Whole-Blood RNA Profiles Associated with Pulmonary Arterial Hypertension and Clinical Outcome

Abstract

Rationale: Idiopathic and heritable pulmonary arterial hypertension (PAH) are rare but comprise a genetically heterogeneous patient group. RNA sequencing linked to the underlying genetic architecture can be used to better understand the underlying pathology by identifying key signaling pathways and stratify patients more robustly according to clinical risk. Objectives: To use a three-stage design of RNA discovery, RNA validation and model construction, and model validation to define a set of PAH-associated RNAs and a single summarizing RNA model score. To define genes most likely to be involved in disease development, we performed Mendelian randomization (MR) analysis. Methods: RNA sequencing was performed on whole-blood samples from 359 patients with idiopathic, heritable, and drug-induced PAH and 72 age- and sex-matched healthy volunteers. The score was evaluated against disease severity markers including survival analysis using all-cause mortality from diagnosis. MR used known expression quantitative trait loci and summary statistics from a PAH genome-wide association study. Measurements and Main Results: We identified 507 genes with differential RNA expression in patients with PAH compared with control subjects. A model of 25 RNAs distinguished PAH with 87% accuracy (area under the curve 95% confidence interval: 0.791–0.945) in model validation. The RNA model score was associated with disease severity and long-term survival ( P = 4.66 × 10 −6 ) in PAH. MR detected an association between SMAD5 levels and PAH disease susceptibility (odds ratio, 0.317; 95% confidence interval, 0.129–0.776; P = 0.012). Conclusions: A whole-blood RNA signature of PAH, which includes RNAs relevant to disease pathogenesis, associates with disease severity and identifies patients with poor clinical outcomes. Genetic variants associated with lower SMAD5 expression may increase susceptibility to PAH.

Dysregulation of BMP9/BMPR2/SMAD signalling pathway contributes to pulmonary fibrosis and pulmonary hypertension induced by bleomycin in rats

“…Previous studies have documented the dysregulation of endothelial BMP9/BMPR2/SMAD signalling in the PA endothelium during the development of PH, based on evidence from both clinical PH patients (Evans et al, 2016; Hodgson et al, 2019; Nikolic et al, 2019; Wang et al, 2019) and experimental PH animal models (Southgate, Machado, Graf, & Morrell, 2020). Mutations in the core components of the BMP9/BMPR2/SMAD signalling pathway have been reported by a number of studies, including the classic BMPR2 mutation, which is found in ~17% of individuals with idiopathic pulmonary arterial hypertension (IPAH) and ~82% with a family history of pulmonary arterial hypertension (PAH) (Evans et al, 2016), SMAD1 , SMAD5 , and SMAD8 (Nasim et al, 2011; Rhodes et al, 2020; Shintani, Yagi, Nakayama, Saji, & Matsuoka, 2009), and the germline BMP9 mutation in IPAH patients (Hodgson et al, 2019; Wang et al, 2019), which leads to reduced expression levels of BMP9 and contributes to the disease development of PH. In terms of the underlying mechanisms, it is known that the reduced BMPR2 levels due to germline mutation or stimulation can facilitate PH pathogenesis through (a) promoting the endothelial‐to‐mesenchymal transition via HMGA1 and its target Slug (Hopper et al, 2016); (b) enhancing the production of the potent chemokine GM‐CSF in response to an inflammatory perturbation and mediating the macrophage recruitment (Sawada et al, 2014); and (c) increasing the risk for neointimal transformation in the pulmonary vasculature and predisposing the inflammation‐induced PH (Tian et al, 2019).…”

Expression Quantitative Trait Locus Mapping in Pulmonary Arterial Hypertension

“…A total of 276 patients with idiopathic, heritable or drug-induced PAH diagnosed following international guidelines [ 15 ] were recruited from expert centres across the UK with whole-genome sequence conducted as part of the UK National Institute for Health Research BioResource (NIHRBR) study [ 16 , 17 ]. Transcriptome profiling through RNAseq was completed as part of the PAH cohort study [ 18 ]. Demographic characteristics and white blood cell counts of the individuals in this study are shown in Supplementary Table S1 .…”

The cancer hypothesis of pulmonary arterial hypertension: are polyamines the new Warburg?

“…For example the ornithine decarboxylase (ODC) inhibitor difluoromethylornithine (DFMO; ornidyl; eflornithine) is approved for treatment of Trypanosome brucei subspecies gambiense and hirsutism and is the focus of multiple cancer clinical trials [8]. Polyamines also regulate ion channels linked to pulmonary arterial hypertension (PAH) such as transient receptor potential C1, which is reduced in patient whole blood RNA [9] and linked to development of PH in hypoxic mice [10].…”

“…5-methylthioadenosine, another polyamine metabolite produced as a by-product in the synthesis of both spermidine and spermine, was also associated with outcomes (survival) in the UK study, emphasising the strong relationship between this family of metabolites and PAH status ( figure 1). In recent transcriptomic analysis of whole blood by microarray [11], RNAseq [9] and lung tissue by RNAseq [12], only one gene was found to be dysregulated in PAH patients across all three studies; AMD1 (encoding adenosylmethionine decarboxylase 1) was consistently lower in PAH. This enzyme catalyses the production of S-adenosyl-methionine-amine, which is required for the conversion of the principal polyamine in humans, putrescine, to spermidine (figure 1).…”