GEO series
Role of Pdk4 in BAPN-induecd aortic dissection in mouse models
GSE314672
Homo sapiens (human)
RNA-seq (gene expression)
39 samples
Submitted 2026/03/27
Platform GPL24676Platform GPL24247
At a glance
RNA-seq (gene expression) · human · 39 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
- 39 samples: 13 conditions, mostly in triplicateGroups 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
- Targeting Endothelial PDK4-EndoMT Feedback Loop Mitigates the Development of Thoracic Aortic Dissection in MiceArteriosclerosis, thrombosis, and vascular biology · 2026
Summary (written by the submitters)
Thoracic aortic dissection (TAD) is a life-threatening acute vascular condition with extremely high morbidity and mortality. Endothelial cells (ECs) are critical for maintaining vascular homeostasis, yet the role of Endothelial-to-Mesenchymal Transition (EndoMT)—a key cell fate process in vascular development and disease—in TAD remains poorly defined.
Read the full summary ↓
Furthermore, the functional significance of EndoMT-gene-program activation mediated by pyruvate dehydrogenase kinase 4 (PDK4) in TAD has not been elucidated. To explore the mechanistic involvement of EndoMT in TAD, a murine TAD model was established through systemic administration of β-aminopropionitrile (BAPN). RNA sequencing was performed to profile the activation landscape of the EndoMT-gene-program in ECs for identifying key regulatory targets. Concurrently, clinical samples from TAD patients and healthy controls were analyzed to quantify mRNA and protein levels of EndoMT-related markers in aortic tissues. Pyruvate dehydrogenase kinase isoenzyme 4 (PDK4) was identified as a critical regulator and validated as a downstream target of EndoMT signaling using an integrated approach combining RNA-seq, luciferase reporter assays, and immunofluorescent staining. The functional role of Pdk4 in TAD was further validated by using conditional knockout (CKO) mouse model. To facilitate better clinical translation, EC-specific Pdk4 deletion or overexpression mouse models were generated via adeno-associated virus (AAV)-mediated delivery and subjected to TAD model. Serum samples from these mice were collected, and enzyme-linked immunosorbent assay (ELISA) was used to measure levels of endothelial injury markers (sICAM1, sVCAM1, sE-Selectin) for assessing endothelial dysfunction. Additionally, the therapeutic potential of dichloroacetate (DCA), a specific PDK4 inhibitor, was evaluated by administering it to BAPN-fed mice to assess its efficacy in ameliorating TAD progression. A significant upregulation of the EndoMT-gene-program was observed in BAPN-fed murine models of TAD, aortic tissues from TAD patients, and HAECs treated with angiotensin II (Ang II). Administration of AAVEndoPdk4 directly induced TAD formation, which was exacerbated by BAPN co-treatment. Conversely, EC-specific knockdown of Pdk4 reduced TAD formation by inhibiting EndoMT signaling. The same results were also obtained in EC-specific conditional Pdk4 knockout mice (CKO, Pdk4flox/flox; Cdh5-CreERT2). PDK4 was identified as a critical factor in both TAD development and EndoMT process, with SNAI1 transcriptionally activating PDK4; vice versa, PDK4 further enhanced the activation of EndoMT signaling in both in vivo and vitro. PDK4 inhibitor, DCA, significantly slowed TAD progression in BAPN-fed mice. Mechanistically, a PDK4-EndoMT feedback loop was identified in TAD, where interruption of this self-reinforcing pathological cycle markedly attenuates the progression of TAD.
Published in
Cao X, Guo X, Huang H et al.
· Arteriosclerosis, thrombosis, and vascular biology 2026
· PMID 41853864
· doi:10.1161/ATVBAHA.125.324031
This dataset
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.
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 GSE314672_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1392438 and SRA study SRP657254. Searching any of these in the dataset finder brings you back here.
Study design
13 conditions, mostly in triplicate
Aorta, BAPN_Control, ×3
Aorta, BAPN_Week2, ×3
Aorta, BAPN_Week4, ×3
Aorta, KD_Pdk4_Saline, ×3
Aorta, KD_Pdk4_BAPN, ×3
Aorta, KD_CTR_Saline, ×3
Aorta, KD_CTR_BAPN, ×3
Cells, OE_Scramble, ×3
+5 more
Supports a between-group comparison across 39 samples.
How we read this: 13 replicated groups read from 39 sample titles; they account for 39 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
- GSM9409030 Aorta, BAPN_Control, R1 Aorta, BAPN_Control,
- GSM9409031 Aorta, BAPN_Control, R2 Aorta, BAPN_Control,
- GSM9409032 Aorta, BAPN_Control, R3 Aorta, BAPN_Control,
- GSM9409033 Aorta, BAPN_Week2, R1 Aorta, BAPN_Week2,
- GSM9409034 Aorta, BAPN_Week2, R2 Aorta, BAPN_Week2,
- GSM9409035 Aorta, BAPN_Week2, R3 Aorta, BAPN_Week2,
- GSM9409036 Aorta, BAPN_Week4, R1 Aorta, BAPN_Week4,
- GSM9409037 Aorta, BAPN_Week4, R2 Aorta, BAPN_Week4,
- GSM9409038 Aorta, BAPN_Week4, R3 Aorta, BAPN_Week4,
- GSM9409039 Aorta, KD_Pdk4_Saline, R1 Aorta, KD_Pdk4_Saline,
- GSM9409040 Aorta, KD_Pdk4_Saline, R2 Aorta, KD_Pdk4_Saline,
- GSM9409041 Aorta, KD_Pdk4_Saline, R3 Aorta, KD_Pdk4_Saline,
- GSM9409042 Aorta, KD_Pdk4_BAPN, R1 Aorta, KD_Pdk4_BAPN,
- GSM9409043 Aorta, KD_Pdk4_BAPN, R2 Aorta, KD_Pdk4_BAPN,
- GSM9409044 Aorta, KD_Pdk4_BAPN, R3 Aorta, KD_Pdk4_BAPN,
- GSM9409045 Aorta, KD_CTR_Saline, R1 Aorta, KD_CTR_Saline,
- GSM9409046 Aorta, KD_CTR_Saline, R2 Aorta, KD_CTR_Saline,
- GSM9409047 Aorta, KD_CTR_Saline, R3 Aorta, KD_CTR_Saline,
- GSM9409048 Aorta, KD_CTR_BAPN, R1 Aorta, KD_CTR_BAPN,
- GSM9409049 Aorta, KD_CTR_BAPN, R2 Aorta, KD_CTR_BAPN,
- GSM9409050 Aorta, KD_CTR_BAPN, R3 Aorta, KD_CTR_BAPN,
- GSM9409051 Cells, OE_Scramble, R1 Cells, OE_Scramble,
- GSM9409052 Cells, OE_Scramble, R2 Cells, OE_Scramble,
- GSM9409053 Cells, OE_Scramble, R3 Cells, OE_Scramble,
- GSM9409054 Cells, OE_PDK4, R1 Cells, OE_PDK4,
- GSM9409055 Cells, OE_PDK4, R2 Cells, OE_PDK4,
- GSM9409056 Cells, OE_PDK4, R3 Cells, OE_PDK4,
- GSM9409057 Aorta, OE_CTR_Saline, R1 Aorta, OE_CTR_Saline,
- GSM9409058 Aorta, OE_CTR_Saline, R2 Aorta, OE_CTR_Saline,
- GSM9409059 Aorta, OE_CTR_Saline, R3 Aorta, OE_CTR_Saline,
- GSM9409060 Aorta, OE_CTR_BAPN, R1 Aorta, OE_CTR_BAPN,
- GSM9409061 Aorta, OE_CTR_BAPN, R2 Aorta, OE_CTR_BAPN,
- GSM9409062 Aorta, OE_CTR_BAPN, R3 Aorta, OE_CTR_BAPN,
- GSM9409063 Aorta, OE_Pdk4_BAPN, R1 Aorta, OE_Pdk4_BAPN,
- GSM9409064 Aorta, OE_Pdk4_BAPN, R2 Aorta, OE_Pdk4_BAPN,
- GSM9409065 Aorta, OE_Pdk4_BAPN, R3 Aorta, OE_Pdk4_BAPN,
- GSM9409066 Aorta, OE_Pdk4_Saline, R1 Aorta, OE_Pdk4_Saline,
- GSM9409067 Aorta, OE_Pdk4_Saline, R2 Aorta, OE_Pdk4_Saline,
- GSM9409068 Aorta, OE_Pdk4_Saline, R3 Aorta, OE_Pdk4_Saline,
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