In Silico Approach to Identify the Relationships between COVID-19 and Coronary Artery Disease/Rheumatoid Arthritis

Global public has been threatened by the coronavirus disease 2019 (COVID-19) pandemic which led to nearly 15 million deaths around the world. People with complex and chronic diseases usually have more severe COVID-19 symptoms than the general population. Mounting evidence indicates individuals with coronary artery disease (CAD) and rheumatoid arthritis (RA) have worse COVID-19 outcomes yet the underlying mechanism still needs to be explored. The aim of our study is to reveal in silico evidence for the molecular mechanisms shared by COVID-19, CAD and RA pathogenesis which may aggravate the COVID-19 disease severity. Public datasets (GSE164805 and GSE23561) were downloaded from the Gene Expression Omnibus (GEO) database and analyzed for differential expression analysis (DEG). Identified differential expressed genes (DEGs) were further analyzed to find common DEGs, common pathways, hub genes, transcription factors (TFs) and microRNAs (miRNAs). Our study identified common hub genes, miRNAs, TFs and shared mechanisms in both mild and severe COVID-19-CAD patients and mild and severe COVID-19-RA patients. We also uncovered that mild and severe forms of COVID-19 differ in potential biomarkers, mechanisms, miRNAs and TFs in both CAD and RA patients. Our study is the first study investigating the potential shared mechanisms, biomarkers, TFs and miRNAs between COVID-19 and CAD patients and COVID-19 and RA patients. Our results could shed on light to the patient management strategies with CAD with COVID-19 and patients with RA with COVID-19 based on the severity of the COVID-19 disease. © 2023 by the authors. Submitted for possible open access publication under the terms and conditions of the Creative Commons Attribution (CC BY NC) license (https://creativecommons.org/licenses/by-nc/4.0/)

Variants discovery in the LPL and CETP genes and their associations with plasma lipid and apolipoprotein levels

Plasma lipid and lipoprotein levels are known to be under strong genetic control and major risk factors for cardiovascular disease (CVD). Identifying novel genetic variants associated with plasma lipoprotein-lipid concentration are of a considerable public health importance because this knowledge may facilitate the design of genetic markers for risk assessment, diagnosis and prognosis of CVD. In this study, we have comprehensively investigated the associations of both common and uncommon/rare variants in two major lipid genes, lipoprotein lipase (LPL) and cholesteryl ester transfer protein (CETP), in relation to plasma lipoprotein-lipid levels in U.S. non-Hispanic whites (NHWs) and African blacks. We resequenced the entire LPL and CETP genes plus their flanking regions in 190 individuals presenting extreme high-density lipoprotein cholesterol (HDL-C)/triglyceride (TG) levels selected from two study samples of 623 NHWs and 788 African blacks. We identified a total of 371 and 279 sequence variants in LPL and CETP genes, respectively, including several novel rare and population-specific variants. Following the discovery stage of resequencing, selected common tagSNPs and uncommon/rare variants from each gene were genotyped in the entire samples of 623 NHWs and 788 African blacks. A total of 171 LPL and 184 CETP variants passed the quality control and were analyzed for their associations with plasma lipoprotein-lipid levels by using single-site, haplotype and rare variant association analyses. Multiple common variants in the two genes demonstrated significant effects on plasma lipoprotein-lipids levels in both populations. Two putative functional SNPs, LPL/ rs13702 (P=0.006 in NHWs; P=0.01 in African blacks) and CETP/rs183130 (P=1.91E-04 in NHWs; P=2.25E-06 in African blacks) exhibited strongest associations with HDL-C in both samples. Rare variant analyses indicated that CETP gene harbors rare variants that contribute to plasma lipoprotein-lipid levels in both ethnic groups. However, rare variants in LPL revealed associations with plasma lipoprotein-lipid levels only in African blacks. Our data reaffirm the important role of LPL and CETP genetic variation has in affecting plasma lipoprotein-lipid levels in the general population

Lipoprotein lipase gene sequencing and plasma lipid profile

In the United States, coronary heart disease (CHD) is the most common cause of death and number one killer of American males and females. Several epidemiological studies have identified risk factors for CHD, like low high-density lipoprotein cholesterol (HDL-C), elevated total cholesterol and low-density lipoprotein (LDL) cholesterol, and high triglycerides (TGs), but underlying genetic variations that cause predisposition to these traits still remain unclear. Lipoprotein lipase (LPL) is one of the major genes involved in lipid metabolism and its gene sequence variation has already been reported to be associated with the risk of CHD and risk of other complex diseases like dyslipidemia, type 2 diabetes, essential hypertension, and Alzheimer's disease. Unraveling the unknown genetic variation in the LPL gene in relation to HDL-C and correlated lipid traits is critically important for public health because identification of genetic markers may lead to promising future public health interventions, like prognostic tools and therapeutic approaches to alleviate the burden of CHD in the U.S. In this study, we investigated the role of common and rare variation in LPL by resequencing individuals having extremely low (n=48) and high (n=47) HDL-C levels selected from a population-based non-Hispanic white (NHW) sample of 623 individuals. A total of 179 variants were identified in 95 individuals by resequencing the entire LPL gene, including 91 uncommon or rare variants [minor allele frequency (MAF) <0.05)] and 88 common variants (MAF ≥ 0.05). Of the 91 relatively uncommon or rare variants, 21 were present only in the low-HDL group and 25 were present only in the high HDL-C group. Overall, the prevalence of uncommon or rare variants was higher in the high HDL-C than the low HDL-C group. Thirty two of the 88 common variants demonstrated significant association (P-value <0.05) between the high and low HDL-C groups. We also examined 12 common variants (MAF ≥ 0.05) in the total NHW sample and identified 7 variants to be significantly associated with lipid levels. In conclusion, our comprehensive resequencing of the LPL gene confirms that both common and rare variants in this gene are associated with interindividual variation in plasma lipid profile

Hsa-miR-584-5p as a novel candidate biomarker in Turkish men with severe coronary artery disease

Coronary artery disease (CAD) is still the preliminary cause of mortality and morbidity in the developed world. Identification of novel predictive and therapeutic biomarkers is crucial for accurate diagnosis, prognosis and treatment of the CAD. The aim of this study was to detect novel candidate miRNA biomarker that may be used in the management of CAD. We performed miRNA profiling in whole blood samples of angiographically confirmed Turkish men with CAD and non-CAD controls with insignificant coronary stenosis. Validation of microarray results was performed by qRT-PCR in a larger cohort of 62 samples. We subsequently assessed the diagnostic value of the miRNA and correlations of miRNA with clinical parameters. miRNA-target identification and network analyses were conducted by Ingenuity Pathway Analysis (IPA) software. Hsa-miR-584-5p was one of the top significantly dysregulated miRNA observed in miRNA microarray. Men-specific down-regulation (p = 0.040) of hsa-miR-584-5p was confirmed by qRT-PCR. ROC curve analysis highlighted the potential diagnostic value of hsa-miR-584-5p with a power area under the curve (AUC) of 0.714 and 0.643 in men and in total sample, respectively. The expression levels of hsa-miR-584-5p showed inverse correlation with stenosis and Gensini scores. IPA revealed CDH13 as the only CAD related predicted target for the miRNA with biological evidence of its involvement in CAD. This study suggests that hsa-miR-584-5p, known to be tumor suppressor miRNA, as a candidate biomarker for CAD and highlighted its putative role in the CAD pathogenesis. The validation of results in larger samples incorporating functional studies warrant further research

In silico identification of putative roles of food-derived xeno-mirs on diet-associated cancer

Aim: Dietary miRNAs in foods were recently suggested to be absorbed into the human circulation and engage in human gene regulation. This started a debate on their possible impacts on human diseases which need further investigation. In this study, we aimed to identify the putative functions and possible implications of selected Xeno-miRs in human diseases by using bioinformatic tools. Methods: Seventy-five human absorbable Xeno-miR candidates were selected from literature and narrowed down the list to miRNAs that share sequence homologies with human miRNAs. Sixteen distinct Xeno-miRs of animal species (cow, pig, chicken) were identified to have homologs in human and they were subsequently analyzed with target prediction, functional and pathway analysis tools. Results and Conclusion: Thirteen human genes were common targets of the miRNA sets grouped by species and shown evidence of associations with various cancer categories, specifically in large intestine adenocarcinoma by Ingenuity Pathway Analysis. miRNA functional enrichment analyses also highlighted the putative involvements of the dietary miRNAs in cancer pathways. Our effort provides ?in silico? evidence for implications of animal-derived dietary miRNAs in cancer-associated pathways, and this shed on light the necessities of future translational research design to investigate the roles of dietary Xeno-miRs in cancer pathophysiology and nutrition-based interventions towards cancer management

Hsa-miR-584-5p as a novel candidate biomarker in Turkish men with severe coronary artery disease

Coronary artery disease (CAD) is still the preliminary cause of mortality and morbidity in the developed world. Identification of novel predictive and therapeutic biomarkers is crucial for accurate diagnosis, prognosis and treatment of the CAD. The aim of this study was to detect novel candidate miRNA biomarker that may be used in the management of CAD. We performed miRNA profiling in whole blood samples of angiographically confirmed Turkish men with CAD and non-CAD controls with insignificant coronary stenosis. Validation of microarray results was performed by qRT-PCR in a larger cohort of 62 samples. We subsequently assessed the diagnostic value of the miRNA and correlations of miRNA with clinical parameters. miRNA-target identification and network analyses were conducted by Ingenuity Pathway Analysis (IPA) software. Hsa-miR-584-5p was one of the top significantly dysregulated miRNA observed in miRNA microarray. Men-specific down-regulation (p = 0.040) of hsa-miR-584-5p was confirmed by qRT-PCR. ROC curve analysis highlighted the potential diagnostic value of hsa-miR-584-5p with a power area under the curve (AUC) of 0.714 and 0.643 in men and in total sample, respectively. The expression levels of hsa-miR-584-5p showed inverse correlation with stenosis and Gensini scores. IPA revealed CDH13 as the only CAD related predicted target for the miRNA with biological evidence of its involvement in CAD. This study suggests that hsa-miR-584-5p, known to be tumor suppressor miRNA, as a candidate biomarker for CAD and highlighted its putative role in the CAD pathogenesis. The validation of results in larger samples incorporating functional studies warrant further research

TMCO1 Gen Sekans Varyanlatlarının Fonksiyonel Özelliklerinin In Silico Analizlerlerle Değerlendirilmesi

Transmembrane and Coiled-Coil Domains 1 (TMCO1) protein is encoded by TMCO1 gene consists of 7 exons. Previous studies have identified multiple TMCO1 variants in patients with cerebro-facio-thoracic dysplasia (CFTD) and TMCO1 locus was also shown to be associated with primary open angle glaucoma (POAG). However, there are limited number of research exist reporting associations of the TMCO1 gene sequence variants and majority of the findings affirm the pathogenicity of the nonsense and frameshift TMCO1 variants and their associations with clinical phenotypes. Thus functional properties of the single nucleotide variants causing amino acid changes in the TMCO1 are yet to be comprehensively elucidated. In this study, we evaluated the effects of amino acid substitutions on protein structure, identified their putative roles in post-translational modifications (PTM) and in regulatory mechanism for TMCO1 protein. We classified 41 missense variants as pathogenic based on combined scores of common in silico tools (SIFT, MutationTaster2, Polyphen2). Of these 41 variants, four (p.K211Q, p.K105E, p.S235F, p.K237R) were identified to be located in PTMs and regulatory protein binding sites; thus they were proposed to be putative functional variants. Moreover, rs1387528611 (p.Lys128Gln) had also strong evidence (RegulomeDB score=2b) for its possible regulatory function. The results of our in silico analyses highlight the functional importance of the missense TMCO1 variants that may contribute to the TMCO1-associated disease phenotypes and further in vivo evaluation yet to be needed to uncover their role in human diseases