Epigenetic Inheritance Underlying Pulmonary Arterial Hypertension

Abstract

In pulmonary arterial hypertension (PAH), the Warburg effect (glycolytic shift) and mitochondrial fission are determinants of phenotype alterations characteristic of the disease, such as proliferation, apoptosis resistance, migration, endothelial-mesenchymal transition, and extracellular matrix stiffness. Current therapies, focusing largely on vasodilation and antithrombotic protection, do not restore these aberrant phenotypes suggesting that additional pathways need be targeted. The multifactorial nature of PAH suggests epigenetic changes as potential determinants of vascular remodeling. Transgenerational epigenetic changes induced by hypoxia can result in permanent changes early in fetal development increasing PAH risk in adulthood. Unlike genetic mutations, epigenetic changes are pharmacologically reversible, making them an attractive target as therapeutic strategies for PAH. This review offers a landscape of the most current clinical, epigenetic-sensitive changes contributing to PAH vascular remodeling both in early and later life, with a focus on a network medicine strategy. Furthermore, we discuss the importance of the application (from morphogenesis to disease onset) of molecular network-based algorithms to dissect PAH molecular pathobiology. Additionally, we suggest an integrated network-based program for clinical disease gene discovery that may reveal novel biomarkers and novel disease targets, thus offering a truly innovative path toward redefining and treating PAH, as well as facilitating the trajectory of a comprehensive precision medicine approach to PAH.

Keywords: apoptosis; biomarkers; hypoxia; mutation; primary prevention.

Conflict of interest statement

Disclosures: The authors declare there are no conflicts of interest.

Figures

Figure 1:. Hallmarks of PAH pathobiology.

Genetic susceptibility, mainly LOF in BMPR2 gene, epigenetic factors, such as DNA methylation, histone modifications, and non-coding RNAs, as well as a variety of environmental risk factors, such as pathogens, ROS, and inflammation are the main trigger factors of the endothelial dysfunction. This letter leads to progressive reduction of vascular tone and arterial remodeling underlying PAH onset. Plexogenic lesions, thrombosis, and fibrosis are the phenotypic hallmarks of right ventricular failure.

Figure 2:. Basic epigenetic mechanisms.

The Figure shows the major epigenetic modifications: DNA methylation, histon modifications and RNA-based mechanisms such as microRNAs. The effect of epigenetic changes is to influence gene expression without modifying DNA sequence by remodeling the chromatin structure and/or targeting RNA messengers.

Figure 3:. The role of epigenetic memory for the induction of arterial remodeling in PAH.

Epigenetic changes represent the means by which environmental factors interact with the genome to alter gene expression. Following the persistence of pathological stimuli, epigenetic memory triggers stimulus-independent cancer-like alterations in ECs, SMCs, and Fs represented by aberrant transcription of pro-proliferative, pro-migratory, pro-ECM stiffness, and anti-apoptotic genes. This phenotypic switch of pulmonary vascular cells largely contributes to the development of complex vascular lesions during the progressive vascular remodeling process in PAH. Hyper-methylation of ABCA1, BMPR2 contributes to block vascular cells in mitotic phase. By increasing acetylation of PGC-1α, SIRT-1 HDAC down-regulation reduces mitochondrial mass and sustains cell proliferation. Hyperacetylation of extracellular CypA, as well as down-regulation of anti-oxidant SOD3 via class I HDAC3 up-regulation, contribute to oxidative stress underlying PAH phenotype. Up-regulation of HDAC4-5 by down-regulating MEF2 adds proliferative stimuli. Downregulation of circulating miR-1281, miR-124, miR-34a-3p, and lnc-RNA MEG3 plays a key role in the development of the proliferative phenotype. All of these epigenetic-sensitive changes might also contribute to transgenerational inheritance, in accordance with the developmental origins of PAH.

Figure 4:. A systems biology approach: from omics science to network-based tools in precision medicine.

Omics sciences offer high-throughput platforms monitoring diabetes onset at molecular level. Genomics (NGS, GWAS, DNA Chip) allows the whole genome or selected gene sequencing; transcriptomics (RNA Chip, RNA-seq) catalogues coding and non-coding RNAs; proteomics (immune assay, MS, protein CHIP) explores structure, function, and interactions of proteins, and epigenomics (MNase-seq, Dnase-seq, ATAC-seq, bisulfite sequencing, EWAS, e.g., meQTL, ChIP) investigated the complete set of chromatin modifications in a particular cell, tissue, or organism. The emerging bioinformatic network-based tools explore systematically PAH-associated modules and pathways to unravel novel candidate genes, the biological significance of PAH-associated polymorphisms, as well as drug targets and biomarkers. The main used algorithms are: 1) PANDA, Genomica (regulatory), and WGCNA (co-expression), at genomic level; 2) WGCNA (co-expression), at trascriptomic level; GenePanda, DIAMOnD, PRINCE, PRODIGE (PPIs), at proteomic level; MMI-network and IPA (regulatory), at epigenetic level. The challenge of network medicine is translate acquired knowledge into clinical practice in order to obtain a more accurate diagnosis, targeted treatment, and personalized therapy, thus ameliorating primary and secondary prevention of PAH.

Figure 5:. Primary prevention of PAH through genetic and epigenetic network-based approaches.

Genetic individual background is invariable during life, whereas epigenetic influences are dynamic and specific to the spatio-temporal status of an organism. Environmental changes can perturb crucial epigenetic-sensitive pathways involved in morphogenesis leading to PAH onset in later stages of life. In order to ameliorate primary prevention of PAH, it is necessary to combine genomics, epigenomics, proteomics, and network-based algorithms to identify innovative biomarkers mainly at the fetal-perinatal stage, as well as at the post-natal stage, during childhood, and in older age.

Figure 6:. An integrated clinical program for discovery of PAH-associated candidate genes.

TThis diagnostic research program, modified from Haghighi et al., (2018), offers an integrated approach to evaluate novel candidate genes in PAH onset and progression. The computational pipeline indicates all processing steps from sample preparation to biomarker validation by bioinformatic approaches. The second step is represented by upstream analysis that validate and prioritize candidate PAH-sensitive genetic and epigenetic variants. The third step includes downstream analysis that are designed to establish the causative effect between variants in candidate genes and PAH. Overall, the main goal is to integrate the findings about gene causality with the clinical management of PAH.