Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension

Abstract

Background: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH.

Methods: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured.

Results: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival.

Conclusions: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation.

Keywords: genetics; hypertension, pulmonary; mutation; prognosis; pulmonary veno-occlusive disease.

Figure 1. Subjects recruited to the NIHR BioResource – Rare Diseases Study and the clinical diagnostic categories of PAH patients included in this study.

Figure 2. The transfer coefficient for carbon monoxide (Kco) is influenced by genotype in pulmonary arterial hypertension.

Patients with FEV₁ < 80 % predicted and FVC < 80 % predicted and diagnosed with PAH or PVOD/PCH after 50 years of age excluded from the plot.

Figure 3. Representative histopathological images from one patient with clinically diagnosed idiopathic PAH but found to have a rare (not reported in the ExAC database) and predicted deleterious (CADD score 32) homozygous EIF2AK4 missense variant (c.1795G>C).

The patient was of Pakistani origin and did not have a family history of PAH or PVOD. At presentation, he was 22 years old and had a reduced Kco (31% predicted) despite preserved spirometry. HRCT of his chest showed subtle but extensive (50-75% involvement) ground glass opacification. No interlobular septal thickening or mediastinal lymphadenopathy was observed. No suspicion of PVOD/PCH was raised based on radiological appearances. Histopathology was reviewed by two independent pathologists each confirming the predominant histological pattern to be one of pulmonary arterial vasculopathy. The pulmonary arteries showed eccentric and concentric intimal fibrosis and medial hypertrophy (A, B) as well as some lesions with features of recanalised thrombus (C). Several concentrically muscularised arterioles were also observed (D). No complex plexiform lesions were present. There was patchy thickening of the alveolar septa with capillary congestion and pigmented intra-alveolar macrophages similar to PCH (E, F). Venous remodelling was difficult to trace and infrequent, but present. Fibrous thickening of the intima in septal veins (G, I) and a micro-vessel (H).