GEO series

Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors (RNA-Seq)

GSE254756 Homo sapiens (human) Single-cell RNA-seq 22 samples Submitted 2024/08/02 Platform GPL28038Platform GPL24676

At a glance

Single-cell RNA-seq · human · 22 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 22 samples: 6 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: Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivorsNature communications · 2024

Summary (written by the submitters)

Long-term toxicities caused by cancer treatments have recently gained increasing recognition due to a steadily growing population of cancer survivors. Radiotherapy (RT) is a common treatment known to unintentionally harm surrounding normal tissues including the skin, hindering wound healing even years after treatment. Our study aimed to elucidate the underlying mechanisms of these late-onset adverse effects caused by RT.

Read the full summary ↓

By comparing paired skin biopsies from previously irradiated (RT+) and non-irradiated (RT-) sites in breast cancer survivors who underwent RT years ago, we discovered compromised wound healing capacity and impaired fibroblast functions in the RT+ skin. By employing ATAC-seq, we identified altered chromatin landscapes in RT+ fibroblasts, pinpointing THBS1 as a crucial epigenetically primed wound repair-related gene. Further confirmation of THBS1's significance during wound repair came from single-cell RNA-sequencing and spatial transcriptomic analysis of human wounds. Remarkably, heightened and sustained THBS1 expression was observed in RT+ fibroblasts in both mouse and human radiation wound models, leading to impaired fibroblast motility and contractility. Encouragingly, our study found that treatment with anti-THBS1 antibodies promoted ex vivo wound closure in RT+ skin from breast cancer survivors. These findings indicate that dermal fibroblasts retain a long-term radiation memory recorded in the form of epigenetic changes. Targeting this maladaptive epigenetic memory shows promise for mitigating the late-onset adverse effects caused by RT, offering potential solutions to improve the quality of life for cancer survivors.

Published in

Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors

Bian X, Piipponen M, Liu Z et al. · Nature communications 2024 · PMID 39468077 · doi:10.1038/s41467-024-53295-1

This dataset

Open GSE254756 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 GSE254756_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1071621 and SRA study SRP487209. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39468077) ↗

Study design

6 conditions, mostly in duplicate

Bulk RNA-seq Ct ×2 Bulk RNA-seq THBS1_OE ×2 Bulk RNA-seq RT- Ct ×2 Bulk RNA-seq RT- TGFb ×2 Bulk RNA-seq RT+ Ct ×2 Bulk RNA-seq RT+ TGFb ×2 Bulk RNA-seq RS1_RT ×1 Bulk RNA-seq RS1_RT+ ×1 +8 more

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 22 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

GSM8057260 Bulk RNA-seq RS1_RT-
GSM8057261 Bulk RNA-seq RS1_RT+
GSM8057262 Bulk RNA-seq RS2_RT-
GSM8057263 Bulk RNA-seq RS2_RT+
GSM8057264 Bulk RNA-seq RS3_RT-
GSM8057265 Bulk RNA-seq RS3_RT+
GSM8057266 Bulk RNA-seq RS4_RT-
GSM8057267 Bulk RNA-seq RS4_RT+
GSM8057268 Bulk RNA-seq RS6_RT-
GSM8057269 Bulk RNA-seq RS6_RT+
GSM8057270 Bulk RNA-seq Ctr_1 Bulk RNA-seq Ct
GSM8057271 Bulk RNA-seq Ctr_2 Bulk RNA-seq Ct
GSM8057272 Bulk RNA-seq THBS1_OE_1 Bulk RNA-seq THBS1_OE
GSM8057273 Bulk RNA-seq THBS1_OE_2 Bulk RNA-seq THBS1_OE
GSM8057274 Bulk RNA-seq RT- Ctr_1 Bulk RNA-seq RT- Ct
GSM8057275 Bulk RNA-seq RT- Ctr_2 Bulk RNA-seq RT- Ct
GSM8057276 Bulk RNA-seq RT- TGFb_1 Bulk RNA-seq RT- TGFb
GSM8057277 Bulk RNA-seq RT- TGFb_2 Bulk RNA-seq RT- TGFb
GSM8057278 Bulk RNA-seq RT+ Ctr_1 Bulk RNA-seq RT+ Ct
GSM8057279 Bulk RNA-seq RT+ Ctr_2 Bulk RNA-seq RT+ Ct
GSM8057280 Bulk RNA-seq RT+ TGFb_1 Bulk RNA-seq RT+ TGFb
GSM8057281 Bulk RNA-seq RT+ TGFb_2 Bulk RNA-seq RT+ TGFb

Datasets on a similar topic

GSE282444 Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [RNA-seq] 56 samples shares epigenetic, rna-seq, memory
GSE275647 Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC RNA-seq] 216 samples shares fibroblasts, rna-seq
GSE234181 Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq] 184 samples shares epigenetic, rna-seq
GSE232076 In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] 89 samples shares epigenetic, rna-seq
GSE306915 Integrated epigenetic and genetic programming of primary human T cells [RNA-seq] 77 samples shares epigenetic, rna-seq
GSE327840 RNA-seq profiling of LPS tolerance in monocytes, THP-1, fibroblasts, smooth muscle cells, and endothelial cells 58 samples shares fibroblasts, rna-seq
GSE275145 Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Human scRNA-seq] 29 samples shares fibroblasts, rna-seq
GSE309392 Cancer-associated fibroblasts promote esophageal carcinogenesis and lung metastasis by CDH11-mediated extracellular matrix environment remodeling [scRNA-Seq] 23 samples shares fibroblasts, rna-seq

Search all human RNA-seq datasets in GEO →

Share this dataset

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.