Aldred, Micheala A.

Abstract Rationale Pulmonary hypertension (PH) is a heterogeneous condition classified into 5 WSPH groups but lacking detailed molecular distinction. The PVDOMICS cohort includes all PH groups alongside healthy and disease comparators, is deeply clinically phenotyped and has RNA sequencing data. Pseudogenes are conserved genome elements that due to sequence-defects cannot be translated into functional proteins. Some pseudogenes never-the-less produce RNA-transcripts which can regulate the expression of other, protein coding genes. Therefore, our study was focused on identifying differentially expressed pseudogene-transcripts within the dataset from the PVDOMICS study and gaining insights into their potential function. Methods Peripheral venous whole blood was collected from PVDOMICS participants [n = 525 PH patients; n = 312 controls without PH who were comparators (n = 256) or healthy (n = 56)]. RNA was isolated, RNA sequencing was performed. After quality control, differential transcript expression between PH and control groups was analyzed using the limma-voom pipeline, rSEA with adjustment for age, sex, race, smoking, WSPH group, latent factors and false discovery rate. We focused on a) transcripts expressed at increased levels (n = 218): the first 200 DEG (differentially-expressed-genes)-transcripts based on log2 difference plus increased DEG within the first 200 most significant p-values; and b) transcripts expressed at decreased levels (n = 292): last 200 DEG based on log2 difference plus decreased DEG within the first 200 most significant p-values. Results Six pseudogene transcripts were among the increased and 35 pseudogene transcripts were among the decreased DEG in the PH group compared to controls. Some of the differentially expressed pseudogenes (DEP) belonged to gene families, like the ribosomal protein family (7 DEP), mitochondria expressed transcripts (3 DEP), zinc finger proteins (2 DEP). Associations of pseudogenes with biological function or disease were extracted via GeneCards(R) and information from GWAS analysis. The DUSP8P5 pseudogene was among the DEP and is known for its association with left heart disease and hypertension; 2 additional DEP have known association with hypertension. Further known associations were with inhibitory or inflammatory immune processes (8 DEP), bone density (6 DEP), metabolism and diabetes (6 DEP), respiratory function or disease (4 DEP), erythrocyte biology (3 DEP), cancer (5 DEP), kidney disease (1 DEP), and demographic parameters like eye or hair color (2 DEP). Ten DEP had no known association with function or disease. Conclusions We identified pseudogene RNA-transcripts associated with PH across WSPH groups. The local vs. systemic effects of these pseudogene transcripts on PH remain to be determined and regulators of pseudogene-transcript expression (e.g. environmental exposures) identified. This abstract is funded by: 1 X01 HL148611 (TopMed), PVDOMICS NHLBI, PVDOMICS Pulmonary Hypertension Association, HT9425-25-1-0533 (GG), 1R21OH012955-01 (GG)

Background Right ventricular (RV) maladaptation to elevated pulmonary afterload is the primary determinant of outcomes in pulmonary artery (PA) hypertension; however, the pathobiological mechanisms underlying RV decompensation remain poorly understood. Methods We performed global untargeted metabolomics on plasma from 55 patients who underwent gold‐standard RV‐PA coupling measurements using multibeat pressure volume loop assessment in a single‐center cohort and from 1027 patients with coupling surrogate measurements in a larger multicenter cohort, the PVDOMICS (Pulmonary Vascular Disease Phenomics) study. Age and sex‐adjusted linear regression was performed to identify associations between metabolites and coupling metrics. Additionally, we performed a metabolic flux analysis using gene expression data from RV tissue in an independent cohort of 32 patients. Partial least squares–discriminant analysis was used to identify metabolites and reactions characteristic of the decompensated RV. Results RV‐PA coupling was negatively associated with tricarboxylic acid (TCA) cycle intermediate levels. Specifically, plasma α‐ketoglutarate and fumarate were significantly associated with all coupling metrics in both cohorts. Metabolic flux analysis indicated that decompensated RVs exhibited aberrant TCA cycle activity, including reduced acetyl coenzyme A entry and increased lactate elimination, suggesting a shift from the TCA cycle toward glycolysis at the RV tissue level. Conclusions We identify an association between circulating TCA cycle intermediate levels and RV‐PA uncoupling in 2 independent cohorts, and dysregulated TCA cycle metabolism in decompensated PA hypertension RVs, suggesting that aberrant TCA cycle metabolism could represent a hallmark of RV maladaptation in PA hypertension. Further study of this pathway is warranted to develop novel biomarkers of RV function or RV‐targeted therapies.

Aims: Alterations of mitochondrial bioenergetics and arginine metabolism are universally present and mechanistically linked to pulmonary arterial hypertension (PAH), but there is little knowledge of arginine metabolism and mitochondrial functions across the different pulmonary hypertension (PH) groups. We hypothesize that abnormalities in mitochondrial functions are present across all PH groups and associated with clinical phenotypes. We test the hypothesis in PH patients and healthy controls from the Pulmonary Vascular Disease Phenomics Program cohort, who had comprehensive clinical phenotyping and follow-up for at least 4 years for death or transplant status. Mitochondrial transmembrane potential, superoxide production, and mass were measured by flow cytometry in fresh platelets. Metabolomics analysis was performed on plasma samples. Global arginine bioavailability was calculated as the ratio of arginine/(ornithine+citrulline). Results: Global arginine bioavailability is consistently lower than controls in all PH groups. Although the mitochondrial mass is similar across all PH groups and controls, superoxide production and transmembrane potential vary across groups. Mitochondrial superoxide is higher in group 1 PAH and lowest in group 3 compared with other groups, while transmembrane potential is lower in group 1 PAH than controls or group 3. The alterations in mitochondrial functions of group 1 PAH are associated with changes in fatty acid metabolism. Mitochondrial transmembrane potential in group 1 PAH is associated with transplant-free survival. Conclusion: While alterations in mitochondrial function are found in all PH groups, group 1 PAH has a unique mitochondrial phenotype with greater superoxide and lower transmembrane potential linked to fatty acid metabolism, and clinically to survival. Antioxid. Redox Signal. 42, 361–377.

Our study shows an early increase in kynurenine pathway metabolism in at-risk subjects with systemic sclerosis who develop pulmonary arterial hypertension (PAH). We show that kynurenine pathway upregulation precedes clinical diagnosis and that this metabolic shift is associated with increased disease severity and shorter survival times. We also show that gene expression of TDO2, an enzyme that generates kynurenine from tryptophan, rises with PAH development.

Abstract The Division of Lung Diseases of the National Heart, Lung, and Blood Institute, with the Office of Rare Diseases Research, held a workshop to identify priority areas and strategic goals to enhance and accelerate research that will result in improved understanding of the lung vasculature, translational research needs, and ultimately the care of patients with pulmonary vascular diseases. Multidisciplinary experts with diverse experience in laboratory, translational, and clinical studies identified seven priority areas and discussed limitations in our current knowledge, technologies, and approaches. The focus for future research efforts include the following: (1) better characterizing vascular genotype–phenotype relationships and incorporating systems biology approaches when appropriate; (2) advancing our understanding of pulmonary vascular metabolic regulatory signaling in health and disease; (3) expanding our knowledge of the biologic relationships between the lung circulation and circulating elements, systemic vascular function, and right heart function and disease; (4) improving translational research for identifying disease-modifying therapies for the pulmonary hypertensive diseases; (5) establishing an appropriate and effective platform for advancing translational findings into clinical studies testing; and (6) developing the specific technologies and tools that will be enabling for these goals, such as question-guided imaging techniques and lung vascular investigator training programs. Recommendations from this workshop will be used within the Lung Vascular Biology and Disease Extramural Research Program for planning and strategic implementation purposes.