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Over 500 million people worldwide are infected with chronic liver pathogens including chronic hepatitis viruses and zoonotic liver flukes, which leads to severe liver diseases. Additionally, several studies have demonstrated that HIV co-infection exacerbate chronic HBV/HCV-induced liver diseases, resulting in increased mortality. The increased prevalence of obesity and metabolic syndrome-associated non-alcoholic fatty liver disease in the United States and other developed countries also contributes to the global liver disease burden, with approximately 25% of the US population affected. The development of therapeutics against these diseases has been hindered by the lack of robust small animal models that accurately recapitulates human disease; in most cases rodents are not susceptible to infections or are resistant to disease. The lack of robust small animal models of human infectious diseases also poses a major hindrance in studying emerging diseases such as Zika virus. Innate immune cell infiltration including macrophage infiltration is a major component of the inflammatory milieu associated with chronic liver infections, non-alcoholic steatohepatitis and most human infections. Importantly, macrophages play a critical role in innate immune response, modulating gut microbiota, macronutrients (i.e., iron, lipids, etc.) sensing and metabolism, and tissue integrity/remodeling; therefore, elucidating the role of macrophage activation in human infectious diseases and metabolic syndrome-associated diseases will provide novel insight into the mechanisms of immune dysregulation and tissue pathogenesis. The Bility lab is broadly interested in elucidating the role of macrophage polarization in human infectious diseases and obesity/metabolic syndrome-associated diseases utilizing humanized mouse models carrying autologous functional human immune system, human liver cells and other human organ systems along with strong emphasis on collaborative translational research with clinical investigators. Major research efforts are: 1) Elucidating the role of macrophage polarization in chronic liver infections (HBV, HCV, liver fluke), HIV-hepatitis virus co-infections and associated liver diseases; 2) Elucidating the nexus between macrophage polarization and gut microbiota in fatty diet-induced non-alcoholic steatohepatitis and associated liver diseases; 3) Developing humanized mouse model for human diseases, including viral hepatitis, HIV, arbovirus, etc. In addition to his biomedical research, Dr. Bility also has strong interests in health security and pandemic/disaster response and management. Dr. Bility has extensive training and expertise in medical planning and operations for various contingencies including pandemic, chemical, biological, radiological, and nuclear (CBRN) disaster events in both domestic and international conditions.
The work of our group (jointly directed by Patrick Moore and Yuan Chang) has focused on human tumor viruses since the early 1990s when we identified Kaposi's sarcoma associated herpesvirus (KSHV/HHV8) and showed that this virus was causally associated with Kaposi's sarcoma, the most common AIDS-related cancer in the United States and the most common malignancy in parts of Africa. We sequenced the KSHV genome, developed serologic assays, determined its prevalence in human populations, and characterized many of its critical viral oncoproteins. We have continued to study virus-host cell interactions in the context of dysregulation of pro-proliferative and anti-apoptotic pathways. We recently identified the seventh human tumor virus, Merkel cell polyomavirus (MCV), from a Merkel cell carcinoma (MCC). We characterized the transcriptional products of MCV and described the early region viral T antigen oncoproteins. Our work has established that MCV causes ~80% of MCC: we determined that the virus is clonally integrated in MCC tumor cells; that human tumor-associated Large T (LT) antigens contain signature truncation mutations; that T antigen proteins are expressed in MCC tumor cells by novel antibodies we developed; and we are the first laboratory to show rodent cell transformation by MCV sT antigen but not the LT antigen. We have identified several novel cellular interactors for MCV T antigens that open new avenues of investigating critical oncogenic signaling pathways. We have focused on many aspects of cancer etiology as modeled through oncogenic tumor viruses.
I study the structure and function of macromolecular complexes, such as virus capsids, using cryo-electron microscopy (cryoEM) to detail protein folds and interfaces. The resolution achieved by cryoEM depends on the sample, and we routinely aim for 3-5 Ångstroms but in some cases can reach below 2 Å resolution. Systems currently being studied include herpesviruses and dsDNA bacteriophages such as HK97, lambda, D3, T5 and others. These tailed phages have important structural similarities with each other and with animal viruses such as herpesvirus, indicating a long evolutionary connection between them. The dynamic aspects of the virus lifecycle – assembly, DNA packaging, infection, and DNA delivery – are better suited to cryoEM study than crystallography, and the non-symmetric but functionally important regions such as the capsid portal vertex and the phage tail-tip can now be resolved due to recent advances in cryoEM technology. In recent work we imaged the phage HK97 portal vertex where the dodecameric portal ring occupies a 5-fold symmetric vertex of the icosahedral capsid. The portal has several vital functions, including nucleating capsid assembly, packaging and releasing the viral dsDNA, and binding the phage tail assembly. However, the nature of the symmetry mismatch with the capsid has been a long-standing puzzle, but one we could solve by cryoEM visualization to reveal that the capsid protein's scaffold domain interfaces with the portal in a quasi-symmetric 12-10 arrangement. This has a number of implications for capsid assembly and maturation that extend to the herpesviruses. With Fred Homa (Dept. MMG) we have visualized a series of herpesvirus capsid mutants that build a picture of the structural steps involved in DNA packaging and we are applying the phage analysis methods to similarly detail the symmetry-breaking portal vertex. Characterizing the structural and functional repertoire of a virus throughout its lifecycle reveals protein-protein and protein-DNA interactions that could be targeted by highly specific anti-virals. In addition to these viral studies, I am involved with numerous groups to enable their structural investigations of SARS2-Covid 19 (Ambrose/Watkins, Cheng/Shi), GPCRs (Cheng/Xie), encapsulins (NIH), lipid nanoparticles and exosomes (Song, CMU, Duquesne), and Merkel Cell Polyomavirus (Chang/Moore).
Terence S. Dermody is the Vira I. Heinz Distinguished Professor and Chair of Pediatrics at the University of Pittsburgh School of Medicine and physician-in-chief and scientific director at UPMC Children’s Hospital of Pittsburgh. He also is professor of microbiology and molecular genetics at the University of Pittsburgh School of Medicine.
With over 36 years of experience in basic virology and viral pathogenesis research, at his core, Dermody is a virologist. Most of his research has focused on reovirus, an important experimental model for studies of viral encephalitis in the young. His research contributions have enhanced an understanding of how these viruses enter into host cells and cause organ-specific disease.
Learn more about Dr. Dermody's work.
Dr. Glorioso has spent his career studying the molecular biology and immunology of HSV and the last 20 years developing HSV gene vectors for local and systemic therapies. He is a world-wide leader in this field and has the expertise to develop the technology related to the treatment of diseases of the peripheral and central nervous system. His interest in peripheral nerve disease has included nerve degeneration due to diabetes and cancer drug therapies that have led to treatments of animal models. Studies to understand the pathophysiology of chronic pain and the identification of gene therapy interventions that create effective pain therapies have been long standing interests and he was among the first to develop HSV vectors to treat pain. This research has culminated in clinical trials for treatment of cancer-related and arthritis pain. Dr. Glorioso has also focused his attention on neurodegenerative diseases that include SCA1 deficiency Alzheimer’s and Huntington's disease and the development of oncolytic vectors to treat brain tumors. Part of this research extends his application of HSV vectors for systemic delivery for treatment of metastatic cancer and muscular dystrophy. He has also recently developed HSV vectors for the creation and neuronal differentiation of human iPS cells derived from fetal brain and human dermal fibroblasts. His vector technology has been licensed to numerous biotech companies in which Dr. Glorioso serves as founder and/or consultant.
Research in my lab combines nuclear magnetic resonance (NMR) spectroscopy and other structural biology methodologies with biophysics, biochemistry, and chemistry to investigate cellular processes at the molecular and atomic levels in relation to human disease. We presently focus on two main areas in biology: gene regulation and HIV pathogenesis. To understand how biological macromolecules work and intervene with respect to activity and function, detailed knowledge of their architecture and dynamic features is required. Evaluation of the major determinants for stability and conformational specificity of normal and disease-causing forms of these molecules will allow us to unravel the complex processes associated with disease. Our group is also developing new NMR methods, such as 19F in-cell NMR.
Research in my lab is focused on the viral pathogenesis of hepatitis B virus (HBV) and antiviral discovery. HBV is the etiologic agent of viral hepatitis B, a disease affecting approximately 300 million people worldwide who suffer the high risk of liver failure, cirrhosis, and liver cancer. My laboratory aims at understanding the molecular mechanisms of HBV DNA replication and morphogenesis, with special focus on the biosynthesis and regulation of HBV covalently closed circular (ccc) DNA, which is the persistent form of HBV infection, and is the culprit for the failure of current antiviral therapies. Making use of the HBV cccDNA reporter cell line systems recently established by us, we are screening small molecule compound libraries for cccDNA inhibitors in a high throughput fashion, and two identified cccDNA formation inhibitors are currently under preclinical development. In addition, we are studying the innate immunity and oncogenic signaling pathways that regulate HBV replication, as well as identification and characterization of host restriction factors that inhibit HBV infection and propagation in human hepatocytes. We are also investigating the molecular mechanisms of HBV-induced liver cancer and finding therapeutic targets.
Dr. Homa's research is focused on understanding the molecular basis of herpes simplex virus type 1 (HSV-1) capsid assembly and viral genome packaging into the viral capsid. DNA encapsidation and cleavage involves the coordinated interaction of several HSV proteins that are essential for production of infectious virions. How these multi-protein assemblies associate and interact to accomplish this complex task touches on fundamental questions in biology. The HSV-1 genome is translocated into the icosahedral procapsid through a donut-shaped 'portal' that is present at one of the 12 vertices of the procapsid. This process is directed by the terminase complex, which consists of the HSV UL15, UL28, and UL33 proteins that function both as part of the ATP-hydrolyzing pump which drives DNA into the capsid, and also as a nuclease that cuts the concatemeric DNA at specific sites to yield a capsid containing the intact genome. The capsid is then stabilized by the addition of the capsid vertex specific component (CVSC), composed of the UL17 and UL25 proteins, which functions to retain the packaged DNA and to signal for nuclear egress of the mature DNA-filled capsid, as well as for nuclear attachment of the incoming, infecting capsid. Seven viral gene products are required for the stable packaging of viral DNA into the preformed HSV procapsid. Orthologs of these HSV DNA packaging genes are found in all three classes (alpha, beta, and gamma) of herpesviruses. Information obtained about the function of these proteins from these studies should therefore apply to other herpesviruses such as human cytomegalovirus, varicella zoster virus and Epstein-Barr virus.
Dr. Kinchington’ s research program focuses on the biology of the human alpha-herpesvirus Varicella Zoster Virus (VZV) and its interaction with human neurons and skin using novel model systems. VZV causes Chickenpox upon primary infection, but then remains with the Host for life in a latent state in sensory neurons. When the Virus reactivates, it causes Herpes Zoster, or Shingles, a painful and debilitating disease that causes significant human morbidity and long-term consequences. Chief among those is the development of long-term, intractable and debilitating chronic pain called post-herpetic neuralgia, or PHN. Zoster also causes many eye diseases that affect vision and even cause blindness, including stromal and retinal disease, ocular inflammation, ophthalmoplegia and total loss of corneal sensation.
Our research addresses two aspects of VZV. The first uses human cultured neurons to understand axonal transport of viruses in neurons, the maintenance of the latent state and reactivation from it. We aim to identify the role of a set of RNAs made during latency termed VLT (For VZV latency Transcript). Human neurons are derived in vitro from human stem cells or progenitors, and we established them as a solid experimental model in which VZV reactivation could be reliably achieved. A second VZV project is to identify the molecular determinants of the attenuation of the widely live attenuated VZV vaccine used to prevent chickenpox. While quite safe in most people, the vaccine is not perfect and sometimes causes a rash or even full-blown chickenpox. It can also go latent and give rise to Zoster. We are evaluating how some of the 200+ changes in the vaccine (compared to its parent) contribute to attenuation, but placing them into wild type virus, and then assessing attenuation in several validated human skin models, as well as in human neuron systems. Together, we may be able to develop an improved vaccine candidate that does not cause skin disease or reactivate to cause zoster.
Many noncoding (nc)RNAs execute diverse cellular functions and are equally important as their coding counterparts. In recent years, owing to the development of cutting-edge technology, such as next-generation sequencing, the detection of ncRNAs and elucidation of their functions have been facilitated. However, compared to the large number of identified ncRNAs, only a minute fraction has been ascribed a specific function, as more and more surprising aspects regarding their mode of action are being uncovered.
Our lab studies the molecular function of two enigmatic ncRNAs from the Epstein-Barr virus (EBV) called EBER1 (EBV-encoded RNA 1) and EBER2. EBV is an oncogenic gamma-herpesvirus with a prevalence of over 90% in the human population and is associated with several types of cancers, such as lymphomas and carcinomas. We apply modern RNA techniques as well as refine existing tools to uncover the modes of action of these viral transcripts. Utilizing these methodologies, our work has revealed a role in transcription regulation for EBER2 and how it ensures efficient viral replication.
A second focus of research is centered on studying the genome architecture of influenza viruses. Given the fact that influenza viruses harbor a genome consisting of RNA, many of the RNA-centric tools we employ to study ncRNAs can be applied to examine how the viral RNA genome is organized during replication. Utilizing these methodologies, we have uncovered molecular details of how the genome associates with viral proteins and how long-range RNA-RNA interactions are essential for viral packaging.
Dr. Mellors' laboratory focuses on resistance to antiretroviral drugs used for treatment and HIV prevention and on mechanisms of HIV persistence and strategies to deplete the reservoirs that are the barrier to curing HIV infection. His work on HIV reservoirs showed that low-level viremia persists in most individuals on long-term suppressive ART, and that the level of residual viremia is predicted by the level of viremia before ART. Current work focuses on identifying agents to reverse HIV latency and to eliminate HIV infected cells. The impact of innovative therapies on HIV reservoirs is being studied in Phase I/II trials of histone deacetylase inhibitors, monoclonal antibodies to immune checkpoint ligands, monoclonal antibodies to HIV envelope glycoproteins, and TLR agonists.
Dr. Moore focuses his research on the link between viruses and cancer. Through his research, he hopes to answer why some viruses evolve to cause cancer while others cause nothing worse than the common cold. Dr. Moore and his wife, Yuan Chang, MD, discovered Kaposi’s sarcoma-associated herpesvirus (KSHV), also called human herpesvirus 8. KSHV causes Kaposi’s sarcoma, the most common malignancy occurring in AIDS patients. Kaposi’s sarcoma, a disease in which cancer cells are found in the tissues under the skin or mucous membranes, can be very aggressive in people whose immune systems are suppressed. Prior to this discovery, scientists had worked for 20 years to find an infectious agent associated with Kaposi’s sarcoma. He and Dr. Chang also are the discoverers of Merkel cell polyomavirus, which is the culprit that causes the rare and deadly skin cancer, Merkel cell carcinoma.
Innate immunity of an organism is the inborn protection against invading pathogens. We are interested in the host innate immune response during virus infection and cancer. Although several basic principles of virus detection and host signaling have been identified, the specific mechanisms by which these pathways are modulated by host components during microbial infection or tumor progression remains poorly understood. Following are some of the specific research topic we are interested:
The Shair Lab studies the human tumor virus “Epstein-Barr virus,” a ubiquitous herpesvirus with 90-95% seropositivity among adults worldwide. The resulting chronic infection can lead to EBV-associated cancer, which can occur in the immune-competent, and the immune-compromised such as post-transplant patients and HIV+ patients. A major focus is to translate these molecular studies to benefit cancer risk assessment and to elucidate EBV molecular pathogenesis in EBV-associated B-cell lymphomas and epithelial cell cancers. One EBV-associated cancer we study is nasopharyngeal carcinoma (NPC), a cancer with high prevalence in specific ethnic populations such as Alaskan Inuits and Southeast Asians. Our projects apply principles in molecular virology, epidemiology, and cell biology. One unique resource at our disposal is a biobank of primary nasopharyngeal cells that we built at the UPMC Hillman Cancer Center. These samples are used to address questions regarding the cellular response to EBV infection in the nasopharyngeal epithelium using techniques such as 3-D cell culture, single cell RNA-sequencing, and microscopy. Furthermore, by studying the molecular signature of the cellular humoral response to EBV antigens, we have profiled the antibody repertoire in persons known to be at risk of developing NPC. This information can be used to develop a risk assessment assay for NPC. We are a highly collaborative team of diverse scientists that tackle questions in molecular virology using interdisciplinary science.
Studies on animal polyomaviruses have provided a wealth of information for cancer biology. Research on the simian and murine polyomaviruses (SV40 and PyV) led to the discovery of tumor suppressor proteins p53 and retinoblastoma (pRb) and unveiled the importance of tyrosine kinase activities in tumorigenic signaling. Our research exploits the human Merkel cell polyomavirus (MCV) that causes most Merkel cell carcinoma (MCC), a rare but deadly skin cancer that exhibits similarity to the tactile sensor “Merkel cells”. Despite the rarity of MCC, MCV infection is common, and nearly all healthy adults were asymptomatically infected and shed MCV from their skin. MCV is a small circular DNA virus that persists in currently unidentified dermal cells. There are two accidental events that are essential for MCV tumorigenesis and act as triggers that turn this common virus into a cancer-causing virus: insertion of linearized viral DNA into host cellular genome and introduction of a specific mutation that inactivates the viral replication enzyme.
By using molecular and cell biological approaches, our lab investigates: (1) MCV lifecycle processes, especially viral DNA replication, gene expression, and viral progeny production (2) MCV target cells wherein MCV persists or transforms into MCC, (3) biological triggers that disrupt the circular MCV DNA and facilitate insertion into host genome, and (4) critical cellular signaling activated by MCV proteins that promote MCC carcinogenesis. A full understanding of these events will help us prevent MCV-associated MCC, as well as identify therapeutic strategies for this deadly cancer.
In theory, inhibition of undesirable enzymatic activity responsible for disease can be accomplished either directly at the active site or indirectly at a distance (allostery). Important examples of selective enzyme inhibition come from the field of protein-tyrosine kinases, an emerging therapeutic target class for cancer and infectious diseases. Virtually all clinically useful kinase inhibitors to date compete for ATP binding at the kinase domain active site. However, the high degree of protein kinase sequence and structural homology limits the development of highly selective ATP-competitive kinase inhibitors. Alternative drug discovery avenues include allosteric inhibitors that target structural features outside of the kinase domain active site that are unique to individual kinase subfamilies. Allosteric inhibitor mechanisms are likely to exhibit greater specificity for their intended kinase targets, and may also stabilize kinase domain conformations that promote the action of existing inhibitors targeting the active site. Based on these principles, we are actively engaged in a drug discovery campaign to find small molecules that enhance the natural allosteric mechanisms associated with kinase domain regulation. We have developed high-throughput screening approaches based on this concept to identify selective inhibitors for protein-tyrosine kinases of the non-receptor class, including members of the Src, Fes/Fps and Abl kinase families. Selective inhibitors emerging from these screens have promise for future development in the treatment of several forms of leukemia, multiple myeloma, and HIV/AIDS.