GEO series

KRIT1 heterozygous mutations are sufficient to induce a pathological phenotype in patient-derived iPSC models of Cerebral Cavernous Malformation

GSE291768 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/04/15 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 6 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: KRIT1 heterozygous mutations are sufficient to induce a pathological phenotype in patient-derived iPSC models of cerebral cavernous malformationCell reports · 2025

Summary (written by the submitters)

Cerebral Cavernous Malformation (CCM) is a neurovascular disease distinguished by clusters of leaky, mulberry-like blood vessels. KRIT1 biallelic loss-of-function mutations in endothelial cells are known to trigger brain cavernomas, however, human pre-clinical models are needed to unveil the importance of germline KRIT1 heterozygous mutations in CCM pathogenesis.

Read the full summary ↓

We generated three iPSCs from CCM patients with hereditary KRIT1 heterozygous mutations. Patient-derived vascularized organoids exhibited intricate and abnormal vascular structures with cavernoma-like morphology, and iPSCs-derived endothelial cells displayed phenotypic abnormalities at the junctional and transcriptional level. Upon injection into brain explants, CCM-endothelial cells integrated into the normal vasculature and created vascular anomalies. Lastly, transcriptional analysis showed that the endothelial progenitor marker PEG3 was highly expressed in iPSCs-derived CCM endothelial cells and further confirmed in familial and sporadic cavernoma biopsies. Overall, our study enlightens the molecular consequence of KRIT1 heterozygous mutations in endothelial cells and the potential implications in cavernoma pathogenesis.

Published in

KRIT1 heterozygous mutations are sufficient to induce a pathological phenotype in patient-derived iPSC models of cerebral cavernous malformation

Arce M, Erzar I, Yang F et al. · Cell reports 2025 · PMID 40238631 · doi:10.1016/j.celrep.2025.115576

This dataset

Open GSE291768 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 GSE291768_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 PRJNA1235214 and SRA study SRP569890. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40238631) ↗

Study design

6 conditions, mostly in triplicate

iECs-CCM01_n ×3 iECs-CCM02_n ×3 iECs-CCM03_n ×3 iECs-HD01_n ×3 Brain-slides-CCM01_n ×3 Brain-slides-HD01_n ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM8842127 iECs-CCM01_n1 iECs-CCM01_n
GSM8842128 iECs-CCM01_n2 iECs-CCM01_n
GSM8842129 iECs-CCM01_n3 iECs-CCM01_n
GSM8842130 iECs-CCM02_n1 iECs-CCM02_n
GSM8842131 iECs-CCM02_n2 iECs-CCM02_n
GSM8842132 iECs-CCM02_n3 iECs-CCM02_n
GSM8842133 iECs-CCM03_n1 iECs-CCM03_n
GSM8842134 iECs-CCM03_n2 iECs-CCM03_n
GSM8842135 iECs-CCM03_n3 iECs-CCM03_n
GSM8842136 iECs-HD01_n1 iECs-HD01_n
GSM8842137 iECs-HD01_n2 iECs-HD01_n
GSM8842138 iECs-HD01_n3 iECs-HD01_n
GSM8842139 Brain-slides-CCM01_n1 Brain-slides-CCM01_n
GSM8842140 Brain-slides-CCM01_n2 Brain-slides-CCM01_n
GSM8842141 Brain-slides-CCM01_n3 Brain-slides-CCM01_n
GSM8842142 Brain-slides-HD01_n1 Brain-slides-HD01_n
GSM8842143 Brain-slides-HD01_n2 Brain-slides-HD01_n
GSM8842144 Brain-slides-HD01_n3 Brain-slides-HD01_n

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