Time since Onset of Disease and Individual Clinical Markers Associate with Transcriptional Changes in Uncomplicated Dengue

Background Dengue virus (DENV) infection causes viral haemorrhagic fever that is characterized by extensive activation of the immune system. The aim of this study is to investigate the kinetics of the transcriptome signature changes during the course of disease and the association of genes in these signatures with clinical parameters. Methodology/Principle Findings Sequential whole blood samples from DENV infected patients in Jakarta were profiled using affymetrix microarrays, which were analysed using principal component analysis, limma, gene set analysis, and weighted gene co-expression network analysis. We show that time since onset of disease, but not diagnosis, has a large impact on the blood transcriptome of patients with non-severe dengue. Clinical diagnosis (according to the WHO classification) does not associate with differential gene expression. Network analysis however, indicated that the clinical markers platelet count, fibrinogen, albumin, IV fluid distributed per day and liver enzymes SGOT and SGPT strongly correlate with gene modules that are enriched for genes involved in the immune response. Overall, we see a shift in the transcriptome from immunity and inflammation to repair and recovery during the course of a DENV infection. Conclusions/Significance Time since onset of disease associates with the shift in transcriptome signatures from immunity and inflammation to cell cycle and repair mechanisms in patients with non-severe dengue. The strong association of time with blood transcriptome changes hampers both the discovery as well as the potential application of biomarkers in dengue. However, we identified gene expression modules that associate with key clinical parameters of dengue that reflect the systemic activity of disease during the course of infection. The expression level of these gene modules may support earlier detection of disease progression as well as clinical management of dengue.

[1]  Jeerayut Chaijaruwanich,et al.  Differences in global gene expression in peripheral blood mononuclear cells indicate a significant role of the innate responses in progression of dengue fever but not dengue hemorrhagic fever. , 2008, The Journal of infectious diseases.

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

[3]  R. Myers,et al.  Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data , 2005, Nucleic acids research.

[4]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[5]  A. Bøyum,et al.  Bioactive cytidine deaminase, an inhibitor of granulocyte-macrophage colony-forming cells, is massively released in fulminant meningococcal sepsis. , 2000, The Journal of infectious diseases.

[6]  Ulisses Braga-Neto,et al.  Gene Expression Profiling during Early Acute Febrile Stage of Dengue Infection Can Predict the Disease Outcome , 2009, PloS one.

[7]  N. M. Dung,et al.  Patterns of gene transcript abundance in the blood of children with severe or uncomplicated dengue highlight differences in disease evolution and host response to dengue virus infection. , 2009, The Journal of infectious diseases.

[8]  Di Wu,et al.  ROAST: rotation gene set tests for complex microarray experiments , 2010, Bioinform..

[9]  A. Nisalak,et al.  Early clinical and laboratory indicators of acute dengue illness. , 1997, The Journal of infectious diseases.

[10]  Niall J. Lennon,et al.  The Early Whole-Blood Transcriptional Signature of Dengue Virus and Features Associated with Progression to Dengue Shock Syndrome in Vietnamese Children and Young Adults , 2010, Journal of Virology.

[11]  A. Nisalak,et al.  Mechanisms of hemorrhage in dengue without circulatory collapse. , 2001, The American journal of tropical medicine and hygiene.

[12]  Mark J. Schreiber,et al.  Characterization of early host responses in adults with dengue disease , 2011, BMC infectious diseases.

[13]  N. M. Dung,et al.  Coagulation abnormalities in dengue hemorrhagic Fever: serial investigations in 167 Vietnamese children with Dengue shock syndrome. , 2002, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[14]  N. Bardeesy,et al.  Adiponectin suppresses hepatic SREBP1c expression in an AdipoR1/LKB1/AMPK dependent pathway. , 2009, Biochemical and biophysical research communications.

[15]  N. M. Dung,et al.  Size and charge characteristics of the protein leak in dengue shock syndrome. , 2004, The Journal of infectious diseases.

[16]  A. Weyrich,et al.  Platelets mediate increased endothelium permeability in dengue through NLRP3-inflammasome activation. , 2013, Blood.

[17]  K. Wong,et al.  Localization of dengue virus in naturally infected human tissues, by immunohistochemistry and in situ hybridization. , 2004, The Journal of infectious diseases.

[18]  P. Bossù,et al.  Lymphocytes from Autoimmune MRL lpr/lpr Mice Are Hyperresponsive to IL-18 and Overexpress the IL-18 Receptor Accessory Chain1 , 2001, The Journal of Immunology.

[19]  Michael T. McManus,et al.  An siRNA Screen in Pancreatic Beta Cells Reveals a Role for Gpr27 in Insulin Production , 2012, PLoS genetics.

[20]  D. Relman,et al.  Temporal Dynamics of the Transcriptional Response to Dengue Virus Infection in Nicaraguan Children , 2012, PLoS neglected tropical diseases.

[21]  S. Inoue,et al.  Association of increased platelet‐associated immunoglobulins with thrombocytopenia and the severity of disease in secondary dengue virus infections , 2004, Clinical and Experimental Immunology.

[22]  D. Speicher,et al.  Cloning of human erythroid dematin reveals another member of the villin family. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A. Osterhaus,et al.  Lipopolysaccharide levels are elevated in dengue virus infected patients and correlate with disease severity. , 2012, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[24]  M. Diamond,et al.  Binding of Flavivirus Nonstructural Protein NS1 to C4b Binding Protein Modulates Complement Activation , 2011, The Journal of Immunology.

[25]  H. Bierman,et al.  HEMATOLOGIC FINDINGS IN THE 1960 HEMORRHAGIC FEVER EPIDEMIC (DENGUE) IN THAILAND. , 1964, The American journal of tropical medicine and hygiene.

[26]  A. Eid,et al.  Sestrin 2 and AMPK Connect Hyperglycemia to Nox4-Dependent Endothelial Nitric Oxide Synthase Uncoupling and Matrix Protein Expression , 2013, Molecular and Cellular Biology.

[27]  T. Hansen,et al.  Identification of KCNJ15 as a susceptibility gene in Asian patients with type 2 diabetes mellitus. , 2010, American journal of human genetics.

[28]  Mark Ellisman,et al.  Maintenance of metabolic homeostasis by Sestrin2 and Sestrin3. , 2012, Cell metabolism.

[29]  Martin Vingron,et al.  Variance stabilization applied to microarray data calibration and to the quantification of differential expression , 2002, ISMB.

[30]  B. Ryffel,et al.  IFN-γ Production Depends on IL-12 and IL-18 Combined Action and Mediates Host Resistance to Dengue Virus Infection in a Nitric Oxide-Dependent Manner , 2011, PLoS neglected tropical diseases.

[31]  M. Cutting,et al.  Platelet adhesion to dengue-2 virus-infected endothelial cells. , 2002, The American journal of tropical medicine and hygiene.

[32]  Ruei-Jiun Hung,et al.  Direct Redox Regulation of F-Actin Assembly and Disassembly by Mical , 2011, Science.

[33]  A. Osterhaus,et al.  Microbial Translocation Is Associated with Extensive Immune Activation in Dengue Virus Infected Patients with Severe Disease , 2013, PLoS neglected tropical diseases.

[34]  J. Farrar,et al.  Patterns of host genome-wide gene transcript abundance in the peripheral blood of patients with acute dengue hemorrhagic fever. , 2007, The Journal of infectious diseases.

[35]  P. Buchy,et al.  Genome-Wide Expression Profiling Deciphers Host Responses Altered during Dengue Shock Syndrome and Reveals the Role of Innate Immunity in Severe Dengue , 2010, PloS one.

[36]  V. Fowler,et al.  Tropomodulins: life at the slow end. , 2003, Trends in cell biology.

[37]  E. Koonin,et al.  Regeneration of Peroxiredoxins by p53-Regulated Sestrins, Homologs of Bacterial AhpD , 2004, Science.

[38]  E. Kalkhoven,et al.  Systemic inflammation in childhood obesity: circulating inflammatory mediators and activated CD14++ monocytes , 2012, Diabetologia.

[39]  Jorge Cime-Castillo,et al.  Crosstalk between coagulation and inflammation during Dengue virus infection , 2008 .

[40]  Charles C. Kim,et al.  Gene Expression Patterns of Dengue Virus-Infected Children from Nicaragua Reveal a Distinct Signature of Increased Metabolism , 2010, PLoS neglected tropical diseases.

[41]  M. Guzmán,et al.  Why dengue haemorrhagic fever in Cuba? 1. Individual risk factors for dengue haemorrhagic fever/dengue shock syndrome (DHF/DSS). , 1987, Transactions of the Royal Society of Tropical Medicine and Hygiene.

[42]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[43]  Jorge Cime-Castillo,et al.  Crosstalk between coagulation and inflammation during Dengue virus infection , 2008, Thrombosis and Haemostasis.

[44]  E. Undurraga,et al.  Economic and Disease Burden of Dengue in Southeast Asia , 2013, PLoS neglected tropical diseases.

[45]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[46]  Rickard Sandberg,et al.  Improved precision and accuracy for microarrays using updated probe set definitions , 2007, BMC Bioinformatics.

[47]  M. Barreto,et al.  Allergies and Diabetes as Risk Factors for Dengue Hemorrhagic Fever: Results of a Case Control Study , 2010, PLoS neglected tropical diseases.

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

[49]  R. Lanciotti,et al.  Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction , 1992, Journal of clinical microbiology.

[50]  A. Bøyum,et al.  Growth inhibition of granulocyte-macrophage colony-forming cells by human cytidine deaminase requires the catalytic function of the protein. , 1998, Blood.

[51]  Zhining Wang,et al.  Sequential Waves of Gene Expression in Patients with Clinically Defined Dengue Illnesses Reveal Subtle Disease Phases and Predict Disease Severity , 2013, PLoS neglected tropical diseases.

[52]  H. Bierman,et al.  DENGUE FEVER: A THROMBOCYTOPENIC DISEASE? , 1964, JAMA.

[53]  J. Lippincott-Schwartz,et al.  Regulation of bile canalicular network formation and maintenance by AMP-activated protein kinase and LKB1 , 2010, Journal of Cell Science.

[54]  Z. Bloomgarden,et al.  Inflammation and insulin resistance. , 2003, Diabetes care.

[55]  Michael S. Diamond,et al.  Modulation of Dengue Virus Infection in Human Cells by Alpha, Beta, and Gamma Interferons , 2000, Journal of Virology.