A Simple Screening Approach To Prioritize Genes for Functional Analysis Identifies a Role for Interferon Regulatory Factor 7 in the Control of Respiratory Syncytial Virus Disease.
Greater understanding of the functions of host gene products in response to infection is required. While many of these genes enable pathogen clearance, some enhance pathogen growth or contribute to disease symptoms. Many studies have profiled transcriptomic and proteomic responses to infection, generating large data sets, but selecting targets for further study is challenging. Here we propose a novel data-mining approach combining multiple heterogeneous data sets to prioritize genes for further study by using respiratory syncytial virus (RSV) infection as a model pathogen with a significant health care impact. The assumption was that the more frequently a gene is detected across multiple studies, the more important its role is. A literature search was performed to find data sets of genes and proteins that change after RSV infection. The data sets were standardized, collated into a single database, and then panned to determine which genes occurred in multiple data sets, generating a candidate gene list. This candidate gene list was validated by using both a clinical cohort andin vitroscreening. We identified several genes that were frequently expressed following RSV infection with no assigned function in RSV control, includingIFI27,IFIT3,IFI44L,GBP1,OAS3,IFI44, andIRF7. Drilling down into the function of these genes, we demonstrate a role in disease for the gene for interferon regulatory factor 7, which was highly ranked on the list, but not forIRF1, which was not. Thus, we have developed and validated an approach for collating published data sets into a manageable list of candidates, identifying novel targets for future analysis.IMPORTANCEMaking the most of "big data" is one of the core challenges of current biology. There is a large array of heterogeneous data sets of host gene responses to infection, but these data sets do not inform us about gene function and require specialized skill sets and training for their utilization. Here we describe an approach that combines and simplifies these data sets, distilling this information into a single list of genes commonly upregulated in response to infection with RSV as a model pathogen. Many of the genes on the list have unknown functions in RSV disease. We validated the gene list with new clinical,in vitro, andin vivodata. This approach allows the rapid selection of genes of interest for further, more-detailed studies, thus reducing time and costs. Furthermore, the approach is simple to use and widely applicable to a range of diseases.
Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary's Campus, London, United Kingdom.
Jacqueline U
JU
McDonald
Section of Paediatrics, Imperial College London, St. Mary's Campus, London, United Kingdom.
Myrsini
M
Kaforou
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Simon
S
Clare
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
Christine
C
Hale
Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary's Campus, London, United Kingdom.
Maria
M
Ivanova
Imperial College Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom.
Derek
D
Huntley
Molecular Virology, Section of Virology, Imperial College London, St. Mary's Campus, London, United Kingdom.
Marcus
M
Dorner
Section of Paediatrics, Imperial College London, St. Mary's Campus, London, United Kingdom.
Victoria J
VJ
Wright
Section of Paediatrics, Imperial College London, St. Mary's Campus, London, United Kingdom.
Michael
M
Levin
Department of Paediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.
Federico
F
Martinon-Torres
Section of Paediatrics, Imperial College London, St. Mary's Campus, London, United Kingdom.
Jethro A
JA
Herberg
Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St. Mary's Campus, London, United Kingdom.
John S
0000-0001-8093-8741
JS
Tregoning
host response; immunity; respiratory syncytial virus; viral immunity