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GeoMx GeoMx-DSP Toxic Lipid-induced Epigenetic Activation of ICAM1 in Liver Sinusoidal Endothelium Regulates Myeloid-Driven Fibro-inflammatory Response in MASH

GSE309979 Homo sapiens (human) Spatial transcriptomics 217 samples Submitted 2026/08/05 Platform GPL30173
At a glance

Spatial transcriptomics · human · 217 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
Homo sapiens (human)
Samples
217 samples: 32 conditions, mostly with about 7 replicates eachGroups 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.
Paper
Toxic lipid-induced epigenetic activation of ICAM1 in liver sinusoidal endothelium regulates myeloid-driven fibro-inflammatory response in MASHHepatology (Baltimore, Md.) · 2026
Summary (written by the submitters)
Background: Liver sinusoidal endothelial cells (LSECs) acquire a proinflammatory phenotype in metabolic dysfunction-associated steatohepatitis (MASH), characterized by elevated adhesion molecules and inflammatory mediators—a process termed lipotoxic endotheliopathy. However, the molecular drivers of this transformation remain incompletely defined.
Read the full summary ↓
Methods: We employed complementary models of lipotoxicity and MASH, including palmitate-treated primary human LSECs (in vitro), cultured precision-cut liver slices from normal human and mice liver with MASH-inducing media as well as MASH mice (ex vivo), and diet-induced MASH models (in vivo). Results: GeoMx digital spatial profiling of human MASH livers revealed enriched proinflammatory and fibrogenic signaling between LSECs and myeloid cells. Among the top upregulated genes and ligand-receptor pairs was ICAM1, whose expression correlated with disease severity and was increased in human MASH by immunostaining. ATAC-seq on primary mouse LSECs showed enhanced chromatin accessibility at the Icam1 promoter in MASH. Chromatin immunoprecipitation confirmed enrichment of the active epigenetic mark H3K27ac and BRD4 binding at the ICAM1 promoter in human LSECs under lipotoxic stress. Mechanistically, we identified the GSK3β/c-Jun/BRD4 axis as a key regulator of ICAM1 induction in LSECs. In vivo, ICAM1-neutralizing antibody or endothelial-specific epigenetic suppression reduced hepatic inflammation, injury, and fibrosis in MASH mice. Conclusion: ICAM1 is epigenetically upregulated in LSECs during lipotoxic stress and promotes myeloid cell recruitment in MASH. Targeting the epigenetic regulation of ICAM1 may offer a novel therapeutic strategy for treating human MASH.
Published in
Toxic lipid-induced epigenetic activation of ICAM1 in liver sinusoidal endothelium regulates myeloid-driven fibro-inflammatory response in MASH
Guo Q, Satthawiwat N, Sano A et al. · Hepatology (Baltimore, Md.) 2026 · PMID 41983905 · doi:10.1097/HEP.0000000000001742
This dataset
Open GSE309979 in finder → Find more human datasets →
Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE309979_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1364859. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41983905) ↗
Study design
32 conditions, mostly with about 7 replicates each
GeoMx-DSP-1001660022457-B-E ×11 GeoMx-DSP-1001660022456-E-A ×10 GeoMx-DSP-1001660022456-E-B ×10 GeoMx-DSP-1001660022457-B-H ×10 GeoMx-DSP-1001660022456-E-D ×9 GeoMx-DSP-1001660022457-B-C ×9 GeoMx-DSP-1001660010639-D-G ×8 GeoMx-DSP-1001660022455-C-D ×8 +24 more

Supports a between-group comparison across 217 samples.

How we read this: 32 replicated groups read from 217 sample titles; they account for 217 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

+ 177 more — browse all 217 samples with per-sample file links →

Datasets on a similar topic

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