Altered Cellular Immunity and Differentially Expressed Immune-Related Genes in Patients With Systemic Sclerosis–Associated Pulmonary Arterial Hypertension

Abstract

Systemic sclerosis (SSc) is the most common connective tissue disease causing pulmonary hypertension (PAH). However, the cause and potential immune molecular events associated with PAH are still unclear. Therefore, it is particularly essential to analyze the changes in SSc-PAH–related immune cells and their immune-related genes. Three microarray datasets (GSE22356, GSE33463, and GSE19617) were obtained by the Gene Expression Omnibus (GEO). Compared with SSc, we found neutrophils have a statistically higher abundance, while T-cell CD4 naive and T-cell CD4 memory resting have a statistically lower abundance in peripheral blood mononuclear cells (PBMCs). Moreover, the results of Gene Set Enrichment Analysis (GSEA) showed there is a differential enrichment of multiple pathways between SSc and SSc-PAH. By combining differentiated expressed genes (DEGs) and immune-related genes (IRGs), fifteen IRGs were selected. In addition, we also analyzed the first five rich Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and the most abundant Gene Ontology (GO)-molecular functional terms. Furthermore, interleukin-7 receptor (IL-7R), tyrosine–protein kinase (LCK), histone deacetylase 1 (HDAC1), and epidermal growth factor receptor (EGFR) genes were identified as hub genes via protein–protein interaction (PPI) network analysis. The Comparative Toxic Genomics Database (CTD) analysis result showed that LCK, HDAC1, and EGFR have a higher score with SSc. Coexpression network analysis confirmed that IL-7R, LCK, and HDAC1 are key genes related to immune regulation in SSc without PAH and are involved in T-cell immune regulation. Subsequently, using GSE22356 and GSE33463 as the test sets and GSE19617 as the verification set, it was verified that the mRNA expression levels of the three central genes of SSc-PAH were significantly lower than those of the SSc without PAH samples. Consistent with previous predictions, the expressions of IL-7R, LCK, and HDAC1 are positively correlated with the numbers of T-cell CD4 naive and T-cell CD4 memory, while the expressions of IL-7R and LCK are negatively correlated with the numbers of neutrophils in the peripheral blood. Therefore, this evidence may suggest that these three immune-related genes: IL-7R, LCK, and HDAC1, may be highly related to the immunological changes in SSc-PAH. These three molecules can reduce T cells in SSc-PAH PBMCs through the regulation of T-cell activation, which suggests that these three molecules may be involved in the development of SSc-PAH. Meanwhile, the low expression of IL-7R, LCK, and HDAC1 detected in the peripheral blood of SSc may indicate the possibility of PAH and hopefully become a biomarker for the early detection of SSc-PAH. Finally, 49 target miRNAs of 3 specifically expressed hub genes were obtained, and 49 mRNA–miRNA pairs were identified, which provided directions for our further research.

Identification of lncRNA–miRNA–mRNA networks in circulating exosomes as potential biomarkers for systemic sclerosis

“…In chronic inflammatory or autoimmune diseases, the high expression of inflammatory cytokines drives neutrophils to form neutrophil extracellular traps (NETs). The number of neutrophils in peripheral blood may reflect the infiltration of neutrophils into tissues ( 64 ). Our results showed that ENST00000313807 and NON-HSAT194388.1 in plasma cirexos were positively correlated with the absolute value and percentage of neutrophils in serum.…”

“…However, hsa-miR-29a-3p in the plasma cirexos was negatively correlated with the percentage of neutrophils in serum. Tu et al ( 64 ) found that the number of neutrophils in peripheral blood of patients with SSc increased significantly. Wareing et al ( 65 ) observed that higher neutrophil counts predicted a worse ILD course and higher long-term mortality in patients with SSc-ILD.…”

Comprehensive analysis and validation of novel immune and vascular remodeling related genes signature associated with drug interactions in pulmonary arterial hypertension

“…Besides, the significant overexpression of RPS27A could enhance the chemoresistance of CML cells to imatinib by trans-activating STAT3 ( Wang et al, 2016 ). However, several studies have identified considerable upregulation of RPS27A expression in the left ventricular myocardium of rats suffering from end-stage PAH (MCT-induced PAH rat model), and abnormal expression of RPS27A has been detected in the peripheral blood of patients with connective tissue disease-associated PAH, and its key regulatory role in the pathogenesis of PAH has been identified ( Hołda et al, 2020 ; Tu et al, 2022 ). Altogether, these findings confirmed that the blood-derived hub transcriptomes are associated with infiltrations of immune cells, hypoxia, and metabolism (glycolysis and fatty acid), which in turn regulates the aberrant vascular remodeling in PAH.…”

Expression profiles of circRNAs and identification of hsa_circ_0007608 and hsa_circ_0064656 as potential biomarkers for COPD-PH patients

“…Bioinformatics tools has been widely applied in oncology to identify genetic changes and new potential biomarkers associated with various diseases [14][15][16] . Likewise, researchers have tried to apply bioinformtics analysis in the study of PH to to elucidate the potential functions of circRNAs related to PH, mostly based on databases and animal experiments [17][18][19][20][21][22][23][24][25][26] . However, few studies have utilized clinical samples with definite diagnosis of PH, and researches for PH in COPD are even fewer.…”