Multi-omics analysis of two rat models reveals potential role of vesicle transport and autophagy in right ventricular remodeling

Abstract

Right ventricular failure as a severe consequence of pulmonary arterial hypertension (PAH) is an independent risk factor for poor prognosis, although the pathogenesis of right ventricular remodeling (RVR) remains unclear. Exploring the shared molecular pathways and key molecules in the right ventricle in monocrotaline (MCT) and pulmonary artery banding (PAB) rat models may reveal critical RVR mechanisms. Untargeted proteome and metabolome analysis were performed on the right ventricular myocardium of two RVR models (MCT-induced PAH rats and PAB-operated rats) to identify the altered proteins and metabolites, followed by validation using parallel reaction monitoring analysis and quantitative real-time polymerase chain reaction (qPCR). The multi-omics profiles of MCT and PAB rat models were compared to explore the key dysregulated molecules and pathways in RVR. Our proteomics study identified 25 shared RVR-altered differentially expressed proteins. Multiple common biological pathways were identified between PAB and MCT rat models, encompassing myocardial remodeling and energy metabolism alternation, etc. Various molecules and pathways related to vesicle transport and autophagy were identified, including nidogen-1, the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) signaling pathway, and the microautophagy pathway (all previously unreported in RVR). Glycerophospholipid metabolism was the sole statistically significant common metabolic pathway enriched by metabolomics. Underreported biological processes, including vesicle transport and autophagy, may contribute to the pathophysiology of PAH-induced RVR.

Keywords: Autophagy; Metabolome; Proteome; Right ventricular remodeling; Vesicle transport.

Fig. 1

Echocardiographic, hemodynamic and morphometric parameters of the PAB rat model and MCT rat model. (A) Hemodynamic measurements of RVSP and RVEDP between PAB rats versus sham rats and MCT rats versus vehicle rats; (B) Representative RVSP waves in 4 groups of rats from hemodynamic experiments; (C) Representative cross-sectional view of the right ventricle in PAB group and MCT group and the quantitative analysis of RVFW /BW and Fulton index; (D) The fibrotic area estimated by Masson trichrome stain with representative section (up); The cross-sectional area of cardiomyocytes evaluated by H&E stain with representative section (down); (E) Echocardiographic measurements of TAPSE and RVID between PAB rats versus sham rats and MCT rats versus vehicle rats; RVSP, right ventricular systolic pressure; RVEDP, right ventricular end-diastolic pressure; RVRW/BW, ratio of right ventricular free wall to body weight; CSA, cross-sectional area; TAPSE, tricuspid annular plane systolic excursion; RVID, right ventricular internal diameter.

Fig. 2

Proteomic profiles and analysis of PAB rat model and MCT rat model. (A) Principal component analyses based on the DIA data of the myocardial proteome between PAB rats versus sham rats (left; blue) and MCT rats versus vehicle rats (right; red); (B) Heat map analyses based on the quantification of differently expressed proteins(DEPs) in of myocardium between PAB rats versus sham rats and MCT rats versus vehicle rats; (C) Venn diagram of the DEPs in the PAB model and MCT model; (D) Protein interaction network based on the 25 shared proteins. Different colors represent different biological processes: phosphoprotein(red), acetylation (blue); fatty acid metabolism (yellow); (E) Hierarchical clustering of shared disease-altered KEGG pathway (both p value < 0.05); (F) Heatmap of the common disease-changed IPA biological function in PAB and MCT models. (both p value < 0.05); (G) Heatmap of the common disease-changed IPA canonical pathways in PAB and MCT models. (both p value < 0.05); (H) Heatmap of the shared upregulated(Z > 0) IPA canonical pathways in PAB and MCT models. The KEGG-related access points in this article are copyrighted.

Fig. 3

qPCR validation of the shared DEPs concerning vesicle transport and autophagy. Relative mRNA expression levels of Fhl1, Nid1, Prkab1, and Flnc in the MCT and PAB groups compared to their respective control groups. Data are presented as mean ± SEM; *p < 0.05, **p < 0.01 vs. control groups.

Fig. 4

Metabolomic profiles and analysis of PAB rat model and MCT rat model. (A) Principal component analyses based on the myocardial metabolomic between MCT rats versus vehicle rats(left) and PAB rats versus sham rats(right); (B) Volcano plots of the identified differently expressed metabolites between MCT rats versus vehicle rats and PAB rats versus sham rats(right); (C) Bubble chart of the top 10 significantly altered metabolic pathway in the comparation of MCT rats and vehicle rats(p < 0.05); (D) Bubble chart of the top 10 significantly altered metabolic pathway in the comparation of PAB rats and sham rats(p < 0.05).

Fig. 5

Correlation between shared DEPs and DEMs in the MCT model and PAB models. (A) Correlation analyses between the common DEPs and the DEMs identified in PAB group; (B) Correlation analyses between the common DEPs and the DEMs identified in MCT group. The circle’s color indicates the correlation coefficient |r|. The size of the circle indicates the significance of the correlation according to the Benjamini–Hochberg [BH] adjusted p-value.

Fig. 6

A summary pattern describing the potential role of vesicle transport and autophagy in right ventricular remodeling. The coordinated actions of cardiomyocyte autophagy and resident macrophages may play a crucial role in cardiomyocytes during PAH-induced RVR. The star symbol (✰) highlights our key finding. Cellular stress, abnormities in metabolic substrates, and mitochondrial dysfunction activate the processes of autophagy (blue, right), vesicle transport and subsequent phagocytic reaction (orange, left). AMPK, Adenosine 5’-monophosphate-activated protein kinase, the β1 regulatory subunit was encoded by Prkab1; Fhl1, Four and a half LIM domains protein 1; mTOR, mammalian target of rapamycin; ULK-1, unc-51-like kinase 1; ATG, autophagy related gene; EIF2, eukaryotic initiation factor 2; SNAREs, soluble N-ethylmaleimide-sensitive factor attachment protein receptors; PERK, Protein kinase R-like endoplasmic reticulum kinase. Created in BioRender. Qin, Y. (2025) https://BioRender.com/z93q463.