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Mitochondrial DNA mutations are associated with response to anti-VEGF therapy in ovarian cancer PDX models

GSE261674 Homo sapiens (human) RNA-seq (gene expression) 19 samples Submitted 2024/12/27 Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 19 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
Ovarian cancerThis series is part of our curated briefing on it.
Samples
19 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
Pathogenic mitochondrial DNA variants are associated with response to anti-VEGF therapy in ovarian cancer PDX modelsJournal of experimental & clinical cancer research : CR · 2024
Summary (written by the submitters)
Mitochondrial DNA (mtDNA) mutations have been reported in several solid tumors including ovarian cancer (OC), the most lethal gynecologic malignancy, and raised interest as they potentially induce mitochondrial dysfunction and rewiring of cellular metabolism. In this study, we characterized mtDNA mutations in ovarian cancer patient derived xenografts (PDX) and investigated their impact on cancer cells at multiple levels.
Read the full summary ↓
To correlate the presence of mtDNA mutations and metabolic pathways that were modulated at the transcriptional level, RNA-seq analysis was performed in ascites-derived cells from 19 OC PDX (here named PDOVCA). Results indicated that mtDNA mutated (>50% VAF) PDX were endowed with upregulated glycolysis and other pathways connected with cancer metabolism. Functional analysis demonstrated that mtDNA mutations modulated mitochondria activity, assembly capacity and morphology of mitochondrial complexes in PDX cells. Moreover, PDX cells bearing homoplasmic mtDNA mutations behave as glucose addicted and could barely survive glucose starvation in vitro. These findings led us to investigate whether mtDNA mutations correlated with response to anti-VEGF therapy, which was shown to reduce glucose availability in tumors. Strikingly, PDX bearing homoplasmic pathogenic mtDNA mutations had improved survival upon anti-VEGF treatment in mouse models, compared with PDX lacking mtDNA mutations or bearing them at low frequency. These results hint at mtDNA mutations as new biomarkers of response to antiangiogenic drugs.
Published in
Pathogenic mitochondrial DNA variants are associated with response to anti-VEGF therapy in ovarian cancer PDX models
Boso D, Piga I, Trento C et al. · Journal of experimental & clinical cancer research : CR 2024 · PMID 39702370 · doi:10.1186/s13046-024-03239-w
This dataset
Open GSE261674 in finder → Find more human RNA-seq datasets → Ovarian cancer 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 GSE261674_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 PRJNA1086910 and SRA study SRP495004. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39702370) ↗
Study design
A cohort of 19 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run PDOVCA_1 … PDOVCA_146 and carry no group information.

Samples in this study
More Ovarian cancer datasets

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.