GEO series

Chemo-senolytic therapeutic potential against angiosarcoma

GSE245935 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2024/03/23 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 13 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: Soft tissue sarcomaThis series is part of our curated briefing on it.
Samples: 13 samples: 5 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.
Paper: Chemo-Senolytic Therapeutic Potential against AngiosarcomaThe Journal of investigative dermatology · 2024

Summary (written by the submitters)

Angiosarcoma is an aggressive soft-tissue sarcoma with a poor prognosis. Chemotherapy for this cancer typically employs paclitaxel, one of the taxanes (genotoxic drugs), although it has a limited effect due to chemoresistance for prolonged treatment. Here we examine a new angiosarcoma treatment approach that combines chemotherapeutic and senolytic agents.

Read the full summary ↓

We first find that the chemotherapeutic drugs, cisplatin and paclitaxel, efficiently induce cellular senescence of angiosarcoma cells. Subsequent treatment with a senolytic agent, ABT-263, eliminates senescent cells through the activation of the apoptotic pathway. In addition, expression analysis indicates that senescence-associated secretory phenotype (SASP) genes are activated in senescent angiosarcoma cells and that ABT-263 treatment eliminates senescent cells expressing genes in the type-I interferon (IFN-I) pathway. Moreover, we show that cisplatin treatment alone requires a high dose to remove angiosarcoma cells, whereas a lower dose of cisplatin is sufficient to induce senescence, followed by the elimination of senescent cells by senolytic treatment. This study sheds light on a potential therapeutic strategy against angiosarcoma by combining a relatively low dose of cisplatin with the ABT-263 senolytic agent, which can help ease the deleterious side effects of chemotherapy.

Published in

Chemo-Senolytic Therapeutic Potential against Angiosarcoma

Wang X, Yik-Lok Chung C, Yoshioka A et al. · The Journal of investigative dermatology 2024 · PMID 38570028 · doi:10.1016/j.jid.2024.03.026

This dataset

Open GSE245935 in finder → Find more human RNA-seq datasets → Soft tissue sarcoma 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 GSE245935_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 PRJNA1030406 and SRA study SRP467588. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38570028) ↗

Study design

5 conditions, mostly in duplicate

MO-LAS-B cells, Control, ×2 MO-LAS-B cells, Cisplatin, ×2 MO-LAS-B cells, Paclitaxel, ×2 ISO-HAS-B cells, Control, ×2 ISO-HAS-B cells, Cisplatin, ×2 MO-LAS-B cells, Cisplatin + ABT ×1 ISO-HAS-B cells, Paclitaxel ×1 ISO-HAS-B cells, Cisplatin + ABT ×1

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 13 sample titles; they account for 10 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

GSM7851418 MO-LAS-B cells, Control, rep1 MO-LAS-B cells, Control,
GSM7851419 MO-LAS-B cells, Control, rep2 MO-LAS-B cells, Control,
GSM7851420 MO-LAS-B cells, Cisplatin, rep1 MO-LAS-B cells, Cisplat…
GSM7851421 MO-LAS-B cells, Cisplatin, rep2 MO-LAS-B cells, Cisplat…
GSM7851422 MO-LAS-B cells, Paclitaxel, rep1 MO-LAS-B cells, Paclita…
GSM7851423 MO-LAS-B cells, Paclitaxel, rep2 MO-LAS-B cells, Paclita…
GSM7851424 MO-LAS-B cells, Cisplatin + ABT-263
GSM7851425 ISO-HAS-B cells, Control, rep1 ISO-HAS-B cells, Contro…
GSM7851426 ISO-HAS-B cells, Control, rep2 ISO-HAS-B cells, Contro…
GSM7851427 ISO-HAS-B cells, Cisplatin, rep1 ISO-HAS-B cells, Cispla…
GSM7851428 ISO-HAS-B cells, Cisplatin, rep2 ISO-HAS-B cells, Cispla…
GSM7851429 ISO-HAS-B cells, Paclitaxel
GSM7851430 ISO-HAS-B cells, Cisplatin + ABT-263

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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.