Principal Investigator

Kara Bernstein, PhD
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Location

2.35 University of Pittsburgh Cancer Institute
5117 Centre Avenue
Pittsburgh, PA 15213

Research Description

Repair of DNA damage is crucial to prevent accumulation of mutations that can cause human disease, such as cancer. Our lab studies how double-strand breaks in the DNA, one of the most lethal types of DNA lesions, are repaired. Many proteins are important for DNA repair including the Shu complex and the Rad51 paralogs, whose mutation is associated with cancer predisposition and Fanconi anemia. Our lab uses cell biological, molecular, and genetic approaches to study the role of double-strand break repair proteins, such as the Shu complex and the Rad51 paralogs, in response to DNA damage. By understanding the mechanism of double-strand break repair and the role of DNA repair proteins in this process, we will uncover mechanisms of tumorigenesis and cancer progression. We will then use this knowledge to aid in diagnosis/prognosis of different types of cancers and to find novel therapeutic targets. 

Dr. Bernstein conducts her research at the University of Pittsburgh Cancer Institute. 

Members 

Braulio Bonilla - Graduate Student

Thong Luong - Graduate Student

Sarah Hengel - Post Doctoral Associate



Principal Investigator

Gutian Xiao, PhD
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and

Zhaoxia (Julia) Qu, PhD
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Location

1.18 Hillman Cancer Center
5117 Centre Avenue
Pittsburgh, PA 15213

Research Description

NF-κB is a family of transcription factors that control expression of numerous genes involved in diverse biological processes, including inflammation, immune response, and cell growth.  NF-κB activity is normally inhibited by IκBs (Inhibitors of NF-κB) or IκB-like protein p100.  Accordingly, NF-κB activation requires IκB degradation or p100 processing to selectively degrade its C-terminal IκB-like domain.  The IκB degradation depends on an IκB kinase (IKK) complex, which consists of two catalytic subunits IKKα (IKK1) and IKKβ (IKK2), and one regulatory subunit IKKγ (NEMO), while the p100 processing is specifically mediated by IKKα and its upstream kinase NIK, NF-κB-inducing kinase.  These two major mechanisms leading to NF-κB activation are now termed canonical and non-canonical NF-κB signaling pathways, respectively.  



 

 

 

 

 

 

 

 

 

 

 

Activation of the NF-κB signaling pathways, particularly the canonical signaling pathway, is tightly regulated and rapidly curtailed following the initial activating stimulus.  Transient activation of NF-κB is physiologically important because persistent activation of either pathway can result in deleterious or even fatal conditions, such as septic shock, inflammatory diseases, autoimmune diseases, and cancers.  Although the molecular mechanisms by which NF-κB is induced under physiological conditions have been well defined, how NF-κB is aberrantly activated for human pathogenesis remains largely unclear. Given the fact that it is unfeasible to block NF-κB activation for disease therapy using ‘classical’ NF-κB inhibitors because of the physiological importance of NF-κB in humans, it is of interest and importance to address the difference in the pathogenic and physiological activation of NF-κB, which is important for the development of novel approaches to specifically target pathogenic NF-κB activation for disease prevention and treatment.  Currently, we are energetically studying how NF-κB is constitutively activated for the pathogenesis and therapy resistance of the following diseases and translating this knowledge into clinical settings.

1. Cancers

A. Viral Oncogenesis. We are focusing on two NF-κB-dependent oncogenic viruses: human T-cell leukemia virus type I (HTLV-I) and Kaposi's sarcoma herpesvirus/human herpesvirus-8 (KSHV/HHV8).  While HTLV-I is the etiologic agent of adult T-cell leukemia/lymphoma (ATL), KSHV causes Kaposi's sarcoma (KS), primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD).  Interestingly, both HTLV-I and KSHV are often detected in individuals infected with HIV. In fact, KS is the most prevalent malignancy among patients with AIDS.  Currently, no effective therapies exist for these fatal diseases.

B. Cellular Oncogenesis. We study the top three deadliest tumors-lung, breast and colon, which account for approximately 241,000 deaths every year in the United States alone.  We are investigating how NF-κB is deregulated in tumor cells and tumor microenvironment, particularly tumor-associated inflammatory cells, as well as how deregulated NF-κB promotes the formation, progression, metastasis and chemoradioresistance of these solid tumors.  We are also actively investigating human leukemia/lymphomas associated with somatic mutations of the nf-κb2 gene and one hematologic malignancy termed early T-cell precursor acute lymphoblastic leukemia (ETP-ALL), a newly identified type of highly lethal pediatric leukemia with no known cause or cure.  Recently, we have established the first reproducible and the only available in vivo model for studying this aggressive childhood leukemia.

2. Inflammatory and Autoimmune Diseases.  In addition to tumors, we are also interested in chronic obstructive pulmonary disease (COPD), colitis, multiple sclerosis (MS) and rheumatoid arthritis (RA).  In particular, we are investigating the molecular and cellular mechanisms by which NF-κB is able to promote COPD and colitis for the development of lung and colon cancers, but NF-κB-driven MS and RA are not associated with tumorigenesis.

3. Graft-Versus-Host Disease (GVHD).  Hematopoietic stem cell transplantation (HSCT) is an effective therapy for patients with a broad range of hematologic malignancies, and is the only potential option for several types of leukemia that no effective therapy exists, such as ATL and EPT-ALL.  However, allogeneic HSCT (alloSCT) causes GVHD in approximately 30-70% of patients, increasing morbidity and mortality as well as the cost of care.  Given the role of NF-κB in inflammation and inflammation-associated diseases, it is interesting to investigate whether and how NF-κB contributes to the development of GVHD and more importantly to target NF-κB for the prevention of GVHD.

Lab Members:

Xin Chen - Postdoctoral Associate

Yixin Zhang - Postdoctoral Associate



Principal Investigator

Saumendra N. Sarkar, PhD
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Location

1.8 Hillman Cancer Center
5117 Centre Avenue
Pittsburgh, PA 15213

Research Description

Innate immunity of an organism is the inborn protection against invading pathogens. Because it is inborn, and entrusted with the protection of host from a vast array of previously unknown invaders, the innate immune system generates a generalized alert response upon pathogen detection. This alert is chemically mediated by a class of molecules called Cytokines. A critical task for this host protection system is to distinguish foreign or non-self, from self, and initiate their destruction or containment. The sensors or the receptors of the innate immune system accomplish this by recognizing specific molecular patterns, which are common to pathogens or pathogen associated molecules, but absent in the host. We focus on a particular subset of these sensors/receptors, which are involved in sensing virus infection.

In order to protect the host from viral invasion, the innate immune system has evolved sensors to detect the viral nucleic acids. Several unique features of virally produced DNA or RNA are exploited to distinguish viral nucleic acids from that of the host. One such unique nucleic acid is double-stranded RNA (dsRNA)—a common byproduct or intermediate in viral genome replication. In mammals, receptors like Toll-like Receptor 3 (TLR3), Retinoic acid-Inducible Gene I (RIG-I) and Melanoma Differentiation-Associated gene-5 (MDA5) are the three known sensors of dsRNA. Single-stranded viral RNA is sensed by Toll-like Receptor 7 and 8 (TLR7 and TLR8), while viral DNA is detected by Toll-like Receptor 9 (TLR9), and other less well characterized receptors.

We study two related aspects of innate immunity: (A) the signaling process involved in cytokine production after virus infection and (B) develop modulators for these signaling pathways. To understand the details of the networks involved in transcriptional induction or ‘switching on’ of genes following the detection of viral nucleic acids, we use various immortalized human cell lines engineered to make TLR3 and TLR7, as model systems. These studies have led us to discover new roles of protein modifications (e.g. tyrosine phosphorylations) involved in TLR3 signaling. We have shown how these phosphorylations control subtle modifications of transcription machinery (transcription factors). Continuing this line of investigation we are now trying to understand how other signaling networks interact and modulate the innate immune signaling pathways in human cells.

In a separate but related project we are identifying new modifiers of innate immune signaling pathways using high throughput screening. Activation of innate immune receptors by their natural microbial agonists leads to up-regulation of a series of pro-inflammatory and cytokine genes to neutralize the infection and shape the subsequent acquired immune response. On the other hand, excess stimulation of the receptor system from invading pathogens or from internal tissue damage products, cause several major inflammatory diseases such as atherosclerosis, asthma, bacterial sepsis and rheumatoid arthritis. Besides chronic inflammatory diseases, innate immune receptors have also been linked to cancer. The most established one is the gastrointestinal malignancy. Epidemiological and genetic evidences have also established links between TLR response and ovarian, prostate, breast and several other cancers. Thus, modulation of innate immune receptor signaling pathways offers an attractive method to fight such diseases. Proofs of this principle have been already established in several cases. Among other TLRs, TLR3 has been shown to mediate inflammation and pathogenesis of viral infection. TLR3 deficient mice are more resistant to lethal infection by West Nile virus than wild type mice. Similarly, TLR3 increases disease morbidity and mortality from Vaccinia and Phlebovirus infection. Therefore, in specific viral infection models, TLR3 may contribute not only to host defense but also to pathogenesis.

We have established cell-based screening systems for dsRNA mediated gene induction. Currently we are screening chemical and genetic modifiers of TLR3 and RIG-I signaling pathway. Additionally, we are in the process of establishing cell-based screening system for TLR7 and TLR8 in order to identify modifiers of their signaling pathways.

Dr. Sarkar conducts his research at the University of Pittsburgh Cancer Institute.

Members

Lulu Shao - Post Doctoral Associate



Principal Investigator

Patrick S. Moore, MD, MPH
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Location

1.8 Hillman Cancer Center
5117 Centre Avenue
Pittsburgh, PA  15213

 

Research Description

We study 1) Kaposi’s sarcoma-associated herpesvirus (KSHV), the viral cause of Kaposi’s sarcoma, 2)  Merkel  cell  polyomavirus  (MCV), the viral cause of Merkel cell carcinoma and 3) methods to search for undiscovered human tumor viruses. Our recent studies on KSHV have shown that its major latency protein evades typical protein processing pathways to avoid provoking a cell-mediated immune response. We also have found that both KSHV and Epstein-Barr virus (EBV) undergo programmed frameshifting to generate novel latent proteins. This allows these viruses to increase their phenotypic diversity within tight biological constraints on their genome size. Surprisingly, these two distantly related viruses generate frameshifted proteins that are nearly identical to each other.

To search for new human tumor viruses, we have developed a technique called digital transcriptome subtraction (DTS) that allows us to sample tumor mRNA profiles for foreign transcripts. Unlike other new pathogen discovery techniques, DTS is quantitative so that we can essentially rule out infection if no foreign transcripts are found. We have successfully used DTS to measure KSHV transcription in infected cell lines, and we have demonstrated that an AIDS-related cancer, squamous cell conjunctival carcinoma, is unlikely to be caused by an exogenous infection.

Using DTS, we discovered Merkel cell polyomavirus (MCV), the likely cause of ~80% of Merkel cell carcinomas. MCV is the first polyomavirus to be found that is a likely cause of human cancer. We are characterizing the basic biology of this virus in host cell transformation, and we are searching for other diseases that may be related to MCV infection. We are developing monoclonal antibodies and serologic tests that will be useful diagnostic markers for infection. We have recently found a unique mutation in tumor-derived MCV that sheds light on tumor cell evolution and the fundamental mechanism for Merkel cell carcinogenesis. Recent studies by others have confirmed our initial findings for the role of MCV in MCC. Our laboratory has now discovered and characterized two of the seven known viral causes of human cancer. We are actively examining other cancers to search for additional human cancer viruses.

Dr. Moore conducts his research through the University of Pittsburgh Cancer Institute.

Lab Members: 

Jennifer Alvarez Orellana - Post Doctoral Associate

Bizunesh Abere Alamirew - Post Doctoral Associate



Principal Investigator

JoAnne L. Flynn, PhD
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Location

5065 Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15260

Research Description

Bone-marrow derived macrophages display heterogeneous phenotypesMy primary interest is in the interaction of pathogens with the host, with special emphasis on the immune mechanisms that protect against or exacerbate disease. Our focus is on Mycobacterium tuberculosis, the organism responsible for tuberculosis, which causes 2 million deaths per year worldwide. We are investigating the immune responses required for protection against tuberculosis, and the effect of these immune responses on both the host and the bacterium. We specifically study cytokine production, macrophage activation, and T cell subsets (CD4+ and CD8+ T cells) that are important in tuberculosis.

CD20... T cell- and B cell-mediated adaptive responses originate from cell-cell interactions that are initiated in lymph nodesFinally, we have a strong interest in the immune mechanisms responsible for maintaining a latent M. tuberculosis infection, and how deficiencies in the immune response can result in reactivation of disease. Our work is done in two model systems: mice and non-human primates. We have vaccine studies, drugs studies, and basic immunologic and pathogenesis studies ongoing. We also participate in projects involving mathematical modeling of the immune response to M. tuberculosis, and our plan is to incorporate nuclear imaging of live animals into our research.

Lab Members

Kara Kracinosky, Vet Tech  Joseph Zeppa, Postdoctoral Associate
Amy Fraser, Lab Manager Jake Borish, System Analyst
Alex White, Data Analyst
Jaime Tomko, Senior Research Specialist
Pauline Maiello, Data Analyst
Cassaundra Ameel, Research Technician
Lonnie Frye, Medical Imaging Technician
Sharie Ganchua, Graduate Student

Chelsea Causgrove, Senior Research Specialist

 

 Tonilynn Baranowski, Research Technician

Caylin Winchell, Post doctoral Associate

Erica Larson, Post doctoral Associate (Scanga Lab)




Principal Investigator

Neal A. DeLuca, PhD
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Location

547 Bridgeside Point II
450 Technology Dr.
Pittsburgh, PA 15219

Research Description

Repression and activation of persisting HSV genomes: Herpes simplex virus can undergo either a productive infection, where all the viral genes are expressed culminating in the production of progeny virus and cell death, or it can enter a latent state, which is characterized by the relative lack of viral gene expression, genome persistence, and cell survival. The latent state typically occurs only in neurons, and may involve the attenuation of immediate early (IE) gene expression, and thus the lack of later viral gene expression. The IE protein ICP0 has been shown to facilitate the transition from the latent to the lytic state, thus leading to reaction episodes that are typical of herpesviruses. We have been investigating the behavior of viruses that do not express any of the five IE proteins upon cellular infection. While the viral genomes are transcriptionally quiescent and cytopathic effects are not seen, they can be rendered transcriptionally active by supplying ICP0 in trans. Thus this system has some of the key features associated with HSV latency, but is also more amenable to biochemical and molecular study. We have found that quiescent genomes are largely repressed and exist in multiple states that differ with respect to nucleosome packaging, histone acetylation and methylation, and heterochromatin formation. The result is a stochastic mix of epigenetic states that differ with respect to the expressibility of the genome. We study the ability of viral activator proteins to overcome these repressive states and their mechanisms of action.

Virus-cell interactions affecting HSV gene expression:  In its productive life cycle, the genes of HSV are expressed in a sequential manner, with those controlling subsequent gene expression produced very early in infection. One of these, ICP4, is required for productive virus infection because it activates the expression of the remaining 80 or so early and late genes. ICP4 activates early and late genes by different mechanisms involving different interaction with TFIID, mediator, and other cellular transcription factors. To study these mechanisms, we examine the association of ICP4 and cellular transcription complexes on HSV promoters during infection, the regions of ICP4 that are important for these interactions are determined, and subsequently the effects of these interactions on the transcription and hence expression of different classes of HSV genes is determined. In addition, we have discovered that there are regions of ICP4 that are not required for productive viral growth in non-neuronal cells, but are absolutely required for function in neurons of the trigeminal ganglia, the site where HSV establishes latency. The basis for this requirement is current under study.

Members

Frances Sivrich, Research Technician

Mitchell Harancher, Research Assistant, Dembowski lab



Principal Investigator

Cristian Apetrei, MD, PhD
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Location

9044 Biomedical Science Tower III
3501 Fifth Avenue
Pittsburgh, PA 15260

Research Description

My laboratory is interested in the study of the HIV/ SIV diversity and pathogenesis. The AIDS pandemic is produced by two different viruses, HIV-1 and HIV-2. These two viruses resulted from cross-species transmissions of SIVs, the viruses that naturally infect nonhuman primate species (NHPs) in Africa. HIV-1 resulted from 4 cross-species transmissions of SIVcpz/gor that infects chimpanzees and gorillas in West-Central Africa. HIV-2 emerged after 8 cross-species transmissions of SIVsmm that infects sooty mangabeys in West Africa. As SIVs naturally infect more than 40 species of non-human primates (NHPs) in Africa, our major concern is whether or not the remaining viruses infecting other species of African NHPs pose a major threat for humans. Our studies revealed that cross-species transmission of SIVs to humans are not the only requirement for the emergence on new virus strains and suggested that viral adaptation in the new host may play a decisive role for this event. Understanding the mechanisms of viral adaptation to new hosts upon cross-species transmission is of major interest for my laboratory. Using monkey models, we study the mechanisms of viral adaptation associated with viral emergence. Also, in order to better understand the AIDS pathogenesis, we are using various models of SIV infection in natural hosts. In African monkeys, SIV are not pathogenic in the vast majority of cases. My group is involved in the study of all currently available models (sooty mangabeys, African  green monkeys and mandrills) and generated significant results that challenged core paradigms of SIV pathogenesis. These studies may help us to control HIV infection in patients. Since no vaccine strategy currently developed seems to be effective, these alternative approaches may be essential in the control of AIDS pandemic.

Dr. Apetrei conducts research through the Center for Vaccine Research.  Learn more>



Principal Investigator

Joseph C. Glorioso, III, PhD
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Location

433 Bridgeside Point II
450 Technology Dr.
Pittsburgh, PA 15219

Research Description

Dr. Glorioso has established a 35-year history of research related to the basic biology and genetics of herpes simplex virus. His contributions to the field include defining antiviral immune responses to infection, the genetics of viral pathogenesis and latency, and mechanisms of viral infection. Furthermore, he has been a pioneer in the design and application of HSV gene vectors for the treatment of nervous system diseases such as peripheral neuropathies, chronic pain and brain tumors. He continues to be a worldwide leader in the HSV gene vector field through the creation of innovative gene vectors and the development of manufacturing methods for Phase I and Phase II human clinical trials for pain gene therapy. His enkephalin vector showed considerable promise in a Phase I human trial to treat cancer pain and phase II testing is underway. These trials were sponsored by Diamyd Medical AB in Stockholm. Dr. Glorioso is a Diamyd stockholder.

Herpes simplex virus infection of a tumor cell monolayer. Uninfected cells are outlined in blue, infected cells are red turning green following virus replication Dr. Glorioso’s most recent research has focused on (i) the design and application of HSV gene vectors for exploring the molecular events that occur in sensory afferents that are involved in the transition from acute to chronic pain, (ii) the development of retargeted oncolytic HSV vectors for specific infection and replication in human glioblastomas and applications to treatment of xenograft models of human brain human brain tumors, (iii) the creation of novel HSV vectors that cross the blood brain barrier by transcytosis followed targeted infection and gene expression in spiny neurons of the striatum; these vectors are being applied to treatment of animal models of Huntington’s disease and (iv) the use of HSV gene vectors for the creation of induced pluripotent stem (iPS) cells and the identification of transcriptional regulatory and signaling processes that participate in cellular reprogramming. 

Over the years, his laboratory has studied the structure/function domains of the HSV envelope glycoproteins that play a role in cognate receptor recognition and activation of the fusion/entry mechanism. HSV relies on 4 essential glycoproteins (gD, gB, gH, gL) to gain entry into cells. gD binding to its natural receptors, HVEM or nectin-1, results in signaling events required for activation of the gB-gH/gL membrane fusion apparatus. Virus envelope fusion with cell membranes releases the virus capsid into the cytoplasm whereupon it is trafficked to the nucleus, viral DNA is released into the nucleoplasm and the replication cycle is initiated. These studies have enabled the genetic manipulation of these attachment/entry function to create viruses with novel tropisms for neurons and tumor cells. For example, we have engineered HSV vectors for infection of stem cell markers, tumor markers and neurotrophic factor receptors. The safety of these vectors have been further enhanced by microRNA control of essential gene expression in normal brain.    

Glorioso, Vero CellsRetargeted, miR controlled vectors are also being exploited for selected gene expression in neurons of the peripheral and central nervous system. Of particular interest are a new generation of vectors that express neuron silencing by drug activated ion channels. The application of neuron silencing methods hold great promise for mapping neurons involved in cognitive processes and chronic pain signaling.

Members

Fang Han, Tsinghua Univ. Visiting Scholar
Mindgi Zhang, Senior Research Specialist

Ceren Tuzmen, Postdoctoral Associate

Sara Artusi, Postdoctoral Associate



Principal Investigator

Jennifer Bomberger, PhD
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Location

445 Bridgeside Point II
450 Technology Dr.
Pittsburgh, PA 15219

Research Description

Viral-bacterial interactions in the lung.  A principal focus in the Bomberger lab is exploring the mechanistic basis by which viral infections promote the development of chronic bacterial infections in the lung, particularly in the setting of chronic lung diseases, like Cystic Fibrosis (CF), bronchiectasis and chronic obstructive pulmonary disease (COPD). Dr. Bomberger’s recent publications provide compelling evidence that respiratory viral infections, and the antiviral immune response to them, drive P. aeruginosa to transition from acute to chronic infection. Current studies in the lab are focused on elucidating molecular mechanisms that govern the innate immune induction of biofilm in the lung. Working to take her work from the bench to the bedside, Dr. Bomberger collaborates with Dr. Stella Lee in Otolaryngology at UPMC to examine viral-bacterial interactions in the sinuses of patients with chronic lung disease. The goal of these studies is to examine the adaptation and transmission of P. aeruginosa between the upper and lower respiratory tracts during viral exacerbations. These studies include novel genomic approaches, in collaboration with Dr. Vaughn Cooper in MMG, to capture the P. aeruginosa diversity in both anatomical sites and determine if this is altered with viral infection in a way that promotes disease progression. The long-term goal of this collaborative project is to translate observations at the bench to new therapeutic strategies to prevent chronic bacterial infections in patients with chronic rhinosinusitis, focusing on iron chelation therapy. 

P. aeruginosa targets pro-resolving lipid mediators in the lung. Approximately ninety-five percent of deaths in CF are attributed to P. aeruginosa infection and the resulting chronic inflammatory response in the airway. Lipoxins are bioactive eicosanoids that mediate resolution of inflammation and are dramatically reduced in the CF airway. Dr. Bomberger’s laboratory has demonstrated that a secreted P. aeruginosa protein Cif reduces lipoxins in the airway and thus, prevents the resolution of inflammation in the CF airways. These studies are the first to show bacterial inhibition of pro-resolving mediators, as well as describe a new bacterial virulence mechanism. In addition to Cif’s regulation of lipoxin in the airways, Dr. Bomberger’s laboratory is also examining antimicrobial functions for lipoxin in the airways, with the long-term goal of adapting stable lipoxin orthologs for therapeutic applications in chronic lung disease. 

Identification of P. aeruginosa biofilm inhibitors.  Dr. Bomberger’s laboratory utilizes in vitro live-cell imaging systems to culture P. aeruginosa biofilms in association with host airway epithelial cells. Due to a lack of small animal models that suitably model P. aeruginosa biofilm growth in vivo, this model allows the study of bacterial biofilm development in the lung. In collaboration with Drs. Ronald Montelaro (MMG, Center for Vaccine Research) and Mark Gladwin (PACCM) at the University of Pittsburgh, Dr. Bomberger’s laboratory is developing new antimicrobial therapies that disrupt P. aeruginosa biofilms growing in the lung. Dr. Bomberger’s laboratory recently reported that an engineered antimicrobial peptide (WLBU2) disrupts incredibly antibiotic resistant bacterial biofilms grown during a viral coinfection, while concurrently reducing viral burden. Dr. Bomberger’s group has also studied the antibiofilm properties of sodium nitrite by targeting bacterial respiration pathways. Truly translating these sodium nitrite studies at the bench to the bedside, the Cystic Fibrosis Center at the University of Pittsburgh is funded to conduct a clinical trial to examine the efficacy of sodium nitrite as a novel antimicrobial therapy for Cystic Fibrosis patients.

Members

Anna Zemke - Asistant Professor, Department of Pulmonary and Critical Care Medicine

Catherine Armbruster - Postdoctoral Associate

Paula Zamora Vargas - Postdoctoral Associate

Leah Krainz - Research Technician

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