The lifespan and kinetics of human Dendritic Cell subsets and their precursors in health and inflammation
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PROVIDER: PRJNA1157768 | ENA |
REPOSITORIES: ENA
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Project description:The lifespan and kinetics of human Dendritic Cell subsets and their precursors in health and inflammation
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Project description:To probe the phenotype of the cDC compartment during pathology, we developed a simplified human experimental skin blister model to sample infiltrating cells in order to examine the function and kinetics of DC populations in response to a bacterial insult in healthy individuals. ASDC were recruited to the inflammatory site, displaying a distinctive effector signature. Human Skin Blister 1.5 x 107 UV killed E.coli (Strain: NCTC 10418, Source: Public Health England, UK) in 100 µl sterile saline was intradermally injected into the forearm approximately 7 cm from the cubital fossa. For the suction blister, a 10 mm diameter suction blister was induced at 24 hours post challenge over the injection site by a negative pressure instrument. Once a blister formed, blister exudate was collected, cells were isolated. Next, Blister cells were stained for DC subsets and index sorted on FACS ARIA III (BD Biosciences) into 96 well plate containing lysis buffer, one cell/well - using the gating strategy in Supplementary Figure 1a. Plates were sealed and stored at -80°C. Single-cell cDNA libraries were prepared using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: (i) 1 mg/mL BSA Lysis buffer (Ambionâ Thermo Fisher Scientific); and (ii) 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina, San Diego, CA, USA), with 300 samples/lane. Pre-processing, quality assessment and control and analysis of SMARTseq2 single cell transcriptome data. Paired-end raw reads were aligned to the human reference genome (GRCh38 version 25 release: Gencode) using RSEM version 1.3.0. Transcript Per Million read (TPM) values were calculated using RSEM and used for downstream analysis. Quality control, selection of highly variable genes, PCA, and differential gene analysis was performed using the Seurat R package. The expression levels of key signature genes by known cell types was used to annotate the cell clusters accordingly.
2024-09-24 | E-MTAB-14451 | biostudies-arrayexpress
Project description:Dendritic cells (DC) are specialised mononuclear phagocytes connecting innate and adaptive immunity. They comprise two principal subsets: plasmacytoid DC and conventional DC. Here, single cell RNA sequencing (scRNA-seq) was performed to analyze the expression levels of different genes in circulating human DC subsets.
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Project description:We exploited label-free quantitative mass spectrometry to compare primary human blood Dendritic cells (DCs) subsets protein expression to identify new markers. Subsets distinguished are: Plasmacytoid DCs (pDC) and BDCA3+ and CD1c+ myeloid DCs and CD16+ monocytes. The dendritic cells were analyzed by LC-MS/MS and processed by MaxQuant for identification and LFQ quantification.
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Project description:The impact of chronic caloric restriction (CR) on health and survival in model organisms is complex and its underlying molecular mechanisms are poorly understood. Genetic background, sex, degree of CR and diet composition are expected modifiers of survival outcomes of this intervention. A recent study in mice addressed the impact of diet composition and feeding patterns used in nonhuman primates. It was found that, while diet composition alone did not impact longevity, fasting and calories were determinant for increased survival. We use here a combined physiological, multi-omics (transcriptomics-metabolomics), and integrated pathway analyses to gain insight into core and specific pathways associated with liver healthspan and lifespan. Main findings show that liver longevity pathways associated with CR predominantly correspond to detoxification, molecular turnover-repair-maintenance, and energy supply processes. Differential responses on lifespan extension provided by the different feeding strategies unveiled a distinct pattern of longevity pathways that centered around amino acid, fatty acid and nucleic acid metabolisms. Glycine-serine-threonine metabolism was a unique metabolic hub associated with lifespan whereas short-chain fatty acids and essential PUFAs metabolism were unique to healthspan. Nonhuman primate serum metabolomics data essentially recapitulated key features in mice.
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Project description:The prevention or delay of the onset of age-related diseases prolongs survival and improves quality of life while reducing the burden on the health care system. Activation of sirtuin 6 (SIRT6), an NAD+-dependent deacetylase, improves metabolism and confers protection against physiological and cognitive disturbances in old age. Here we show that MDL-800 is a specific SIRT6 activator that has health and lifespan benefits in adult mice fed a standard diet. We found extension in lifespan, delayed onset of age-related metabolic diseases, and improved general health in mice fed a standard diet after MDL-800 supplementation. Treatment with MDL-800 induced synthesis of anti-oxidation related proteins, and this rejuvenated HSCs and ISCs in aged mice. Inhibition of pro-inflammatory gene expression in both liver and muscle of MDL-800-treated animals was noted. MDL-800 lowered the level of NF-kB pathway and improved fatty acid metabolism in liver. Combined with our previous work, the current study further supports the beneficial effects of MDL-800 on health across the lifespan in mice.
2023-01-30 | GSE144749 | GEO
Project description:Plasmacytoid and conventional dendritic cells (pDC, and cDC) are generated from distinct lymphoid and myeloid progenitor cells in murine bone marrow. Despite the early separation of pDC and cDC lineages, CD11c+ MHCII-/lo Siglec-H+ CCR9lo pDC-like precursor cells are able to differentiate into both pDC and cDC. Single-cell transcriptomics and high-dimensional flow cytometry combined with cell fate analysis revealed the heterogeneity and commitment of subsets in this compartment. While Ly6D– cells within this fraction were cDC-committed and B220hi Ly6Dhi Zbtb46– cells were immediate precursors of pDCs, B220lo Ly6Dhi Zbtb46– cells still had the potential to generate cDCs in addition to pDCs. Transition to cDCs occurred via an intermediary stage marked by coexpression of Siglec-H, Ly6D and Zbtb46. Type I IFN stimulation limited cDC and promoted pDC output from these precursors, demonstrating their plasticity in response to inflammation. Thus, flexibility to divert to cDCs is retained in the pDC lineage at later differentiation stages.
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