GEO series

IL-8+ neutrophils drive inexorable inflammation in severe alcohol-associated hepatitis [scRNA-seq]

GSE255772 Homo sapiens (human) Single-cell RNA-seq 13 samples Submitted 2024/05/13 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 13 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: 13 samples: 5 × Liver_sAH vs 4 × WBC_sAH vs 3 × WBC_ACGroups are read from the sample names, not from the paper. Check the list below.
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.
Paper: IL-8+ neutrophils drive inexorable inflammation in severe alcohol-associated hepatitisThe Journal of clinical investigation · 2024

Summary (written by the submitters)

Patients with alcohol-associated liver cirrhosis (AC) may develop severe alcohol-associated hepatitis (sAH), but the mechanisms underlying the transition from AC to sAH still remain unclear. We performed single cell RNA (scRNA) sequencing analysis of livers and peripheral white blood cells (WBC) from sAH and AC patients. We found that the significant difference between sAH and AC was that sAH livers had a markedly higher number of neutrophil subsets than AC livers.

Read the full summary ↓

Thus, we further focused on the neutrophil cluster and found two distinct sAH-specific liver neutrophils are notably characterized by heightened expression of CXCL8 (IL-8) defined as IL-8+ neutrophils blood. Our current study has demonstrated that sAH had self-sustaining IL-8+ neutrophil accumulation that likely drives inexorable liver inflammation and failure in sAH. Based on our study, we believe targeting IL-8+ neutrophils is a promising therapeutic strategy for sAH.

Published in

IL-8+ neutrophils drive inexorable inflammation in severe alcohol-associated hepatitis

Guan Y, Peiffer B, Feng D et al. · The Journal of clinical investigation 2024 · PMID 38502218 · doi:10.1172/JCI178616

This dataset

Open GSE255772 in finder → Find more human RNA-seq datasets →

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 GSE255772_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 PRJNA1076500 and SRA study SRP489753. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38502218) ↗

Study design

5 × Liver_sAH vs 4 × WBC_sAH vs 3 × WBC_AC

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 13 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8079816 Liver_AC29
GSM8079817 Liver_sAH100 Liver_sAH
GSM8079818 Liver_sAH101 Liver_sAH
GSM8079819 Liver_sAH102 Liver_sAH
GSM8079820 Liver_sAH103 Liver_sAH
GSM8079821 Liver_sAH104 Liver_sAH
GSM8079822 WBC_AC27 WBC_AC
GSM8079823 WBC_AC28 WBC_AC
GSM8079824 WBC_AC29 WBC_AC
GSM8079825 WBC_sAH101 WBC_sAH
GSM8079826 WBC_sAH102 WBC_sAH
GSM8079827 WBC_sAH103 WBC_sAH
GSM8079828 WBC_sAH104 WBC_sAH

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GSE333389 Platelet-derived S100A9 contributes to Endotheliopathy in Alcohol-Associated Hepatitis 15 samples shares alcohol-associated, hepatitis
GSE247467 Transcriptomic characterization of circulating neutrophils isolated from patients with metabolic dysfunction-associated steatohepatitis (MASH), formerly known as nonalcoholic steatohepatitis (NASH). 12 samples shares neutrophils, hepatitis
GSE255379 Interleukin-6 Trans Signaling and STAT-3 Activation Promote Neutrophilic Inflammation in Alcohol-Associated Hepatitis 9 samples shares alcohol-associated, hepatitis
GSE269566 Alcohol-associated hepatitis induces hepatocyte senescence which is reduced following disease resolution I 8 samples shares alcohol-associated, hepatitis

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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.