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Ganekal P, Vastrad B, Vastrad C, Kotrashetti S. Identification of biomarkers, pathways, and potential therapeutic targets for heart failure using next-generation sequencing data and bioinformatics analysis. Ther Adv Cardiovasc Dis 2023; 17:17539447231168471. [PMID: 37092838 PMCID: PMC10134165 DOI: 10.1177/17539447231168471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
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.
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Affiliation(s)
- Prashanth Ganekal
- Department of General Medicine, Basaveshwara Medical College, Chitradurga, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy, Gadag, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, #253, Bharthinagar, Dharwad 580001, India
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Philippe R, Mignen O. Measuring Calumenin Impact on ER-Calcium Depletion Using Transient Calumenin Overexpression and Silencing. Methods Mol Biol 2019; 1929:539-550. [PMID: 30710295 DOI: 10.1007/978-1-4939-9030-6_33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Calumenin is a secretory pathway protein regulating different endoplasmic reticulum (ER) proteins such as the sarco-endoplasmic reticulum calcium ATPase (SERCA) pumps. Combined with its diverse cellular distribution, its calcium-binding ability, and its interaction with proteins involved in calcium signaling, it is easy to speculate on future description of important roles of calumenin in calcium homeostasis in many cell types, as it was initially observed in muscle cells. In this chapter, we describe basic techniques to modulate calumenin expression and detect its impact on ER calcium content using classic transfection and Western blot techniques, as well as ER calcium measurement using microplate reader.
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Affiliation(s)
- Réginald Philippe
- Institut National de la Santé et de la Recherche Médicale, U1151, Paris, France
| | - Olivier Mignen
- Laboratoire Canalopathies & Signalisation Calcique, Inserm U1227, Université de Bretagne Occidentale (UBO), Brest, France.
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Tzveova R, Dimitrova-Karamfilova A, Saraeva R, Solarova T, Naydenova G, Petrova I, Hristova N, Popov I, Nachev G, Mitev V, Kaneva R. Estimation and validation of acenocoumarol dosing algorithms in Bulgarian patients with cardiovascular diseases. Per Med 2015; 12:209-220. [PMID: 29771648 DOI: 10.2217/pme.14.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim & Methods: A total of 169 Bulgarian patients were genotyped for CYP2C9*2,*3, VKORC1-1639G>A and VKORC11173C>T. The effect of genetic and nongenetic factors on acenocoumarol dose variability was tested in a derivation cohort of patients and the obtained algorithm was validated in a test cohort. RESULTS & DISCUSSION It was found that VKORC-1639G>A (25.5%), CYP2C9*2 (7.8%), CYP2C9*3 (6.1%), age (13.6%) and diagnosis (6.0%) significantly affected acenocoumarol dose variability in the derivation cohort. These factors with additional factors, such as sex (0.1%, p = 0.76), weight (2.6%, p = 0.14) and amiodarone use (3.0%, p = 0.059) accounted for 46.5% and 23.0% of the dose variability for genetic and clinical models, respectively. CONCLUSION Based on the results of this investigation, validated clinical and pharmacogenetic algorithms for the prediction of a stable anticoagulant dose were developed, specifically designed for the Bulgarian population.
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Affiliation(s)
- Reni Tzveova
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Antoaneta Dimitrova-Karamfilova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Radoslava Saraeva
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Tanya Solarova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Galya Naydenova
- Second Department of Cardiology, University NationalMulti-profile Active Treatment Hospital "Dr. G. Stansky"- Pleven, 8A Georgi Kochev str., Pleven 5800, Bulgaria
| | - Irina Petrova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Nataliya Hristova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Ivan Popov
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Gencho Nachev
- Department of Cardiac Surgery, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
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Jover E, Marín F, Quintana M, Pérez-Andreu J, Hurtado JA, Rodríguez C, Martínez-González J, González-Conejero R, Valdés M, Hernández-Romero D. CALU polymorphism A29809G affects calumenin availability involving vascular calcification. J Mol Cell Cardiol 2015; 82:218-27. [PMID: 25823396 DOI: 10.1016/j.yjmcc.2015.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/09/2015] [Accepted: 03/24/2015] [Indexed: 01/07/2023]
Abstract
Calumenin inhibits gamma-carboxylation of matrix-Gla-protein preventing BMP2-dependent calcification. Our aim was to explore the clinical relevance and functionality of the CALU polymorphism rs1043550, and the relationship of calumenin time-dependent expression profile with the active calcification of human vascular smooth muscle cells (hVSMC). Coronary artery calcium score and lesion severity were assessed by cardiac computed tomography in 139 consecutive low-risk patients genotyped for rs1043550. Polymorphic (G) allele carriage was associated with lower calcium (OR: 6.19, p=0.042). Calcified arteries from CALU 'A' allele carriers undergoing cardiovascular surgery exhibited higher residual calcification, higher calumenin immunostaining and lower matrix-Gla-protein, contrary to 'G' allele carriers. In a luciferase reporter system in vascular cells, polymorphic 'G' allele reduced the mRNA stability by 30% (p < 0.05). Osteogenic high-phosphate media induced active differentiation of hVSMC onto functional osteoblast-like cells as demonstrated by extracellular matrix mineralization and osteoblast markers expression. Calumenin was early over-expressed at day 3 (p < 0.05), but decreased thereafter (mRNA and protein) with implications on gamma-carboxylation system. Calumenin was found released and co-localizing with extracellular matrix calcifications. The CALU polymorphism rs1043550 affects mRNA stability and tissue availability of calumenin thus supporting the protective clinical significance. Calumenin shows a time-dependent profile during induced calcification. These data demonstrate a novel association of vascular calcification with the VSMC phenotypic transition into osteoblast-like cells. Moreover, hyperphosphatemic stimuli render calumenin accumulation in the mineralized extracellular matrix.
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MESH Headings
- Alleles
- Calcium/metabolism
- Calcium-Binding Proteins/genetics
- Calcium-Binding Proteins/metabolism
- Cell Culture Techniques
- Cell Differentiation
- Cells, Cultured
- Coronary Vessels/metabolism
- Coronary Vessels/pathology
- Extracellular Matrix/metabolism
- Extracellular Matrix Proteins/metabolism
- Humans
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/cytology
- Myocytes, Smooth Muscle/metabolism
- Osteoblasts/cytology
- Osteoblasts/metabolism
- Polymorphism, Single Nucleotide
- RNA Stability/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Vascular Calcification/genetics
- Vascular Calcification/metabolism
- Matrix Gla Protein
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Affiliation(s)
- Eva Jover
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Francisco Marín
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain.
| | - Míriam Quintana
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Joaquín Pérez-Andreu
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - José Antonio Hurtado
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Cristina Rodríguez
- Centro de Investigación Cardiovascular, CSIC-ICCC, Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - José Martínez-González
- Centro de Investigación Cardiovascular, CSIC-ICCC, Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | | | - Mariano Valdés
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Diana Hernández-Romero
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
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Daskalopoulos EP. CALibrating the CALumenin gene: New insights in overcoming the vascular CALcification CALamity? J Mol Cell Cardiol 2015; 84:81-3. [PMID: 25912188 DOI: 10.1016/j.yjmcc.2015.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 11/13/2022]
Affiliation(s)
- Evangelos P Daskalopoulos
- Pôle de Recherche Cardiovasculaire (CARD), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain (UCL), Brussels, Belgium; Cardiovascular Research (Care) Institute, Athens & Ioannina, Greece.
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Ongoing treatment with non-steroidal anti-inflammatory drugs at time of admission is associated with poorer prognosis in patients with first-time acute myocardial infarction. Int J Cardiol 2012; 168:832-7. [PMID: 23117013 DOI: 10.1016/j.ijcard.2012.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 09/21/2012] [Accepted: 10/07/2012] [Indexed: 11/24/2022]
Abstract
BACKGROUND Use of non-steroidal anti-inflammatory drugs (NSAIDs) has been associated with increased cardiovascular morbidity and mortality. The purpose of this study was to examine the effect of ongoing NSAID treatment at time of admission for myocardial infarction (MI) on prognosis. METHODS All patients admitted with first-time MI in 1997-2006 were included by use of individual-level linkage of nationwide registries. By claimed prescription of NSAIDs, availability of tablets was estimated within 14 days prior to inclusion and defined ongoing use. Risk of death within 30 days and risk of death or MI within 1 year was analyzed by logistic regression and Cox proportional-hazard models, respectively. RESULTS A total of 97,458 patients were included (mean age 69.9 [SD 13.2] years and 62% males); the 30 day and 1 year mortality rates were 18.1% and 27.7%, respectively. Ongoing NSAID treatment was identified in 12,156 (12.5%) patients and 30-day mortality was significantly increased in patients receiving rofecoxib (odds ratio [OR] 1.43; 95% confidence interval [CI] 1.22-1.68) and celecoxib (OR 1.23; CI 1.03-1.47) relative to no use of NSAIDs. Correspondingly, the 1-year rate of death or recurrent MI was significantly increased in patients receiving rofecoxib (hazard ratio [HR] 1.15; CI 1.04-1.27), celecoxib (HR 1.13; CI 1.01-1.26), diclofenac (HR 1.12; CI 1.04-1.20) or any NSAID use (HR 1.05; CI 1.02-1.09). No association was found for naproxen or ibuprofen. CONCLUSION Ongoing treatment with NSAIDs and in particular the cyclooxygenase-2-selective inhibitors rofecoxib, celecoxib, and diclofenac is associated with worsened prognosis in patients admitted with first-time MI.
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Tavridou A, Petridis I, Vasileiadis M, Ragia G, Heliopoulos I, Vargemezis V, Manolopoulos VG. Association of VKORC1 -1639 G>A polymorphism with carotid intima-media thickness in type 2 diabetes mellitus. Diabetes Res Clin Pract 2011; 94:236-41. [PMID: 21767890 DOI: 10.1016/j.diabres.2011.06.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 06/16/2011] [Accepted: 06/22/2011] [Indexed: 10/17/2022]
Abstract
AIMS Media calcification is a predictor of cardiovascular mortality in type 2 diabetes mellitus (T2DM). Undercarboxylation of some vitamin K-dependent proteins, due to genetic polymorphisms of VKORC1, can lead to calcification. We examined a potential association between VKORC1 -1639 G>A polymorphism and T2DM and, also, the association of this polymorphism with carotid intima-media thickness (cIMT). METHODS VKORC1 -1639 G>A polymorphism was determined in 299 T2DM patients and 328 controls of Caucasian origin using PCR-RFLP. cIMT was measured in a subgroup of 118 T2DM patients. RESULTS The frequency of VKORC1 genotypes between diabetic and nondiabetic subjects differed significantly (p=0.01). VKORC1 genotype was associated with T2DM in an adjusted model (OR 1.36, p=0.009). A statistically significant difference was observed in the maximum value of cIMT among different genotypes. VKORC1 -1639 G>A polymorphism was an independent predictor of cIMT (p=0.029) after adjusting for established risk factors. CONCLUSIONS The association between VKORC1 -1639 G>A polymorphism and risk of T2DM could be due to the higher prevalence of calcification in T2DM patients. This is supported by the independent association between VKORC1 -1639 G>A polymorphism and maximum cIMT in T2DM patients which is likely due to atherosclerosis characterized by increased calcification.
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Affiliation(s)
- Anna Tavridou
- Lab of Pharmacology, Medical School, Democritus University of Thrace, Dragana Campus, 68100 Alexandroupolis, Greece.
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Abstract
Artery calcification reflects an admixture of factors such as ectopic osteochondral differentiation with primary host pathological conditions. We review how genetic factors, as identified by human genome-wide association studies, and incomplete correlations with various mouse studies, including knockout and strain analyses, fit into "pieces of the puzzle" in intimal calcification in human atherosclerosis, and artery tunica media calcification in aging, diabetes mellitus, and chronic kidney disease. We also describe in sharp contrast how ENPP1, CD73, and ABCC6 serve as "cogs in a wheel" of arterial calcification. Specifically, each is a minor component in the function of a much larger network of factors that exert balanced effects to promote and suppress arterial calcification. For the network to normally suppress spontaneous arterial calcification, the "cogs" ENPP1, CD73, and ABCC6 must be present and in working order. Monogenic ENPP1, CD73, and ABCC6 deficiencies each drive a molecular pathophysiology of closely related but phenotypically different diseases (generalized arterial calcification of infancy (GACI), pseudoxanthoma elasticum (PXE) and arterial calcification caused by CD73 deficiency (ACDC)), in which premature onset arterial calcification is a prominent but not the sole feature.
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Affiliation(s)
- Frank Rutsch
- Department of General Pediatrics, Münster University Children's Hospital, Albert-Schweitzer-Campus 1, D-48149 Münster, Germany.
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