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Perivascular fibrosis is mediated by a KLF10-IL-9 signaling axis in CD4+ T cells

GSE199288 Mus musculus (mouse) Single-cell RNA-seq 27 samples Submitted 2024/10/06 Platform GPL21103
At a glance

Single-cell RNA-seq · mouse · 27 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
Mus musculus (mouse)
Samples
27 samples: 6 conditions, mostly with about 6 replicates eachGroups 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
Perivascular Fibrosis Is Mediated by a KLF10-IL-9 Signaling Axis in CD4+ T CellsCirculation research · 2022
Summary (written by the submitters)
Perivascular fibrosis, characterized by increased amount of connective tissue around vessels, is a hallmark for vascular disease. Angiotensin II (Ang II) contributes to vascular disease and end-organ damage via promoting T-cell activation. Despite recent data suggesting the role of T cells in the progression of perivascular fibrosis, the underlying mechanisms are poorly understood.
Read the full summary ↓
Kruppel-like Factor 10 is a transcription factor expressed in T cell subsets. We sought to investigate the role of KLF10 in CD4+ T cells in regulating vascular damage in an AngII mouse model. CD4-targeted KLF10 deficient (TKO) and CD4-Cre (WT) mice were generated and subjected to 28 days of Ang II infusion. Differential gene expression profiling of non-stripped aorta, stripped aorta, isolated aortic fibroblasts from CD4-Cre (Cre) or CD4-Cre KLF10-fl/fl mice(TKO) mice after 28 days Angiotensin II (Ang II) treatment were performed to ascertain the underlying global transcriptomic changes involved in perivascular fibrosis. Since increased IL-9 is a profibrotic cytokine, we hypothesized that perivascular fibrosis might be rescued by administration of anti-IL-9 neutralizing monoclonal antibodies (mAbs) in Ang II-treated TKO mice. Then differential gene expression profiling of non-stripped aorta from TKO mice with or without anti-IL9-antibody treatment after 28 days Ang II infusion. To further understand the differences in phenotypic heterogeneity in fibroblasts during the progression of perivascular fibrosis between TKO and control mice in response to Ang II treatment, we performed single-cell RNA-sequencing (scRNA-seq) of the descending aorta. Collectively, comparative RNA-seq transcript profiling identified several pathways associated with periadventitial remodeling and that the calcium signaling pathway is dominantly upregulated in non-stripped aortas of TKO mice after Ang II treatment. Indeed, the profibrotic genes Col8a1, Mmp2, Fmod, and Angptl1, which were identified as significantly increased in TKO aortas and in isolated fibroblasts by both bulk RNA seq and scRNA seq, were all decreased after treatment with anti-IL-9 mAbs. These results indicate that the KLF10-IL-9 signaling axis in CD4+ T cells tightly regulate the processes of Ang II-induced pathological perivascular fibrosis and provide novel therapeutic opportunities for the treatment of hypertensive-associated diseases. 1) Differential gene expression profiling of non-stripped aotra, stripped aorta, aortic fibroblasts from CD4-Cre(Cre) or CD4-Cre KLF10-fl/fl mice(TKO) mice after 28 days Angiotensin II (Ang II) treatment. 2) Differential gene expression profiling of non-stripped aotra from TKO mice with or without anti-IL9-antibody treatment after 28 days Ang II infusion. 3) Single cell RNA-sequencing was perform on descending aorta from Cre or TKO after Ang II treatment.
Published in
Perivascular Fibrosis Is Mediated by a KLF10-IL-9 Signaling Axis in CD4+ T Cells
Zhuang R, Chen J, Cheng HS et al. · Circulation research 2022 · PMID 35440172 · doi:10.1161/CIRCRESAHA.121.320420
This dataset
Open GSE199288 in finder → Find more mouse 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 GSE199288_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 PRJNA819170 and SRA study SRP365568. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 35440172) ↗
Study design
6 conditions, mostly with about 6 replicates each
01_Nonstripped_aorta_AO ×6 02_Nonstripped_aorta_A ×6 03_Aotric_fibroblast ×6 04_IL9_blocker_nonstripped_aorta_IL9-Blocke ×5 05_single cell_Cre ×2 05_single cell_TKO ×2

Supports a between-group comparison across 27 samples.

How we read this: 6 replicated groups read from 27 sample titles; they account for 27 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
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