Integrative proteomics and phosphoproteomics in pulmonary arterial hypertension

Abstract

Pulmonary arterial endothelial cells (PAEC) are mechanistically linked to origins of pulmonary arterial hypertension (PAH). Here, global proteomics and phosphoproteomics of PAEC from PAH (n = 4) and healthy lungs (n = 5) were performed using LC-MS/MS to confirm known pathways and identify new areas of investigation in PAH. Among PAH and control cells, 170 proteins and 240 phosphopeptides were differentially expressed; of these, 45 proteins and 18 phosphopeptides were located in the mitochondria. Pathologic pathways were identified with integrative bioinformatics and human protein-protein interactome network analyses, then confirmed with targeted proteomics in PAH PAEC and non-targeted metabolomics and targeted high-performance liquid chromatography of metabolites in plasma from PAH patients (n = 30) and healthy controls (n = 12). Dysregulated pathways in PAH include accelerated one carbon metabolism, abnormal tricarboxylic acid (TCA) cycle flux and glutamate metabolism, dysfunctional arginine and nitric oxide pathways, and increased oxidative stress. Functional studies in cells confirmed abnormalities in glucose metabolism, mitochondrial oxygen consumption, and production of reactive oxygen species in PAH. Altogether, the findings indicate that PAH is typified by changes in metabolic pathways that are primarily found in mitochondria.

Single Mutation in the NFU1 Gene Metabolically Reprograms Pulmonary Artery Smooth Muscle Cells

“…In the GO-based assessment using Database for Annotation, Visualization and Integrated Discovery, we focused on pathways closely associated with the mitochondria and were implicated in proliferation. Proteomic evidence from a recent report by Xu Weiling et al 29 showed that endothelial cells derived from human PAH patients had deranged mitochondrial respiration, abnormal FA metabolism, enhanced oxidative stress, and apoptosis resistance. 29 The study concluded that PAH is characterized by metabolic pathways that are primarily associated with the mitochondria.…”

“…Proteomic evidence from a recent report by Xu Weiling et al 29 showed that endothelial cells derived from human PAH patients had deranged mitochondrial respiration, abnormal FA metabolism, enhanced oxidative stress, and apoptosis resistance. 29 The study concluded that PAH is characterized by metabolic pathways that are primarily associated with the mitochondria. 29 In addition to this, other reports also indicated that dysregulation of oxidative phosphorylation, FA metabolism, oxidative stress, and regulation of apoptosis were significantly associated with PAH and proliferation.…”

“… 29 The study concluded that PAH is characterized by metabolic pathways that are primarily associated with the mitochondria. 29 In addition to this, other reports also indicated that dysregulation of oxidative phosphorylation, FA metabolism, oxidative stress, and regulation of apoptosis were significantly associated with PAH and proliferation. 6 , 30 – 34 Our data identify significantly enriched top 20 pathways in the Kyoto Encyclopedia of Genes and Genomes and the top 30 processes in the GO pathways for the biological processes (Figure 2 A).…”

“… 30 , 68 , 69 In addition to this, recent proteomic studies in cells derived from PAH patients have strongly associated abnormal and increased FA metabolism with PAH. 29 Increased expression of the main long-chain FA transporter CD36 has been shown to be elevated in PAH, causing chronic elevation of long-chain FA uptake. 30 Also, CD36 accounts for around 70% of the FA uptake in cardiomyocytes.…”

The application of ‘omics’ to pulmonary arterial hypertension

“…Most of the down-regulated proteins were related to mitochondrial structure and function(Malenfant et al, 2015). A recent proteomic study in pulmonary arterial endothelial cells obtained from PAH patients after lung transplantation found that changes of protein levels in these pulmonary cells can be linked to the mitochondria(Xu et al, 2019). An analysis of 1,124 plasma proteins from a defined PAH population using the 1K Somamer platform established the potential clinical utility of proteome screening of venous blood; a nine-protein panel was defined that predicts survival at baseline in PAH with an accuracy equivalent to clinical measures, such as provided by the REVEAL prognostic equation(Benza et al, 2019;.The proteins cover a range of pathological processes relevant to PAH, such as myocardial stress (IL-1 receptor-like 1 also known as ST-2), pulmonary endothelial repair (tissue inhibitors of metalloproteinases, TIMPs −1 and −2), inflammation and metabolism (insulin growth factor binding protein-1 and apolipoprotein E), innate immunity (complement factors H, reduced and D, increased), abnormal iron status (erythropoietin) and thrombogenesis (reduced plasminogen).…”