Project description:MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.
Project description:MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.
Project description:Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that have a critical impact on plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present an atlas of gene regulatory logic involving transcription factors, potential cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integration of our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic. Overall, this study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.
Project description:Encystment is a common response of most protists to stress. Although some signaling pathways regulating this process were reported, our knowledge remains limited. Here, we mapped the molecular changes occurring in the amoeba Acanthamoeba castellanii during the early steps of encystment. De novo analysis of the transcriptome identified more than 150,000 previously undescribed transcripts that were utilized for mass spectrometry-based proteomics analysis after triggering starvation. With this strategy, we identified thousands of protein sequences absent from the reference genome. These results revealed the regulation of expected biological processes, such as the shutdown of cell proliferation at transcript level followed by down-regulation of proteins. The phosphoproteome showed a quick regulation of phosphorylation sites involved in cytoskeleton remodeling and translation regulation, among other processes underlying A. castellanii encystment. To our knowledge, this work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource to further investigating amoebae encystment.
Project description:We employed time-resolved microRNA expression analyses upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in patients at different stages of PD