Program Members

Summary

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.

Summary

Millions of people are infected with both HIV and HBV. Morbidity and mortality in HIV/HBV co-infection is higher than mono-infections and co-infection accelerates HBV-related liver disease with more frequent development of hepatocellular carcinoma (HCC), particularly when CD4 cell counts are low. Together with Dr. Haitao Guo, we are developing a murine model to study pathogenesis and HCC progression during HIV/HBV co-infection, which will be essential in evaluating mechanisms of infection as well as novel prevention methods, improved therapies, and curative strategies.

Summary

The Chang-Moore Laboratory at the Hillman Cancer Center, led by Patrick Moore and Yuan Chang, has focused on human tumor viruses. We identified Kaposi sarcoma-associated herpesvirus (KSHV/HHV8) and established its link to Kaposi sarcoma, a common AIDS-related cancer in the U.S. and parts of Africa. We sequenced the KSHV genome, developed serologic assays, assessed its prevalence, and characterized key viral oncoproteins. 
Recently, we discovered Merkel cell polyomavirus (MCV), and established its causal role in ~80% of MCC.  We characterized the early T antigen oncoproteins (large T and small T), and identified several novel cellular interactors for T antigens that open new avenues of investigating critical oncogenic signaling pathways. 

Our group has focused on many aspects of cancer etiology as modeled through oncogenic tumor viruses; as well as investigations of the epidemiology and basic biology of these viruses. Our ongoing research explores virus-host interactions, particularly in pro-proliferative and innate immune signaling pathways. Characteristics of our laboratory include the ability to work collaboratively with colleagues, to incorporate innovative technologies, and to develop a rigorous training/research environment. 

Summary

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. 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, Whiteside, Hiller, Lee, Manickam), Chikungunya virus (Silva) and Merkel cell polyomavirus (Chang/Moore).

Summary

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 38 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. He also has established a link between reovirus and blockade of immunological tolerance to newly introduced food antigen.

Learn more about Dr. Dermody's work.

Summary

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.

Summary

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. 

Summary

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.

Summary

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.

Summary

In my role as leader in AI for Cancer Research, I work closely with Hillman PIs and Hillman leadership to develop the AI infrastructure and capability to advance clinical operation, clinical research, and basic cancer research. I envision building a robust AI capability at Hillman that can meet the AI needs for cutting-edge cancer research and be adapted to address new challenges. My current cancer-related research includes:

1. Mechanism of infection and oncogenesis by KSHV
Goals: Using a combination of bioinformatics/machine learning, high throughput profiling (scRNA-seq, in-situ-seq, 16s-seq, etc), and bench experiments to delineate the mechanism of KSHV-induced cellular transform and oncogenesis, elucidate the pathogenesis of KSHV-associated cancers, and identify effective therapeutic targets and prognostic biomarkers. Through a long-term collaboration with Dr. SJ Gao, we have identified targets and pathways regulated by KSHV miRNAs (Nat. cell Biology, 2010), delineated the addicted cellular genes and networks by genome-wide CRISPR-Cas9 screening (MBIO 2019), performed the first genome-wide viral and cellular m6A profiling in multiple KSHV-infected systems (Nat. Microbiology 2018), and identified the signatures of oral microbiome in HIV-infected individuals with oral KSHV (PLOS PATHOGENS, 2019).

2. m6A mRNA modification/epitranscriptome and cancer
Goals: 1) Develop bioinformatics/machine learning tools to facilitate the functional study of m6A mRNA methylation and cancer. Using a combination of bioinformatics/machine learning and high throughput profiling technologies to 1) understand the mechanisms by which m6A regulates cancer and viral infection; 2) identify m6A-related clinical makers. m6A/epitranscriptome is a new and rapidly advancing area that studies modifications in mRNAs. My lab leads the development of computation tools for analyzing m6A profiling data and predicting m6A functions. The analysis pipeline for m6A sequencing, exomePeak, has been used widely and cited > 400 times (Google Scholar) by many high impact papers in Cell, Cell Stem Cell, Nature, Nature Cell Biology, Nature Neuroscience, Nature Genetics, and Cancer Cell. Using these tools, we have uncovered the reprogramming of viral and cellular m6A epitranscriptome during the life cycle of Kaposi sarcoma-associated herpesvirus (KSHV) (Nature Microbiology, (2018) 3(1):108-120) and reported common and distinct m6A regulation of innate immune response during bacterial and viral infection (Cell Death & Disease 2022, 13(3)). Besides, I have collaborated with other cancer biologists to uncover a cross-talk among m6A writers, erasers, and readers that regulates cancer progression (Science Advances, 2018 4(10)) and linked the increased activity of ALKBH5 with dysregulation of histone ubiquitination in cancers (Cancer Research, 2022/5).
 
3. Single-cell spatially-resolved transcriptomics (scSRT) analysis
Goals: 1) Develop the analysis and visualization pipeline for scSRT data(Nanostring CosMx, 10X Xenium, and Vizgen MERSCOPE), 2) Develop AI/machine learning tools for modeling tissue structure and disease pathology, and 3) apply scSRT to study immune microenvironment associated with tumor and viral infection. We have recently applied scSRT to reveal the molecular and immune signatures as well as pathological trajectories of fatal COVID-19 lungs (JMV, 2023)

4. Functional interpretable deep learning models and large language models for cancer genomics
Goals: 1) Develop novel deep learning models capable of cancer phenotype predictions and explain the underlying mechanisms. 2) ChatGPT-based prompt engineering for extracting knowledge about molecular regulatory mechanisms from literature. We have developed several genomics-based deep learning/AI tools for cancer prognosis and survival analysis, drug response prediction, and gene dependence prediction (Science Advances, 2021; Cancers, 2023). 

Summary

I am the principal investigator of an R21 grant titled Development of a biparatopic-domain antibody screening system, with the long-term goal of developing MSLN-targeting domain antibodies that will be utilized to design therapeutic reagents. I am also collaborating on a project involving Src-family kinase.

Summary

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.  Zoster is a major side consequence of many types of cancer or their treatment, particularly when either cause immune suppression. 

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) using human neuron cultures derived in vitro by differentiation of human stem cells or progenitors. We established this system 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 used live attenuated VZV vaccine, currently used to prevent chickenpox. While quite safe, the vaccine is not perfect, as  it often causes a rash, can cause full-blown chickenpox, and also go latent. It can give rise to Zoster in vaccinees.  We are evaluating how some of the 200+ changes in the vaccine (compared to its parent) contribute to attenuation, but placing them into a wild type virus background and assessing how the recombinant virus grows in validated human skin models and 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. 

Summary

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.

Summary

Epstein-Barr virus (EBV) is the causative agent of nasopharyngeal cancer (a type of head and neck cancer), stomach cancer and several types of lymphomas. Each year 200,000 cancers worldwide are caused by EBV. The presence of EBV in cancer cells also provides a unique opportunity for targeted therapy by forcing tumor cells to reactivate latent EBV. The Li lab is focusing on understanding the molecular mechanisms by which viral and host factors control the transition of EBV from latency to reactivation with a goal of developing novel therapeutic strategies to cure EBV-associated cancer.

Summary

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.

Summary

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.

Summary

Joseph T. Newsome is an Associate Professor in the Department of Pathology and Associate Director – Division of Laboratory Animal Resources at the University of Pittsburgh. He is also the Director of the UPMC Hillman Cancer Center Animal Facility Shared Resource. He is a team member of the Cancer Virology Program. His current focus and expertise are in management, biosecurity, biocontainment, facility design and operations, and cancer modeling, immunology, and virology. He is involved in national and industry level organizations such as the American College of Laboratory Animal Medicine, the Association of Primate Veterinarians, the Association of Laboratory Animal Science, The NASEM ILAR Roundtable, and the American Veterinary Medical Association. Newsome received a B.Sc. in microbiology, an M.S.  in pathobiology, and a DVM from the Ohio State University College of Veterinary Medicine. He is certified as a Diplomate of the American College of Laboratory Animal Medicine.

Summary

Dr. Rinaldo's research is focused on the relation of disease progression to dendritic cell function and reactivity of CD8 killer T cells to HIV and human herpesvirus 8 (HHV-8, or KSHV, the cause of Kaposi's sarcoma).

Summary

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.

Summary

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.

Summary

Antiretroviral drug discovery. While current antiretroviral drugs have transformed HIV infection from a life-threatening illness to a chronic condition, they do not clear the virus and require life-long administration. Chronic antiretroviral drug exposure can be toxic and promote drug resistance, underscoring the urgent need for new approaches to combat HIV. We have discovered compounds that interfere with the functions of HIV-1 Nef as a new approach to antiretroviral therapy. Unique to primate lentiviruses, Nef is critical for HIV-1 replication in vivo, immune escape of HIV-infected cells, and AIDS progression. Our small molecule HIV-1 Nef inhibitors potently suppress HIV replication and restore immune recognition of HIV-positive cells, raising the exciting possibility of their translational potential in new strategies to eliminate latent viral reservoirs.

Non-receptor tyrosine kinase structure, function and chemical biology. Protein-tyrosine kinases represent exciting drug targets for leukemia and many other cancers. Most current kinase inhibitors compete for ATP binding at the kinase domain active site. However, structural conservation of kinase active sites limits the clinical applications of ATP-competitive kinase inhibitors as well as their utility as chemical probes of individual kinase functions. To address these issues, we are pursuing drug discovery strategies to find small molecules that enhance the natural allosteric mechanisms associated with kinase domain regulation. Chemical library screening assays based on this concept are targeting members of the Src and Tec kinase families that are drivers of several hematopoietic malignancies.