GEO series

ANGPTL3 regulates the peroxisomal translocation of SmarcAL1 in response to cell growth states

GSE221371 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/02/19 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 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: Homo sapiens (human)
Samples: 12 samples: 6 × Control vs 6 × ANGPTL3_KOGroups 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: ANGPTL3 regulates the peroxisomal translocation of SmarcAL1 in response to cell growth statesScientific reports · 2025

Summary (written by the submitters)

Angiopoietin-like 3 (ANGPTL3) is a key regulator of lipoprotein metabolism, known for its potent inhibition on intravascular lipoprotein and endothelial lipase activities. Recent studies have shed light on the cellular functions of ANGPTL3. However, the precise mechanism underlying its regulation of cellular lipid metabolism remains elusive.

Read the full summary ↓

We recently reported that ANGPTL3 interacts with the chromatin regulator SMARCAL1, which plays a pivotal role in maintaining cellular lipid homeostasis. Here, through a combination of in vitro and in vivo functional analyses, we provide evidence that ANGPTL3 indeed influences cellular lipid metabolism. Increased expression of Angptl3 prompted the formation of lipid droplets (LDs) in response to slow growth conditions. Notably, under the conditions, Angptl3 accumulated within cytoplasmic peroxisomes, where it interacts with SmarcAL1, which translocated from nucleus as observed previously. This translocation induced changes in gene expression favoring triglyceride (TG) accumulation. Indeed, ANGPTL3 gene knockout (KO) in human cells increased the expression of key lipid genes, which could be linked to elevated nuclear localization of SMARCAL1, whereas the expression of these genes decreased in SMARCAL1 KO cells. Consistent with these findings, the injection of Angptl3 protein to mice led to hepatic fat accumulation derived from circulating blood, a phenotype likely indicative of its long-term effect on blood TG, linked to SmarcAL1 activities. Thus, our results suggest that the Angptl3-SmarcAL1 pathway may confer the capacity for TG storage in cells in response to varying growth states, which may have broad implications for this pathway in regulating energy storage and trafficking.

Published in

ANGPTL3 regulates the peroxisomal translocation of SmarcAL1 in response to cell growth states

Nagai TH, Mizoguchi T, Wang Y et al. · Scientific reports 2025 · PMID 39934259 · doi:10.1038/s41598-025-89552-6

This dataset

Open GSE221371 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 GSE221371_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 PRJNA914047 and SRA study SRP413981. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39934259) ↗

Study design

6 × Control vs 6 × ANGPTL3_KO

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

GSM6862059 Control_0 Control
GSM6862060 Control_1 Control
GSM6862061 Control_2 Control
GSM6862062 Control_3 Control
GSM6862063 Control_4 Control
GSM6862064 Control_5 Control
GSM6862065 ANGPTL3_KO_0 ANGPTL3_KO
GSM6862066 ANGPTL3_KO_1 ANGPTL3_KO
GSM6862067 ANGPTL3_KO_2 ANGPTL3_KO
GSM6862068 ANGPTL3_KO_3 ANGPTL3_KO
GSM6862069 ANGPTL3_KO_4 ANGPTL3_KO
GSM6862070 ANGPTL3_KO_5 ANGPTL3_KO

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