{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan Schroeder"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16291"],"description":["Classically, dendritic cells (DC) capture pathogen material and upon activation by pathogen products (or damage), initiate adaptive immunity. Here, we describe an additional layer to this process, required when the pathogen-derived signals themselves do not provide effective DC activation.  Immunisation with sporozoites from Plasmodium leads to the generation of protective anti-malarial immunity mediated by liver resident memory T (TRM) cells, in a complex response that is crucially dependent upon gd T cells.  Here, we show that CD40L signals to antigen-presenting DC are CD4 T cell derived, but Vg1 gd T cells play an initiating role by providing essential IL-4 signals to DC. IL-4 acts together with IFNg to induce IL-12 and promote CD8 T cell expansion. This study shows that responses to some pathogens, such as Plasmodium, require help from innate-like T cells to pass the initiation threshold, and demonstrates the critical role of IL-4 in this process."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Illumina NovaSeq X Plus","Library Construction - Libraries were prepared using Illumina stranded mRNA library kits and the outputs sequenced to a depth of 20M reads per sample on a 150PE on Illumina NovaSeq X Plus 10B flow cell. Library preparation and sequencing was conducted at the Australian Genome Research Facility.","Nucleic Acid Extraction - To determine gene expression in cDC1s, mRNA was extracted using a Direct-zol RNA MicroPrep kit (Zymo Research) as per manufacturer’s protocol.","Sample Collection - Dendritic cells were isolated from spleens of B16.Flt3L tumour-bearing mice. Briefly, spleens were finely minced in 1mg/ml Collagenase Type 3, 20 µg/ml DNase I and continuously agitated for 15 minutes. DC-T cell complexes were disrupted with the addition of 0.1M EDTA (pH7.2). Undigested fragments were removed by filtering through a 70 µM mesh before light-density separation with 1.077g/cm3 Nycodenz medium via centrifugation at 1700rpm at 4°C for 12min. To increase the purity of cDC1 precursors, the light density fraction was collected, and cDC1s/pre-cDC1s were negatively enriched for through incubation with rat mAb against CD3ε (KT3), Thy1.1 (T24/31.7), Gr-1 (RB6-8C5), B220 (RA3-6B2), Ter-119 and CD11b (M1/70) prior to incubation with BioMag goat anti-rat IgG coupled magnetic beads (Qiagen) and magnetic separation. Target cells were characterised as CD11c+, MHC-IIint/+, CD11b−, CD24hi, CD8a+ with purities from 60-80%. CD11c+, MHC-IIint/+, CD11b−, CD24hi, B220−, CD172− cells were then sorted using a BD FACSAriaTM III Cell Sorter into filtered RPMI supplemented with 50% heat-inactivated FCS and pelleted. In a 24-well plate, 5 x 105 cells were plated in complete Kenneth D Shortman RPMI (KDS-RPMI 1640, 10% FCS, 2mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 50 mM 2-mercaptoethanol). To assess cDC1 gene expression in response to IL-4, cells were incubated in the presence of -CD40 (10g/ml), IL-4 (60ng/mL), IFN- (20ng/mL), or LPS (1g/ml). Plates were then incubated at 37°C and 5% CO2 for 4 hours. For RNA isolation, cells were washed and resuspended using TRIzol (Life Technologies), snap frozen and stored at -80°C.","Growth Protocol - See treatment","Sample Treatment - CD11c+, MHC-IIint/+, CD11b−, CD24hi, B220−, CD172a− cells were then sorted using a BD FACSAriaTM III Cell Sorter into filtered RPMI supplemented with 50% heat-inactivated FCS and pelleted. In a 24-well plate, 5 x 105 cells were plated in complete Kenneth D Shortman RPMI (KDS-RPMI 1640, 10% FCS, 2mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 50 mM 2-mercaptoethanol). To assess cDC1 gene expression in response to IL-4, cells were incubated in the presence of a-CD40 (10mg/ml), IL-4 (60ng/mL), IFN-g (20ng/mL), or LPS (1mg/ml). Plates were then incubated at 37°C and 5% CO2 for 4 hours. For RNA isolation, cells were washed and resuspended using TRIzol (Life Technologies), snap frozen and stored at -80°C."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The processed data was not normalised and contains raw counts.","Sequence Alignment - Bulk sequencing reads were aligned to the GRCm39 reference genome and transcriptome (version 105) using the STAR aligner (version 2.7.8a) and counted using featureCounts (version 2.0.0)"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Jan Schroeder"],"additional_accession":[]},"is_claimable":false,"name":"Vg1+ gd T cells promote DC activation and CD8 T cell expansion via IL-4","description":"Classically, dendritic cells (DC) capture pathogen material and upon activation by pathogen products (or damage), initiate adaptive immunity. Here, we describe an additional layer to this process, required when the pathogen-derived signals themselves do not provide effective DC activation.  Immunisation with sporozoites from Plasmodium leads to the generation of protective anti-malarial immunity mediated by liver resident memory T (TRM) cells, in a complex response that is crucially dependent upon gd T cells.  Here, we show that CD40L signals to antigen-presenting DC are CD4 T cell derived, but Vg1 gd T cells play an initiating role by providing essential IL-4 signals to DC. IL-4 acts together with IFNg to induce IL-12 and promote CD8 T cell expansion. This study shows that responses to some pathogens, such as Plasmodium, require help from innate-like T cells to pass the initiation threshold, and demonstrates the critical role of IL-4 in this process.","dates":{"release":"2025-11-18T00:00:00Z","modification":"2026-06-16T11:20:59.374Z","creation":"2025-11-25T16:02:36.409Z"},"accession":"E-MTAB-16291","cross_references":{"ENA":["ERP185635"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}