EDEM3 Modulates Plasma Triglyceride Level through Its Regulation of LRP1 Expression

Identifying biomarkers of endoplasmic reticulum stress and analyzing immune cell infiltration in chronic obstructive pulmonary disease using machine learning

Background

Endoplasmic reticulum stress (ERS) is a crucial factor in the progression of chronic obstructive pulmonary disease (COPD). However, the key genes associated with COPD and immune cell infiltration remain to be elucidated. Therefore, this study aimed to identify biomarkers pertinent to the diagnosis of ERS in COPD and delve deeper into the association between pivotal genes and their possible interactions with immune cells.

Methods

We selected the genetic data of 189 samples from the Gene Expression Omnibus database, including 91 control and 98 COPD samples. First, we identified the differentially expressed genes between patients with COPD and controls and then screened the ERS genes associated with COPD. Second, 22 core ERS genes associated with COPD were screened using the Least Absolute Shrinkage and Selection Operator (LASSO) regression model and Support Vector Machine Recursive Feature Elimination (SVM-RFE), and the predictive effects of the screened core genes in COPD were evaluated. Third, we explored immune cell infiltration associated with COPD and conducted an in-depth analysis to explore the possible connections between the identified key genes and their related immune cells.

Results

A total of 66 differentially expressed endoplasmic reticulum stress-related genes (DE-ERGs) were identified in this study, among which 12 were upregulated and 54 were downregulated. The 22 key genes screened were as follows: AGR3, BCHE, CBY1, CHRM3, CYP1B1, DCSTAMP, DDHD1, DMPK, EDEM3, EDN1, FKBP10, HSPA2, KPNA2, LGALS3, MAOB, MMP9, MPO, MTTP, PIK3CA, PTGIS, PURA, and TMCC1. Their expression was significantly different between COPD and healthy samples, and the difference between the groups was significant. Receiver operating characteristic curve analysis revealed that CBY1 (area under the curve [AUC] = 0.800), BCHE (AUC = 0.773), EDEM3 (AUC = 0.768), FKBP10 (AUC = 0.760), MAOB (AUC = 0.736), and MMP9 (AUC = 0.729) showed a strong ability to distinguish COPD samples from normal samples. Immune cell infiltration results associated with the three key genes were also obtained.

Conclusion

The insights of our study have the potential to present new evidence for exploring emerging diagnostic signs of COPD while also contributing to a better understanding of its developmental mechanisms.

Potential drug targets for gastroesophageal reflux disease and Barrett's esophagus identified through Mendelian randomization analysis

Gastroesophageal reflux disease (GERD) is a prevalent chronic ailment, and present therapeutic approaches are not always effective. This study aimed to find new drug targets for GERD and Barrett's esophagus (BE). We obtained genetic instruments for GERD, BE, and 2004 plasma proteins from recently published genome-wide association studies (GWAS), and Mendelian randomization (MR) was employed to explore potential drug targets. We further winnowed down MR-prioritized proteins through replication, reverse causality testing, colocalization analysis, phenotype scanning, and Phenome-wide MR. Furthermore, we constructed a protein-protein interaction network, unveiling potential associations among candidate proteins. Simultaneously, we acquired mRNA expression quantitative trait loci (eQTL) data from another GWAS encompassing four different tissues to identify additional drug targets. Meanwhile, we searched drug databases to evaluate these targets. Under Bonferroni correction (P < 4.8 × 10-5), we identified 11 plasma proteins significantly associated with GERD. Among these, 7 are protective proteins (MSP, GPX1, ERBB3, BT3A3, ANTR2, CCM2, and DECR2), while 4 are detrimental proteins (TMEM106B, DUSP13, C1-INH, and LINGO1). Ultimately, C1-INH and DECR2 successfully passed the screening process and exhibited similar directional causal effects on BE. Further analysis of eQTLs highlighted 4 potential drug targets, including EDEM3, PBX3, MEIS1-AS3, and NME7. The search of drug databases further supported our conclusions. Our study indicated that the plasma proteins C1-INH and DECR2, along with 4 genes (EDEM3, PBX3, MEIS1-AS3, and NME7), may represent potential drug targets for GERD and BE, warranting further investigation.

Chromatin regulator SMARCAL1 modulates cellular lipid metabolism

Biallelic mutations of the chromatin regulator SMARCAL1 cause Schimke Immunoosseous Dysplasia (SIOD), characterized by severe growth defects and premature mortality. Atherosclerosis and hyperlipidemia are common among SIOD patients, yet their onset and progression are poorly understood. Using an integrative approach involving proteomics, mouse models, and population genetics, we investigated SMARCAL1's role. We found that SmarcAL1 interacts with angiopoietin-like 3 (Angptl3), a key regulator of lipoprotein metabolism. In vitro and in vivo analyses demonstrate SmarcAL1's vital role in maintaining cellular lipid homeostasis. The observed translocation of SmarcAL1 to cytoplasmic peroxisomes suggests a potential regulatory role in lipid metabolism through gene expression. SmarcAL1 gene inactivation reduces the expression of key genes in cellular lipid catabolism. Population genetics investigations highlight significant associations between SMARCAL1 genetic variations and body mass index, along with lipid-related traits. This study underscores SMARCAL1's pivotal role in cellular lipid metabolism, likely contributing to the observed lipid phenotypes in SIOD patients.

Genetic disruption of mammalian endoplasmic reticulum-associated protein degradation: Human phenotypes and animal and cellular disease models

Endoplasmic reticulum-associated protein degradation (ERAD) is a stringent quality control mechanism through which misfolded, unassembled and some native proteins are targeted for degradation to maintain appropriate cellular and organelle homeostasis. Several in vitro and in vivo ERAD-related studies have provided mechanistic insights into ERAD pathway activation and its consequent events; however, a majority of these have investigated the effect of ERAD substrates and their consequent diseases affecting the degradation process. In this review, we present all reported human single-gene disorders caused by genetic variation in genes that encode ERAD components rather than their substrates. Additionally, after extensive literature survey, we present various genetically manipulated higher cellular and mammalian animal models that lack specific components involved in various stages of the ERAD pathway.

The multifaceted roles of ER and Golgi in metabolic cardiomyopathy

Metabolic cardiomyopathy is a significant global financial and health challenge; however, pathophysiological mechanisms governing this entity remain poorly understood. Among the main features of metabolic cardiomyopathy, the changes to cellular lipid metabolism have been studied and targeted for the discovery of novel treatment strategies obtaining contrasting results. The endoplasmic reticulum (ER) and Golgi apparatus (GA) carry out protein modification, sorting, and secretion activities that are more commonly studied from the perspective of protein quality control; however, they also drive the maintenance of lipid homeostasis. In response to metabolic stress, ER and GA regulate the expression of genes involved in cardiac lipid biogenesis and participate in lipid droplet formation and degradation. Due to the varied roles these organelles play, this review will focus on recapitulating the alterations and crosstalk between ER, GA, and lipid metabolism in cardiac metabolic syndrome.

Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation

EDEM3 encodes a protein that converts Man8GlcNAc2 isomer B to Man7-5GlcNAc2. It is involved in the endoplasmic reticulum-associated degradation pathway, responsible for the recognition of misfolded proteins that will be targeted and translocated to the cytosol and degraded by the proteasome. In this study, through a combination of exome sequencing and gene matching, we have identified seven independent families with 11 individuals with bi-allelic protein-truncating variants and one individual with a compound heterozygous missense variant in EDEM3. The affected individuals present with an inherited congenital disorder of glycosylation (CDG) consisting of neurodevelopmental delay and variable facial dysmorphisms. Experiments in human fibroblast cell lines, human plasma, and mouse plasma and brain tissue demonstrated decreased trimming of Man8GlcNAc2 isomer B to Man7GlcNAc2, consistent with loss of EDEM3 enzymatic activity. In human cells, Man5GlcNAc2 to Man4GlcNAc2 conversion is also diminished with an increase of Glc1Man5GlcNAc2. Furthermore, analysis of the unfolded protein response showed a reduced increase in EIF2AK3 (PERK) expression upon stimulation with tunicamycin as compared to controls, suggesting an impaired unfolded protein response. The aberrant plasma N-glycan profile provides a quick, clinically available test for validating variants of uncertain significance that may be identified by molecular genetic testing. We propose to call this deficiency EDEM3-CDG.

Large-Scale Analysis of Apolipoprotein CIII Glycosylation by Ultrahigh Resolution Mass Spectrometry

Apolipoprotein-CIII (apo-CIII) is a glycoprotein involved in lipid metabolism and its levels are associated with cardiovascular disease risk. Apo-CIII sialylation is associated with improved plasma triglyceride levels and its glycosylation may have an effect on the clearance of triglyceride-rich lipoproteins by directing these particles to different metabolic pathways. Large-scale sample cohort studies are required to fully elucidate the role of apo-CIII glycosylation in lipid metabolism and associated cardiovascular disease. In this study, we revisited a high-throughput workflow for the analysis of intact apo-CIII by ultrahigh-resolution MALDI FT-ICR MS. The workflow includes a chemical oxidation step to reduce methionine oxidation heterogeneity and spectrum complexity. Sinapinic acid matrix was used to minimize the loss of sialic acids upon MALDI. MassyTools software was used to standardize and automate MS data processing and quality control. This method was applied on 771 plasma samples from individuals without diabetes allowing for an evaluation of the expression levels of apo-CIII glycoforms against a panel of lipid biomarkers demonstrating the validity of the method. Our study supports the hypothesis that triglyceride clearance may be regulated, or at least strongly influenced by apo-CIII sialylation. Interestingly, the association of apo-CIII glycoforms with triglyceride levels was found to be largely independent of body mass index. Due to its precision and throughput, the new workflow will allow studying the role of apo-CIII in the regulation of lipid metabolism in various disease settings.

The molecular mechanism of LRP1 in physiological vascular homeostasis and signal transduction pathways

Interactions between vascular smooth muscle cells (VSMCs), endothelial cells (ECs), pericytes (PCs) and macrophages (MФ), the major components of blood vessels, play a crucial role in maintaining vascular structural and functional homeostasis. Low-density lipoprotein (LDL) receptor-related protein-1 (LRP1), a transmembrane receptor protein belonging to the LDL receptor family, plays multifunctional roles in maintaining endocytosis, homeostasis, and signal transduction. Accumulating evidence suggests that LRP1 modulates vascular homeostasis mainly by regulating vasoactive substances and specific intracellular signaling pathways, including the plasminogen activator inhibitor 1 (PAI-1) signaling pathway, platelet-derived growth factor (PDGF) signaling pathway, transforming growth factor-β (TGF-β) signaling pathway and vascular endothelial growth factor (VEGF) signaling pathway. The aim of the present review is to focus on recent advances in the discovery and mechanism of vascular homeostasis regulated by LRP1-dependent signaling pathways. These recent discoveries expand our understanding of the mechanisms controlling LRP1 as a target for studies on vascular complications.