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Cytokine-driven glycosphingolipid metabolism modulates endoplasmic reticulum calcium homeostasis in primary human renal mesangial cells

GSE311014 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2025/11/25 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 9 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
Cytokine-driven glycosphingolipid metabolism modulates endoplasmic reticulum calcium homeostasis in primary human renal mesangial cellsFrontiers in immunology · 2025
Summary (written by the submitters)
Glycosphingolipids (GSLs), including hexosylceramides (HexCers), lactosylceramides (LacCers), and gangliosides composed of one or more sugar residues attached to ceramide, are essential components of cell membranes. Dysregulated GSL metabolism has been implicated in various inflammatory and autoimmune diseases, including lupus nephritis; however, its contribution to renal cell dysfunction remains largely unexplored.
Read the full summary ↓
In this study, we demonstrate that in primary human renal mesangial cells (hRMCs), proinflammatory cytokines relevant to lupus elicit significant upregulation and secretion of inflammatory mediators that parallel intracellular and extracellular accumulation of HexCers and elevated cytosolic calcium (Ca2+) levels. The increase in cytosolic Ca2+ was attributed to a decrease in endoplasmic reticulum (ER) Ca2+ store capacity. Pharmacological inhibition of GSL synthesis with eliglustat significantly reduced HexCers levels and restored ER Ca2+ stores, but did not impact cytokine-induced cytokine/chemokine secretion or cell viability/proliferation. Together, these data suggest that elevated GSL synthesis modulates cytokine-induced ER Ca²⁺ dysregulation in mesangial cells and may play a role in the pathogenesis of lupus nephritis.
Published in
Cytokine-driven glycosphingolipid metabolism modulates endoplasmic reticulum calcium homeostasis in primary human renal mesangial cells
Stefanenko M, Ortiz TM, Mungaray SG et al. · Frontiers in immunology 2025 · PMID 41451198 · doi:10.3389/fimmu.2025.1688916
This dataset
Open GSE311014 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 GSE311014_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 PRJNA1368490 and SRA study SRP647926. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41451198) ↗
Study design
9 conditions, mostly in triplicate
E ×3 F ×3 G ×3 H ×3 I ×3 J ×3 K ×3 L ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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
Datasets on a similar topic

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