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MFRP in the retina is a molecular hub that organizes the apical membrane of RPE cells by engaging in interactions with specific protein and lipid molecules

GSE283089 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/01/31 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 12 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
Mus musculus (mouse)
Samples
12 samples: 6 × RPE cells from 1mo rd6 mice vs 6 × RPE cells from 1mo wt (C57BL/6J) miceGroups 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
MFRP is a molecular hub that organizes the apical membrane of RPE cells by engaging in interactions with specific proteins and lipidsProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
Membrane frizzled-related protein (MFRP) is an integral membrane protein present in the retinal pigment epithelium (RPE) and is essential for ocular development and the physiology of the retina. Mutations in MFRP are associated with autosomal recessive non-syndromic nanophthalmos, leading to severe hyperopia and early-onset retinitis pigmentosa.
Read the full summary ↓
While several preclinical gene augmentation and gene editing trials hold promise for future therapies aimed at stopping degeneration and restoring retinal function, the molecular mechanisms underlying MFRP biology remain largely undefined. Here, we studied the biochemical properties of MFRP and the molecular consequences of its loss in a mouse model. Using transcriptomic and lipidomic approaches, we observed that DHA accumulation constitutes a primary defect in the MFRP-deficient RPE. In biochemical assays, we showed that MFRP undergoes extensive glycosylation and preferentially binds several classes of lipids, including phosphatidylserine and phosphatidylinositol 4-phosphate, as well as several other transmembrane proteins, notably adiponectin receptor 1 (ADIPOR1) and inward rectifier potassium channel 13 (KCNJ13). Moreover, MFRP determines ADIPOR1 and KCNJ13 subcellular localization in the RPE in vivo. This feature is affected upon MFRP deficiency and can be restored by gene therapy approaches. Overall, our observations suggest that MFRP constitutes an important interaction hub within the apical membrane of RPE cells, essential for protein trafficking and subcellular localization within the RPE and lipid homeostasis within the entire retina.
Published in
MFRP is a molecular hub that organizes the apical membrane of RPE cells by engaging in interactions with specific proteins and lipids
Tworak A, Smidak R, Rodrigues Menezes C et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40249779 · doi:10.1073/pnas.2425523122
This dataset
Open GSE283089 in finder → Find more mouse 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 GSE283089_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 PRJNA1191850 and SRA study SRP548224. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40249779) ↗
Study design
6 × RPE cells from 1mo rd6 mice vs 6 × RPE cells from 1mo wt (C57BL/6J) mice

Supports a between-group comparison across 12 samples.

How we read this: 2 replicated groups read from 12 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
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