Mehra, R

Abstract Introduction Interstitial lung disease-associated pulmonary hypertension (ILD-PH) is a clinically challenging entity that lies on a pathophysiologic spectrum between pulmonary arterial hypertension (PAH) and interstitial lung disease (ILD). We compared the metabolomes of patients with ILD-PH to those with PAH and ILD to characterize the PAH-ILD axis and determine whether ILD-PH patients can be phenotyped based on their metabolomic similarity to PAH. Methods Using untargeted metabolomics profiles from patients with PAH, ILD, and ILD-PH in the large, U.S.-based, NIH-funded, multi-center PVDOMICS cohort, we trained an anchor-based classifier on PAH and ILD metabolomes using supervised PLS-DA with a 75/25 train/test split. Primary and secondary PH or risk-group classifications in PVDOMICS were based on expert adjudication of clinical data including right heart catheterization hemodynamics, pulmonary function testing, chest imaging, and laboratory results. We then applied the trained model to each ILD-PH patient to assign a PAH similarity score. We classified patients as having a PAH-like or ILD-like metabolomic phenotype using an optimal PAH similarity score cutoff of 0.5 then compared PAH metabolomic similarity to expert-adjudicated primary and secondary WSPH classifications in PVDOMICS. We implemented FELLA, a network-based metabolomics enrichment method, to holistically characterize the biologic underpinnings of PAH, ILD-PH, and ILD metabolomes. Results We analyzed 244 patients with PAH, 54 with ILD, and 47 with ILD-PH. The anchor-based classifier demonstrated high train-test performance with a c-statistic of 0.81 and 78% agreement with expert-adjudicated diagnoses. Among the ILD-PH patients, 23 were classified as PAH-like and 24 as ILD-like (74% agreement with expert adjudication, Cohen’s kappa 0.49, Hedge’s g estimate of 0.86). FELLA enrichment revealed core glycolytic and bioenergetic pathways were enriched in both pure PAH and ILD-PH. Comparison of diffusion Z-scores between groups demonstrated subtle but biologically coherent differences in several reaction-level nodes, including lactate, NADPH oxidoreductase, and phosphofructokinase, which were enriched in ILD-PH. Conclusion Patients with ILD-PH demonstrate clinically relevant metabolomic phenotypes. Examination of the network biology underlying ILD-PH may point to potential therapeutic targets in this vulnerable subgroup with lagging clinical outcomes. This abstract is funded by: Pulmonary Fibrosis Foundation PFF Scholars Program

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)