title: Transcription factor regulatory network for early lung immune response to tuberculosis in mice.
abstract: Numerous transcription factors (TFs) have been suggested to have a role in Mycobacterium tuberculosis infection; however, the TFs involved in the early immune response of lung cells remains to be fully elucidated. The present study aimed to identify TFs which may have a role in the early immune response to tuberculosis and the gene regulatory networks in which they are involved. Gene expression data obtained from microarray analysis of the early lung immune response to tuberculosis (Gene Expression Omnibus; accession no. GSE23014) was integrated with data for TF binding sites and protein-protein interactions in order to construct a TF regulatory network. The role of TFs in protein complexes, active modules, topology of the network and regulation of immune processes were investigated. The results demonstrated that the constructed gene regulatory network harbored 1,270 differentially expressed (DE) genes with 4,070 regulatory and protein-protein interactions. In addition, it was revealed that 17 DE TFs were involved in the positive regulation of numerous immunological and biological processes, including T cell activation, T cell proliferation and tuberculosis-associated gene expression, in the constructed regulatory network. Signal transducer and activator of transcription 4, interferon regulatory factor 8, spleen focus-forming virus proviral integration 1, enhancer of zeste homolog 2 and kruppel-like factor 4 were predicted to be the primary TFs regulating the DE genes during early lung infection by M. tuberculosis, as determined through various analyses of the gene regulatory network. In conclusion, the present study identified novel TFs involved in the early response to M. tuberculosis infection, which may enhance current understanding of the molecular mechanism underlying tuberculosis infection and introduced potential targets for novel tuberculosis therapies.
authors.affiliation: Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran 14178-63171, Iran.
authors.forename: Moein
authors.initials: M
authors.lastname: Yaqubi
authors.affiliation: Department of Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran 14178-63171, Iran.
authors.forename: Abdulshakour
authors.initials: A
authors.lastname: Mohammadnia
authors.affiliation: Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah 67149‑67346, Iran.
authors.forename: Hossein
authors.initials: H
authors.lastname: Fallahi
mesh_terms: D000818:Animals; D053263:Gene Regulatory Networks; D000090062:Kruppel-Like Factor 4; D008168:Lung / Q000276:immunology / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis; D060066:Protein Interaction Maps; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014376:Tuberculosis / Q000276:immunology / Q000473:pathology* / Q000662:veterinary
chemical_list: C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4; D014157:Transcription Factors