GEO series

Cholesterol biosynthesis and mutant IDH activity are linked to cellular glycogen through PPP1R3C in growth plate chondrocytes and chondrosarcoma [RNA-seq]

GSE286965 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/04/02 Platform GPL24676

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
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: Protein Phosphatase 1 Regulatory Subunit 3C integrates cholesterol metabolism and isocitrate dehydrogenase in chondrocytes and neoplasiaProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

Enchondromas are common bone tumors composed of chondrocytes originating from growth plate cells, which can progress to malignant chondrosarcoma. Mutations in the genes encoding isocitrate dehydrogenase (IDH1 and IDH2) are identified in a large proportion of these tumors. IDH enzymes convert isocitrate to alpha-ketoglutarate (α-KG), an essential component of the citric acid cycle.

Read the full summary ↓

The mutant IDH enzymes produce 2-hydroxyglutarate (2-HG), which has epigenetic effects important in tumor initiation. Tumor maintenance and growth rely on additional factors as well. Prior work shows that intracellular cholesterol and glycogen are upregulated in mutant IDH chondrocytes. Here, we show that Protein Phosphatase 1 Regulatory Subunit 3C (PPP1R3C, previously termed Protein Targeting to Glycogen or PTG) is upregulated in chondrocytes harboring a mutant IDH. PPP1R3C expression correlates with the level of intracellular cholesterol biosynthesis and can be regulated by Sterol Regulatory Element-Binding Proteins (SREBPs), which are transcriptional regulators of enzymes involved in sterol biosynthesis. We found that PPP1R3C regulates glycolysis and glycolytic capacity in chondrocytes. Depletion of PPP1R3C in mouse chondrocytes in vivo suppresses the enchondroma phenotype. The growth plate phenotype associated with the inhibition of cholesterol biosynthesis is partially rescued by PPP1R3C overexpression. Taken together, our data show that PPP1R3C integrates the effects of cholesterol metabolism and isocitrate dehydrogenase on growth plate and neoplastic chondrocyte metabolism by regulating intracellular glycogen levels.

Published in

Protein Phosphatase 1 Regulatory Subunit 3C integrates cholesterol metabolism and isocitrate dehydrogenase in chondrocytes and neoplasia

Nakagawa M, Shimada E, Guardino N et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40232792 · doi:10.1073/pnas.2501519122

This dataset

Open GSE286965 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 GSE286965_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 PRJNA1210610 and SRA study SRP557298. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40232792) ↗

Samples in this study

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+ 18 more — browse all 18 samples with per-sample file links →

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