Gene Variation of Endoplasmic Reticulum Aminopeptidases 1 and 2, and Risk of Blood Pressure Progression and Incident Hypertension among 17,255 Initially Healthy Women

Identification of biomarkers, pathways, and potential therapeutic targets for heart failure using next-generation sequencing data and bioinformatics analysis

BACKGROUND

Heart failure (HF) is the most common cardiovascular diseases and the leading cause of cardiovascular diseases related deaths. Increasing molecular targets have been discovered for HF prognosis and therapy. However, there is still an urgent need to identify novel biomarkers. Therefore, we evaluated biomarkers that might aid the diagnosis and treatment of HF.

METHODS

We searched next-generation sequencing (NGS) dataset (GSE161472) and identified differentially expressed genes (DEGs) by comparing 47 HF samples and 37 normal control samples using limma in R package. Gene ontology (GO) and pathway enrichment analyses of the DEGs were performed using the g: Profiler database. The protein-protein interaction (PPI) network was plotted with Human Integrated Protein-Protein Interaction rEference (HiPPIE) and visualized using Cytoscape. Module analysis of the PPI network was done using PEWCC1. Then, miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed by Cytoscape software. Finally, we performed receiver operating characteristic (ROC) curve analysis to predict the diagnostic effectiveness of the hub genes.

RESULTS

A total of 930 DEGs, 464 upregulated genes and 466 downregulated genes, were identified in HF. GO and REACTOME pathway enrichment results showed that DEGs mainly enriched in localization, small molecule metabolic process, SARS-CoV infections, and the citric acid tricarboxylic acid (TCA) cycle and respiratory electron transport. After combining the results of the PPI network miRNA-hub gene regulatory network and TF-hub gene regulatory network, 10 hub genes were selected, including heat shock protein 90 alpha family class A member 1 (HSP90AA1), arrestin beta 2 (ARRB2), myosin heavy chain 9 (MYH9), heat shock protein 90 alpha family class B member 1 (HSP90AB1), filamin A (FLNA), epidermal growth factor receptor (EGFR), phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), cullin 4A (CUL4A), YEATS domain containing 4 (YEATS4), and lysine acetyltransferase 2B (KAT2B).

CONCLUSIONS

This discovery-driven study might be useful to provide a novel insight into the diagnosis and treatment of HF. However, more experiments are needed in the future to investigate the functional roles of these genes in HF.

ERAP1 and ERAP2 Enzymes: A Protective Shield for RAS against COVID-19?

Patients with coronavirus disease 2019 (COVID-19) have a wide variety of clinical outcomes ranging from asymptomatic to severe respiratory syndrome that can progress to life-threatening lung lesions. The identification of prognostic factors can help to improve the risk stratification of patients by promptly defining for each the most effective therapy to resolve the disease. The etiological agent causing COVID-19 is a new coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that enters cells via the ACE2 receptor. SARS-CoV-2 infection causes a reduction in ACE2 levels, leading to an imbalance in the renin-angiotensin system (RAS), and consequently, in blood pressure and systemic vascular resistance. ERAP1 and ERAP2 are two RAS regulators and key components of MHC class I antigen processing. Their polymorphisms have been associated with autoimmune and inflammatory conditions, hypertension, and cancer. Based on their involvement in the RAS, we believe that the dysfunctional status of ERAP1 and ERAP2 enzymes may exacerbate the effect of SARS-CoV-2 infection, aggravating the symptomatology and clinical outcome of the disease. In this review, we discuss this hypothesis.

Impact of Natural Occurring ERAP1 Single Nucleotide Polymorphisms within miRNA-Binding Sites on HCMV Infection

Human cytomegalovirus (HCMV) is a β-herpesvirus that causes serious problems in people with a compromised immune system, whereas it coexists asymptomatically within the host with a healthy immune system. Like other viruses, HCMV has adopted multiples strategies to manipulate the host’s immune responses. Among them, expression of viral microRNAs (miRNAs) is one of the most intriguing. HCMV miR-UL112-5p and miR-US4-1 have been found to contribute to immune evasion by targeting the endoplasmic reticulum aminopeptidase 1 (ERAP1), a highly polymorphic key component of antigen processing. The current incomplete picture on the interplay between viral miRNAs and host immunity implies the need to better characterize the host genetic determinants. Naturally occurring single nucleotide polymorphisms (SNPs) within the miRNA binding sites of target genes may affect miRNA–target interactions. In this review, we focus on the relevance of 3′ untranslated region (3′UTR) ERAP1 SNPs within miRNA binding sites in modulating miRNA–mRNA interactions and the possible consequent individual susceptibility to HCMV infection. Moreover, we performed an in silico analysis using different bioinformatic algorithms to predict ERAP1 variants with a putative powerful biological function. This evidence provides a basis to deepen the knowledge on how 3′UTR ERAP1 variants may alter the mechanism of action of HCMV miRNAs, in order to develop targeted antiviral therapies.

Aminopeptidases in Cardiovascular and Renal Function. Role as Predictive Renal Injury Biomarkers

Aminopeptidases (APs) are metalloenzymes that hydrolyze peptides and polypeptides by scission of the N-terminus amino acid and that also participate in the intracellular final digestion of proteins. APs play an important role in protein maturation, signal transduction, and cell-cycle control, among other processes. These enzymes are especially relevant in the control of cardiovascular and renal functions. APs participate in the regulation of the systemic and local renin-angiotensin system and also modulate the activity of neuropeptides, kinins, immunomodulatory peptides, and cytokines, even contributing to cholesterol uptake and angiogenesis. This review focuses on the role of four key APs, aspartyl-, alanyl-, glutamyl-, and leucyl-cystinyl-aminopeptidases, in the control of blood pressure (BP) and renal function and on their association with different cardiovascular and renal diseases. In this context, the effects of AP inhibitors are analyzed as therapeutic tools for BP control and renal diseases. Their role as urinary biomarkers of renal injury is also explored. The enzymatic activities of urinary APs, which act as hydrolyzing peptides on the luminal surface of the renal tubule, have emerged as early predictive renal injury biomarkers in both acute and chronic renal nephropathies, including those induced by nephrotoxic agents, obesity, hypertension, or diabetes. Hence, the analysis of urinary AP appears to be a promising diagnostic and prognostic approach to renal disease in both research and clinical settings.

The roles of ERAP1 and ERAP2 in autoimmunity and cancer immunity: New insights and perspective

Autoimmunity and cancer affect millions worldwide and both, in principal, result from dysregulated immune responses. There are many well-known molecules involved in immunological process playing as a double-edged sword, by which associating autoimmune diseases and cancer. In this regard, Endoplasmic reticulum aminopeptidases (ERAP) 1, which belongs to the M1 family of aminopeptidases, plays a central role as a "molecular ruler", proteolyzing of N-terminal of the antigenic peptides before their loading onto HLA-I molecules for antigen presentation in the Endoplasmic Reticulum (ER). Several genome-wide association studies (GWAS) highlighted the significance of ERAP1 and ERAP2 in autoimmune diseases, including Ankylosing spondylitis, Psoriasis, Bechet's disease, and Birdshot chorioretinopathy, as well as in cancers. The expression of ERAP1/2 is mostly altered in different cancers compared to normal cells, but how this affects anti-cancer immune responses and cancer growth has been little explored. Recent studies on the immunological outcomes and the catalytic functions of ERAP1 and ERAP2 have provided a better understanding of their potential pathogenetic role in autoimmunity and cancer. In this review, we summarize the role of ERAP1 and ERAP2 in the autoimmune diseases and cancer immunity based on the recent advances in GWAS studies.

Ankylosing Spondylitis: A Trade Off of HLA-B27, ERAP, and Pathogen Interconnections? Focus on Sardinia

The frequency of HLA-B27 in patients with Ankylosing Spondylitis (AS) is over 85%. There are more than 170 recognized HLA-B27 alleles but the majority of them is not sufficiently represented for genetic association studies. So far only two alleles, the HLA-B^*2706 in Asia and the HLA-B^*2709 in Sardinia, have not been found to be associated with AS. The highly homogenous genetic structure of the Sardinian population has favored the search of relevant variants for disease-association studies. Moreover, malaria, once endemic in the island, has been shown to have contributed to shape the native population genome affecting the relative allele frequency of relevant genes. In Sardinia, the prevalence of HLA-B^*2709, which differs from the strongly AS-associated B^*2705 prototype for one amino acid (His/Asp116) in the F pocket of the peptide binding groove, is around 20% of all HLA-B27 alleles. We have previously hypothesized that malaria could have contributed to the establishment of this allele in Sardinia. Based on our recent findings, in this perspective article we speculate that the Endoplasmic Reticulum Amino Peptidases, ERAP1 and 2, associated with AS and involved in antigen presentation, underwent co-selection by malaria. These genes, besides shaping the immunopeptidome of HLA-class I molecules, have other biological functions that could also be involved in the immunosurveillance against malaria.

Intracellular antigen processing by ERAP2: Molecular mechanism and roles in health and disease

Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) is an intracellular enzyme localized in the ER that has been shown to play roles in the generation of peptides that serve as ligands for MHC class I (MHC-1) molecules. Although ERAP2 has been primarily described as an accessory and complementary enzyme to the homologous ERAP1, several lines of evidence during the last few years suggest that it can play distinct and important roles in processing antigenic peptides and influencing cellular cytotoxic immune responses. Such emerging evidence has been shaping ERAP2 as a potentially tractable target for regulating select autoimmune and anti-cancer responses for therapeutic purposes. Here, we review the state-of-the-art knowledge on the role of ERAP2 in antigen processing, its structure and molecular mechanism, influence on shaping MHC-I-bound immunopeptidomes and its involvement in disease pathogenesis.

How ERAP1 and ERAP2 Shape the Peptidomes of Disease-Associated MHC-I Proteins

Four inflammatory diseases are strongly associated with Major Histocompatibility Complex class I (MHC-I) molecules: birdshot chorioretinopathy (HLA-A^*29:02), ankylosing spondylitis (HLA-B^*27), Behçet's disease (HLA-B^*51), and psoriasis (HLA-C^*06:02). The endoplasmic reticulum aminopeptidases (ERAP) 1 and 2 are also risk factors for these diseases. Since both enzymes are involved in the final processing steps of MHC-I ligands it is reasonable to assume that MHC-I-bound peptides play a significant pathogenetic role. This review will mainly focus on recent studies concerning the effects of ERAP1 and ERAP2 polymorphism and expression on shaping the peptidome of disease-associated MHC-I molecules in live cells. These studies will be discussed in the context of the distinct mechanisms and substrate preferences of both enzymes, their different patterns of genetic association with various diseases, the role of polymorphisms determining changes in enzymatic activity or expression levels, and the distinct peptidomes of disease-associated MHC-I allotypes. ERAP1 and ERAP2 polymorphism and expression induce significant changes in multiple MHC-I-bound peptidomes. These changes are MHC allotype-specific and, without excluding a degree of functional inter-dependence between both enzymes, reflect largely separate roles in their processing of MHC-I ligands. The studies reviewed here provide a molecular basis for the distinct patterns of genetic association of ERAP1 and ERAP2 with disease and for the pathogenetic role of peptides. The allotype-dependent alterations induced on distinct peptidomes may explain that the joint association of both enzymes and unrelated MHC-I alleles influence different pathological outcomes.