RESUMEN
Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enhanced yeast one-hybrid (eY1H) assays to derive a comprehensive network comprising 1380 interactions between 265 TFs and 108 cytokine gene promoters. Our eY1H-derived network greatly expands the known repertoire of TF-cytokine gene interactions and the set of TFs known to regulate cytokine genes. We found an enrichment of nuclear receptors and confirmed their role in cytokine regulation in primary macrophages. Additionally, we used the eY1H-derived network as a framework to identify pairs of TFs that can be targeted with commercially-available drugs to synergistically modulate cytokine production. Finally, we integrated the eY1H data with single cell RNA-seq and phenotypic datasets to identify novel TF-cytokine regulatory axes in immune diseases and immune cell lineage development. Overall, the eY1H data provides a rich resource to study cytokine regulation in a variety of physiological and disease contexts.
Asunto(s)
Linaje de la Célula/inmunología , Citocinas/genética , Redes Reguladoras de Genes/inmunología , Linfocitos/inmunología , Regiones Promotoras Genéticas , Factores de Transcripción/genética , Linaje de la Célula/genética , Citocinas/clasificación , Citocinas/inmunología , Conjuntos de Datos como Asunto , Células Dendríticas/citología , Células Dendríticas/inmunología , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Ontología de Genes , Células HEK293 , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Linfocitos/clasificación , Linfocitos/citología , Macrófagos/citología , Macrófagos/inmunología , Anotación de Secuencia Molecular , Monocitos/citología , Monocitos/inmunología , Cultivo Primario de Células , Unión Proteica , Receptores Citoplasmáticos y Nucleares/genética , Receptores Citoplasmáticos y Nucleares/inmunología , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Análisis de la Célula Individual , Células THP-1 , Factores de Transcripción/clasificación , Factores de Transcripción/inmunología , Transcripción Genética , Técnicas del Sistema de Dos HíbridosRESUMEN
RATIONALE: Individuals with a history of tuberculosis (TB) disease are at elevated risk of disease recurrence. The underlying cause is not known, but one explanation is that previous disease results in less-effective immunity against Mycobacterium tuberculosis (Mtb). OBJECTIVES: We hypothesized that the repertoire of Mtb-derived epitopes recognized by T cells from individuals with latent Mtb infection differs as a function of previous diagnosis of active TB disease. METHODS: T-cell responses to peptide pools in samples collected from an adult screening and an adolescent validation cohort were measured by IFN-γ enzyme-linked immunospot assay or intracellular cytokine staining. MEASUREMENTS AND MAIN RESULTS: We identified a set of "type 2" T-cell epitopes that were recognized at 10-fold-lower levels in Mtb-infected individuals with a history of TB disease less than 6 years ago than in those without previous TB. By contrast, "type 1" epitopes were recognized equally well in individuals with or without previous TB. The differential epitope recognition was not due to differences in HLA class II binding, memory phenotypes, or gene expression in the responding T cells. Instead, "TB disease history-sensitive" type 2 epitopes were significantly (P < 0.0001) more homologous to sequences from bacteria found in the human microbiome than type 1 epitopes. CONCLUSIONS: Preferential loss of T-cell reactivity to Mtb epitopes that are homologous to bacteria in the microbiome in persons with previous TB disease may reflect long-term effects of antibiotic TB treatment on the microbiome.