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Cerebrospinal fluid from HAM/TSP patients with rapid evolution affects mitochondrial DNA transcription and structure in human glioblastoma cell lines

GSE290808 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2025/04/15 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 30 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)
Topic
GlioblastomaThis series is part of our curated briefing on it.
Samples
30 samples: 15 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
Human T-lymphotropic virus 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive neurodegenerative disease impacting motor and sensorial functions. While the cerebrospinal fluid (CSF) alterations have been used to identify biomarkers for this disease, the effects of HTLV-1 CSF on neural cells remain unexplored.
Read the full summary ↓
Herein, we investigated the impact of CSF from HTLV-1 infected patients on glioblastoma cell lines. CSF samples were obtained from HTLV-1 asymptomatic carriers (HAC) (n=13), and HAM/TSP patients (n=21) categorized according to the speed of disease progression: very slow (HAMvs), typical (HAMt), and rapid (HAMr). RNA sequencing of glioblastoma cells treated with HTLV-1 CSF revealed notable gene expression changes, particularly with HAMr CSF, which caused significant downregulation of mitochondrial DNA transcripts. Confocal microscopy showed phenotypical changes in the mitochondrial network: astrocytes exposed to HAMr CSF exhibited a less complex mitochondrial network compared to CSF from other patient groups. It is characterized by reduced mitochondrial branching, fewer junctions per branch length, and slightly increased branch diameter. Compared to untreated cells, HTLV+ CSF disturbed mitochondrial metabolism. However, these changes are limited at the metabolic level and do not appear to vary significantly with HTLV donor status. In conclusion, our findings suggest that HTLV+ CSF induces mitochondrial reorganization in glioblastoma cells, potentially helping to compensate for the stress caused by the CSF exposure.
This dataset
Open GSE290808 in finder → Find more human RNA-seq datasets → Glioblastoma landscape →
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 GSE290808_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 PRJNA1230155 and SRA study SRP572921. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
15 conditions, mostly in duplicate
U87-MG cells, untreated, replicate 1, hou ×2 U87-MG cells, untreated, replicate 2, hou ×2 U87-MG cells, untreated, replicate 3, hou ×2 U87-MG cells, asymptomatic, replicate 1, hou ×2 U87-MG cells, asymptomatic, replicate 2, hou ×2 U87-MG cells, asymptomatic, replicate 3, hou ×2 U87-MG cells, HAM very slow, replicate 1, hou ×2 U87-MG cells, HAM very slow, replicate 2, hou ×2 +7 more

Supports a between-group comparison across 30 samples.

How we read this: 15 replicated groups read from 30 sample titles; they account for 30 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
More Glioblastoma datasets

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