04 February 2019

Epigenome-wide profiling uncovers novel gene regulatory networks in human pulmonary arterial hypertension

Background:

Evidence of epigenome-wide alterations that facilitates normal vascular cells to acquire and exhibit pro-proliferative, apoptotic-resistant, pro-inflammatory phenotypes in pulmonary arterial hypertension (PAH) remains unexplored at a genome-wide scale.

Objectives and Methods:

Our major objectives were to (1) employ multiple next-generation sequencing (NGS) approaches to profile vascular cell-specific epigenomic alterations in human setting, (2) identify gene regulatory signatures, (3) identify transcription factor networks associated with hypertensive phenotypes, (4) evaluate the therapeutic potential of epigenetic intervention.

Results:

Cell-specific transcriptome profiling revealed differential expression of 2069 genes (2-fold) in ex vivo isolated pulmonary artery adventitial fibroblasts (PAFBs) from idiopathic PAH (IPAH) and human donors, which strongly indicated the existence of genome-scale alterations in transcription regulatory mechanisms of PAH. To map the PAH-associated epigenomic alterations in the chromatin landscape of PAH vascular cells, we employed ChIP-seq to generate genome-wide maps for RNA polymerase II occupancy, histone modifications associated with euchromatin (H3K9/K14ac, H3K4me3, pan-H4Kac), heterochromatin (H3K27me3, H3K9me3) and enhancers (H3K27ac, H3K4me1). Bioinformatic analysis confirmed massive epigenetic alterations in both histone acetylation and methylation pattern in IPAH, which corroborated with aberrant expression and recruitment of histone modifying enzymes in IPAH. KEGG analysis of epigenetic signatures revealed association with ABC transporters, smooth muscle contraction, cGMP-PKG, renin secretion, NF-κB, TGFβ and cancer signaling pathways. Integrative analysis also revealed acquisition of pro-hypertensive gene expression signatures in PAH, that includes differential regulation of novel transcription factor networks (SOX, ID, HES, GLI, GATA, REL) that may altogether coordinate the pro-proliferative and pro-inflammatory phenotypes in PAH. Aberrant epigenetic signatures in PAH were reversed by targeting chromatin modifying enzymes.

Conclusions:

Integrative analysis of vascular cell-specific epigenomics data confirmed genome-scale alterations in the chromatin landscape and DNA accessibility leading to aberrant transcriptional responses in PAH. This genome-scale study also uncovered novel regulatory factors, signaling networks and potential targets for therapeutic intervention.

Key Contributors

Prakash Chelladurai 1,2, Carsten Künne 1, Christine Weber 3, René Reiner Nötzold 3, Mario Schmoranzer 1, Mario Looso 1, Uta-Maria Bauer 3, Werner Seeger 1,2, Soni Savai Pullamsetti 1,2 : (1) Max-Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; (2) Universities ofGiessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research(DZL), Giessen, Germany; (3) Institute of Molecular Biology and Tumor Research, Marburg,Germany.


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