GEO series

Candida albicans-specific Th17 cell-mediated response contributes to alcohol-associated liver disease [scRNA & scTCR-seq]

GSE215930 Homo sapiens (human) Single-cell RNA-seq 4 samples Submitted 2023/02/16 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 4 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 4 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Alcohol-associated liver disease is accompanied by changes in the intestinal mycobiome. How fungal dysbiosis contributes to liver disease is not clear. T-helper (Th17) cells mediate immune responses against fungi, but the interleukin 17 (IL17) pathway has been associated with pathogenesis of alcohol-associated liver disease. Here, we demonstrate that Candida albicans (C.

Read the full summary ↓

albicans)-specific Th17 cells are increased in the circulation and present in the liver of patients with alcohol-associated liver disease. Chronic ethanol administration to mice results in migration of C. albicans-reactive Th17 cells from the intestine to the liver. The antifungal agent nystatin reduced intestinal fungal overgrowth, decreased C. albicans-specific Th17 cells in the liver, and reduced features of ethanol-induced liver disease in mice. Transgenic mice that express a T-cell receptor (TCR) reactive to Candida antigens develop more severe ethanol-induced liver disease than transgene-negative littermates; disease severity was reduced by administration of an antibody against IL17 to the TCR transgenic mice. Adoptive transfer of C. albicans-reactive Th17 cells exacerbated ethanol-induced liver disease in wild-type mice. IL17 receptor A (IL17ra) signaling in Kupffer cells was required for the effects of C. albicans-reactive Th17 cells. Our findings indicate that ethanol increases C. albicans-reactive Th17 cells, which contribute to alcohol-associated liver disease.

This dataset

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Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE215930_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA891302 and SRA study SRP403052. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 36893735) ↗

Samples in this study

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+ 4 more — browse all 4 samples with per-sample file links →

Datasets on a similar topic

GSE215929 Candida albicans-specific Th17 cell-mediated response contributes to alcohol-associated liver disease [bulk TCR-seq] 8 samples shares th17, alcohol-associated, albicans-specific, cell-mediated, contributes, candida, liver
GSE329527 Antigen-restricted Candida albicans Th17 cells link oral-gut immunity and adopt pathogenic features during intestinal inflammation 81 samples shares th17, candida
GSE272014 Bulk RNA sequencing of liver biopsy-derived organoids from patients with alcohol-associated liver disease and paired tissues 50 samples shares alcohol-associated, liver
GSE333389 Platelet-derived S100A9 contributes to Endotheliopathy in Alcohol-Associated Hepatitis 15 samples shares alcohol-associated, contributes
GSE281574 Dysregulated RNA splicing induces regeneration failure in alcohol-associated liver disease 12 samples shares alcohol-associated, liver
GSE273146 Patient-derived liver organoids recapitulate epithelial heterogeneity and enable precision disease modelling of alcohol-associated liver disease 10 samples shares alcohol-associated, liver
GSE320339 Blocking the Gut–Liver IgA Axis Attenuates Macrophage-Mediated Inflammation and Injury in Alcohol-Associated Liver Disease [RNA-Seq] 6 samples shares alcohol-associated, liver
GSE243064 RORA proximal enhancer regulates its expression during early human Th17 cell differentiation 72 samples shares th17

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.