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Rare Modifier Variants Alter the Severity of Cardiovascular Disease in Pseudoxanthoma Elasticum

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Rare Modifier Variants Alter the Severity of Cardiovascular Disease in Pseudoxanthoma Elasticum fcell-09-612581 June 8, 2021 Time: 11:34 # 1 BRIEF RESEARCH REPORT published: 08 June 2021 doi: 10.3389/fcell.2021.612581 Rare Modifier Variants Alter the Severity of Cardiovascular Disease in Pseudoxanthoma Elasticum: Identification of Novel Candidate Modifier Genes and Disease Pathways Through Mixture of Effects Analysis Eva Y. G. De Vilder1,2,3, Ludovic Martin4, Georges Lefthériotis5, Paul Coucke1,6, Filip Van Nieuwerburgh7 and Olivier M. Vanakker1,6* Edited by: 1 2 Svetlana Komarova, Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium, The Research Foundation – Flanders, Ghent, 3 4 McGill University, Canada Belgium, Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium, Department of Dermatology, Angers University Hospital, Angers, France, 5 Department of Vascular Physiology and Sports Medicine, Angers University, Angers, Reviewed by: France, 6 Department of Biomolecular Medicine, Ghent University, Ghent, Belgium, 7 Department of Pharmaceutics, Carolina Beraldo Meloto, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium McGill University, Canada Koen van de Wetering, Thomas Jefferson University, Introduction: Pseudoxanthoma elasticum (PXE), an ectopic mineralization disorder United States caused by pathogenic ABCC6 variants, is characterized by skin, ocular and Jessica Bertrand, University Hospital Magdeburg, cardiovascular (CV) symptoms. Due to striking phenotypic variability without genotype- Germany phenotype correlations, modifier genes are thought to play a role in disease variability. *Correspondence: In this study, we evaluated the collective modifying effect of rare variants on the Olivier M. Vanakker [email protected] cardiovascular phenotype of PXE. Materials and Methods: Mixed effects of rare variants were assessed by Whole Exome Specialty section: This article was submitted to Sequencing in 11 PXE patients with an extreme CV phenotype (mild/severe). Statistical Molecular Medicine, analysis (SKAT-O and C-alpha testing) was performed to identify new modifier genes for a section of the journal Frontiers in Cell and Developmental the CV PXE phenotype and enrichment analysis for genes significantly associated with Biology the severe cohort was used to evaluate pathway and gene ontology features. Received: 30 September 2020 Results: Respectively 16 (SKAT-O) and 74 (C-alpha) genes were significantly associated Accepted: 11 May 2021 Published: 08 June 2021 to the severe cohort. Top significant genes could be stratified in 3 groups– Citation: calcium homeostasis, association with vascular disease and induction of apoptosis. De Vilder EYG, Martin L, Comparative analysis of both analyses led to prioritization of four genes (NLRP1, SELE, Lefthériotis G, Coucke P, Van Nieuwerburgh F and TRPV1, and CSF1R), all signaling through IL-1B. Vanakker OM (2021) Rare Modifier Variants Alter the Severity Conclusion: This study explored for the first time the cumulative effect of rare variants of Cardiovascular Disease on the severity of cardiovascular disease in PXE, leading to a panel of novel candidate in Pseudoxanthoma Elasticum: modifier genes and disease pathways. Though further validation is essential, this panel Identification of Novel Candidate Modifier Genes and Disease may aid in risk stratification and genetic counseling of PXE patients and will help to gain Pathways Through Mixture of Effects new insights in the PXE pathophysiology. Analysis. Front. Cell Dev. Biol. 9:612581. Keywords: pseudoxanthoma elasticum, ABCC6, candidate modifier gene, cardiovascular disease, mixture of doi: 10.3389/fcell.2021.612581 effects analysis, C-alpha test, SKAT-O Frontiers in Cell and Developmental Biology| www.frontiersin.org 1 June 2021| Volume 9| Article 612581 fcell-09-612581 June 8, 2021 Time: 11:34 # 2 De Vilder et al. Novel Candidate Modifiers in PXE INTRODUCTION a candidate gene approach (Boraldi et al., 2014; De Vilder et al., 2020). Further, the allelic variant epsilon2/epsilon3 of the APOE Pseudoxanthoma elasticum (PXE, OMIM#264800) is gene was suggested as a modifying factor for the cardiovascular an autosomal recessive ectopic mineralization disorder, PXE phenotype with a seemingly protective effect in older age characterized by elastic fiber mineralization in the mid- (Clarke et al., 2013). dermis of the skin, the elastic media of blood vessels and the Contrary to modifiers with a high penetrance, it is assumed Bruch’s membrane in the eye. The main vascular feature of that multiple rare variants of low penetrance either within or the disease is medial calcification, leading to peripheral artery across genes collectively may influence complex human traits, disease and narrowing of arteries of mainly the lower limbs for with a combined protective, deleterious or null effect. While the which surgical intervention may be necessary in advanced stages effects of each individual rare variant can be modest, collectively (Leftheriotis et al., 2013). they can sufficiently increase or decrease the disease risk or PXE is caused by bi-allelic pathogenic variants in the severity (Konigorski et al., 2017). To identify new modifier genes, ABCC6 gene (ATP binding cassette, subfamily C, member 6, a multiple-marker test can be used, which tests multiple variants OMIM∗603234), encoding an ATP-dependent transmembrane simultaneously with the use of multivariate methods (Lee et al., transporter. To date, over 300 different potentially pathogenic 2012). Examples of such tests are the classical burden tests, variants have been reported (Vanakker et al., 2008; Finger et al., which have an optimal result when the direction of effect is the 2009). Pathogenic variants in the ENPP1 gene (ectonucleotide same for all assessed variants (Lee et al., 2012). However, this pyrophosphatase/phosphodiesterase 1; OMIM∗173335), the gene is not always the case, therefore testing for the presence of a associated with Generalized Arterial Calcification of Infancy mixture of effects of multiple rare variants on a trait may prove (GACI; OMIM#208000), were also found to cause PXE, although beneficial, for which the C-alpha and the (optimized) sequence less frequently (Nitschke et al., 2012). Kernel Association (SKAT-O) test can be used (Emond et al., The pathophysiology of PXE is incompletely understood, but 2012; Konigorski et al., 2017). holds an important role for the calcification inhibitor inorganic Here, we implemented extreme phenotype sampling, in which pyrophosphate (PPi). The production of PPi relies on hydrolysis individuals who are at both ends of the phenotypic distribution of ATP by the ENPP1 enzyme, after is has been transported from are analyzed. The rationale for this approach is that it can the liver to the vasculature. PPi serum levels are considerably be assumed that the frequency of alleles that contribute to decreased in PXE patients and ABCC6 deficiency has been the trait are enriched in patients with an extreme phenotype, demonstrated to hamper cellular ATP release, hence hindering hereby improving the power of the analysis. Especially in the PPi production (Jansen et al., 2014). Nonetheless, it is known setting of rare diseases, where limited sample sizes are available, that a lack of PPi is not the only disease mechanism in PXE. such an approach helps to obtain valid results (Lanktree et al., Also mitochondrial dysfunction and oxidative stress, apoptosis, 2010; Emond et al., 2015). For example, in cystic fibrosis (CF; inflammation and dysfunctional inhibitors of calcification, such OMIM#219700), this approach was used to successfully identify as matrix gla protein (MGP) and fetuin-A have been described several disease modifiers (Emond et al., 2015). to contribute to the elastic fiber calcification in PXE patients, In this study, we evaluated the collective modifying effect cell- and animal models (Uitto et al., 2010; Hosen et al., 2014; of rare variants on the cardiovascular phenotype of PXE. For Brampton et al., 2021). this, we performed whole exome sequencing in 11 PXE patients Striking for PXE is an extensive inter- and intrafamilial clinical with an extremely mild or severe cardiovascular phenotype, variability, with no strong underlying genotype-phenotype based on clinical severity and Agatston score of the lower correlations. Indeed, patients with the same pathogenic ABCC6 limbs. Subsequently, we performed SKAT-O and C-alpha tests variants may develop a different phenotype with respect to to help identify modifiers of the cardiovascular disease severity, the type and severity of the symptoms. Moreover, identical leading to a panel of novel candidate modifier genes and pathogenic variants in ABCC6 or ENPP1 were shown to cause disease pathways. either PXE or GACI in different patients (Nitschke et al., 2012). All these findings suggest that other factors must contribute to the clinical variability in PXE besides the causal genes, e.g., MATERIALS AND METHODS environmental factors such as life-style, epigenetic modifications and modifier genes (Stitziel et al., 2011; Kwon et al., 2020). Patient Characteristics Different approaches could be followed for genetic modifier All patients were diagnosed with PXE based on a combination of discovery. One approach is the single-marker test, whereby skin pathology (elastic fiber mineralization and fragmentation in individual variants within a gene are tested for an association with the mid-dermis of lesional skin, using Verhoef-van Giesson and the disease outcome, with standard univariate statistical tests, Von Kossa staining), and typical (sub)retinal abnormalities on controlled by
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