Altered Smooth Muscle Cell Histone Acetylome by the SPHK2/S1P Axis Promotes Pulmonary Hypertension

Identification of an immune-related gene panel for the diagnosis of pulmonary arterial hypertension using bioinformatics and machine learning

OBJECTIVE

This study aimed to screen an immune-related gene (IRG) panel and develop a novel approach for diagnosing pulmonary arterial hypertension (PAH) utilizing bioinformatics and machine learning (ML).

METHODS

Gene expression profiles were retrieved from the Gene Expression Omnibus (GEO) database to identify differentially expressed immune-related genes (IRG-DEGs). We employed five machine learning algorithms-LASSO, random forest (RF), boosted regression trees (BRT), XGBoost, and support vector machine recursive feature elimination (SVM-RFE) to identify biomarkers derived from IRG-DEGs associated with the diagnosis of PAH, incorporating them into the IRG-DEGs panel. Validation of these biomarker levels in lung tissue was conducted in a hypoxia-induced mouse model of PAH, investigating the correlation between AIMP1, IL-15, GLRX, SOD1, Fulton's index (RVHI), and the ratio of pulmonary artery medial thickness to external diameter (MT%). Subsequently, we developed a nomogram model based on the IRG-DEGs panel in lung tissue for diagnosing PAH. The expression, distribution, and pseudotime analysis of these biomarkers across various immune cell types were assessed using single-cell sequencing datasets. Finally, we evaluated the diagnostic utility of the nomogram model based on the IRG-DEGs panel in peripheral blood mononuclear cells (PBMCs) for diagnosing PAH.

RESULTS

A total of 36 upregulated and 17 downregulated IRG-DEGs were identified in lung tissue from patients with PAH. AIMP1, IL-15, GLRX, and SOD1 were subsequently selected as novel immune-related biomarkers for PAH through the aforementioned machine learning algorithms and incorporated into the IRG-DEGs panel. Experimental results from mice with PAH validated that the expression levels of AIMP1, IL-15, and GLRX in lung tissue were elevated, while SOD1 expression was significantly reduced. Additionally, GLRX and AIMP1 exhibited positive correlations with Fulton's index (RVHI). The expression levels of GLRX, IL-15, and AIMP1 showed positive correlations with MT%, whereas SOD1 exhibited negative correlations with MT%. Analysis of single-cell sequencing data further revealed that the levels of IRG-DEG panel members gradually increased during the pseudotime trajectory from PBMCs to macrophages, correlating with macrophage activation. The area under the curve (AUC) for diagnosing PAH using a nomogram model based on the IRG-DEGs panel derived from lung tissue samples and PBMCs was ≥0.969 and 0.900, respectively.

CONCLUSIONS

We developed an IRG-DEGs panel containing AIMP1, IL-15, GLRX, and SOD1, which may facilitate the diagnosis of pulmonary arterial hypertension (PAH). These findings provide novel insights that may enhance diagnostic and therapeutic approaches for PAH.

Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application

The dynamic regulation of chromatin accessibility is one of the prominent characteristics of eukaryotic genome. The inaccessible regions are mainly located in heterochromatin, which is multilevel compressed and access restricted. The remaining accessible loci are generally located in the euchromatin, which have less nucleosome occupancy and higher regulatory activity. The opening of chromatin is the most important prerequisite for DNA transcription, replication, and damage repair, which is regulated by genetic, epigenetic, environmental, and other factors, playing a vital role in multiple biological progresses. Currently, based on the susceptibility difference of occupied or free DNA to enzymatic cleavage, solubility, methylation, and transposition, there are many methods to detect chromatin accessibility both in bulk and single-cell level. Through combining with high-throughput sequencing, the genome-wide chromatin accessibility landscape of many tissues and cells types also have been constructed. The chromatin accessibility feature is distinct in different tissues and biological states. Research on the regulation network of chromatin accessibility is crucial for uncovering the secret of various biological processes. In this review, we comprehensively introduced the major functions and mechanisms of chromatin accessibility variation in different physiological and pathological processes, meanwhile, the targeted therapies based on chromatin dynamics regulation are also summarized.

A role for plasma membrane Ca2+ ATPases in regulation of cellular Ca2+ homeostasis by sphingosine kinase-1

Sphingosine-1-phosphate (S1P) is a ubiquitous lipid mediator, acting via specific G-protein-coupled receptors (GPCR) and intracellularly. Previous work has shown that deletion of S1P lyase caused a chronic elevation of cytosolic [Ca2+]i and enhanced Ca2+ storage in mouse embryonic fibroblasts. Here, we studied the role of sphingosine kinase (SphK)-1 in Ca2+ signaling, using two independently generated EA.hy926 cell lines with stable knockdown of SphK1 (SphK1-KD1/2). Resting [Ca2+]i and thapsigargin-induced [Ca2+]i increases were reduced in both SphK1-KD1 and -KD2 cells. Agonist-induced [Ca2+]i increases, measured in SphK1-KD1, were blunted. In the absence of extracellular Ca2+, thapsigargin-induced [Ca2+]i increases declined rapidly, indicating enhanced removal of Ca2+ from the cytosol. In agreement, plasma membrane Ca2+ ATPase (PMCA)-1 and -4 and their auxiliary subunit, basigin, were strongly upregulated. Activation of S1P-GPCR by specific agonists or extracellular S1P did not rescue the effects of SphK1 knockdown, indicating that S1P-GPCR were not involved. Lipid measurements indicated that not only S1P but also dihydro-sphingosine, ceramides, and lactosylceramides were markedly depleted in SphK1-KD2 cells. SphK2 and S1P lyase were upregulated, suggesting enhanced flux via the sphingolipid degradation pathway. Finally, histone acetylation was enhanced in SphK1-KD2 cells, and the histone deacetylase inhibitor, vorinostat, induced upregulation of PMCA1 and basigin on mRNA and protein levels in EA.hy926 cells. These data show for the first time a transcriptional regulation of PMCA1 and basigin by S1P metabolism. It is concluded that SphK1 knockdown in EA.hy926 cells caused long-term alterations in cellular Ca2+ homeostasis by upregulating PMCA via increased histone acetylation.

Emerging Epigenetic Targets and Their Molecular Impact on Vascular Remodeling in Pulmonary Hypertension

Pulmonary Hypertension (PH) is a terminal disease characterized by severe pulmonary vascular remodeling. Unfortunately, targeted therapy to prevent disease progression is limited. Here, the vascular cell populations that contribute to the molecular and morphological changes of PH in conjunction with current animal models for studying vascular remodeling in PH will be examined. The status quo of epigenetic targeting for treating vascular remodeling in different PH subtypes will be dissected, while parallel epigenetic threads between pulmonary hypertension and pathogenic cancer provide insight into future therapeutic PH opportunities.