GEO series

Impaired vitamin D signaling causes LMNA mutation-related cardiomyopathy

GSE182219 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/03/01 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 15 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: 15 samples: 5 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.

Summary (written by the submitters)

Mutations of the lamin A/C gene (LMNA) cause a variety of diseases including dilated cardiomyopathy (DCM). LMNA-related DCM often leads to severe heart failure, but the underlying pathophysiology is unknown. Here we show that vitamin D receptor (VDR) signaling is critically involved in LMNA-related DCM. We established iPS cells from DCM patients with an LMNA mutation and found that the iPS cell-derived cardiomyocytes (iPSCMs) showed remarkable DNA damage and reduced contractility compared with the isogenic control.

Read the full summary ↓

Screening of a chemical library revealed that vitamin D2 reduced DNA damage of the mutant iPSCMs. RNA sequencing analysis showed that expression levels of putative downstream genes of VDR including DNA repair factors were downregulated in the mutant iPSCMs, which were upregulated by vitamin D2. Protein-protein interaction screening revealed that the binding of VDR to mutant LMNA was more robust than to wild-type LMNA, resulting in attenuated VDR signaling in the mutant iPSCMs. Vitamin D2 administration reduced DNA damage and improved cardiac function in pressure overload-induced heart failure mice. These results indicate that impaired DNA repair caused by reduced transcriptional activity of VDR induces cardiac dysfunction of LMNA-related DCM and suggest that VDR signaling is a potential therapeutic target for patients with DCM and heart failure.

This dataset

Open GSE182219 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 GSE182219_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 PRJNA755320 and SRA study SRP332733. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 conditions, mostly in triplicate

Cor_DMSO ×3 Mut1_DMSO ×3 Mut1_VD2 ×3 Mut2_DMSO ×3 Mut2_VD2 ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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

GSM5525263 Cor_DMSO_rep1 Cor_DMSO
GSM5525264 Cor_DMSO_rep2 Cor_DMSO
GSM5525265 Cor_DMSO_rep3 Cor_DMSO
GSM5525266 Mut1_DMSO_rep1 Mut1_DMSO
GSM5525267 Mut1_DMSO_rep2 Mut1_DMSO
GSM5525268 Mut1_DMSO_rep3 Mut1_DMSO
GSM5525269 Mut1_VD2_rep1 Mut1_VD2
GSM5525270 Mut1_VD2_rep2 Mut1_VD2
GSM5525271 Mut1_VD2_rep3 Mut1_VD2
GSM5525272 Mut2_DMSO_rep1 Mut2_DMSO
GSM5525273 Mut2_DMSO_rep2 Mut2_DMSO
GSM5525274 Mut2_DMSO_rep3 Mut2_DMSO
GSM5525275 Mut2_VD2_rep1 Mut2_VD2
GSM5525276 Mut2_VD2_rep2 Mut2_VD2
GSM5525277 Mut2_VD2_rep3 Mut2_VD2

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GSE312730 Simtuzumab Attenuates Loxl2-Mediated Extracellular Matrix Remodeling and Preserves Cardiac Function in LMNA Mutation-Induced Dilated Cardiomyopathy 6 samples shares lmna, cardiomyopathy
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GSE284630 RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [siZNF207_Rescue_mRNA-Seq] 8 samples shares lmna
GSE284629 RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [siZNF207_mRNA-Seq] 8 samples shares lmna
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