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The immune system generates pathogen-tailored responses. The precise innate immune cell types and pathways that direct robust adaptive immune responses have not been fully characterized. By using fluorescent pathogens combined with massively parallel single-cell RNA-seq, we comprehensively characterized the initial 48 h of the innate immune response to diverse pathogens. We found that across all pathogens tested, most of the lymph node cell types and states showed little pathogen specificity. In contrast, the rare antigen-positive cells displayed pathogen-specific transcriptional programs as early as 24 h after immunization. In addition, mycobacteria activated a specific NK-driven IFNγ response. Depletion of NK cells and IFNγ showed that IFNγ initiated a monocyte-specific signaling cascade, leading to the production of major chemokines and cytokines that promote Th1 development. Our systems immunology approach sheds light on early events in innate immune responses and may help further development of safe and efficient vaccines.
Pubmed ID: 30772378 RIS Download
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View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role.
View all literature mentionsSoftware R package for analyzing and interactively exploring large single cell RNAseq datasets.
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View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsThis isotype control targets HRP
View all literature mentionsThis monoclonal targets NK1.1
View all literature mentionsThis monoclonal targets Mouse TCR β Chain
View all literature mentionsThis monoclonal targets CD326 (Ep-CAM)
View all literature mentionsThis monoclonal targets CD11b (Mac-1)
View all literature mentionsThis isotype control targets Unknown Specificity
View all literature mentionsThis monoclonal targets IFNγ
View all literature mentionsThis monoclonal targets NK1.1
View all literature mentionsThis monoclonal targets KLRG1
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