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GETomics based bulk-RNA sequencing revealed HIF-3α prevents COPD by inhibiting alveolar epithelial cell ferroptosis via the HIF-3α-GPx4 axis.

GSE275503 Homo sapiens (human) Single-cell RNA-seq 36 samples Submitted 2024/10/09 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 36 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: 36 samples: 9 × H vs 9 × S vs 9 × E vs 9 × CGroups 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: Hypoxia inducible factor (HIF) 3α prevents COPD by inhibiting alveolar epithelial cell ferroptosis via the HIF-3α-GPx4 axisTheranostics · 2024

Summary (written by the submitters)

COPD patients are largely asymptomatic until later stages when prognosis is generally poor. Here, by shifting the focus forward to pre-COPD and smoking stages, we found the peak of reactive oxygen species (ROS) level and hypoxia character are enriched in pre-COPD samples, and hypoxia inducible factor (HIF)-3α is the key factor. Smoking induced regional tissue hypoxia and emphysema have been found in COPD patients.

Read the full summary ↓

However, the mechanisms underlying hypoxia especially HIF-3α and COPD have not been investigated. In this study, by leveraging scRNA-seq and EpCAM co-localization analysis we identified HIF-3α is downregulated in alveolar epithelial cells in COPD. In vitro experiments using lentivirus transfection, bulk-RNA seq and RSL3 we found the activation of HIF-3α-GPx4 axis inhibits alveolar epithelial cell ferroptosis under the treatment of cigarettes smoking extracts (CSE). Further results from SftpcCreert2/+R26LSL-Hif3a knock-in mice demonstrated overexpression of HIF-3α inhibits alveolar epithelial cells ferroptosis and prevents the declining of lung function. Our data suggest the activation of HIF-3α-GPx4 axis prevents COPD by inhibiting alveolar epithelial cells ferroptosis. By leveraging this comprehensive analysis method, more promising treatment targets will be found and enhance our understanding to the pathogenesis.

Published in

Hypoxia inducible factor (HIF) 3α prevents COPD by inhibiting alveolar epithelial cell ferroptosis via the HIF-3α-GPx4 axis

Jiang J, Zheng Z, Chen S et al. · Theranostics 2024 · PMID 39310101 · doi:10.7150/thno.99237

This dataset

Open GSE275503 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 GSE275503_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 PRJNA1151128 and SRA study SRP534215. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39310101) ↗

Study design

9 × H vs 9 × S vs 9 × E vs 9 × C

Supports a between-group comparison across 36 samples.

How we read this: 4 replicated groups read from 36 sample titles; they account for 36 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

GSM8478653 H1 H
GSM8478654 H2 H
GSM8478655 H4 H
GSM8478656 H5 H
GSM8478657 H6 H
GSM8478658 H7 H
GSM8478659 H8 H
GSM8478660 H9 H
GSM8478661 H10 H
GSM8478662 S1 S
GSM8478663 S3 S
GSM8478664 S4 S
GSM8478665 S5 S
GSM8478666 S6 S
GSM8478667 S7 S
GSM8478668 S8 S
GSM8478669 S9 S
GSM8478670 S10 S
GSM8478671 E1 E
GSM8478672 E2 E
GSM8478673 E3 E
GSM8478674 E4 E
GSM8478675 E6 E
GSM8478676 E9 E
GSM8478677 E10 E
GSM8478678 E11 E
GSM8478679 E13 E
GSM8478680 C1 C
GSM8478681 C2 C
GSM8478682 C3 C
GSM8478683 C4 C
GSM8478684 C5 C
GSM8478685 C6 C
GSM8478686 C8 C
GSM8478687 C9 C
GSM8478688 C10 C

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GSE290910 Cellular mechanisms of early brain overgrowth in autistic children: elevated levels of GPX4 and resistance to ferroptosis 24 samples shares gpx4, ferroptosis
GSE313809 Bronchial epithelial cell-derived extracellular vesicles drive inflammasome activation and NTHi infection in COPD 12 samples shares copd, epithelial
GSE296939 Neuroblastoma tumors are sensitive to ferroptosis inducers – GPX4 inhibitors 12 samples shares gpx4, ferroptosis
GSE307575 A covalent fragment screen identifies ferroptosis induced by GPX4 inhibition as a vulnerability of senescent cells 11 samples shares gpx4, ferroptosis
GSE267812 Daphnetin induces ferroptosis in ovarian cancer by inhibiting NAD(P)H: Quinone oxidoreductase 1 (NQO1) 18 samples shares ferroptosis, inhibiting
GSE240656 Multi-center Korean cohort study based on RNA-sequencing data targeting COPD patients 294 samples shares copd

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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.