Search results for: Michael G. Katze

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article

Evaluation of the innate immune responses to influenza and live-attenuated influenza vaccine infection in primary differentiated human nasal epithelial cells

Adriana Forero, Katherine Fenstermacher, Nicholas Wohlgemuth, Andrew Nishida, more

Vaccine > 2017 > 35 > 45 > 6112-6121

The host innate immune response to influenza virus is a key determinant of pathogenic outcomes and long-term protective immune responses against subsequent exposures. Here, we present a direct contrast of the host responses in primary differentiated human nasal epithelial cell (hNEC) cultures following infection with either a seasonal H3N2 influenza virus (WT) or the antigenically-matched live-attenuated...

article

A Systems Approach Reveals MAVS Signaling in Myeloid Cells as Critical for Resistance to Ebola Virus in Murine Models of Infection

Mukta Dutta, Shelly J. Robertson, Atsushi Okumura, Dana P. Scott, more

Cell Reports > 2017 > 18 > 3 > 816-829

The unprecedented 2013–2016 outbreak of Ebola virus (EBOV) resulted in over 11,300 human deaths. Host resistance to RNA viruses requires RIG-I-like receptor (RLR) signaling through the adaptor protein, mitochondrial antiviral signaling protein (MAVS), but the role of RLR-MAVS in orchestrating anti-EBOV responses in vivo is not known. Here we apply a systems approach to MAVS^−/− mice infected with either...

article

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus

Jason E. McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, more

BMC Systems Biology > 2016 > 10 > 1 > 1-12

Background The complex interplay between viral replication and host immune response during infection remains poorly understood. While many viruses are known to employ anti-immune strategies to facilitate their replication, highly pathogenic virus infections can also cause an excessive immune response that exacerbates, rather than reduces pathogenicity. To investigate this dichotomy in severe acute...

article

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology

Angela L. Rasmussen, Michael G. Katze

Cell Host & Microbe > 2016 > 19 > 5 > 611-618

Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehensive studies of population-level responses to infection and provides novel methods for predicting clinical...

article

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism

Jennifer Tisoncik-Go, David J. Gasper, Jennifer E. Kyle, Amie J. Eisfeld, more

Cell Host & Microbe > 2016 > 19 > 2 > 254-266

Pandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data uncovered relationships...

article

Flavivirus Antagonism of Type I Interferon Signaling Reveals Prolidase as a Regulator of IFNAR1 Surface Expression

Kirk J. Lubick, Shelly J. Robertson, Kristin L. McNally, Brett A. Freedman, more

Cell Host & Microbe > 2015 > 18 > 1 > 61-74

Type I interferon (IFN-α/β or IFN-I) signals through two receptor subunits, IFNAR1 and IFNAR2, to orchestrate sterile and infectious immunity. Cellular pathways that regulate IFNAR1 are often targeted by viruses to suppress the antiviral effects of IFN-I. Here we report that encephalitic flaviviruses, including tick-borne encephalitis virus and West Nile virus, antagonize IFN-I signaling by inhibiting...

article

A proteomic glimpse into the initial global epigenetic changes during HIV infection

Laura‐Mae P. Britton, Pavel Sova, Sarah Belisle, Shichong Liu, more

PROTEOMICS > 14 > 19 > 2226 - 2230

HIV‐1 replication requires the insertion of viral DNA into the host genome, which is catalyzed by HIV‐1 integrase. This integration event can lead to vast changes in the chromatin landscape and gene transcription. In this study, we sought to correlate the extensive changes of histone PTM abundances with the equally dynamic shifts in host transcriptional activity. To fully capture the changes that...

article

Assessment and improvement of Indian‐origin rhesus macaque and Mauritian‐origin cynomolgus macaque genome annotations using deep transcriptome sequencing data

Xinxia Peng, Lenore Pipes, Hao Xiong, Richard R. Green, more

Journal of Medical Primatology > 43 > 5 > 317 - 328

BackgroundThe genome annotations of rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques, two of the most common non‐human primate animal models, are limited. MethodsWe analyzed large‐scale macaque RNA‐based next‐generation sequencing (RNAseq) data to identify un‐annotated macaque transcripts. ResultsFor both macaque species, we uncovered thousands of novel isoforms for annotated...

article

Enabling large‐scale next‐generation sequence assembly with Blacklight

M. Brian Couger, Lenore Pipes, Fabio Squina, Rolf Prade, more

Concurrency and Computation: Practice and Experience > 26 > 13 > 2157 - 2166

A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. These include genomic sequence assembly, very large metagenomic sequence assembly, transcriptome assembly, and sequencing error correction. The data sets used in these analyses...

article

Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates

Christian Selinger, Jennifer Tisoncik-Go, Vineet D Menachery, Sudhakar Agnihothram, more

BMC Genomics > 2014 > 15 > 1 > 1-16

Background The recent emergence of a novel coronavirus in the Middle East (designated MERS-CoV) is a reminder of the zoonotic and pathogenic potential of emerging coronaviruses in humans. Clinical features of Middle East respiratory syndrome (MERS) include atypical pneumonia and progressive respiratory failure that is highly reminiscent of severe acute respiratory syndrome (SARS) caused by SARS-CoV...

article

Moving H5N1 studies into the era of systems biology

Laurence Josset, Jennifer Tisoncik-Go, Michael G. Katze

Virus Research > 2013 > 178 > 1 > 151-167

The dynamics of H5N1 influenza virus pathogenesis are multifaceted and can be seen as an emergent property that cannot be comprehended without looking at the system as a whole. In past years, most of the high-throughput studies on H5N1–host interactions have focused on the host transcriptomic response, at the cellular or the lung tissue level. These studies pointed out that the dynamics and magnitude...

article

Drug repurposing: a better approach for infectious disease drug discovery?

G Lynn Law, Jennifer Tisoncik-Go, Marcus J Korth, Michael G Katze

Current Opinion in Immunology > 2013 > 25 > 5 > 588-592

The advent of publicly available databases containing system-wide phenotypic data of the host response to both drugs and pathogens, in conjunction with bioinformatics and computational methods now allows for in silico predictions of FDA-approved drugs as treatments against infection diseases. This systems biology approach captures the complexity of both the pathogen and drug host response in the form...

article

Transcriptional signatures of pathogenesis and successful type I interferon and ribavirin therapy in a rhesus macaque model of MERS-CoV infection

Angela L. Rasmussen, Darryl Falzarano, Emmie de Wit, Friederike Feldmann, more

Cytokine > 2013 > 63 > 3 > 291-292

A novel betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), emerged on the Arabian Peninsula in 2012. MERS-CoV was found to produce severe respiratory illness with case-fatality rates near 50%, and may be transmitted person-to-person in instances of close physical contact, such as among family members and to health care workers. As mice, hamsters, ferrets, and cynomolgus macaques...

article

Mathematical models of viral latency

Christian Selinger, Michael G Katze

Current Opinion in Virology > 2013 > 3 > 4 > 402-407

While viral latency remains one of the biggest challenges for successful antiviral therapy, it has also inspired mathematical modelers to develop dynamical system approaches with the aim of predicting the impact of drug efficacy on disease progression and the persistence of latent viral reservoirs. In this review we present several differential equation models and assess their relative success in...

article

Playing the waiting game

Michael G Katze

Current Opinion in Virology > 2013 > 3 > 4 > 377-379

article

Accumulation of CD11b⁺Gr-1⁺ cells in the lung, blood and bone marrow of mice infected with highly pathogenic H5N1 and H1N1 influenza viruses

James P. Long, Mark S. Kotur, Gregory V. Stark, Richard L. Warren, more

Archives of Virology > 2013 > 158 > 6 > 1305-1322

Infection with pathogenic influenza viruses is associated with intense inflammatory disease. Here, we investigated the innate immune response in mice infected with H5N1 A/Vietnam/1203/04 and with reassortant human H1N1 A/Texas/36/91 viruses containing the virulence genes hemagglutinin (HA), neuraminidase (NA) and NS1 of the 1918 pandemic virus. Inclusion of the 1918 HA and NA glycoproteins rendered...

article

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Nicolas Tchitchek, Amie J Eisfeld, Jennifer Tisoncik-Go, Laurence Josset, more

BMC Systems Biology > 2013 > 7 > 1 > 1-24

Background Influenza infection causes respiratory disease that can lead to death. The complex interplay between virus-encoded and host-specific pathogenicity regulators – and the relative contributions of each toward viral pathogenicity – is not well-understood. Results By analyzing a collection of lung samples from mice infected by A/Vietnam/1203/2004 (H5N1; VN1203), we characterized a signature...

article

Chronic immune activation is a distinguishing feature of liver and PBMC gene signatures from HCV/HIV coinfected patients and may contribute to hepatic fibrogenesis

Angela L. Rasmussen, I-Ming Wang, Margaret C. Shuhart, Sean C. Proll, more

Virology > 2012 > 430 > 1 > 43-52

Hepatitis C virus/human immunodeficiency virus (HCV/HIV) coinfected patients demonstrate accelerated progression to severe liver injury in comparison to HCV monoinfected patients, although the underlying mechanisms are unclear owing to infection of separate tissue compartments with two distinct viral pathogens. Microarray analysis of paired liver biopsy and peripheral blood mononuclear cell (PBMC)...

article

Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: Protein synthesis, cell proliferation, and T-cell activation

Arti T. Navare, Pavel Sova, David E. Purdy, Jeffrey M. Weiss, more

Virology > 2012 > 429 > 1 > 37-46

Human immunodeficiency virus (HIV-1) depends upon host-encoded proteins to facilitate its replication while at the same time inhibiting critical components of innate and/or intrinsic immune response pathways. To characterize the host cell response on protein levels in CD4+ lymphoblastoid SUP-T1 cells after infection with HIV-1 strain LAI, we used mass spectrometry (MS)-based global quantitation with...

article

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus–mediated liver disease posttransplantation

Deborah L. Diamond, Alexei L. Krasnoselsky, Kristin E. Burnum, Matthew E. Monroe, more

Hepatology > 56 > 1 > 28 - 38

Liver transplant tissues offer the unique opportunity to model the longitudinal protein abundance changes occurring during hepatitis C virus (HCV)‐associated liver disease progression in vivo. In this study, our goal was to identify molecular signatures, and potential key regulatory proteins, representative of the processes influencing early progression to fibrosis. We performed global protein profiling...

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Search results for: Michael G. Katze

Evaluation of the innate immune responses to influenza and live-attenuated influenza vaccine infection in primary differentiated human nasal epithelial cells

A Systems Approach Reveals MAVS Signaling in Myeloid Cells as Critical for Resistance to Ebola Virus in Murine Models of Infection

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism

Flavivirus Antagonism of Type I Interferon Signaling Reveals Prolidase as a Regulator of IFNAR1 Surface Expression

A proteomic glimpse into the initial global epigenetic changes during HIV infection

Assessment and improvement of Indian‐origin rhesus macaque and Mauritian‐origin cynomolgus macaque genome annotations using deep transcriptome sequencing data

Enabling large‐scale next‐generation sequence assembly with Blacklight

Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates

Moving H5N1 studies into the era of systems biology

Drug repurposing: a better approach for infectious disease drug discovery?

Transcriptional signatures of pathogenesis and successful type I interferon and ribavirin therapy in a rhesus macaque model of MERS-CoV infection

Mathematical models of viral latency

Playing the waiting game

Accumulation of CD11b⁺Gr-1⁺ cells in the lung, blood and bone marrow of mice infected with highly pathogenic H5N1 and H1N1 influenza viruses

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Chronic immune activation is a distinguishing feature of liver and PBMC gene signatures from HCV/HIV coinfected patients and may contribute to hepatic fibrogenesis

Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: Protein synthesis, cell proliferation, and T-cell activation

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus–mediated liver disease posttransplantation

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