Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism

BackgroundComparative analysis of genome-wide expression profiles are increasingly being used to study virus-specific host interactions. In order to gain mechanistic insights, gene expression profiles can be combined with information on DNA-binding sites of transcription factors to detect transcription factor activity (by analysis of target gene sets) during viral infections. Here, we apply this approach to study mechanisms of immune antagonism elicited by Influenza A virus (New Caledonia/20/1999) by comparing the transcriptional response with the non-pathogenic Newcastle disease virus (NDV), which lacks human immune antagonism.ResultsExisting gene set approaches do not quantify activity in a way that can be statistically compared between responses. We thus developed a new method for Bayesian Estimation of Transcription factor Activity (BETA) that allows for such quantification and comparative analysis across multiple responses. BETA predicted decreased ISGF3 activity during influenza A infection of human dendritic cells (reflected in lower expression of Interferon Stimulated Genes, ISGs). This prediction was confirmed through a combination of mathematical modeling and experiments at different multiplicities of infection to show that ISGs were specifically blocked in infected cells. Suppression of the transcription factor SATB1 was also predicted as a novel effect of influenza-mediated immune antagonism, and validated experimentally.ConclusionsComparative analysis of genome-wide transcriptional profiles can reveal new effects of viral immune antagonism. We have developed a computational framework (BETA) that enables quantitative comparative analysis of transcription factor activities. This method will aid future studies to identify mechanistic differences in the host-pathogen interactions. Application of BETA to genome-wide transcriptional profiling data from human DCs identified SATB1 as a novel effect of influenza antagonism.

[1]  R. Lamb,et al.  A new influenza virus virulence determinant: The NS1 protein four C-terminal residues modulate pathogenicity , 2008, Proceedings of the National Academy of Sciences.

[2]  M. Lozano,et al.  Nuclear Matrix Binding Regulates SATB1-mediated Transcriptional Repression* , 2005, Journal of Biological Chemistry.

[3]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[4]  R. Webster.  1918 Spanish influenza: the secrets remain elusive. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Michael G. Katze,et al.  Systems approaches to influenza-virus host interactions and the pathogenesis of highly virulent and pandemic viruses , 2012, Seminars in Immunology.

[6]  P. Doherty,et al.  Immunity to seasonal and pandemic influenza A viruses. , 2011, Microbes and infection.

[7]  John Steel,et al.  Differential Contribution of PB1-F2 to the Virulence of Highly Pathogenic H5N1 Influenza A Virus in Mammalian and Avian Species , 2011, PLoS pathogens.

[8]  Steven H. Kleinstein,et al.  Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection , 2013, BMC Bioinformatics.

[9]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Jonathan W. Yewdell,et al.  A novel influenza A virus mitochondrial protein that induces cell death , 2001, Nature Medicine.

[11]  R. Balderas,et al.  Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation , 2011, Nature Immunology.

[12]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[13]  T. Kohwi-Shigematsu,et al.  SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes , 2006, Nature Genetics.

[14]  Erin Burns,et al.  Estimates of deaths associated with seasonal influenza --- United States, 1976-2007. , 2010, MMWR. Morbidity and mortality weekly report.

[15]  J. Taubenberger,et al.  The 1918 influenza virus: A killer comes into view. , 2000, Virology.

[16]  Clifford H. Wagner.  Simpson's Paradox in Real Life , 1982 .

[17]  Michael G. Katze,et al.  Distinct RIG-I and MDA5 Signaling by RNA Viruses in Innate Immunity , 2007, Journal of Virology.

[18]  Sanjay Tyagi,et al.  Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infection , 2015, Science Signaling.

[19]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[20]  L. Carin,et al.  Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection , 2011, PLoS genetics.

[21]  Roger E Bumgarner,et al.  Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: The role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Thomas M. Moran,et al.  Influenza Virus Evades Innate and Adaptive Immunity via the NS1 Protein , 2006, Journal of Virology.

[23]  A. Chakrabarti,et al.  Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th‐century pandemics , 2012, Influenza and other respiratory viruses.

[24]  K. Honda,et al.  Type I Inteferon Gene Induction by the Interferon Regulatory Factor Family of Transcription Factors , 2006 .

[25]  A. García-Sastre,et al.  Inefficient Control of Host Gene Expression by the 2009 Pandemic H1N1 Influenza A Virus NS1 Protein , 2010, Journal of Virology.

[26]  Irene Ramos,et al.  The Influenza Virus Protein PB1-F2 Inhibits the Induction of Type I Interferon at the Level of the MAVS Adaptor Protein , 2011, PLoS pathogens.

[27]  H. Ploegh,et al.  Viral subversion of the immune system. , 2000, Annual review of immunology.

[28]  Jing Chen,et al.  Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules , 2013, PLoS Comput. Biol..

[29]  R. Storn,et al.  Differential Evolution - A simple and efficient adaptive scheme for global optimization over continuous spaces , 2004 .

[30]  Heinz Feldmann,et al.  2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models , 2012, BMC Genomics.

[31]  Juilee Thakar,et al.  Overcoming NS1-mediated immune antagonism involves both interferon-dependent and independent mechanisms. , 2013, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[32]  A. García-Sastre,et al.  Newcastle Disease Virus V Protein Is a Determinant of Host Range Restriction , 2003, Journal of Virology.

[33]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[34]  Bernd Hartke,et al.  Global optimization , 2011 .

[35]  J. Thakar,et al.  Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations , 2013, Nucleic acids research.

[36]  G. Kochs,et al.  Inverse interference: how viruses fight the interferon system. , 2004, Viral immunology.

[37]  K. Rohr,et al.  Single‐cell‐based image analysis of high‐throughput cell array screens for quantification of viral infection , 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[38]  K. Honda,et al.  Type I interferon [corrected] gene induction by the interferon regulatory factor family of transcription factors. , 2006, Immunity.

[39]  E. Wingender,et al.  MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.

[40]  Jeremy Seto,et al.  Antiviral Response Dictated by Choreographed Cascade of Transcription Factors , 2010, The Journal of Immunology.

[41]  Michael G. Katze,et al.  Systems virology: host-directed approaches to viral pathogenesis and drug targeting , 2013, Nature Reviews Microbiology.

[42]  R. Andrews,et al.  Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression , 2014, Science.

[43]  B. G. Hale,et al.  The multifunctional NS1 protein of influenza A viruses. , 2008, The Journal of general virology.

[44]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[45]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[46]  Alexander E. Kel,et al.  MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..

[47]  Charles M. Rice,et al.  Corrigendum: A diverse range of gene products are effectors of the type I interferon antiviral response , 2015, Nature.

[48]  A. Chakrabarti,et al.  An insight into the PB1F2 protein and its multifunctional role in enhancing the pathogenicity of the influenza A viruses. , 2013, Virology.

[49]  D. Levy,et al.  Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems. , 1998, Virology.

[50]  S. Galande,et al.  Global Regulator SATB1 Recruits β-Catenin and Regulates TH2 Differentiation in Wnt-Dependent Manner , 2010, PLoS biology.

[51]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[52]  L. Stein,et al.  Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome , 2012, Cancers.

[53]  Boris M. Hartmann,et al.  Antiviral-Activated Dendritic Cells: A Paracrine-Induced Response State1 , 2008, The Journal of Immunology.

[54]  A. García-Sastre,et al.  PB1-F2 Expression by the 2009 Pandemic H1N1 Influenza Virus Has Minimal Impact on Virulence in Animal Models , 2010, Journal of Virology.

[55]  D. Marquardt.  An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[56]  A. García-Sastre,et al.  Protection against Respiratory Syncytial Virus by a Recombinant Newcastle Disease Virus Vector , 2006, Journal of Virology.

[57]  Kenneth Levenberg.  A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .

[58]  T. Taniguchi,et al.  Type I interferons are essential mediators of apoptotic death in virally infected cells , 1998, Genes to cells : devoted to molecular & cellular mechanisms.

[59]  Rainer Storn,et al.  Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces , 1997, J. Glob. Optim..

[60]  L. Simonsen,et al.  The impact of influenza epidemics on mortality: introducing a severity index. , 1997, American journal of public health.

[61]  Steven H. Kleinstein,et al.  Quantifying selection in high-throughput Immunoglobulin sequencing data sets , 2012, Nucleic acids research.

[62]  R. Albrecht,et al.  The M Segment of the 2009 New Pandemic H1N1 Influenza Virus Is Critical for Its High Transmission Efficiency in the Guinea Pig Model , 2011, Journal of Virology.