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SRX10240706: GSM5135522: WT (F7); Mus musculus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 381.4M spots, 34.7G bases, 7.2Gb downloads

Submitted by: NCBI (GEO)
Study: cDC1 retain a niche for precursor exhausted T cells during chronic viral infection
show Abstracthide Abstract
Tumors and chronic infections result in sustained antigen exposure, which promotes impaired functional responsiveness in T cells referred to as exhaustion. Checkpoint immunotherapy can induce the reinvigoration of cellular immunity by activating a recently identified precursor of exhausted T (TPEX) cell population. This activation requires cellular interactions between TPEX cells and professional antigen-presenting cells, likely conventional dendritic cells (cDC). Currently, it is unknown where cDC - TPEX cell interactions take place and which cDC subsets are involved. To address these questions, we first mapped the differentiation trajectory of TPEX cell subsets via transitory cellular states towards terminally exhausted T (TEX) cells, identified transcriptionally distinct subpopulations and defined their localization in the spleen during chronic viral infection. We found that cDC were required for TPEX cell proliferation, differentiation and viral control during PD-L1 treatment. In particular cDC1, a specialized subset of dendritic cells, colocalized with TPEX cells and regulated their maintenance by promoting the functionality of stromal cells that support TPEX cell survival. Additionally, during PD-L1 treatment, the splenic cDC1 network was significantly reorganized at the marginal zone, a site of TPEX cell differentiation. As a consequence, viral control during checkpoint immunotherapy and cellular integrity of the marginal zone depended on the presence of cDC1. Since cDC2 were sufficient to drive initial TPEX cell proliferation and TEX cell generation but not viral control, our data suggest a new concept in which cDC1 decelerate the speed of differentiation of TPEX cells via transitory cellular states and thereby generate a therapeutic window for effective immunotherapy. Together, our findings reveal how the dynamic spatial organization of the DC network supports cellular niches that guide the maintenance and differentiation of TPEX cells and opens new avenues to optimize checkpoint immunotherapy. Overall design: B/6 Mice were infected with 2x10^6 IU LCMV clone13 after 2 times CD4 T cell depletion (d2 and d0) with 300µg GK1.5 antibody. At the chronic infection phase (> d30), splenocytes were isolated and CD8+, PD-1+, Tim-3 low cells were sorted using FACS AriaIII. Treated mice were injected i.p. 200µg aPD-L1 antibody (clone 10F.9G2) 24h before sacrificing the mice. Cells were pooled form 4 mice per group.
Sample: WT (F7)
SAMN18142680 • SRS8382105 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Mice were sacrificed and spleen isolated. Single cell suspnesion was created by grinding spleens though a filter. Afterwards, red blood cells were lysed with ACK-buffer for 4min. Splenocytes were staining with antibodies for 30min at 4 degrees and sorted for the desired population using FACS AriaIII. CD8+, PD-1+, TIM-3 negative single-cells were sorted from the spleen of chronically infected mice using a FACSAria III (BD Biosciences), before being encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer's specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3' Library & Gel Bead Kit v2 for the WT untreated sample or v3 for WT and XCR1-DTR samples treated with aPD-L1 and DTx (10x Genomics) following the detailed protocol provided by the manufacturer.
Experiment attributes:
GEO Accession: GSM5135522
Links:
Runs: 1 run, 381.4M spots, 34.7G bases, 7.2Gb
Run# of Spots# of BasesSizePublished
SRR13859724381,362,82734.7G7.2Gb2022-05-06

ID:
13368282

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