early in the virus lifecycle. We are trying identify the antiviral protein and to understand how it blocks virus replication. Current and Future Research Opportunities
David Levy, Ph.D.David Levy, Ph.D., Professor, Pathology, NYUSOM Signaling and transcriptional regulation in the innate immune response to viral infection. Virus infection of mammalian cells induces expression of genes involved in establishing a protective antiviral state. Primary genes in this process include the type I interferon (IFN) family which are targeted for induction by virus infection and subsequently act on cells to induce antiviral genes through a signal transduction pathway. We are studying the signaling and biochemistry of IFN gene induction in response to virus infection, the signal transduction pathway through which IFN activates subsequent gene expression, the mechanisms of viral evasion that allow viruses to impair or elude the IFN pathway, and the mechanism of action of IFN-induced proteins. Many viruses induce IFN through activation of a cytoplasmic signal transduction pathway targeting the related transcription factors, IRF3 and IRF7. Viral nucleic acids are crucial activators of this pathway, but the cellular sensors involved and their mechanism of signaling are incompletely understood. Moreover, most viruses encode virulence factors that impair innate immune responses, and we are studying the mechanisms of action of these viral proteins and their interaction with cellular signaling molecules. We have also found that different viruses induce distinct subsets of the IFN multigene family, and the underlying signaling and transcriptional mechanisms for differential gene regulation are being investigated. Following synthesis and secretion, IFN proteins induce an antiviral state in target cells by activating the JAK-STAT pathway, through activation of the essential transcription factors, STAT1 and STAT2. We have defined unique aspects of the transcriptional program exploited by STAT1 and STAT2 to induce gene expression, especially an unexpected role for histone deacetylase (HDAC) enzymes and epigenetic regulation in transcriptional elongation and mRNA processing of IFN stimulated genes. While most cell types are capable of producing and responding to IFN, dendritic cells (DCs) play a central role in resistance to pathogens by modulating the interface between innate and adaptive immunity. We have found that DCs exhibit distinct mechanisms of viral response and IFN action, and we are exploiting an ex vivo conditional immortalization system to analyze this important cell type. Current and Future Research Opportunities
Daniel Littman. M.D., Ph.D.Daniel Littman, M.D., Ph.D., Professor, Pathology, NYUSOM Our laboratory has interest in three major areas: (1) mechanisms of T lymphocyte development, particularly how thymocytes differentiate into CD4+ T helper cells versus CD8+ cytotoxic T cells; (2) regulation of effector T cell differentiation in response to commensal and pathogenic microorganisms, with a focus on the mechanism of differentiation of Th17 cells and the transcriptional regulatory network that defines these cells; and (3) host restrictions in replication of HIV, emphasizing differences between human T cells and dendritic cells and similar lineages from mice, with the goal of developing a mouse model for HIV disease and understanding how HIV is detected by the host innate immune system. Current Research Opportunities
Future Research Opportunities
Ian Mohr, Ph.D.Ian Mohr, Ph.D., Associate Professor, Microbiology, NYUSOM Virus - host interactions that regulate mRNA translation in infected cellsA critical event in the lifecycle of all viruses entails recruiting host ribosomes to their mRNAs. For cellular and viral mRNAs that harbor 7-methyl GTP caps on their 5' ends, this process involves the translation initiation factor eIF4F, a tripartite complex comprised of a cap-binding subunit (eIF4E), and an RNA helicase (eIF4A) anchored to a large molecular scaffold (eIF4G) capable of associating with eIF3-bound 40S ribosome subunits. Whereas viruses whose mRNAs are translated by cap-independent mechanisms often negatively regulate eIF4F to suppress cap-dependent translation, we have found that some viruses, which utilizing a cap-dependent mechanism to translate their mRNAs, actually stimulate eIF4F-activity. Representative herpesviruses family members (herpes simplex virus, cytomegalovirus, and Kaposis' sarcoma associated herpesvirus) and a model poxvirus (Vaccinia) all inactivate the translational repressor 4E-BP1, stimulate the assembly of eIF4F complexes, and promote phosphorylation of the cap-binding subunit eIF4E. Strikingly, while all the viral model systems share the ability to promote eIF4F assembly, they use markedly different mechanisms to achieve this goal. Each of these mechanisms acts to manipulate the effective, available concentration of eIF4F-core and associated components, a critical parameter in regulating translation. Ongoing work in the lab is directed towards understanding how each of these different viruses regulates eIF4F assembly and activity. Current and Future Research Opportunities
Thomas Moran, Ph.D.Thomas Moran, Ph.D., Professor, Microbiology, MSSM The major emphasis of the Moran lab is the investigation of the interaction of virus with the mammalian immune system. Investigative studies are carried out in mouse model systems where the entire process from infection to recovery can be analyzed. Innate immunity and the transition to adaptive immunity, are studied using sophisticated cutting edge technology. When possible, information derived from animal models is translated into human immune studies using cells collected from donor blood samples. The mammalian immune response is comprised of two major components, the innate response that serves to prevent or slow the replication of invading pathogens, and the adaptive response that, upon activation, is responsible for eliminating the invader and protecting against reinfection. Once an infection is established, the innate response signals the activation of adaptive immunity. A key cell type responsible for the transition from innate to adaptive immunity is the dendritic cell. Dendritic cells (DCs) possess receptors that are capable of sensing the presence of bacteria, viruses or parasites. Receptor signaling leads to a maturational change in the DCs that endows them with the capacity to trigger adaptive immunity. The study of the interaction of microbes with DCs is a primary interest of the Moran lab. This work is currently being performed in vivo and in vitro using a mouse model system. In vivo studies monitoring the movement and function of DCs are providing unique insight into the initiation of adaptive immunity. The lab has demonstrated that different strains of Sendai and influenza virus exhibit differential abilities to induce DC maturation and secretion of type 1 interferon (an innate viral cytokine). These studies led to the identification of a mechanism involved in the triggering of DC maturation by viruses that depends upon virus replication and is independent of secreted type 1 interferon and toll-like receptor signaling. In collaboration with Dr. Carolina Lopez, a particular species of defective interfering particles produced in Sendai virus has been identified as a potent trigger of DC maturation. This molecule has enormous potential as an enhancer of immunity and continues to be a focus of exploration in the lab. Influenza virus codes for a protein called NS1 that has been reported to prevent the release of the important anti-viral cytokine, type 1 interferon. Work from our lab and others has shown that in addition to its inhibition of interferon, NS1 functions as a general anti-inflammatory agent and prevents the maturation of DCs. Thus, in a mouse model of influenza infection, the NS1 protein interferes with the transition to adaptive immunity allowing the virus time to replicate to high levels in lung tissue and assuring its dissemination to other hosts. Current studies include the analysis of NS function and the immune system's mechanisms for overcoming its antagonism. Another area of research is the study of the initiation of immunity by viruses using human cells. Three types of DCs are studied: those present in circulating blood: CD11c positive DCs and plasmacytoid DCs as well as DCs generated in culture from CD14 positive monocytes. The activation of these cells is measured by release of immunologically active proteins and genetic profiling analyzed by qRT-PCR. Using these techniques, we have identified genes that code for cytokines and chemokines, receptors and transcription factors and are activated in DCs after infection by virus . Of particular interest is the impact of viral antagonists on the maturation of DCs following exposure to virus. The interferon antagonist, NS1, found in all influenza viruses has been shown to inhibit DC maturation as well as innate immune functions. Robert Schneider, Ph.D.Robert Schneider, Ph.D., Professor, Microbiology, NYUSOM Molecular Mechanisms for Viral Induced Carcinoma and PathogenesisOur research effort is concerned with two areas of gene regulation related to viral mediated oncogenesis and disease pathogenesis: (1) inhibition of cellular protein synthesis by adenovirus (Ad), and (2) the function of hepatitis B virus (HBV) X protein (HBx) in cell transformation, pathogenesis and viral replication.
Current and Future Research Opportunities
Megan Shaw, Ph.D.Megan Shaw, Ph.D., Assistant Professor, Microbiology, MSSM My lab is interested in the interactions that occur between a virus and its host at the molecular level and how this knowledge may be used for designing better vaccines and for finding new antiviral drugs. The research involves basic molecular biology and virology techniques combined with RNAi, proteomics and high-throughput screening. Traditionally antiviral drugs have been designed to target viral proteins and four such drugs exist for influenza virus: the M2 inhibitors, amantadine and rimantadine and the neuraminidase (NA) inhibitors, oseltamivir and zanamivir. Unfortunately, widespread use of the M2 inhibitors has led to the development of resistant virus strains and there are also some recent reports of oseltamivir resistance. This leaves us in a vulnerable position, especially at a time when there is concern over the potential for another influenza pandemic. Viruses (particularly RNA viruses) encode a limited number of proteins and therefore they must rely on many host cell functions to complete their replication cycles. Therefore an alternative strategy would be to direct the drug at one of these essential host factors. The advantages of this are that the virus is far less likely to develop resistance and these drugs should also be effective against viruses that are already resistant to the current antivirals. Furthermore, as the dependence on cellular pathways is often a conserved feature of viral replication strategies it may be possible to find a single drug that is broadly effective against several viruses. Another focus of my lab is the host antiviral response and specifically the mechanisms that viruses use to block this response. Viral proteins with this activity are termed interferon antagonists and they are important determinants of pathogenicity. Nipah virus is a highly pathogenic, emerging paramyxovirus that produces four proteins from its P gene, all of which have the ability to prevent the induction of an antiviral response. The W protein which is found in the nucleus has particularly strong activity and the goal of the research is to understand its mechanism of action. This information could be used to design attenuated viruses for vaccine purposes or to find antiviral drugs that interfere with the function of the W protein. Current and Future Research Opportunities
Carol Shoshkes Reiss, Ph.D.Carol Shoshkes Reiss, Ph.D., Biology, NYU and Adjunct Professor, Microbiology, NYUSOM Viruses can enter the central nervous system (CNS) via the olfactory neuroepithelium. With one such virus, vesicular stomatitis virus, infection can result in lethal encephalitis or in the host's ability to activate both innate and acquired immune responses and clear the infection. Viral infections of the CNS occur in an immunologically privileged site. We have been studying the mechanisms by which interferons and other cytokines promote an antiviral milieu in neurons; this translational work focuses on influence of commonly available drugs on the host's innate immune responses to viral encephalitis. We have been studying the cell biology which is essential for viral assembly and release. Finally, we have been examining a recombinant VSV which is highly attenuated in the CNS and may potentially be a new vaccine vehicle or an oncolytic therapeutic. Current Research Opportunities
Future Research OpportunitiesThis work builds on previous studies on the recovery-promoting benefit of IL-12 administration and the mechanism of cytokine-mediated antiviral activities in neurons. The studies will be carried out using molecular biological approaches (rt-PCR, RNAse protection, in situ hybridization, microarray analysis), immunohistochemistry, knockout strains of mice, and drug treatment specific for enzyme systems to be explored such as isoprenylation and cannabinoids. This work has basic and translational applications for viral encephalitis, tumor treatment and vaccination. Viviana A. Simon, M.D., Ph.D.Viviana A. Simon, M.D., Ph.D., Assistant Professor, Medicine / Infectious Diseases, Microbiology, MSSM Dr. Simon's research focuses on HIV-1 pathogenesis and viral host interactions. We are especially interested in the human defense mechanisms and viral counter strategies. Host cells use DNA/RNA editing enzymes as ways to curb invasion from viruses. For example, members of the human APOBEC3G (APOlipoprotein B Editing Complex 3G) family have been shown to be active against exogenous retroviruses (HIV-1, HIV-2, Foamy), endogenous mobile genetic elements (e.g., LTR retrotransposons) and also DNA viruses (e.g., Hepatitis B). These cytidine deaminases restrict viruses by editing and non-editing mechanisms. Sequence variation is central to the ability of HIV-1 to evade immune responses and antiretroviral therapeutics. Over the past years, it has become clear that, if left unchecked, APOBEC3 editing enzymes are potent mutagens of retroviral genomes. The HIV-1 gene Vif effectively counters the antiretroviral activity of some of the APOBEC3 enzymes by inducing proteosomal degradation. Current Research Opportunities
Future Research Opportunities
Naoko Tanese, Ph.D.Naoko Tanese, Ph.D., Microbiology, NYUSOM Histone-binding properties of SWI/SNF chromatin remodeling complex and viral protein LANA. Genetic and biochemical approaches have led to the discovery of multiple protein complexes that activate or repress transcription by targeting histones or nucleosomes. Our lab isolated cDNA clones encoding the two largest subunits of the human SWI/SNF chromatin remodeling complex and demonstrated their role in transcriptional activation by steroid hormone receptors. We found that cell lines induced to over-express these proteins exhibit growth and cell cycle defects. Our results suggest that in addition to their role in transcription, SWI/SNF subunits that associate with chromatin might also function as a sensor in the DNA damage response pathway. Further, we have discovered that the largest SWI/SNF subunit binds to histones. In collaboration with Angus Wilson's lab (participating faculty) we are comparing nucleosome-binding properties of SWI/SNF with that of LANA, a viral chromatin-binding protein critical for establishment of latency in Kaposi's sarcoma-associated herpesvirus (KSHV). Benjamin R. tenOever, Ph.D.Benjamin R. tenOever, Ph.D., Assistant Professor, Microbiology, Emerging Pathogens Institute, MSSM Given the ever-present global burden of influenza virus and newly emerging pathogens such as yellow fever, and Dengue virus, the study of host-virus interactions can result in discoveries that have immediate impact on human health. We focus on the study of cellular recognition to these RNA virus infections, the host response to their replication, and the dynamic relationship between the virus and these cellular responses. Our laboratory uses many techniques to study host-virus interactions including genetic manipulation of both host and pathogen and classical molecular biology- and biochemistry-based applications. We are presently working in the following areas.
Current and Future Research Opportunities
Domenico Tortorella, Ph.D.Domenico Tortorella, Ph.D., Assistant Professor, Microbiology, MSSM Research InterestsHuman cytomegalovirus (HCMV) is a herpes virus that can establish persistence and latent infections. HCMV significantly contributes to the cause of birth defects in newborns such as hearing disturbances and mortality in immuno-compromised individuals such as transplant-recipients and HIV-infected persons. HCMV encodes for proteins that modulate cellular immune responses, in particular CD8+ cytotoxic T cell (CTL) activation, that allows HCMV to escape immune detection and establish latency. HCMV encodes for at least four gene products from the unique short region of the genome US2, US3, US6 and US11 that interfere with the CTL recognition of HCMV-infected cells by preventing the surface expression of major histocompatibility complex (MHC) class I molecules. This strategy would limit the frequency of CTLs directed against HCMV epitopes during the early-phase of HCMV infection. The HCMV US3 gene products are expressed during the immediate-early phase while HCMV US6 is turned on during the late-phase of HCMV infection. HCMV US2 is expressed during the early phase of infection shortly followed by HCMV US11 expression. HCMV appears to employ US2 and US11 during the early-phase of infection to avoid immune detection. HCMV appears to employ US2 and US11 during the early-phase of infection to avoid immune detection. The US2 and US11 proteins activate cellular complexes to target MHC class I molecules for degradation by the proteasome. The viral proteins utilize a cellular process that extracts and destroys aberrant proteins from the ER referred to as ER quality control, a process related to human diseases such as cystic fibrosis and emphysema. The laboratory projects focus on understanding the molecular details of how HCMV unique short proteins US2, US3, US6 and US11 down-regulate MHC class I molecules. These projects include the identification of the cellular components that participate in MHC class I destruction and defining the regions of the viral gene products that target class I molecules for degradation. These data would provide a paradigm of how these viral gene products manipulate the cellular machinery to block MHC class I antigen presentation. Current and Future Research OpportunitiesThe research opportunities extend to the immunological study of how HCMV manipulates the cellular machinery of dendritic cells. These studies include the analysis of the innate and adaptive markers to a HCMV infection. Derya Unutmaz, M.D.Derya Unutmaz, M.D., Associate Professor, Microbiology, NYUSOM The Molecular Machinery of human T Cell Activation, Differentiation and its Exploitation by HIVThe first long-term focus is to understand how T cells compute and integrate the signals from the environment to initiate different effector functions or differentiation programs. The complex signaling machinery of T cells allows the immune system to have a flexible and vigorous response against different pathogen challenges. The second and major focus of our lab is to understand how HIV exploits T cell activation and differentiation for its own survival. HIV has infected over 60 million and killed more than 20 million individuals worldwide. The infection continues to spread exponentially and kills 3 million people every year. Massive efforts over the past 20 years have failed to produce an effective and urgently needed vaccine. Infection of T cells by HIV requires their activation. Therefore it is not surprising that the hallmarks of HIV infection are chronic immune activation and destruction of its targets, the CD4+ T cells. However, we still do not understand how HIV exploits chronic immune activation and how it causes severe developmental and homeostatic dysfunction of the immune system. In the last several years we have made several very exciting discoveries that we believe have began to shed light into the highly complex immune pathogenesis of HIV infection. We initially demonstrated that HIV uses a Trojan horse like mechanism to be captured by the sentinels of the immune system, the dendritic cells, thus avoiding destruction, and possibly uses this mechanism to gain a foothold in the body during its transmission. We are now working to understand the mechanism by which HIV hijacks dendritic cells. Recently a subset of CD4+ T cells was identified as regulatory T cells (Tregs). The function of these cells is to suppress excessive T cell activation during unwanted immune responses such autoimmunity. We hypothesized that HIV targets and gradually depletes Tregs, thus removing the brakes of T cell activation, causing persistent immune activation. We have now discovered that Tregs are highly susceptible to HIV infection and are depleted during the late stages of the disease. Remarkably, we also found a highly significant correlation between the loss of Treg cells and the increase in activated CD4+ T cells in HIV infected individuals, as precisely predicted by our hypothesis. How Tregs suppress activation of other T cells is not known. A major impediment in working with Tregs is that they are only about 2% of human T cells and are difficult to grow in vitro. In order to decode the function of Tregs and their role during HIV infection we have developed a method to genetically reprogram conventional T cells into Tregs by ectopically expressing a master transcription factor called FoxP3. The FoxP3-engineered T cells behave just like naturally occurring Treg cells and can be generated in unlimited numbers. This method has now paved the way for identifying mechanisms that mediate Treg cell suppressive function. In summary, we would like to decode the complex sensory system of T cells that execute adaptable biological programs and to understand how HIV hacks into the "operating system" of these cells and exploits their "biocode" for its own survival. Current and Future Research OpportunitiesCurrently we don't have any open positions and future ones depend on funding. Lu-Hai Wang, Ph.D.Lu-Hai Wang, Ph.D., Professor, Microbiology, MSSM Our laboratory is interested in exploring the normal and oncogenic signal transduction processes of receptor protein tyrosine kinases (RPTKs) and their down stream signaling molecules focusing on Ros, insulin and insulin-like growth factor I receptors protein tyrosine kinases. From each of the three native RPTKs, we have generated oncogenic and various loss-of-function mutants and used them as tools to dissect the signaling pathways to identify specific signaling molecules important in the processes of cell transformation and oncogenicity. The techniques used include various molecular genetic approaches such as knock-out cell lines, anti-sense, siRNA, dominant negative blocking, as well as clinical specimens and transgenic animal models. These studies are coupled with biochemical analyses of protein-protein interactions to elucidate the functional roles of those signaling molecules. Yeast two-hybrid system approach has been used to unveil novel substrates of those RPTKs. The physiological functions of those novel signaling molecules are being investigated. Human cancer cell lines including those derived from breast, ovarian and prostate cancers are being used to explore the role of various RPTKs and related-signaling molecules in the development and progression of tumors. Current Research Opportunities
Future Research Opportunities
Angus Wilson, Ph.D.Angus Wilson, Ph.D., Assistant Professor, Microbiology, NYUSOM Herpesviruses constitute an important and widespread family of viral pathogens implicated in numerous human and animal diseases. A characteristic of these DNA viruses is their ability to follow two very different modes of infection: an acute or lytic mode that results in the production of new viral particles and a quiescent or latent mode that allows long-term persistence in the infected host. Our laboratory studies the mechanisms that allow an incoming virus herpesviruses to choose one mode over the other and the process of reactivation in which a latent virus is prompted by external signals to switch into lytic replication. We study two human viruses: Kaposi's sarcoma-associated herpesvirus (KSHV), for which latency is the predominant outcome of a new infection and herpes simplex virus-1 (HSV-1), which strongly favors lytic replication and only establishes latency in sensory neurons. In immunocompromised people (such as those with HIV/AIDS or following organ transplant), KSHV can give rise to endothelial and lymphoid tumors and in some regions of the world are a major source of mortality. Lytic replication by HSV-1 gives rise to everything from cold sores to irreversible corneal scarring and life-threatening encephalitis. Our work concentrates on viral transcription factors that serve as master regulators of these elaborate genetic switches. In KSHV, we study the lytic determinant RTA and pro-latent factor LANA, focusing on the dynamic interplay of these products and cellular factors that determines the lytic-latent switch. For HSV-1, our focus is the viral transcription factor VP16, which again is thought to be a key regulator of the developmental switch. VP16 is reliant on a cellular co-activator, HCF-1, for its activity. HCF-1 is critical for cell cycle progression, stem cell pluripotency and other developmental processes. Our goal is to understand how the transcriptional properties of HCF-1 relate to the viral life cycle and tissue tropism. Current Research OpportunitiesWe are using a variety of molecular and cell biology approaches to dissect the lytic/latent switches in KSHV and HSV. We have initiated a genome-wide screen to identify all of the RTA responsive promoters in the 140-kbp KSHV genome and are using molecular and bioinformatics approaches to understand how RTA directs the highly elaborate lytic replication program. This work will highlight points at which cellular signaling pathways impact on the basic genetic program, allowing the virus to adjust to differences in cell type and respond to different environmental cues. Work on LANA is focused on its interaction with cellular chromatin, a necessary function for the persistence of the latent viral genome. Lastly our studies of VP16/HCF-1 address the mechanisms that control the stability and subcellular localization of the HCF-1 protein as these are likely to be major determinants of HSV-1 lytic replication. By exploring these networks of virus-host interactions, we expect to discover novel regulatory mechanisms that are used by cells and subsequently pirated by the viral invaders. Future Research OpportunitiesA variety of projects are available for highly-motivated graduate students and postdoctoral fellows invoking everything from the mapping of mRNA transcripts and promoter elements using state-of-the-art tools of molecular biology to studies of subcellular localization by confocal microscopy. We have established a number of exciting collaborations with colleagues in New York and beyond that aim to broaden our studies of the lytic/latent switch to include changes in translational control, the influence of signal transduction cascades and the construction of recombinant viruses that carry mutations in defined regulatory sequences. Susan Zolla-Pazner, Ph.D.Susan Zolla-Pazner, Ph.D., Professor, Pathology, NYUSOM Because human immunodeficiency virus (HIV) is a chronic infection, patients are continuously stimulated by the viral antigens, which leads to very high levels of antibody to HIV and the presence in the blood of antibody-producing B cells. Thus, despite the immunosuppression of HIV-infected individuals, their HIV antibody response is extremely vigorous. We exploit this aspect of the disease to produce human monoclonal antibodies (mAbs). To do so, we culture infected individuals' peripheral blood cells in the presence of Epstein-Barr virus, which transforms the B cells and allows them to grow indefinitely. We use immunologic tests to identify those B cells producing HIV antibodies; we expand and clone them, and then fuse them to other cells to form "heterohybridomas," which indefinitely synthesize and secrete human mAbs to HIV. Using this technique, we made over 70 cell lines and produced mAbs to various parts of the virus. Although some of these mAbs have only slight biologic activity, others are extremely potent neutralizers of virus infectivity. We also investigate the antibodies responsible for protection and slowing disease spread throughout the body. These studies enable us to characterize the protective aspects of anti-HIV immunity, about which surprisingly little is known. Current Research Opportunities
Future Research Opportunities
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