Biomarker For Pulmonary Arterial Hypertension Research Articles

Anti-fibroblast and anti-endothelial cell autoantibodies in pulmonary arterial hypertension (PAH) in patients with connective tissue diseases (CTD).

Pulmonary arterial hypertension (PAH) is a rare disease that may be associated with connective tissue diseases (CTD). Anti-fibroblast (AFA) and anti-endothelial cell autoantibodies (AECA) have been identified in idiopathic and systemic sclerosis (SSc)-associated PAH. The aim was to identify autoantibodies discriminating for PAH associated with systemic lupus erythematosus (SLE), mixed connective tissue disease (MCTD) and primary Sjögren's syndrome (SS), and their target antigens. Sera were collected in the French multicentre Auto-HTAP study from 86 patients with CTD excluding SSc, including 32 with PAH (PAH+) and 54 without (PAH-). AFA and AECA were identified using one (1D) and two dimensions (2D) immunoblots and proteomics. ELISA tests using human recombinant proteins were used to confirm PAH-associated IgG reactivities. PAH+ patients had similar IgG AFA and AECA reactivities in 56.2% and 40.6% of the cases in 1D immunoblots, respectively. In 2D immunoblots, serum IgG pools from SLE patients (n = 14), MCTD (n = 10), SS (n = 9) and 14 healthy controls (n = 1) recognized respectively 273 ± 79, 205 ± 77, 109 ± 11 and 109 protein spots in fibroblasts and 189 ± 48, 146 ± 30, 88 ± 33 and 190 protein spots in endothelial cell extracts. Serum IgG from PAH+ patients recognized 39 fibroblast and 34 endothelial cell protein spots that were not recognized by IgG from PAH- patients, including Annexin A5 (ANXA5). Anti-ANXA5 IgG reactivity was significantly higher in PAH+ compared with PAH- patients with MCTD (73% vs 0%, p< 0.001) and SLE (33% vs 0%, p= 0.009). Anti-ANXA5 IgG autoantibody reactivity might represent a predictive biomarker for PAH associated with MCTD and SLE.

Advancing Prognostic Biomarkers in Pulmonary Arterial Hypertension: The Role of Plasma Immunoglobulin G Fucosylation

Advancing Prognostic Biomarkers in Pulmonary Arterial Hypertension: The Role of Plasma Immunoglobulin G Fucosylation

Serum proteome profiling reveals HGFA as a candidate biomarker for pulmonary arterial hypertension

BackgroundIdentification and validation of potential biomarkers could facilitate the identification of pulmonary arterial hypertension (PAH) and thus aid to study their roles in the disease process.MethodsWe used the isobaric tag for relative and absolute quantitation approaches to compare the protein profiles between the serum of PAH patients and the controls. Bioinformatics analyses and enzyme-linked immunosorbent assay (ELISA) identification of PAH patients and the controls were performed to identify the potential biomarkers. The receiver operating characteristic curve (ROC) analysis was used to evaluate the diagnostic performance of these potential biomarkers. Mendelian randomization (MR) analysis further clarified the relationship between the potential biomarkers and PAH. Additionally, the expression levels of the potential biomarkers were further validated in two PAH animal models (monocrotaline-PH and Sugen5416 plus hypoxia-PH) using ELISA and reverse transcription-quantitative PCR (RT-qPCR).ResultsWe identified significant changes in three proteins including heparanase (HPSE), gelsolin (GSN), and hepatocyte growth factor activator (HGFA) in PAH patients. The ROC analysis showed that the areas under the curve of HPSE, GSN, and HGFA in differentiating PAH patients from controls were 0.769, 0.777, and 0.964, respectively. HGFA was correlated with multiple parameters of right ventricular functions in PAH patients. Besides proteomic analysis, we also used MR method to demonstrate the causal link between genetically reduced HGFA levels and an increased risk of PAH. In subsequent validation study in PAH animal models, the mRNA expression levels of HGFA in the lung tissues were significantly lower in PAH rat models than in controls. In the rat models, serum levels of HGFA were lower compared to the control group and showed a negative correlation with right ventricular systolic pressure.ConclusionThe study demonstrated that HGFA might be a promising biomarker for noninvasive detection of PAH.

Abstract 4138019: eQTL Analysis of the PAH Biomarker CCN2 Identifies a Novel SNP that Associates with Survival

Background: We recently determined that cellular communication network factor 2 (CCN2) (also known as IGFBP8) levels associate with metrics of severity, and survival, in pulmonary arterial hypertension (PAH). While genetic variants that modify CCN2 gene expression have been described, the variants across the genome that associate with CCN2 protein levels in human circulation remain unknown. Research Question: We sought to identify genetic variants associated with circulating levels of CCN2 and to determine those variants’ relationship with clinical severity and survival. Methods: Serum CCN2 was measured by ELISA in subjects from a national sample repository, the PAH Biobank. A genome wide association study (GWAS) for CCN2 (natural log transformed) was performed in White idiopathic PAH (IPAH) PAH Biobank participants (n = 768) using Illumina OMNI5 genotypes in plink after standard quality control. Subsequent exploration of the SNP of interest was conducted in a separate dataset of 687 White PAH participants (n=360 IPAH, n=313 APAH) linked to genetic and clinical data, including REVEAL 2.0 risk score assessment (divided into low, medium, and high-risk levels) and outcomes (the STRIDE (Sitaxsentan To Relieve Impaired Exercise) trials cohort). Results: In the PAH Biobank, using GWAS, we found CCN2 levels were significantly associated with rs9493157 (p = 2.8 x10 -12 ) ( Figure A ). rs9493157 is reported in the Genotype-Tissue Expression (GTEx) portal to be an eQTL for CCN2 expression in the left ventricle. In the STRIDE cohort, the hazard ratio (HR) for death was 1.33 (99% CI 1.03 to 1.72) for participants with one or more T alleles (p=0.027; ( Figure B )). On multivariate analysis, the HR for death was 1.28 (95% CI 0.99 to 1.66; p=0.060). Among subjects with the highest REVEAL2.0 risk, those with a T allele had worse survival than those no T allele, with best survival among those with low a REVEAL2.0 score and no T allele. Conclusions: In White PAH subjects, rs9493157 associates with human levels of serum CCN2, a known biomarker for PAH. While additional studies are warranted, the T allele associates with worse survival and may enhance the prognostic value of the REVEAL2.0 risk score.

Inflammatory and cardiac biomarkers in pulmonary arterial hypertension: The prognostic role of IL-34

BackgroundPulmonary arterial hypertension (PAH) is characterized by increased pulmonary artery pressure with significant morbidity and mortality. Inflammatory processes are crucial in PAH pathogenesis, with inflammatory cells and mediators present early in disease progression. IL-34 involvement in inflammatory pathways suggests that IL-34 could be an important player in the progression of PAH, influencing both pulmonary pressures and vascular changes. ObjectiveThe purpose of this study was to investigate the correlation between IL-34 levels and pulmonary arterial hypertension (PAH), aiming to enhance the understanding of the molecular mechanisms underlying PAH and explore IL-34′s potential as a biomarker. MethodsConsecutive PAH patients diagnosed via right-heart catheterization at Malatya Turgut Ozal Eğitim ve Araştırma Hastanesi (Dec 2022 - Apr 2024) were enrolled. Patients were classified into low-risk and high-risk groups based on comprehensive risk assessments that included clinical parameters, hemodynamic measurements and biomarkers, in-line with ESC/ERS guidelines. Serum IL-34, hs-CRP, and NT-proBNP levels were measured and compared with those of healthy controls. Echocardiographic assessments and statistical analyses, including ROC analysis, were conducted to evaluate biomarker significance and predictive capabilities. ResultsThe mean age of low-risk and high-risk PAH patients was 42 ± 7.2 years and 45 ± 5.5 years, respectively. The mean age of the control group was 40 ± 6.4 years. Males comprised 54.29 % of the low-risk group, 56 % of the high-risk group, and 53.3 % of the control group. IL-34 and hs-CRP levels were significantly elevated in PAH patients compared to controls. IL-34 correlated positively with systolic pulmonary artery pressure, RA area, and NT-proBNP levels. Multivariate analysis revealed that IL-34 and hs-CRP were independent predictors of PAH. IL-34 levels>29.8 pg/mL predicted PAH with 78 % sensitivity and 69 % specificity, while levels >44.4 pg/mL predicted high-risk PAH with 84 % sensitivity and 77 % specificity. ConclusionElevated IL-34 and hs-CRP levels are associated with PAH severity and right ventricular dysfunction, suggesting IL-34′s potential as a diagnostic and prognostic biomarker. Further research is needed to validate these findings and explore IL-34-targeted therapies in pH management.

Exploring IRGs as a Biomarker of Pulmonary Hypertension Using Multiple Machine Learning Algorithms.

Pulmonary arterial hypertension (PAH) is a severe disease with poor prognosis and high mortality, lacking simple and sensitive diagnostic biomarkers in clinical practice. This study aims to identify novel diagnostic biomarkers for PAH using genomics research. We conducted a comprehensive analysis of a large transcriptome dataset, including PAH and inflammatory response genes (IRGs), integrated with 113 machine learning models to assess diagnostic potential. We developed a clinical diagnostic model based on hub genes, evaluating their effectiveness through calibration curves, clinical decision curves, and ROC curves. An animal model of PAH was also established to validate hub gene expression patterns. Among the 113 machine learning algorithms, the Lasso + LDA model achieved the highest AUC of 0.741. Differential expression profiles of hub genes CTGF, DDR2, FGFR2, MYH10, and YAP1 were observed between the PAH and normal control groups. A diagnostic model utilizing these hub genes was developed, showing high accuracy with an AUC of 0.87. MYH10 demonstrated the most favorable diagnostic performance with an AUC of 0.8. Animal experiments confirmed the differential expression of CTGF, DDR2, FGFR2, MYH10, and YAP1 between the PAH and control groups (p < 0.05); Conclusions: We successfully established a diagnostic model for PAH using IRGs, demonstrating excellent diagnostic performance. CTGF, DDR2, FGFR2, MYH10, and YAP1 may serve as novel molecular diagnostic markers for PAH.

Circulating extracellular vesicles as novel biomarkers for pulmonary arterial hypertension in patients with systemic lupus erythematosus.

Pulmonary arterial hypertension (PAH) is a serious complication of systemic lupus erythematosus (SLE) with increased mortality. A prothrombotic state may contribute to pathogenesis of SLE-PAH. Extracellular vesicles (EVs) are known to be associated with thrombosis. Here, we investigated circulating EVs and their associations with SLE-PAH. Eighteen SLE-PAH patients, 36 SLE-non-PAH patients, and 36 healthy controls (HCs) were enrolled. Flow cytometry was used to analyze circulating EVs from leukocytes (LEVs), red blood cells (REVs), platelets (PEVs), endothelial cells (EEVs), and Annexin V+ EVs with membrane phosphatidylserine (PS) exposure. Plasma levels of all EV subgroups were elevated in SLE patients with or without PAH compared to HCs. Furthermore, plasma Annexin V+ EVs, LEVs, PEVs, REVs, EEVs, and Annexin V+ REVs were significantly elevated in SLE-PAH patients compared to SLE-non-PAH patients. Additionally, PAH patients with moderate/high SLE showed a significant increase in LEVs, PEVs, REVs, Annexin V+ EVs, and Annexin V+ REVs compared to SLE-non-PAH patients. However, PAH patients with inactive/mild SLE only exhibited elevations in Annexin V+ EVs, REVs, and Annexin V+ REVs. In the SLE-PAH patients, EEVs were positively correlated with pulmonary arterial systolic pressure, while PEVs and EEVs were positively correlated with right ventricular diameter. Moreover, the receiver operating characteristic curve indicated that Annexin V+ EVs, LEVs, PEVs, REVs, EEVs and Annexin V+ REVs could predict the presence of PAH in SLE patients. Importantly, multivariate logistic regression analysis showed that circulating levels of LEVs or REVs, anti-nRNP antibody, and serositis were independent risk factors for PAH in SLE patients. Findings reveal that specific subgroups of circulating EVs contribute to the hypercoagulation state and the severity of SLE-PAH. Higher plasma levels of LEVs or REVs may serve as biomarkers for SLE-PAH.

Serum uric acid and pulmonary arterial hypertension: A two-sample Mendelian randomization study

BackgroundObservational studies have suggested a correlation between hyperuricemia and pulmonary arterial hypertension (PAH), yet the causal relationship remains uncertain. We aimed to establish this link using Mendelian Randomization (MR) methods. ObjectivesBased on publicly accessible data, our study employs MR to determine the causal relationship between uric acid (UA) and PAH. MethodMR analysis was conducted among individuals of European descent. Genetic instruments linked to UA (p-value < 5 × 10–8) were extracted from the Chronic Kidney Disease Genetic Consortium and genome-wide association study databases. PAH risk genetic associations were sourced separately. We employed four MR methods (MR-Egger, weighted median, inverse variance weighted, and weighted mode) with selected instrumental variables to assess the causal association between UA and PAH. MR-PRESSO was used to evaluate pleiotropy and outlier Single Nucleotide Polymorphisms (SNPs), while Cochran's Q test and funnel plot assessed SNP heterogeneity. Leave-one-out analysis examined SNP impacts on causal assessment. ResultTwo-sample MR analysis revealed a positive, causal relationship between UA levels and PAH. ConclusionOur MR analysis provides robust evidence of a causal link between serum UA and PAH, suggesting UA's potential as a biomarker and therapeutic target for PAH.

Inhibition of DLL4/Notch Signaling Pathway Promotes M2 Polarization and Cell Proliferation in Pulmonary Arterial Hypertension.

In this study, we conducted a comprehensive analysis to identify key genes and pathways associated with pulmonary arterial hypertension (PAH) and investigated the role of delta-like ligand 4 (DLL4) in PAH pathogenesis. Through integrated analysis of multiple data sets, we identified 6 candidate differentially expressed genes (DEGs), notably DLL4, which showed the highest distinguishing efficiency between PAH and control samples. Functional and pathway enrichment analyses revealed the involvement of DLL4 in critical biological processes and pathways related to PAH, including notch signaling, immune cell function, and inflammatory responses. Further investigation demonstrated that decreased DLL4 expression correlated with increased M2 macrophage polarization, suggesting a potential role for DLL4 in preventing M2 differentiation. Additionally, the DLL4/Notch1 axis was found to influence the Notch profile and regulate signaling mediators during M2 differentiation. These findings highlight DLL4 as a promising biomarker and therapeutic target for PAH, shedding light on the underlying molecular mechanisms and providing insights for the development of novel treatment strategies.

Identification of TFRC as a biomarker for pulmonary arterial hypertension based on bioinformatics and experimental verification

BackgroundPulmonary arterial hypertension (PAH) is a life-threatening chronic cardiopulmonary disease. However, there is a paucity of studies that reflect the available biomarkers from separate gene expression profiles in PAH.MethodsThe GSE131793 and GSE113439 datasets were combined for subsequent analyses, and batch effects were removed. Bioinformatic analysis was then performed to identify differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) and a protein-protein interaction (PPI) network analysis were then used to further filter the hub genes. Functional enrichment analysis of the intersection genes was performed using Gene Ontology (GO), Disease Ontology (DO), Kyoto encyclopedia of genes and genomes (KEGG) and gene set enrichment analysis (GSEA). The expression level and diagnostic value of hub gene expression in pulmonary arterial hypertension (PAH) patients were also analyzed in the validation datasets GSE53408 and GSE22356. In addition, target gene expression was validated in the lungs of a monocrotaline (MCT)-induced pulmonary hypertension (PH) rat model and in the serum of PAH patients.ResultsA total of 914 differentially expressed genes (DEGs) were identified, with 722 upregulated and 192 downregulated genes. The key module relevant to PAH was selected using WGCNA. By combining the DEGs and the key module of WGCNA, 807 genes were selected. Furthermore, protein–protein interaction (PPI) network analysis identified HSP90AA1, CD8A, HIF1A, CXCL8, EPRS1, POLR2B, TFRC, and PTGS2 as hub genes. The GSE53408 and GSE22356 datasets were used to evaluate the expression of TFRC, which also showed robust diagnostic value. According to GSEA enrichment analysis, PAH-relevant biological functions and pathways were enriched in patients with high TFRC levels. Furthermore, TFRC expression was found to be upregulated in the lung tissues of our experimental PH rat model compared to those of the controls, and the same conclusion was reached in the serum of the PAH patients.ConclusionsAccording to our bioinformatics analysis, the observed increase of TFRC in the lung tissue of human PAH patients, as indicated by transcriptomic data, is consistent with the alterations observed in PAH patients and rodent models. These data suggest that TFRC may serve as a potential biomarker for PAH.

BMP9 attenuates IL-33 signaling and prevents endothelial-to-mesenchymal transition in pulmonary arterial hypertension

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): Dutch Cardiovascular Alliance - PHAEDRA IMPACT Background Pulmonary Arterial hypertension (PAH) is a rare and progressive disease characterized by increased vascular resistance and remodeling of the pulmonary arteries. Disturbed Transforming growth factor (TGF)-β signaling, often associated with mutations in the gene encoding for the bone morphogenic protein receptor type II (BMPR2) and endothelial-to-mesenchymal transition (EndMT), emerges as a central culprit in the pathogenesis of PAH. Interleukin-33 (IL-33) has been identified as an inducer of EndMT, and its soluble receptor ST2 (sST2) has emerged as a potential biomarker for PAH. Bone morphogenic protein (BMP) 9, a BMPR2 ligand, showing a high affinity for endothelial cells, is being explored as a therapeutic approach. Purpose We hypothesize that a crosstalk between the TGF-β pathway and IL-33, a known promoter of vascular remodeling, occurs in PAH. This study aims to unravel the protective role of BMP9 in PAH, with a specific focus on the involvement of EndMT, a key player in the pathogenesis of vascular diseases. Methods The expression of IL-33 protein levels was assessed in Pulmonary Arterial Endothelial Cells (PAEC) and in lung tissues from experimentally induced PH (Sugen/Hypoxia (SuHx)) or control mice. Signal transduction and EndMT were investigated in PAECs exposed to IL-33, BMP9 and sST2, by gene expression analysis (qPCR), western blotting, ELISA and immunostaining. BMP9 and sST2 levels were measured in plasma from PAH patients by ELISA. Results Elevated IL-33 expression was observed in PAEC from PAH patients and lung tissues from SuHx mice compared to healthy controls. In vitro, BMP9 significantly induced the expression of the IL-33 soluble receptor ST2, while concurrently reducing IL-33 target gene expression. IL-33-induced EndoMT in PAEC was effectively mitigated by pre-incubation with BMP9, proving more efficacious than ST2 neutralizing antibody. Furthermore, a correlation between BMP9 and sST2 levels in plasma from PAH patients was identified. Conclusion Our findings demonstrate that BMP9 offers superior protections against IL-33-induced EndMT in PAECs compared to a ST2 neutralizing antibody. BMP9 induces expression of sST2, leading to IL-33 neutralization and subsequent EndMT inhibition. Therefore, targeting the IL-33 pathway in PAH patients presents a promising therapeutic option for preventing EndMT. This study provides novel insights into the pathogenesis of PAH, revealing a potential therapeutic target for this rare disease.BMP9 inhibits IL-33 downstream signalingBMP9 protects from IL-33-induced EndMT

Circulating Biomarkers in Pulmonary Arterial Hypertension: An Update.

Pulmonary arterial hypertension (PAH) is a rare subtype of group 1 pulmonary hypertension (PH) diseases, characterized by high pulmonary artery pressure leading to right ventricular dysfunction and potential life-threatening consequences. PAH involves complex mechanisms: vasoconstriction, vascular remodeling, endothelial dysfunction, inflammation, oxidative stress, fibrosis, RV remodeling, cellular hypoxia, metabolic imbalance, and thrombosis. These mechanisms are mediated by several pathways, involving molecules like nitric oxide and prostacyclin. PAH diagnosis requires clinical evaluation and right heart catheterization, confirming a value of mPAP ≥ 20 mmHg at rest and often elevated pulmonary vascular resistance (PVR). Even if an early and accurate diagnosis is crucial, PAH still lacks effective biomarkers to assist in its diagnosis and prognosis. Biomarkers could contribute to arousing clinical suspicion and serve for prognosis prediction, risk stratification, and dynamic monitoring in patients with PAH. The aim of the present review is to report the main novelties on new possible biomarkers for the diagnosis, prognosis, and treatment monitoring of PAH.

Differential expression and analysis of extrachromosomal circular DNAs as serum biomarkers in pulmonary arterial hypertension

BackgroundExtrachromosomal circular DNAs (eccDNAs) have been reported to play a key role in the occurrence and development of various diseases. However, the characterization and role of eccDNAs in pulmonary arterial hypertension (PAH) remain unclear.MethodsIn the discovery cohort, we first explored eccDNA expression profiles by Circle-sequencing analysis. The candidate eccDNAs were validated by routine polymerase chain reaction (PCR), TOPO-TA cloning and Sanger sequencing. In the validation cohort, 30 patients with PAH and 10 healthy controls were recruited for qPCR amplification to detect the candidate eccDNAs. Datas at the baseline were collected, including clinical background, biochemical variables, echocardiography and hemodynamic factors. Receiver operating characteristic curve was used to investigate the diagnostic effect of the eccDNA.ResultsWe identified a total of 21,741 eccDNAs in plasma samples of 3 IPAH patients and 3 individuals in good health, and the expression frequency, GC content, length distribution, and genome distribution of the eccDNAs were thoroughly characterized and analyzed. In the validation cohort, 687 eccDNAs were differentially expressed in patients with IPAH compared with healthy controls (screening threshold: |FC|≥2 and P < 0.05). Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the specific eccDNAs in IPAH were significantly enriched in calcium channel activity, the mitogen-activated protein kinase pathway, and the wnt signaling pathway. Verification queue found that the expression of eccDNA-chr2:131208878–131,424,362 in PAH was considerably higher than that in healthy controls and exhibited a high level of accuracy in predicting PAH with a sensitivity of 86.67% and a specificity of 90%. Furthermore, correlation analysis disclosed a significant association between serum eccDNA-chr2:131208878–131,424,362 and mean pulmonary artery pressure (mPAP) (r = 0.396, P = 0.03), 6 min walking distance (6MWD) (r = -0.399, P = 0.029), N-terminal pro-B-type natriuretic peptide (NT-proBNP) (r = 0.685, P < 0.001) and cardiac index (CI) (r = − 0.419, P = 0.021).ConclusionsThis is the first study to identify and characterize eccDNAs in patients with PAH. We revealed that serum eccDNA-chr2:131208878–131,424,362 is significantly overexpressed and can be used in the diagnosis of PAH, indicating its potential as a novel non-invasive biomarker.

Identification of MACC1 as a potential biomarker for pulmonary arterial hypertension based on bioinformatics and machine learning

BackgroundPulmonary arterial hypertension (PAH) is a life-threatening disease characterized by abnormal early activation of pulmonary arterial smooth muscle cells (PASMCs), yet the underlying mechanisms remain to be elucidated. MethodsNormal and PAH gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database and analyzed using gene set enrichment analysis (GSEA) to uncover the underlying mechanisms. Weighted gene co-expression network analysis (WGCNA) and machine learning methods were deployed to further filter hub genes. A number of immune infiltration analysis methods were applied to explore the immune landscape of PAH. Enzyme-linked immunosorbent assay (ELISA) was employed to compare MACC1 levels between PAH and normal subjects. The important role of MACC1 in the progression of PAH was verified through Western blot and real-time qPCR, among others. Results39 up-regulated and 7 down-regulated genes were identified by ‘limma’ and ‘RRA’ packages. WGCNA and machine learning further narrowed down the list to 4 hub genes, with MACC1 showing strong diagnostic capacity. In vivo and in vitro experiments revealed that MACC1 was highsly associated with malignant features of PASMCs in PAH. ConclusionsThese findings suggest that targeting MACC1 may offer a promising therapeutic strategy for treating PAH, and further clinical studies are warranted to evaluate its efficacy.

The Potential of Circular RNAs as Biomarkers in Pulmonary Arterial Hypertension Related to Congenital Heart Disease

The Potential of Circular RNAs as Biomarkers in Pulmonary Arterial Hypertension Related to Congenital Heart Disease

Identification and validation of CCL5 as a key gene in HIV infection and pulmonary arterial hypertension.

The relationship between human immunodeficiency virus (HIV) infection and pulmonary arterial hypertension (PAH) has garnered significant scrutiny. Individuals with HIV infection have a higher risk of developing PAH. However, the specific mechanism of HIV-associated PAH remains unclear. Our study aims at investigating the shared biomarkers in HIV infection and PAH and predicting the potential therapeutic target for HIV-associated PAH. Data for HIV infection and PAH were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) analysis was performed to detect shared genes in HIV infection and PAH. Enrichment analysis was conducted to identify the function of common DEGs. Protein-protein interaction (PPI) analysis was used to detect key genes. These crucial genes were subsequently verified by RT-qPCR. Finally, candidate drugs were identified by using the Drug Signatures Database (DSigDB). Nineteen common DEGs were identified in HIV infection and PAH. Enrichment analysis exhibited that the functions of these genes were mainly enriched in inflammatory responses, mainly including cellular immunity and interaction between viral proteins and cytokines. By constructing PPI networks, we identified the key gene CC-type chemokine ligand 5 (CCL5), and we verified that CCL5 was highly expressed in hypoxia induced human pulmonary artery endothelial cells (hPAECs) and human pulmonary artery smooth muscle cells (hPASMCs). In addition, we predicted 10 potential drugs targeting CCL5 by Autodock Vina. This study revealed that CCL5 might be a common biomarker of HIV infection and PAH and provided a new therapeutic target for HIV-associated PAH. However, further clinical validation is still indispensable.

A comprehensive analysis of genes associated with hypoxia and cuproptosis in pulmonary arterial hypertension using machine learning methods and immune infiltration analysis: AHR is a key gene in the cuproptosis process.

Pulmonary arterial hypertension (PAH) is a serious condition characterized by elevated pulmonary artery pressure, leading to right heart failure and increased mortality. This study investigates the link between PAH and genes associated with hypoxia and cuproptosis. We utilized expression profiles and single-cell RNA-seq data of PAH from the GEO database and genecad. Genes related to cuproptosis and hypoxia were identified. After normalizing the data, differential gene expression was analyzed between PAH and control groups. We performed clustering analyses on cuproptosis-related genes and constructed a weighted gene co-expression network (WGCNA) to identify key genes linked to cuproptosis subtype scores. KEGG, GO, and DO enrichment analyses were conducted for hypoxia-related genes, and a protein-protein interaction (PPI) network was created using STRING. Immune cell composition differences were examined between groups. SingleR and Seurat were used for scRNA-seq data analysis, with PCA and t-SNE for dimensionality reduction. We analyzed hub gene expression across single-cell clusters and built a diagnostic model using LASSO and random forest, optimizing parameters with 10-fold cross-validation. A total of 113 combinations of 12 machine learning algorithms were employed to evaluate model accuracy. GSEA was utilized for pathway enrichment analysis of AHR and FAS, and a Nomogram was created to assess risk impact. We also analyzed the correlation between key genes and immune cell types using Spearman correlation. We identified several diagnostic genes for PAH linked to hypoxia and cuproptosis. PPI networks illustrated relationships among these hub genes, with immune infiltration analysis highlighting associations with monocytes, macrophages, and CD8 T cells. The genes AHR, FAS, and FGF2 emerged as key markers, forming a robust diagnostic model (NaiveBayes) with an AUC of 0.9. AHR, FAS, and FGF2 were identified as potential biomarkers for PAH, influencing cell proliferation and inflammatory responses, thereby offering new insights for PAH prevention and treatment.

Whole-genome microRNA sequencing analysis in patients with pulmonary hypertension.

Pulmonary hypertension (PH) is a pathological disorder with multiple clinical manifestations that lead to cardiovascular and respiratory diseases in most patients. Recent studies have revealed that microRNAs (miRNAs) play important roles as upstream signaling molecules in several diseases, including PH. However, miRNAs that can be used as diagnostic or prognostic biomarkers for PH have not been identified. Thus, in this study, peripheral blood samples obtained from patients with PH and healthy individuals were subjected to genome-wide miRNA sequencing and transcriptome analysis. We screened 136 differentially expressed miRNAs in patients with PH and verified that four differentially expressed miRNAs, namely, hsa-miR-1304-3p, hsa-miR-490-3p, hsa-miR-11400, and hsa-miR-31-5p, could be used as clinical diagnostic biomarkers for pulmonary arterial hypertension. Our findings provide a basis for further in-depth investigations of the specific mechanisms of miRNAs in PH.

RNA ve protein seviyelerinde temel biyobelirteçleri belirlemek için pulmoner arteriyel hipertansiyonun in silico analizi

Pulmonary arterial hypertension (PAH) is a chronic cardiopulmonary disorder marked by a raised hypertension in the pulmonary arteries. There is no remedy for PAH, existing medications can help reduce the disease’s progression. This research aimed to investigate potential protein and RNA biomarkers of PAH by bioinformatic analysis. Two PAH datasets accessed from the publicly available Gene Expression Omnibus (GEO) database were used to discover differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for common DEGs were conducted by the DAVID tool. Cytoscape was used to create the protein-protein interaction (PPI) and pick the top 10 hub genes. The transcription factors (TFs) and microRNAs (miRNAs) that target DEGs and hub genes were investigated using the JASPAR database. Potential therapeutics that target the top hub genes have been discovered. Ten hub genes were discovered to be linked to the pathogenesis of PAH (CCL5, TLR4, TLR1, SPP1, CYBB, HGF, IGF1, SELL, CD163, and POSTN). “Positive regulation of tumor necrosis factor biosynthetic process” and a “toll-like receptor signaling pathway” are the most enriched GO term and KEGG pathway, respectively. “hsa-mir-26b-5p, hsa-mir-146a-5p, hsa-mir-335-5p” and FOXC1, YY1, GATA2 are the top TFs targeting hub genes. 21 drugs targeting ten hub genes have been discovered. Our results would help to discover the pathogenesis of PAH and hub genes, miRNAs and 10 TFs that might serve as potential therapeutic targets at protein and RNA levels for PAH patients.

Kynurenine pathway metabolism evolves with development of preclinical and scleroderma-associated pulmonary arterial hypertension.

Understanding metabolic evolution underlying pulmonary arterial hypertension (PAH) development may clarify pathobiology and reveal disease-specific biomarkers. Patients with systemic sclerosis (SSc) are regularly surveilled for PAH, presenting an opportunity to examine metabolic change as disease develops in an at-risk cohort. We performed mass spectrometry-based metabolomics on longitudinal serum samples collected before and near SSc-PAH diagnosis, compared with time-matched SSc subjects without PAH, in a SSc surveillance cohort. We validated metabolic differences in a second cohort and determined metabolite-phenotype relationships. In parallel, we performed serial metabolomic and hemodynamic assessments as the disease developed in a preclinical model. For differentially expressed metabolites, we investigated corresponding gene expression in human and rodent PAH lungs. Kynurenine and its ratio to tryptophan (kyn/trp) increased over the surveillance period in patients with SSc who developed PAH. Higher kyn/trp measured two years before diagnostic right heart catheterization increased the odds of SSc-PAH diagnosis (OR 1.57, 95% CI 1.05-2.36, P = 0.028). The slope of kyn/trp rise during SSc surveillance predicted PAH development and mortality. In both clinical and experimental PAH, higher kynurenine pathway metabolites correlated with adverse pulmonary vascular and RV measurements. In human and rodent PAH lungs, expression of TDO2, which encodes tryptophan 2,3 dioxygenase (TDO), a protein that catalyzes tryptophan conversion to kynurenine, was significantly upregulated and tightly correlated with pulmonary hypertensive features. Upregulated kynurenine pathway metabolism occurs early in PAH, localizes to the lung, and may be modulated by TDO2. Kynurenine pathway metabolites may be candidate PAH biomarkers and TDO warrants exploration as a potential novel therapeutic target.NEW & NOTEWORTHY Our study shows an early increase in kynurenine pathway metabolism in at-risk subjects with systemic sclerosis who develop pulmonary arterial hypertension (PAH). We show that kynurenine pathway upregulation precedes clinical diagnosis and that this metabolic shift is associated with increased disease severity and shorter survival times. We also show that gene expression of TDO2, an enzyme that generates kynurenine from tryptophan, rises with PAH development.