GEO series

Soluble Glycoprotein VI Predicts Abdominal Aortic Aneurysm Growth Rate and is a Novel Therapeutic Target

GSE269845 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/06/22 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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)
Samples: 12 samples: 5 × Control-Aortic-Wall vs 3 × AAA-Aortic-Wall vs 3 × AAA.ThrombusGroups 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: Soluble glycoprotein VI predicts abdominal aortic aneurysm growth rate and is a novel therapeutic targetBlood · 2024

Summary (written by the submitters)

A common feature in patients with abdominal aortic aneurysms (AAA) is the formation of a nonocclusive intraluminal thrombus (ILT) in regions of aortic dilation. Platelets are known to maintain hemostasis and propagate thrombosis through several redundant activation mechanisms, yet the role of platelet activation in the pathogenesis of AAA associated ILT is still poorly understood.

Read the full summary ↓

Thus, we sought to investigate how platelet activation impacts the pathogenesis of AAA. Using RNA-sequencing, we identify that the platelet-associated transcripts are significantly enriched in the ILT compared to the adjacent aneurysm wall and healthy control aortas. We found that the platelet specific receptor glycoprotein VI (GPVI) is among the top enriched genes in AAA ILT and is increased on the platelet surface of AAA patients. Examination of a specific indicator of platelet activity, soluble GPVI (sGPVI), in two independent AAA patient cohorts is highly predictive of a AAA diagnosis and associates more strongly with aneurysm growth rate when compared to D-dimer in humans. Finally, intervention with the anti-GPVI antibody (JAQ1) in mice with established aneurysms blunted the progression of AAA in two independent mouse models. In conclusion, we show that levels of sGPVI in humans can predict a diagnosis of AAA and AAA growth rate, which may be critical in the identification of high-risk patients. We also identify GPVI as a novel platelet-specific AAA therapeutic target, with minimal risk of adverse bleeding complications, where none currently exist.

Published in

Soluble glycoprotein VI predicts abdominal aortic aneurysm growth rate and is a novel therapeutic target

Benson TW, Pike MM, Spuzzillo A et al. · Blood 2024 · PMID 38900973 · doi:10.1182/blood.2023021655

This dataset

Open GSE269845 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 GSE269845_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 PRJNA1124005 and SRA study SRP516052. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38900973) ↗

Study design

5 × Control-Aortic-Wall vs 3 × AAA-Aortic-Wall vs 3 × AAA.Thrombus

Supports a between-group comparison across 11 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 11 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

GSM8328834 Control-Aortic-Wall-1 Control-Aortic-Wall
GSM8328835 Control-Aortic-Wall-2 Control-Aortic-Wall
GSM8328836 Control-Aortic-Wall-3 Control-Aortic-Wall
GSM8328837 Control-Aortic-Wall-4 Control-Aortic-Wall
GSM8328838 Control-Aortic-Wall-5 Control-Aortic-Wall
GSM8328839 AAA-Aortic-Wall-1 AAA-Aortic-Wall
GSM8328840 AAA-Aortic-Wall-2 AAA-Aortic-Wall
GSM8328841 AAA-Aortic-Wall-3 AAA-Aortic-Wall
GSM8328842 AAA.Aortic.Wall-5
GSM8328843 AAA.Thrombus-1 AAA.Thrombus
GSM8328844 AAA.Thrombus-3 AAA.Thrombus
GSM8328845 AAA.Thrombus-5 AAA.Thrombus

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