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Effect of ADAR1 and MDA5 knock down by siRNA on human SMC phenotypic modulation and calcification in vitro

GSE254862 Homo sapiens (human) RNA-seq (gene expression) 42 samples Submitted 2025/07/29 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 42 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
42 samples: 14 conditions, mostly in triplicateGroups 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
Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of the RNA sensor MDA5 in atherosclerosisNature cardiovascular research · 2025
Summary (written by the submitters)
Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression1. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing2.
Read the full summary ↓
This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 (IFIH1)3,4. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing to be an important mechanism of coronary artery disease (CAD) risk2,5. Here, we provide a crucial link between observations in human genetics and the mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that MDA5 activation occurs in SMC phenotypic modulation — demonstrating a cell type and context specific role of RNA editing. We further show Adar1 controls SMC phenotypic state, is required to maintain vascular integrity, and controls progression of vascular calcification. Through this work, we describe a fundamental mechanism of CAD, where cell type and context specific RNA editing and sensing of dsRNA mediates disease progression, bridging our understanding of human genetics and disease causality.
Published in
Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of the RNA sensor MDA5 in atherosclerosis
Weldy CS, Li Q, Monteiro JP et al. · Nature cardiovascular research 2025 · PMID 40958051 · doi:10.1038/s44161-025-00710-5
This dataset
Open GSE254862 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 GSE254862_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1072104 and SRA study SRP487540. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40958051) ↗
Study design
14 conditions, mostly in triplicate
Primary HCASMC cells, siRNA control, serum st… ×3 Primary HCASMC cells, siRNA ADAR1, serum star… ×3 Primary HCASMC cells, siRNA ADAR1 IFIH1, seru… ×3 Primary HCASMC cells, siRNA ADAR1, serum stim… ×3 Immortalized HCASMC cell line, siRNA control,… ×3 Immortalized HCASMC cell line, siRNA ADAR1, c… ×3 Immortalized HCASMC cell line, siRNA ADAR1 IF… ×3 Immortalized HCASMC cell line, siRNA IFIH1, c… ×3 +8 more

Supports a case/control comparison: 6 samples read as cases, 18 as controls.

How we read this: 14 replicated groups read from 42 sample titles; they account for 40 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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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.