Project description:Bone marrow derived phagocytes from mouse, rat, rabbit and pig stimulated with LPS (100ng/mL) or with dsRNA (poly I:C) (1ug/mL) for 0,2,4,6 hours. Processed files include UMI matrices of QCed cells that belong to the first cluster (as described in the publication), which were used for all the analyses presented in the publication.
Project description:We developed PERCEPT, an approach that uses ex vivo perturbational single-cell RNA sequencing to compare the response of immunomodulatory treatments with unstimulated controls directly in patient samples. Using PERCEPT, we tested cytokines and innate immune agonists in melanoma and Merkel cell carcinoma (MCC) and identified the dsRNA mimetic, RIG-I agonist, Stem Loop RNA (SLR) 14 as a powerful inducer of anti-viral states and enhancer of T cell activation. Our results demonstrate the utility of high-dimensional controlled perturbation of patient samples to identify mechanisms of innate immune response and resistance.
Project description:Dermal fibroblasts from bat and human, stimulated with dsRNA (poly(I:C)) and controls. Bats can harbor some of the most deadliest viruses to humans while rarely displaying pathogenicity themselves. To study the transcriptional divergence and cell-to-cell variability of their innate immune response - the expression program that is initiated once a pathogen is sensed, we stimulated dermal fibroblast cells from Rousettus aegyptiacus and from human for four hours with dsRNA - a viral RNA mimic that triggers a rapid innate immune response. Subsequently, we profiled the response using scRNA-seq.
Project description:Plasmacytoid dendritic cells (pDCs) are a rare immune cell population that plays a key role in antiviral innate immunity. In our analysis, secretin (SCT) emerged as one of the most highly expressed hormones in both circulating and tissue-resident pDCs. To validate this finding, we performed spatial transcriptomic analysis of adult tonsil tissue, which demonstrated co-localization of SCT transcripts with the pDC marker LILR4A. We further confirmed SCT expression at the protein level by immunofluorescence staining of primary human peripheral blood pDCs, showing co-expression of secretin with the canonical pDC markers CLEC4C and TLR9. In a longitudinal single-cell RNA-sequencing dataset from individuals with COVID-19, we observed modest upregulation of SCT in interferon-activated pDCs. To determine whether SCT expression is linked to immune function, we purchased primary human peripheral blood pDCs and stimulated them in vitro with the TLR9 agonist cytosine-phosphate-guanine (CpG) oligodeoxynucleotide, followed by single-cell transcriptomic profiling.
Project description:The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.<br>This experiment contains data of dermal fibroblasts from 3 human individuals, stimulated with dsRNA (poly I:C) for 6 hours, sequenced by 10X Genomics technology. Corresponding data from unstimulated cells are found under ArrayExpress accession <a href="/arrayexpress/experiments/E-MTAB-5988">E-MTAB-5988</a>.