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Javanshir E, Ebrahimi ZJ, Mirzohreh ST, Ghaffari S, Banisefid E, Alamdari NM, Roshanravan N. Disparity of gene expression in coronary artery disease: insights from MEIS1, HIRA, and Myocardin. Mol Biol Rep 2024; 51:712. [PMID: 38824221 DOI: 10.1007/s11033-024-09657-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024]
Abstract
INTRODUCTION Coronary artery disease (CAD) in young adults can have devastating consequences. The cardiac developmental gene MEIS1 plays important roles in vascular networks and heart development. This gene effects on the regeneration capacity of the heart. Considering role of MEIS1 in cardiac tissue development and the progression of myocardial infarction this study investigated the expression levels of the MEIS1, HIRA, and Myocardin genes in premature CAD patients compared to healthy subjects and evaluated the relationships between these genes and possible inflammatory factors. METHODS AND RESULTS The study conducted a case-control design involving 35 CAD patients and 35 healthy individuals. Peripheral blood mononuclear cells (PBMCs) were collected, and gene expression analysis was performed using real-time PCR. Compared with control group, the number of PBMCs in the CAD group exhibited greater MEIS1 and HIRA gene expression, with fold changes of 2.45 and 3.6. The expression of MEIS1 exhibited a negative correlation with IL-10 (r= -0.312) expression and positive correlation with Interleukin (IL)-6 (r = 0.415) and tumor necrosis factor (TNF)-α (r = 0.534) gene expression. Moreover, there was an inverse correlation between the gene expression of HIRA and that of IL-10 (r= -0.326), and a positive correlation was revealed between the expression of this gene and that of the IL-6 (r = 0.453) and TNF-α (r = 0.572) genes. CONCLUSION This research demonstrated a disparity in expression levels of MEIS1, HIRA, and Myocardin, between CAD and healthy subjects. The results showed that, MEIS1 and HIRA play significant roles in regulating the synthesis of proinflammatory cytokines, namely, TNF-α and IL-6.
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Affiliation(s)
- Elnaz Javanshir
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Samad Ghaffari
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Erfan Banisefid
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Neda Roshanravan
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Zhang Q, Meng H, Wang X, Chen Y, Yan Z, Ruan J, Meng F. Low expression of Notch1 may be associated with acute myocardial infarction. Front Cardiovasc Med 2024; 11:1367675. [PMID: 38841263 PMCID: PMC11150703 DOI: 10.3389/fcvm.2024.1367675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
Background The transmembrane protein Notch1 is associated with cell growth, development, differentiation, proliferation, apoptosis, adhesion, and the epithelial mesenchymal transition. Proteomics, as a research method, uses a series of sequencing techniques to study the composition, expression levels, and modifications of proteins. Here, the association between Notch1 and acute myocardial infarction (AMI) was investigated using proteomics, to assess the possibility of using Notch1 as a biomarker for the disease. Methods Fifty-five eligible patients with AMI and 74 with chronic coronary syndrome (CCS) were enrolled, representing the experimental and control groups, respectively. The mRNA levels were assessed using RT-qPCR and proteins were measured using ELISA, and the results were compared and analyzed. Results Notch1 mRNA levels were 0.52 times higher in the peripheral blood mononuclear cells of the AMI group relative to the CCS group (p < 0.05) while Notch1 protein levels were 0.63 times higher in peripheral blood plasma in AMI patients (p < 0.05). Notch1 levels were not associated with older age, hypertension, smoking, high abdominal-blood glucose, high total cholesterol, and high LDL in AMI. Logistic regression indicated associations between AMI and reduced Notch1 expression, hypertension, smoking, and high fasting glucose. Conclusions Notch1 expression was reduced in the peripheral blood of patients with AMI relative to those with CCS. The low expression of Notch1 was found to be an independent risk factor for AMI and may thus be an indicator of the disease.
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Affiliation(s)
- Qing Zhang
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Changchun, Jilin, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Changchun, Jilin, China
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Changchun, Jilin, China
| | - Heyu Meng
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Changchun, Jilin, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Changchun, Jilin, China
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Changchun, Jilin, China
| | - Xue Wang
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Changchun, Jilin, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Changchun, Jilin, China
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Changchun, Jilin, China
| | - Yanqiu Chen
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Changchun, Jilin, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Changchun, Jilin, China
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Changchun, Jilin, China
| | - Zhaohan Yan
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Changchun, Jilin, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Changchun, Jilin, China
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Changchun, Jilin, China
| | - Jianjun Ruan
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Changchun, Jilin, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Changchun, Jilin, China
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Changchun, Jilin, China
| | - Fanbo Meng
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Changchun, Jilin, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Changchun, Jilin, China
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Changchun, Jilin, China
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Saba L, Maindarkar M, Johri AM, Mantella L, Laird JR, Khanna NN, Paraskevas KI, Ruzsa Z, Kalra MK, Fernandes JFE, Chaturvedi S, Nicolaides A, Rathore V, Singh N, Isenovic ER, Viswanathan V, Fouda MM, Suri JS. UltraAIGenomics: Artificial Intelligence-Based Cardiovascular Disease Risk Assessment by Fusion of Ultrasound-Based Radiomics and Genomics Features for Preventive, Personalized and Precision Medicine: A Narrative Review. Rev Cardiovasc Med 2024; 25:184. [PMID: 39076491 PMCID: PMC11267214 DOI: 10.31083/j.rcm2505184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/24/2024] [Accepted: 03/05/2024] [Indexed: 07/31/2024] Open
Abstract
Cardiovascular disease (CVD) diagnosis and treatment are challenging since symptoms appear late in the disease's progression. Despite clinical risk scores, cardiac event prediction is inadequate, and many at-risk patients are not adequately categorised by conventional risk factors alone. Integrating genomic-based biomarkers (GBBM), specifically those found in plasma and/or serum samples, along with novel non-invasive radiomic-based biomarkers (RBBM) such as plaque area and plaque burden can improve the overall specificity of CVD risk. This review proposes two hypotheses: (i) RBBM and GBBM biomarkers have a strong correlation and can be used to detect the severity of CVD and stroke precisely, and (ii) introduces a proposed artificial intelligence (AI)-based preventive, precision, and personalized ( aiP 3 ) CVD/Stroke risk model. The PRISMA search selected 246 studies for the CVD/Stroke risk. It showed that using the RBBM and GBBM biomarkers, deep learning (DL) modelscould be used for CVD/Stroke risk stratification in the aiP 3 framework. Furthermore, we present a concise overview of platelet function, complete blood count (CBC), and diagnostic methods. As part of the AI paradigm, we discuss explainability, pruning, bias, and benchmarking against previous studies and their potential impacts. The review proposes the integration of RBBM and GBBM, an innovative solution streamlined in the DL paradigm for predicting CVD/Stroke risk in the aiP 3 framework. The combination of RBBM and GBBM introduces a powerful CVD/Stroke risk assessment paradigm. aiP 3 model signifies a promising advancement in CVD/Stroke risk assessment.
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Affiliation(s)
- Luca Saba
- Department of Radiology, Azienda Ospedaliero Universitaria, 40138 Cagliari, Italy
| | - Mahesh Maindarkar
- School of Bioengineering Sciences and Research, MIT Art, Design and Technology University, 412021 Pune, India
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA 95661, USA
| | - Amer M. Johri
- Department of Medicine, Division of Cardiology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Laura Mantella
- Department of Medicine, Division of Cardiology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - John R. Laird
- Heart and Vascular Institute, Adventist Health St. Helena, St Helena, CA 94574, USA
| | - Narendra N. Khanna
- Department of Cardiology, Indraprastha APOLLO Hospitals, 110001 New Delhi, India
| | | | - Zoltan Ruzsa
- Invasive Cardiology Division, University of Szeged, 6720 Szeged, Hungary
| | - Manudeep K. Kalra
- Department of Radiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Seemant Chaturvedi
- Department of Neurology & Stroke Program, University of Maryland, Baltimore, MD 20742, USA
| | - Andrew Nicolaides
- Vascular Screening and Diagnostic Centre and University of Nicosia Medical School, 2368 Agios Dometios, Cyprus
| | - Vijay Rathore
- Nephrology Department, Kaiser Permanente, Sacramento, CA 95823, USA
| | - Narpinder Singh
- Department of Food Science and Technology, Graphic Era Deemed to be University, Dehradun, 248002 Uttarakhand, India
| | - Esma R. Isenovic
- Department of Radiobiology and Molecular Genetics, National Institute of The Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | | | - Mostafa M. Fouda
- Department of Electrical and Computer Engineering, Idaho State University, Pocatello, ID 83209, USA
| | - Jasjit S. Suri
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA 95661, USA
- Department of Computer Engineering, Graphic Era Deemed to be University, Dehradun, 248002 Uttarakhand, India
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Zeng G, Jin YZ, Huang Y, Hu JS, Li MF, Tian M, Lu J, Huang R. Transcriptomic Analysis of Type 2 Diabetes Mellitus Combined with Lower Extremity Atherosclerotic Occlusive Disease. Diabetes Metab Syndr Obes 2024; 17:997-1011. [PMID: 38435631 PMCID: PMC10909374 DOI: 10.2147/dmso.s432698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Abstract
Background The pathological damage mechanism of type 2 diabetes (T2D) and macroangiopathy is extremely complex, and T2D and arteriosclerosis obliterans have different biological behaviors and clinical features. To explore the mechanism of lower extremity arteriosclerosis occlusion (LEAOD) in T2D patients, we utilized RNA-seq to identify unique gene expression signatures of T2D and LEAOD through transcriptomic analysis. Methods We obtained blood samples and performed RNA sequencing from four patients with T2D, five of whom had LEAOD. Another six age- and gender-matched blood samples from healthy volunteers were used for control. By exploring the general and specific differential expression analysis after transcriptome sequencing, specific gene expression patterns of T2D and LEAOD were verified. Results Transcriptome analysis found differentially expressed genes in T2D, and T2D + LEAOD (vs normal) separately, of which 35/486 (T2D/T2D + LEAOD) were up-regulated and 1290/2970 (T2D/T2D + LEAOD) were down-regulated. A strong overlap of 571 genes across T2D, LEAOD, and coexisting conditions was mainly involved in extracellular exosomes and the transcription process. By exploring the sex difference gene expression features between T2D, T2D + LEAOD, and healthy controls, we noticed that sex chromosome-associated genes do not participate in the sexual dimorphism gene expression profiles of T2D and LEAOD. Protein-Protein Interaction Network analysis and drug target prediction provided the drug candidates to treat T2D and LEAOD. Conclusion This study provides some evidence at the transcript level to uncover the association of T2D with LEAOD. The screened hub genes and predicted target drugs may be therapeutic targets.
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Affiliation(s)
- Guang Zeng
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Yong-Zhi Jin
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Yi Huang
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Jun-Sheng Hu
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Meng-Fan Li
- Department of General Surgery, LiQun Hospital, Shanghai, 200333, People’s Republic of China
| | - Ming Tian
- Department of Burn, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People’s Republic of China
| | - Jun Lu
- Department of Endocrinology, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
| | - Rong Huang
- Department of General Surgery, Putuo Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, People’s Republic of China
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You Y, Wang W, Zhu W, Xu J. Identification of functional lncRNAs in atrial fibrillation based on RNA sequencing. BMC Cardiovasc Disord 2023; 23:539. [PMID: 37932671 PMCID: PMC10626701 DOI: 10.1186/s12872-023-03573-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Atrial fibrillation (AF) is one of the most common arrhythmia contributing to serious conditions such as stroke and heart failure. Recent studies demonstrated that long noncoding RNAs (lncRNAs) were related to cardiovascular disease. However, the molecular mechanisms of AF are not fully clear. This study intended to discover lncRNAs that are differentially expressed in AF compared with controls and evaluate the potential functions of these lncRNAs. METHODS Ninety-seven patients (49 patients with AF and 48 patients without AF) were included in this study. Among these patients, leucocyte suspensions of 3 AF patients and 3 controls were sent for RNA-seq analysis to select differentially expressed lncRNA and mRNA. Different lncRNA expressions were validated in another samples (46 AF patients and 45 controls). Gene ontology (GO) enrichment analysis was conducted to annotate the function of selected mRNAs. Alternative splicing (AS) analysis was performed and a lncRNA-mRNA network was also constructed. The receiver operating characteristics (ROC) curve was used to evaluate diagnostic values. Logistic regression analysis was utilized to assess the risk or protective factor of AF. RESULTS A total of 223 mRNAs and 105 lncRNAs were detected in AF patients compared with controls. Total 4 lncRNAs (LINC01781, AC009509.2, AL662844.3, AL662844.4) associated with AF were picked out for validation in another samples by quantitative real-time PCR (qRT-PCR), detecting that upregulated AC009509.2 and downregulated LINC01781 in AF patients. Multivariate logistic regression analysis illustrated that left atrial diameter (OR 1.201; 95% CI 1.093-1.320; P=0.000) and AC009509.2 (OR 1.732; 95% CI 1.092-2.747; P=0.020) were related to AF respectively. ROC curve showed that AC009509.2, LINC01781 and left atrial diameter (LAD) were predictors of AF. For LINC01781, the area under the curve (AUC) was 0.654 (95% CI 0.541-0.767, P=0.0113). For AC009509.2, the AUC was 0.710 (95% CI 0.599-0.822, P=0.0005). Bioinformatic methods (GO enrichment, AS analysis and lncRNA-mRNA network construction) were performed to reveal the role of lncRNAs. CONCLUSIONS This study discussed differentially expressed lncRNA and their potential interaction with mRNA in AF. LncRNA AC009509.2 could be a new potential biomarker for AF prediction.
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Affiliation(s)
- Yangyang You
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Wei Wang
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Wenshu Zhu
- Department of Cardiology, Bengbu First People's Hospital, Bengbu, Anhui, 233000, China
| | - Jian Xu
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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Al-Maini M, Maindarkar M, Kitas GD, Khanna NN, Misra DP, Johri AM, Mantella L, Agarwal V, Sharma A, Singh IM, Tsoulfas G, Laird JR, Faa G, Teji J, Turk M, Viskovic K, Ruzsa Z, Mavrogeni S, Rathore V, Miner M, Kalra MK, Isenovic ER, Saba L, Fouda MM, Suri JS. Artificial intelligence-based preventive, personalized and precision medicine for cardiovascular disease/stroke risk assessment in rheumatoid arthritis patients: a narrative review. Rheumatol Int 2023; 43:1965-1982. [PMID: 37648884 DOI: 10.1007/s00296-023-05415-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
The challenges associated with diagnosing and treating cardiovascular disease (CVD)/Stroke in Rheumatoid arthritis (RA) arise from the delayed onset of symptoms. Existing clinical risk scores are inadequate in predicting cardiac events, and conventional risk factors alone do not accurately classify many individuals at risk. Several CVD biomarkers consider the multiple pathways involved in the development of atherosclerosis, which is the primary cause of CVD/Stroke in RA. To enhance the accuracy of CVD/Stroke risk assessment in the RA framework, a proposed approach involves combining genomic-based biomarkers (GBBM) derived from plasma and/or serum samples with innovative non-invasive radiomic-based biomarkers (RBBM), such as measurements of synovial fluid, plaque area, and plaque burden. This review presents two hypotheses: (i) RBBM and GBBM biomarkers exhibit a significant correlation and can precisely detect the severity of CVD/Stroke in RA patients. (ii) Artificial Intelligence (AI)-based preventive, precision, and personalized (aiP3) CVD/Stroke risk AtheroEdge™ model (AtheroPoint™, CA, USA) that utilizes deep learning (DL) to accurately classify the risk of CVD/stroke in RA framework. The authors conducted a comprehensive search using the PRISMA technique, identifying 153 studies that assessed the features/biomarkers of RBBM and GBBM for CVD/Stroke. The study demonstrates how DL models can be integrated into the AtheroEdge™-aiP3 framework to determine the risk of CVD/Stroke in RA patients. The findings of this review suggest that the combination of RBBM with GBBM introduces a new dimension to the assessment of CVD/Stroke risk in the RA framework. Synovial fluid levels that are higher than normal lead to an increase in the plaque burden. Additionally, the review provides recommendations for novel, unbiased, and pruned DL algorithms that can predict CVD/Stroke risk within a RA framework that is preventive, precise, and personalized.
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Affiliation(s)
- Mustafa Al-Maini
- Allergy, Clinical Immunology and Rheumatology Institute, Toronto, ON, L4Z 4C4, Canada
| | - Mahesh Maindarkar
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, 95661, USA
- Asia Pacific Vascular Society, New Delhi, 110001, India
| | - George D Kitas
- Academic Affairs, Dudley Group NHS Foundation Trust, Dudley, DY1 2HQ, UK
- Arthritis Research UK Epidemiology Unit, Manchester University, Manchester, M13 9PL, UK
| | - Narendra N Khanna
- Asia Pacific Vascular Society, New Delhi, 110001, India
- Department of Cardiology, Indraprastha APOLLO Hospitals, New Delhi, 110001, India
| | | | - Amer M Johri
- Division of Cardiology, Department of Medicine, Queen's University, Kingston, Canada
| | - Laura Mantella
- Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Canada
| | - Vikas Agarwal
- Department of Immunology, SGPIMS, Lucknow, 226014, India
| | - Aman Sharma
- Department of Immunology, SGPIMS, Lucknow, 226014, India
| | - Inder M Singh
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, 95661, USA
| | - George Tsoulfas
- Department of Surgery, Aristoteleion University of Thessaloniki, 54124, Thessaloniki, Greece
| | - John R Laird
- Heart and Vascular Institute, Adventist Health St. Helena, St Helena, CA, 94574, USA
| | - Gavino Faa
- Department of Pathology, Azienda Ospedaliero Universitaria, 09124, Cagliari, Italy
| | - Jagjit Teji
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Monika Turk
- The Hanse-Wissenschaftskolleg Institute for Advanced Study, 27753, Delmenhorst, Germany
| | - Klaudija Viskovic
- Department of Radiology and Ultrasound, UHID, 10 000, Zagreb, Croatia
| | - Zoltan Ruzsa
- Invasive Cardiology Division, University of Szeged, Szeged, Hungary
| | - Sophie Mavrogeni
- Cardiology Clinic, Onassis Cardiac Surgery Centre, Athens, Greece
| | - Vijay Rathore
- Nephrology Department, Kaiser Permanente, Sacramento, CA, 95823, USA
| | - Martin Miner
- Men's Health Centre, Miriam Hospital Providence, Providence, RI, 02906, USA
| | - Manudeep K Kalra
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Esma R Isenovic
- Department of Radiobiology and Molecular Genetics, National Institute of the Republic of Serbia, University of Belgrade, 11000, Belgrade, Serbia
| | - Luca Saba
- Department of Radiology, Azienda Ospedaliero Universitaria, 40138, Cagliari, Italy
| | - Mostafa M Fouda
- Department of Electrical and Computer Engineering, Idaho State University, Pocatello, ID, 83209, USA
| | - Jasjit S Suri
- Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, 95661, USA.
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Dehghani K, Stanek A, Bagherabadi A, Atashi F, Beygi M, Hooshmand A, Hamedi P, Farhang M, Bagheri S, Zolghadri S. CCND1 Overexpression in Idiopathic Dilated Cardiomyopathy: A Promising Biomarker? Genes (Basel) 2023; 14:1243. [PMID: 37372424 DOI: 10.3390/genes14061243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Cardiomyopathy, a disorder of electrical or heart muscle function, represents a type of cardiac muscle failure and culminates in severe heart conditions. The prevalence of dilated cardiomyopathy (DCM) is higher than that of other types (hypertrophic cardiomyopathy and restrictive cardiomyopathy) and causes many deaths. Idiopathic dilated cardiomyopathy (IDCM) is a type of DCM with an unknown underlying cause. This study aims to analyze the gene network of IDCM patients to identify disease biomarkers. Data were first extracted from the Gene Expression Omnibus (GEO) dataset and normalized based on the RMA algorithm (Bioconductor package), and differentially expressed genes were identified. The gene network was mapped on the STRING website, and the data were transferred to Cytoscape software to determine the top 100 genes. In the following, several genes, including VEGFA, IGF1, APP, STAT1, CCND1, MYH10, and MYH11, were selected for clinical studies. Peripheral blood samples were taken from 14 identified IDCM patients and 14 controls. The RT-PCR results revealed no significant differences in the expression of the genes APP, MYH10, and MYH11 between the two groups. By contrast, the STAT1, IGF1, CCND1, and VEGFA genes were overexpressed in patients more than in controls. The highest expression was found for VEGFA, followed by CCND1 (p < 0.001). Overexpression of these genes may contribute to disease progression in patients with IDCM. However, more patients and genes need to be analyzed in order to achieve more robust results.
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Affiliation(s)
- Khatereh Dehghani
- Department of Cardiology, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Agata Stanek
- Department and Clinic of Internal Medicine, Angiology and Physical Medicine, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Batorego 15 Street, 41-902 Bytom, Poland
| | - Arash Bagherabadi
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil 5619911367, Iran
| | - Fatemeh Atashi
- Faculty of Medicine, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Mohammad Beygi
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 8415683111, Iran
| | - Amirreza Hooshmand
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences & Technology, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran
| | - Pezhman Hamedi
- Research Center, Department of Medical Laboratory Sciences, Faculty of Medicine, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Mohsen Farhang
- Molecular Study and Diagnostic Center, Jahrom University of Medical Sciences, Jahrom 7414846199, Iran
| | - Soghra Bagheri
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415185, Iran
| | - Samaneh Zolghadri
- Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom 7414785318, Iran
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Abdallah HY, Fareed A, Abdelmaogood AKK, Allam S, Abdelgawad M, Deen LATE. Introducing Circulating Vasculature-Related Transcripts as Biomarkers in Coronary Artery Disease. Mol Diagn Ther 2023; 27:243-259. [PMID: 36538237 PMCID: PMC10008268 DOI: 10.1007/s40291-022-00622-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Atherosclerotic plaque is considered the hallmark of atherosclerotic lesions in coronary atherosclerosis (CAS), the primary pathogenesis in coronary artery disease (CAD), which develops and progresses through a complex interplay between immune cells, vascular cells, and endothelial shear stresses. Early diagnosis of CAS is critical for avoiding plaque rupture and sudden death. Therefore, identifying new CAD biomarkers linked to vessel wall functions, such as RNA molecules with their distinct signature, is a promising development for these patients. With this rationale, the present study investigated the expression level of the vascular-related RNA transcripts (lncRNA ANRIL, miRNA-126-5p, CDK4, CDK6, TGF-β, E-cadherin, and TNF-α) implicated in the cellular vascular function, proliferation, and inflammatory processes. METHODS A case-control study design with a total of 180 subjects classified participants into two groups; CAD and control groups. The relative expression levels of the seven transcripts under study-selected using online bioinformatics tools and current literature-were assessed in the plasma of all study participants using RT-qPCR. Their predictive significance testing, scoring of disease prioritization, enrichment analysis, and the miRNA-mRNA regulatory network was investigated. RESULTS The relative expression levels of all seven of the circulating vascular-related transcripts under study were statistically significant between CAD patients and controls. Receiver operating characteristic (ROC) analysis results indicated the statistical significance of all the transcripts under study with CDK4 showing the highest area under the curve (AUC) equivalent to 0.91, followed by E-cadherin (0.90), miRNA-126-5p (0.83), ANRIL (0.82), TNF-α (0.63), TGF-β (0.62), and CDK6 (0.59), in descending order. A strong association was detected between most of the transcripts studied in CAD patients with a significant Spearman's correlation coefficient with a two-tailed significance of p < 0.001. Network analysis revealed a strong relationship between the five circulating vasculature transcripts studied and their target miRNAs and miR-126-5p, but not for ANRIL. CONCLUSION The seven circulating vascular-related RNA transcripts under study could serve as potential CAD biomarkers, reflecting the cellular vascular function, proliferation, and inflammatory processes in CAD patients. Therefore, blood transcriptome analysis opens new frontiers for the non-invasive diagnosis of CAD.
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Affiliation(s)
- Hoda Y Abdallah
- Medical Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt. .,Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
| | - Ahmed Fareed
- Department of Cardiology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Asmaa K K Abdelmaogood
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Sahar Allam
- Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Mai Abdelgawad
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, Egypt
| | - Loaa A Tag El Deen
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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Meng H, Ruan J, Yan Z, Chen Y, Liu J, Li X, Meng F. New Progress in Early Diagnosis of Atherosclerosis. Int J Mol Sci 2022; 23:ijms23168939. [PMID: 36012202 PMCID: PMC9409135 DOI: 10.3390/ijms23168939] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/30/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Coronary atherosclerosis is a potentially chronic circulatory condition that endangers human health. The biological cause underpinning cardiovascular disease is coronary atherosclerosis, and acute cardiovascular events can develop due to thrombosis, platelet aggregation, and unstable atherosclerotic plaque rupture. Coronary atherosclerosis is progressive, and three specific changes appear, with fat spots and stripes, atherosclerosis and thin-walled fiber atherosclerosis, and then complex changes in arteries. The progression and severity of cardiovascular disease are correlated with various levels of calcium accumulation in the coronary artery. The therapy and diagnosis of coronary atherosclerosis benefit from the initial assessment of the size and degree of calcification. This article will discuss the new progress in the early diagnosis of coronary atherosclerosis in terms of three aspects: imaging, gene and protein markers, and trace elements. This study intends to present the latest methods for diagnosing patients with early atherosclerosis through a literature review.
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Affiliation(s)
- Heyu Meng
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Jianjun Ruan
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Zhaohan Yan
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Yanqiu Chen
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Jinsha Liu
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Xiangdong Li
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
| | - Fanbo Meng
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease, Jilin Provincial Cardiovascular Research Institute, Jilin University, Changchun 130033, China
- Correspondence: ; Tel.: +86-15948346855
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Andreini D, Melotti E, Vavassori C, Chiesa M, Piacentini L, Conte E, Mushtaq S, Manzoni M, Cipriani E, Ravagnani PM, Bartorelli AL, Colombo GI. Whole-Blood Transcriptional Profiles Enable Early Prediction of the Presence of Coronary Atherosclerosis and High-Risk Plaque Features at Coronary CT Angiography. Biomedicines 2022; 10:biomedicines10061309. [PMID: 35740331 PMCID: PMC9219643 DOI: 10.3390/biomedicines10061309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 12/10/2022] Open
Abstract
Existing tools to estimate cardiovascular (CV) risk have sub-optimal predictive capacities. In this setting, non-invasive imaging techniques and omics biomarkers could improve risk-prediction models for CV events. This study aimed to identify gene expression patterns in whole blood that could differentiate patients with severe coronary atherosclerosis from subjects with a complete absence of detectable coronary artery disease and to assess associations of gene expression patterns with plaque features in coronary CT angiography (CCTA). Patients undergoing CCTA for suspected coronary artery disease (CAD) were enrolled. Coronary stenosis was quantified and CCTA plaque features were assessed. The whole-blood transcriptome was analyzed with RNA sequencing. We detected highly significant differences in the circulating transcriptome between patients with high-degree coronary stenosis (≥70%) in the CCTA and subjects with an absence of coronary plaque. Notably, regression analysis revealed expression signatures associated with the Leaman score, the segment involved score, the segment stenosis score, and plaque volume with density <150 HU at CCTA. This pilot study shows that patients with significant coronary stenosis are characterized by whole-blood transcriptome profiles that may discriminate them from patients without CAD. Furthermore, our results suggest that whole-blood transcriptional profiles may predict plaque characteristics.
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Affiliation(s)
- Daniele Andreini
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Biomedical and Clinical Science “Luigi Sacco”, University of Milan, 20121 Milan, Italy
- Correspondence: (D.A.); (G.I.C.); Tel.: +39-0258002577 (D.A.); +39-0258002464 (G.I.C.)
| | - Eleonora Melotti
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Chiara Vavassori
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Clinical Sciences and Community Health, University of Milan, 20121 Milan, Italy
| | - Mattia Chiesa
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Electronics, Information and Biomedical Engineering, Politecnico di Milano, 20133 Milan, Italy
| | - Luca Piacentini
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Edoardo Conte
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Biomedical Sciences for Health, University of Milan, 20121 Milan, Italy
| | - Saima Mushtaq
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Martina Manzoni
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Eleonora Cipriani
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Paolo M. Ravagnani
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
| | - Antonio L. Bartorelli
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Department of Biomedical and Clinical Science “Luigi Sacco”, University of Milan, 20121 Milan, Italy
| | - Gualtiero I. Colombo
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (E.M.); (C.V.); (M.C.); (L.P.); (E.C.); (S.M.); (M.M.); (E.C.); (P.M.R.); (A.L.B.)
- Correspondence: (D.A.); (G.I.C.); Tel.: +39-0258002577 (D.A.); +39-0258002464 (G.I.C.)
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Lee M, Chang Y, Ahmadinejad N, Johnson-Agbakwu C, Bailey C, Liu L. COVID-19 mortality is associated with pre-existing impaired innate immunity in health conditions. PeerJ 2022; 10:e13227. [PMID: 35547187 PMCID: PMC9083528 DOI: 10.7717/peerj.13227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/15/2022] [Indexed: 01/12/2023] Open
Abstract
COVID-19 can be life-threatening to individuals with chronic diseases. To prevent severe outcomes, it is critical that we comprehend pre-existing molecular abnormalities found in common health conditions that predispose patients to poor prognoses. In this study, we focused on 14 pre-existing health conditions for which increased hazard ratios of COVID-19 mortality have been documented. We hypothesized that dysregulated gene expression in these pre-existing health conditions were risk factors of COVID-19 related death, and the magnitude of dysregulation (measured by fold change) were correlated with the severity of COVID-19 outcome (measured by hazard ratio). To test this hypothesis, we analyzed transcriptomics data sets archived before the pandemic in which no sample had COVID-19. For a given pre-existing health condition, we identified differentially expressed genes by comparing individuals affected by this health condition with those unaffected. Among genes differentially expressed in multiple health conditions, the fold changes of 70 upregulated genes and 181 downregulated genes were correlated with hazard ratios of COVID-19 mortality. These pre-existing dysregulations were molecular risk factors of severe COVID-19 outcomes. These genes were enriched with endoplasmic reticulum and mitochondria function, proinflammatory reaction, interferon production, and programmed cell death that participate in viral replication and innate immune responses to viral infections. Our results suggest that impaired innate immunity in pre-existing health conditions is associated with increased hazard of COVID-19 mortality. The discovered molecular risk factors are potential prognostic biomarkers and targets for therapeutic intervention.
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Affiliation(s)
- Matthew Lee
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
| | - Yung Chang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Navid Ahmadinejad
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
| | | | - Celeste Bailey
- Valleywise Health Medical Center, Phoenix, AZ, United States
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States,Biodesign Institute, Arizona State University, Tempe, AZ, United States
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12
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Expression of ATP-binding cassette subfamily B member 1 gene in peripheral blood of patients with acute myocardial infarction. Bioengineered 2022; 13:11095-11105. [PMID: 35473443 PMCID: PMC9161866 DOI: 10.1080/21655979.2022.2068881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
This study aimed to determine the amount of expression of the ATP-binding cassette subfamily B member 1 (ABCB1) gene chip as a prospective diagnostic marker for acute myocardial infarction (AMI) in a wide population . In the AMI and control groups, 113 patients with AMI and 83 persons with non-coronary artery disease were selected for peripheral venous leukocyte collection. Western blot and real-time polymerase chain reaction (RT-PCR) were employed to detect relative ABCB1 expression in both groups. The results showed that the ABCB1 transcription and protein levels in the AMI group were higher than in the control. The relative mRNA expression of ABCB1 was 0.26 (0.03-0.79) in the AMI group and 0.13 (0.01-0.52) in the control group (P < 0.05). The expression of the ABCB1 gene at the protein level in the AMI group was 1.65 times that in the control (P < 0.05). Further, the subjects in the AMI group were older (P < 0.001), had lower levels of high-density lipoprotein cholesterol (P = 0.038), and had higher incidence of type II diabetes mellitus (P = 0.003) compared with the control. Logistic regression analysis showed that the expression of ABCB1 in peripheral blood was correlated with the occurrence of AMI (P = 0.003). High ABCB1 expression, type II diabetes, and advanced age were found to serve as potential independent risk factors for AMI, with a 4.88-fold, 2.99-fold, and 2.63-fold increased risk of AMI. Overall, the high expression of ABCB1 in peripheral blood might be related to the occurrence of AMI.
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Association of Low Expression of NUMB in Peripheral Blood with Acute Myocardial Infarction. Cardiol Res Pract 2022; 2022:7981637. [PMID: 35529060 PMCID: PMC9072008 DOI: 10.1155/2022/7981637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022] Open
Abstract
Objective Our study's goal was to find out acute myocardial infarction (AMI) patients' NUMB gene expression patterns and to evaluate its role as a diagnostic marker for AMI detection. Methods Peripheral blood was drawn from 124 individuals who had an AMI and 115 patients who had stable coronary artery disease (SCAD). The real-time quantitative polymerase chain reaction was used to measure the mRNA expression level of the NUMB gene in peripheral blood. Results The AMI group's NUMB gene expression was 0.906 (0.181–0.954), whereas the SCAD group's expression was 1.024 (0.207–1.127). However, the AMI group had 0.885 times lower NUMB mRNA expression than the SCAD group (P < 0.05). Conclusion Multivariate logistic regression evaluation found that lower NUMB expression was correlated with an increased risk of coronary artery disease. However, age and fasting plasma glucose levels were not associated with decreased NUMB expression.
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Li L, Meng H, Wang X, Ruan J, Tian X, Meng F. Low ZCCHC9 Gene Expression in Peripheral Blood May Be an Acute Myocardial Infarction Genetic Molecular Marker in Patients with Stable Coronary Atherosclerotic Disease. Int J Gen Med 2022; 15:1795-1804. [PMID: 35210844 PMCID: PMC8863191 DOI: 10.2147/ijgm.s346335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
Purpose Patients and Methods Results Conclusion
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Affiliation(s)
- Lihong Li
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Heyu Meng
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Xue Wang
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Jianjun Ruan
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Xiaomin Tian
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
| | - Fanbo Meng
- Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China
- Correspondence: Fanbo Meng, Department of Cardiology, The Third Hospital of Jilin University, Changchun, People’s Republic of China, Tel +86-15948346855, Fax + 86-431-84995228, Email
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Differential Analysis and Putative Roles of Genes, Cytokines and Apoptotic Proteins in Blood Samples of Patients with Respiratory Viral Infections: A Single Center Study. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insights into the molecular pathogenesis of respiratory viral infections were investigated using serum and peripheral blood from patients with clinical syndromes. Signatures of expression of cytokines, genes and apoptotic proteins that discriminate symptomatic individuals from healthy individuals were determined among 21 patients. In symptomatic patients, significant upregulation of IL-1β, IL-2, IL-4, IL-6, IL-8, IL-12, IL-15, TNF-a and IFN-g (P<0.05) was noted, while IL-10 was significantly downregulated (P<0.05). This is accompanied by either up or down-regulation of various pro-apoptotic and anti-apoptotic markers, suggesting a protective role of immune responses against viral infection and the capacity of viruses to subvert host cell apoptosis. Gene expression analysis for both T and B cells were categorized according to their functional status of activation, proliferation, and differentiation. Of note, genes SH2D1A and TCL1A were upregulated only in rhinovirus samples, while PSMB7, CD4, CD8A, HLA-DMA, HLA-DRA and CD69 were upregulated in samples of Flu A and RSV but were not significant in samples of rhinovirus as compared to healthy individuals. These results demonstrated Flu A and RSV elicit different alterations in human peripheral blood gene expression as compared to rhinovirus. Overall, despite the small number of study subjects, the current study for the first time has recognized signature genes, cytokines and proteins that are used by some respiratory viruses that may serve as candidates for rapid diagnosis as well as targets for therapeutic interventions.
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Meng H, Ruan J, Tian X, Li L, Chen W, Meng F. High retinoic acid receptor-related orphan receptor A gene expression in peripheral blood leukocytes may be related to acute myocardial infarction. J Int Med Res 2021; 49:3000605211019663. [PMID: 34101510 PMCID: PMC8191083 DOI: 10.1177/03000605211019663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE This study aimed to investigate whether differential expression of the retinoic acid receptor-related orphan receptor A (RORA) gene is related to occurrence of acute myocardial infarction (AMI). METHODS This was a retrospective study. White blood cells of 93 patients with acute myocardial infarction and 74 patients with stable coronary artery disease were collected. Reverse transcription quantitative polymerase chain reaction and western blotting were used to measure RORA mRNA and protein expression, respectively. RESULTS RORA mRNA expression levels in peripheral blood leukocytes in patients with AMI were 1.57 times higher than those in patients with stable coronary artery disease. Protein RORA levels in peripheral blood of patients with AMI were increased. Binary logistic regression analysis showed that high expression of RORA was an independent risk factor for AMI, and it increased the risk of AMI by 2.990 times. CONCLUSION RORA expression levels in patients with AMI is significantly higher than that in patients with stable coronary artery disease. High expression of RORA is related to AMI and it may be an independent risk factor for AMI.
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Affiliation(s)
- Heyu Meng
- Department of Cardiology, Third Hospital of Jilin University, Jilin Provincial Cardiovascular Research Institute, Jilin, China
| | - Jianjun Ruan
- Department of Cardiology, Third Hospital of Jilin University, Jilin Provincial Cardiovascular Research Institute, Jilin, China
| | - Xiaomin Tian
- Department of Cardiology, Third Hospital of Jilin University, Jilin Provincial Cardiovascular Research Institute, Jilin, China
| | - Lihong Li
- Department of Cardiology, Third Hospital of Jilin University, Jilin Provincial Cardiovascular Research Institute, Jilin, China
| | - Weiwei Chen
- Department of Cardiology, Third Hospital of Jilin University, Jilin Provincial Cardiovascular Research Institute, Jilin, China
| | - Fanbo Meng
- Department of Cardiology, Third Hospital of Jilin University, Jilin Provincial Cardiovascular Research Institute, Jilin, China
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Fang Q, Li T, Chen P, Wu Y, Wang T, Mo L, Ou J, Nandakumar KS. Comparative Analysis on Abnormal Methylome of Differentially Expressed Genes and Disease Pathways in the Immune Cells of RA and SLE. Front Immunol 2021; 12:668007. [PMID: 34079550 PMCID: PMC8165287 DOI: 10.3389/fimmu.2021.668007] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
We identified abnormally methylated, differentially expressed genes (DEGs) and pathogenic mechanisms in different immune cells of RA and SLE by comprehensive bioinformatics analysis. Six microarray data sets of each immune cell (CD19+ B cells, CD4+ T cells and CD14+ monocytes) were integrated to screen DEGs and differentially methylated genes by using R package “limma.” Gene ontology annotations and KEGG analysis of aberrant methylome of DEGs were done using DAVID online database. Protein-protein interaction (PPI) network was generated to detect the hub genes and their methylation levels were compared using DiseaseMeth 2.0 database. Aberrantly methylated DEGs in CD19+ B cells (173 and 180), CD4+ T cells (184 and 417) and CD14+ monocytes (193 and 392) of RA and SLE patients were identified. We detected 30 hub genes in different immune cells of RA and SLE and confirmed their expression using FACS sorted immune cells by qPCR. Among them, 12 genes (BPTF, PHC2, JUN, KRAS, PTEN, FGFR2, ALB, SERB-1, SKP2, TUBA1A, IMP3, and SMAD4) of RA and 12 genes (OAS1, RSAD2, OASL, IFIT3, OAS2, IFIH1, CENPE, TOP2A, PBK, KIF11, IFIT1, and ISG15) of SLE are proposed as potential biomarker genes based on receiver operating curve analysis. Our study suggests that MAPK signaling pathway could potentially differentiate the mechanisms affecting T- and B- cells in RA, whereas PI3K pathway may be used for exploring common disease pathways between RA and SLE. Compared to individual data analyses, more dependable and precise filtering of results can be achieved by integrating several relevant data sets.
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Affiliation(s)
- Qinghua Fang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Tingyue Li
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peiya Chen
- Department of Science and Education, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuzhe Wu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Tingting Wang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Lixia Mo
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jiaxin Ou
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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Long-term prognostic value of myocardin expression levels in non-ischemic dilated cardiomyopathy. Heart Vessels 2021; 36:1841-1847. [PMID: 33983455 DOI: 10.1007/s00380-021-01869-0] [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] [Received: 01/30/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
The mortality of patients with non-ischemic dilated cardiomyopathy (NIDCM) remains substantial. We evaluated gene expression levels of myocardin, an early cardiac gene, in the peripheral blood cells of NIDCM patients as a prognostic biomarker in their long-term outcome and mortality from congestive HF (CHF). We retrospectively analyzed 101 consecutives optimally treated NIDCM patients of Cretan origin who were enrolled from the HF clinic of our hospital from November 2005 to December 2008. Our patient data were either taken from their medical files or recorded during visits to the HF unit or hospitalizations. Follow-up was carried out by telephone interview and by accessing information from general practitioners and cardiologists in private practice. The median follow-up period was 8 years (mean follow-up 7 ± 3.4 years). The overall mortality during follow-up was 61.4%, while mortality due to congestive heart failure (CHF) was 49.5%. Higher CHF and all-cause mortality were observed in patients with myocardin levels < 14.26 (p < 0.001 for both CHF and all-cause mortality). A multivariate Cox regression analysis showed that myocardin level of expression had independent significant prognostic value for the risk of death from CHF (HR 14.5, 95% confidence interval (CI) 5.3-39) in those patients. Peripheral blood cells gene expression of myocardin, an early myocardial marker, may serve as prognostic biomarkers of the long-term outcome of patients with NIDCM. Our findings open new prospects in the risk stratification of these patients.
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Lu S, Lijuan R, Tang QH, Liu QL, Xian-Lan Z. Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Venous Thromboembolism (VTE). Ann Vasc Surg 2021; 74:389-399. [PMID: 33819580 DOI: 10.1016/j.avsg.2021.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 01/14/2021] [Accepted: 02/26/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To explore the key genes, and correlated pathways in venous thromboembolism (VTE) via bioinformatic analysis, and expected our findings could contribute to the development of new biomarkers and therapeutic target for VTE. METHODS Two VTE-related microarray expression profiles (GSE48000 and GSE19151) were downloaded from the Gene Expression Ominibus (GEO) database. Differentially expressed genes (DEGs) were analyzed using limma package, and overlapping DEGs were identified form the above two expression profiles. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEEG) pathway enrichment analyses were performed by DAVID. Protein-protein interaction (PPI) network was constructed by using STRING and visualized with Cytoscape. Furthermore, module analysis plus centrality analysis of the PPI network were executed to identify the potential key genes. Finally, the pathway analysis was performed using GenCLiP 3.0. RESULTS A total of 173 DEGs (125 upregulated and 48 downregulated) were identified. GO analysis demonstrated that DEGs were mainly enriched in viral life cycle, ribosome and structural constituent of ribosome. Meanwhile, KEGG pathway analysis showed that these genes were enriched in ribosome, Parkinson's disease and cell cycle. Additionally, one most significant module and 12 hub genes were found. Finally, 6 key genes, namely ISG15, RPS15A, MRPL13, ICT1, MRPL15 and RPLP0, with high centrality features were identified. These key genes were mainly involved in translation, metabolism of proteins and ribosome pathway. CONCLUSIONS In summary, these 6 identified genes and correlated pathways should play an important role in VTE, which can provide new insight into the molecular mechanism, potential biomarkers and therapeutic targets associated with VTE.
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Affiliation(s)
- Shun Lu
- Department of Interventional Radiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Department of Vascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Ren Lijuan
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qian-Hui Tang
- Department of Vascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Qi-Li Liu
- Department of Vascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Zhang Xian-Lan
- Department of Vascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, China.
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Yan CC, Zhang XS, Zhou L, Yang Q, Zhou M, Zhang LW, Xing JC, Yan ZF, Price M, Li J, Yue BS, Fan ZX. Effects of aging on gene expression in blood of captive Tibetan macaques ( Macaca thibetana) and comparisons with expression in humans. Zool Res 2021; 41:557-563. [PMID: 32746507 PMCID: PMC7475009 DOI: 10.24272/j.issn.2095-8137.2020.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Changes in gene expression occur as animals, including primates, age. Macaques have long been used as a model species for primate evolution and biomedical studies. Here, to study gene expression in Tibetan macaques (Macaca thibetana, TMs) and its differences to humans, we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs. In total, 2 523 age-associated differentially expressed genes (DEGs) were identified. Several pathways and processes that regulate aging, including the FoxO signaling pathway, autophagy, and platelet activation, were significantly enriched in the up-regulated DEGs. Two significantly age-related modules were identified by weighted gene co-expression network analysis (WGCNA). The TMs and humans shared 279 common DEGs, including 111 up-regulated and 141 down-regulated genes with advancing age in the same expression direction. However, 27 age-related DEGs presented the opposite expression direction in TMs as that in humans. For example, INPPL1, with inhibitory effects on the B cell receptor signaling pathway, was up-regulated in humans but down-regulated in TMs. In general, our study suggests that aging is a critical factor affecting gene expression in the captive TM population. The similarities and differences in gene expression patterns between TMs and humans could provide new insights into primate evolution and benefit TM model development.
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Affiliation(s)
- Chao-Chao Yan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xin-Shang Zhang
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Liang Zhou
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Qiao Yang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Min Zhou
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Lin-Wan Zhang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jin-Chuan Xing
- Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Zhi-Feng Yan
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jing Li
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Bi-Song Yue
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhen-Xin Fan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China. E-mail:
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El Shamieh S, Stathopoulou MG, Bonnefond A, Ndiaye NC, Lecoeur C, Meyre D, Dadé S, Chedid P, Salami A, Shahabi P, Dedoussis GV, Froguel P, Visvikis-Siest S. Obesity status modifies the association between rs7556897T>C in the intergenic region SLC19A3-CCL20 and blood pressure in French children. Clin Chem Lab Med 2020; 58:1819-1827. [PMID: 32238601 DOI: 10.1515/cclm-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 02/24/2020] [Indexed: 12/16/2022]
Abstract
Background Growing evidence reports an association between inflammatory markers, obesity and blood pressure (BP). Specifically, the intergenic single nucleotide polymorphism (SNP) rs7556897T > C (MAF = 0.34) located between SLC19A3 and the CCL20 was shown to be associated with chronic inflammatory diseases. In addition, CCL20 expression was found increased in pancreatic islets of obese rodents and human pancreatic β cells under the influence of inflammation. In this study, we hypothesized that SNP rs7556897 could affect BP levels, thus providing a link between inflammation, BP and obesity. Methods BP was measured under supine position with a manual sphygmomanometer; values reported were the means of three readings. We analyzed rs7556897 in 577 normal weight and 689 obese French children. Using real-time polymerase chain reaction (PCR), we quantified CCL20 and SLC19A3 expression in adipose tissue and peripheral blood mononuclear cells (PBMCs) of normal weight and overweight children. Results The rs7556897C allele was negatively associated with diastolic BP in normal weight children (β = -0.012 ± 0.004, p = 0.006) but positively associated in obese children (β = 2.178 ± 0.71, p = 0.002). A significant interaction between rs7556897T > C and the obesity status (obese or normal weight) was detected (β = 3.49, p = 9.79 × 10-5) for BP in a combined population analysis. CCL20 mRNA was only expressed in the adipose tissue of overweight children, and its expression levels were 10.7× higher in PBMCs of overweight children than normal weight children. Finally, CCL20 mRNA levels were positively associated with rs7556897T > C in PBMCs of 58 normal weight children (β = 0.43, p = 0.002). SLC19A3 was not expressed in PBMCs, and in adipose tissue, it showed same levels of expression in normal weight and overweight children. The gene expression results may highlight a specific involvement of CCL20 via communicating obesity/inflammation pathways that regulate BP. Conclusions Childhood obesity reverses the effect of rs7556897T > C on diastolic BP, possibly via the modulation of CCL20 expression levels.
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Affiliation(s)
- Said El Shamieh
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France.,Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Maria G Stathopoulou
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France
| | - Amélie Bonnefond
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France.,CNRS 8199-University Lille North of France, Institut Pasteur de Lille, Lille, France
| | - Ndeye Coumba Ndiaye
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France
| | - Cécile Lecoeur
- CNRS 8199-University Lille North of France, Institut Pasteur de Lille, Lille, France
| | - David Meyre
- CNRS 8199-University Lille North of France, Institut Pasteur de Lille, Lille, France.,Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Sébastien Dadé
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France
| | - Pia Chedid
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France
| | - Ali Salami
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France.,Rammal Hassan Rammal Research Laboratory, Physio-toxicity (PhyTox) Research Group, Lebanese University, Faculty of Sciences (V), Nabatieh, Lebanon
| | - Payman Shahabi
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France
| | - George V Dedoussis
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France.,Department of Nutrition - Dietetics, Harokopio University, Athens, Greece
| | - Philippe Froguel
- CNRS 8199-University Lille North of France, Institut Pasteur de Lille, Lille, France.,Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
| | - Sophie Visvikis-Siest
- Research Unit EA_1122; IGE-PCV - Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Faculté de Pharmacie, Nancy, France
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Insight into atrial fibrillation through analysis of the coding transcriptome in humans. Biophys Rev 2020; 12:817-826. [PMID: 32666467 DOI: 10.1007/s12551-020-00735-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Atrial fibrillation is the most common sustained cardiac arrhythmia in humans, and its prevalence continues to increase because of the aging of the world population. Much still needs to be learned about the molecular pathways involved in the development and the persistence of the disease. Analysis of the transcriptome of cardiac tissue has provided valuable insight into diverse aspects of atrial remodeling, in particular concerning electrical remodeling-related to ion channels-and structural remodeling identified by dysregulation of processes linked to inflammation, fibrosis, oxidative stress, and thrombogenesis. The huge amount of data produced by these studies now represents a valuable source for the identification of novel potential therapeutic targets. In addition, the shift from cardiac tissue to peripheral blood as a substrate for transcriptome analysis revealed this strategy as a promising tool for improved diagnosis and therefore better patient care.
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23
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Simantirakis Ε, Arkolaki E, Kontaraki J, Chlouverakis G, Mavrakis H, Kallergis E, Parthenakis F, Vardas P. The impact of paced QRS duration on the expression of genes related to contractile function of the left ventricle in chronically paced patients from the right ventricular apex. Hellenic J Cardiol 2020; 61:274-278. [DOI: 10.1016/j.hjc.2019.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/17/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022] Open
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Meng H, Wang X, Ruan J, Chen W, Meng F, Yang P. High Expression Levels of the SOCS3 Gene Are Associated with Acute Myocardial Infarction. Genet Test Mol Biomarkers 2020; 24:443-450. [PMID: 32589469 DOI: 10.1089/gtmb.2020.0040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aims: The present study was designed to evaluate whether the expression of the suppressor of cytokine signaling 3 (SOCS3) gene could serve as a biomarker to predict the risk of acute myocardial infarction (AMI). Basic Methods: Peripheral white blood cells were collected from 113 patients with AMI and 92 patients with stable coronary artery disease (SCAD). SOCS3 mRNA expression levels in peripheral blood cells were determined by a real-time quantitative polymerase chain reaction, and levels of the SOCS3 protein were determined by Western blotting. Results: The mRNA expression levels of the SOCS3 gene in AMI patients was 1.33-fold higher than that in the SCAD patients, and the level of the SOCS3 protein was 1.25-fold higher (p < 0.05 for both). Bivariate logistic regression analysis documented that elevated expression of the SOCS3 gene was an independent risk factor for AMI. A regression analysis demonstrated a lack of correlation between elevated expression levels of SOCS3 and the levels of fasting blood glucose high- and low-density lipoprotein, and cardiac troponin. Conclusions: Elevated expression of the SOCS3 gene results most likely from enhanced inflammatory responses and is an independent risk factor for AMI.
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Affiliation(s)
- Heyu Meng
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis (Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease; Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease; Jilin Provincial Cardiovascular Research Institute), Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xue Wang
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis (Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease; Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease; Jilin Provincial Cardiovascular Research Institute), Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jianjun Ruan
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis (Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease; Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease; Jilin Provincial Cardiovascular Research Institute), Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Weiwei Chen
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis (Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease; Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease; Jilin Provincial Cardiovascular Research Institute), Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Fanbo Meng
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis (Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease; Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease; Jilin Provincial Cardiovascular Research Institute), Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Ping Yang
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis (Jilin Provincial Engineering Laboratory for Endothelial Function and Genetic Diagnosis of Cardiovascular Disease; Jilin Provincial Molecular Biology Research Center for Precision Medicine of Major Cardiovascular Disease; Jilin Provincial Cardiovascular Research Institute), Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
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25
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Whole blood transcriptome profile at hospital admission discriminates between patients with ST-segment elevation and non-ST-segment elevation acute myocardial infarction. Sci Rep 2020; 10:8731. [PMID: 32457432 PMCID: PMC7250845 DOI: 10.1038/s41598-020-65527-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Whether ST-segment (STEMI) and non-ST-segment elevation myocardial infarction (NSTEMI) should be regarded as distinct pathophysiological entities is a matter of debate. We tested the hypothesis that peripheral blood gene-expression profiles at presentation distinguish STEMI from NSTEMI. We performed a case-control study collecting whole-blood from 60 STEMI and 58 NSTEMI (defined according to the third universal definition of MI) consecutive patients on hospital admission. We used RNA-sequencing for the discovery phase, comparing 15 STEMI vs. 15 NSTEMI patients, matched for age, sex, and cardiovascular risk factors, and quantitative PCR in the remaining unmatched patients for validating top-significant genes. Gene-level differential expression analysis identified significant differences in the expression of 323 genes: 153 genes withstood correction for admission cardiac troponin I (cTnI), differentiating the two conditions independently of myocardial necrosis extent. Functional annotation analysis uncovered divergent modulation in leukocyte and platelet activation, cell migration, and mitochondrial respiratory processes. Linear regression analysis revealed gene expression patterns on admission predicting infarct size, as indexed by cTnI peak (R2 = 0.58–0.75). Our results unveil distinctive pathological traits for these two MI subtypes and provide insights into the early assessment of injury extent. This could translate into RNA-based disease-specific biomarkers for precision diagnosis and risk stratification.
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26
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Logan JG, Yun S, Bao Y, Farber E, Farber CR. RNA-sequencing analysis of differential gene expression associated with arterial stiffness. Vascular 2020; 28:655-663. [PMID: 32375599 DOI: 10.1177/1708538120922650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Arterial stiffness is recognized as an important predictor of cardiovascular disease morbidity and mortality, independent of traditional cardiovascular disease risk factors. Given that arterial tissue is not easily accessible, most gene expression studies on arterial stiffness have been conducted on animals or on patients who have undergone by-pass surgeries. In order to obtain a deeper understanding of early changes of arterial stiffness, this study compared transcriptome profiles between healthy adults with higher and lower arterial stiffness. METHODS The sample included 20 healthy female adults without cardiovascular disease. Arterial stiffness was measured by carotid-femoral pulse wave velocity, the "gold-standard" measure of central arterial stiffness. Peripheral blood samples collected to PAXgene™ RNA tubes were used for RNA sequencing (RNA-seq). The potential confounding effects of age, body mass index, and mean arterial pressure were controlled for in RNA-seq analysis. To validate RNA-seq results, quantitative real-time PCR (qRT-PCR) was performed for six selected genes. RESULTS The findings demonstrated that genes including CAPN9, IL32, ERAP2, RAB6B, MYBPH, and miRNA626 were down-regulated, and that MOCS1 gene was up-regulated among the people with higher arterial stiffness. Real-time PCR showed that the changes of CAPN9, IL32, ERAP2, and RAB6B were in concordance with RNA-seq data, and confirmed the validity of the gene expression profiles obtained by RNA-seq analysis. CONCLUSIONS Previous studies have suggested the potential roles of CAPN9, IL32, and ERAP2 in structural changes of the arterial wall through up-regulation of metalloproteinases. However, the current study showed that CAPN9, IL32, and ERAP2 were down-regulated in the individuals with higher arterial stiffness, compared with those with lower arterial stiffness. The unexpected directions of expression of these genes may indicate an effort to maintain vascular homeostasis during increased arterial stiffness among healthy individuals. Further studies are guaranteed to investigate the roles of CAPN9, IL32, and ERAP2 in regulating arterial stiffness in people with and without cardiovascular disease.
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Affiliation(s)
| | | | - Yongde Bao
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, USA
| | - Emily Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, USA
| | - Charles R Farber
- Department of Public Health Sciences and Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, USA
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Integrated miRNA/mRNA Counter-Expression Analysis Highlights Oxidative Stress-Related Genes CCR7 and FOXO1 as Blood Markers of Coronary Arterial Disease. Int J Mol Sci 2020; 21:ijms21061943. [PMID: 32178422 PMCID: PMC7139611 DOI: 10.3390/ijms21061943] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/10/2020] [Indexed: 11/23/2022] Open
Abstract
Our interest in the mechanisms of atherosclerosis progression (ATHp) has led to the recent identification of 13 miRNAs and 1285 mRNAs whose expression was altered during ATHp. Here, we deepen the functional relationship among these 13 miRNAs and genes associated to oxidative stress, a crucial step in the onset and progression of vascular disease. We first compiled a list of genes associated to the response to oxidative stress (Oxstress genes) by performing a reverse Gene Ontology analysis (rGO, from the GO terms to the genes) with the GO terms GO0006979, GO1902882, GO1902883 and GO1902884, which included a total of 417 unique Oxstress genes. Next, we identified 108 putative targets of the 13 miRNAs among these unique Oxstress genes, which were validated by an integrated miRNA/mRNA counter-expression analysis with the 1285 mRNAs that yielded 14 genes, Map2k1, Mapk1, Mapk9, Dapk1, Atp2a2, Gata4, Fos, Egfr, Foxo1, Ccr7, Vkorc1l1, Rnf7, Kcnh3, and Mgat3. GO enrichment analysis and a protein–protein-interaction network analysis (PPI) identified most of the validated Oxstress transcripts as components of signaling pathways, highlighting a role for MAP signaling in ATHp. Lastly, expression of these Oxstress transcripts was measured in PBMCs from patients suffering severe coronary artery disease, a serious consequence of ATHp. This allowed the identification of FOXO1 and CCR7 as blood markers downregulated in CAD. These results are discussed in the context of the interaction of the Oxstress transcripts with the ATHp-associated miRNAs.
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28
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Yao L, Zhou B, You L, Hu H, Xie R. LncRNA MIAT/miR-133a-3p axis regulates atrial fibrillation and atrial fibrillation-induced myocardial fibrosis. Mol Biol Rep 2020; 47:2605-2617. [DOI: 10.1007/s11033-020-05347-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 02/25/2020] [Indexed: 02/07/2023]
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Low Expression of FFAR2 in Peripheral White Blood Cells May Be a Genetic Marker for Early Diagnosis of Acute Myocardial Infarction. Cardiol Res Pract 2020; 2020:3108124. [PMID: 32411444 PMCID: PMC7204345 DOI: 10.1155/2020/3108124] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/08/2019] [Accepted: 12/26/2019] [Indexed: 12/25/2022] Open
Abstract
Objective To find molecular markers for the diagnosis of acute myocardial infarction (AMI), this research further verified the relationship between the expression level of FFAR2 gene and AMI by expanding the sample size based on the previous gene chip results. Methods Peripheral venous leukocytes were collected from 113 patients with AMI and 94 patients with noncoronary artery disease as the experimental group and the control group, respectively. Real-time fluorescence quantitative polymerase chain reaction was used to detect the expression of the FFAR2 gene. Western blot analysis was applied to detect the relative expression of the FFAR2 gene at the level of protein. Furthermore, the relationship between gene expression and clinical data was also analyzed and compared. Results The level of expression of FFAR2 gene in peripheral blood of patients with AMI was significantly lower than that of the control group (0.33 [0.04–1.08], 0.62 [0.07–1.86], respectively; p < 0.05), which was 0.53 times that of the control group. Western blot results presented that the FFAR2 protein level in the peripheral blood of the AMI group was lower than that of the control group (0.114; p=0.004). Analyzing clinical data of the subjects indicated that the average age of the AMI group was significantly higher than the age of control group (p < 0.01). Also, the fasting blood glucose level was higher (p < 0.01), and the high-density lipoprotein cholesterol (HDL-C) level was lower (p=0.03). The FFAR2 mRNA level correlated positively with the HDL-C level (p < 0.01). Logistic regression analysis suggested that the low expression of the FFAR2 gene in peripheral blood may be a risk factor for AMI independent of age, family history of diabetes, fasting blood glucose level, and HDL-C level (p=0.025). Compared with the high FFAR2 expression group, the risk of AMI in the low FFAR2 expression group was 6.308 times higher. Conclusion The expression level of the FFAR2 gene in peripheral blood of patients with AMI was significantly lower than that in the control group. Low expression of the FFAR2 gene in peripheral blood is an independent risk factor for AMI. Hence, it may also be a potential biomarker to predict AMI.
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30
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Peng X, Zhang Z, Ye D, Xing P, Zou Z, Lei H, Duan L. Gene dysregulation in peripheral blood of moyamoya disease and comparison with other vascular disorders. PLoS One 2019; 14:e0221811. [PMID: 31532776 PMCID: PMC6750579 DOI: 10.1371/journal.pone.0221811] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022] Open
Abstract
Objective Moyamoya disease (MMD) is a chronic occlusive cerebrovascular disease with unknown etiology, sharing many similar clinical symptoms with other vascular disorders. This study aimed to investigate gene dysregulation in peripheral blood of MMD and compare it with other vascular disorders. Methods Transcriptomic profiles of 12 MMD patients and 8 healthy controls were obtained using RNA sequencing. Differentially expressed genes (DEGs) were identified and several were validated by quantitative real-time PCR in independent samples. Biological pathway enrichment analysis of DEGs and deconvolution of leukocyte subsets in peripheral blood were performed. Expression profiles for other vascular diseases were downloaded from public database and consistent DEGs were calculated. Gene set enrichment analysis (GSEA) was conducted to compare gene dysregulation pattern between MMD and other vascular diseases. Results A total of 533 DEGs were identified for MMD. Up-regulated genes were mainly involved in extracellular matrix (ECM) organization, whereas down-regulated genes were primarily associated with inflammatory and immune responses. As for cell populations, significantly increased naïve B cells and naïve CD4 cells as well as obviously decreased resting natural killer cells were observed in peripheral blood of MMD patients. GSEA analysis indicated that only up-regulated genes of ischemic stroke and down-regulated genes of coronary artery disease and myocardial infarction were enriched in up-regulated and down-regulated genes of MMD, respectively. Conclusion Dysregulated genes in peripheral blood of MMD mainly played key roles in ECM organization, inflammatory and immune responses. This gene dysregulation pattern was specific compared with other vascular diseases. Besides, naïve B cells, naïve CD4 cells and resting natural killer cells were aberrantly disrupted in peripheral blood of MMD patients. These results will help elucidate the complicated pathogenic mechanism of MMD.
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Affiliation(s)
- Xing Peng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengshan Zhang
- Department of Neurosurgery, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Dongqing Ye
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Peiqi Xing
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengxing Zou
- Department of Neurosurgery, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Lian Duan
- Department of Neurosurgery, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
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Gorenjak V, Vance DR, Petrelis AM, Stathopoulou MG, Dadé S, Shamieh SE, Murray H, Masson C, Lamont J, Fitzgerald P, Visvikis-Siest S. Peripheral blood mononuclear cells extracts VEGF protein levels and VEGF mRNA: Associations with inflammatory molecules in a healthy population. PLoS One 2019; 14:e0220902. [PMID: 31419243 PMCID: PMC6697334 DOI: 10.1371/journal.pone.0220902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/25/2019] [Indexed: 01/09/2023] Open
Abstract
Background Vascular endothelial growth factor (VEGF) is a signal protein, implicated in various physiological and pathophysiological processes together with other common inflammatory biomarkers. However, their associations have not yet been fully elucidated. In the present study, we investigated associations between VEGF and four specific VEGF mRNA isoforms with levels of 11 inflammation molecules, derived from peripheral blood mononuclear cells (PBMCs) extracts. Methods Healthy participants from the STANISLAS Family Study (n = 285) were included. Levels of VEGF (four mRNA isoforms and protein levels) and inflammatory molecules (IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, INF-γ, TNF-α, MCP-1, EGF) were measured in PBMCs extracts. Multiple regression analyses were performed, adjusted for age and gender. Results The analyses revealed significant associations between VEGF protein levels and levels of IL-4 (β = 0.028, P = 0.013), MCP-1 (β = 0.015, P<0.0001) and EGF (β = 0.017, P<0.0001). Furthermore, mRNA isoform VEGF165 was associated with MCP-1 and IL-1α (P = 0.002 and P = 0.008, respectively); and mRNA isoform VEGF189 was associated with IL-4 and IL-6 (P = 0.019 and P = 0.034, respectively). Conclusions To our knowledge, the present study represents the first investigation that successfully demonstrates links between VEGF protein levels and inflammatory molecules levels derived from PBMCs extracts and identifies associations between specific VEGF mRNA isoforms and inflammatory molecules. Impact These findings provide novel insights that may assist in the development of new tissue and mRNA isoform specific measurements of VEGF levels, which may positively contribute to predicting the risk of common complex diseases and response of currently used anti-VEGF agents, and developing of novel targeted therapies for VEGF-related pathophysiology.
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Affiliation(s)
| | - Dwaine R. Vance
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | | | | | | | - Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Helena Murray
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | | | - John Lamont
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | - Peter Fitzgerald
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | - Sophie Visvikis-Siest
- Université de Lorraine, Inserm, IGE-PCV, Nancy, France
- Department of Internal Medicine and Geriatrics, CHU Technopôle Nancy-Brabois, Rue du Morvan, Vandoeuvre-lès-Nancy, France
- * E-mail:
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32
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Póliska S, Besenyei T, Végh E, Hamar A, Pusztai A, Váncsa A, Bodnár N, Szamosi S, Csumita M, Kerekes G, Szabó Z, Nagy Z, Szűcs G, Szántó S, Zahuczky G, Nagy L, Szekanecz Z. Gene expression analysis of vascular pathophysiology related to anti-TNF treatment in rheumatoid arthritis. Arthritis Res Ther 2019; 21:94. [PMID: 30987671 PMCID: PMC6466794 DOI: 10.1186/s13075-019-1862-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/08/2019] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES Impaired vascular pathophysiology and increased cardiovascular (CV) mortality are associated with rheumatoid arthritis (RA). To date, no genomic analysis of RA- and RA treatment-related vascular pathophysiology has been published. In this pilot study, we performed gene expression profiling in association with vascular pathophysiology in RA patients. METHODS Sixteen and 19 biologic-naïve RA patients were included in study 1 and study 2, respectively. In study 1, genetic signatures determined by microarray were related to flow-mediated vasodilation (FMD), pulse-wave velocity (PWV), and common carotid intima-media thickness (IMT) of patients. In study 2, clinical response (cR) vs non-response (cNR) to 1-year etanercept (ETN) or certolizumab pegol (CZP) treatment, as well as "vascular" response (vR) vs non-response (vNR) to biologics, were also associated with genomic profiles. Multiple testing could not be performed due to the relatively small number of patients; therefore, our pilot study may lack power. RESULTS In study 1, multiple genes were up- or downregulated in patients with abnormal vs normal FMD, IMT, and PWV. In study 2, there were 13 cR and 6 cNR anti-tumor necrosis factor (TNF)-treated patients. In addition, 10, 9, and 8 patients were FMD-20%, IMT-20%, and PWV-20% responders. Again, vascular responder status was associated with changes of the expression of various genes. The highest number of genes showing significant enrichment were involved in positive regulation of immune effector process, regulation of glucose transport, and Golgi vesicle budding. CONCLUSION Differential expression of multiple genetic profiles may be associated with vascular pathophysiology associated with RA. Moreover, distinct genetic signatures may also be associated with clinical and vascular responses to 1-year anti-TNF treatment.
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Affiliation(s)
- Szilárd Póliska
- Department of Biochemistry and Molecular Biology, University of Debrecen Faculty of Medicine, Debrecen, Hungary.,Department of Sports Medicine, University of Debrecen Faculty of Medicine, Debrecen, Hungary
| | - Timea Besenyei
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary.,Department of Internal Medicine, University of Debrecen Faculty of Medicine, Debrecen, Hungary
| | - Edit Végh
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Attila Hamar
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Anita Pusztai
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Andrea Váncsa
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Nóra Bodnár
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Szilvia Szamosi
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Mária Csumita
- Department of Biochemistry and Molecular Biology, University of Debrecen Faculty of Medicine, Debrecen, Hungary.,Department of Sports Medicine, University of Debrecen Faculty of Medicine, Debrecen, Hungary
| | - György Kerekes
- Department of Angiology, University of Debrecen Faculty of Medicine, Debrecen, Hungary
| | - Zoltán Szabó
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Zoltán Nagy
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Gabriella Szűcs
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary
| | - Sándor Szántó
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary.,Department of Sports Medicine, University of Debrecen Faculty of Medicine, Debrecen, Hungary
| | | | - László Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen Faculty of Medicine, Debrecen, Hungary
| | - Zoltán Szekanecz
- Department of Rheumatology, University of Debrecen Faculty of Medicine, Nagyerdei str 98, Debrecen, 4032, Hungary.
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Tan B, Liu M, Yang Y, Liu L, Meng F. Low expression of PIK3C2A gene: A potential biomarker to predict the risk of acute myocardial infarction. Medicine (Baltimore) 2019; 98:e15061. [PMID: 30946353 PMCID: PMC6456027 DOI: 10.1097/md.0000000000015061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
AIMS Phosphoinositide 3-kinases (PI3Ks) are a family of enzymes that phosphorylate the 3'-OH of inositol ring of phosphatidylinositol (PI) and regulate a broad range of signaling pathways. PIK3C2A is structurally distinct from the other members of this class and is expressed in endothelial cells, vascular endothelium, and smooth muscle. In ischemic cardiovascular diseases, such as coronary artery disease, pathology is associated with endothelial damage and inflammation, downregulation of the EPC cell population and function, and impaired angiogenesis. This study aims to make an assessment on whether expression of PIK3C2A gene can be used as a biomarker for predicting the risk of acute myocardial infarction (AMI). METHODS We collected peripheral blood from 84 subjects with non-coronary heart disease and 70 patients with AMI. The real-time quantitative PCR test was applied to measure levels of PIK3C2A gene expression at mRNA level in peripheral blood. RESULTS Our results indicated that the level of PIK3C2A gene expression in peripheral blood of AMI patients was significantly lower than one in the non-coronary heart disease subjects. Binary logistic regression analysis showed that low expression of PIK3C2A gene was an independent risk factor of AMI and increased the risk of AMI by 2.231 folds. Moreover, it was found that low expression of PIK3C2A gene was not associated with level of fasting blood glucose, platelet count, Gensini score of coronary artery, and quantity of cardiac troponin. CONCLUSION The level of PIK3C2A gene expression in patients with AMI is significantly lower than that of healthy people. Low expression of PIK3C2A gene is an independent risk factor of AMI. Low expression of PIK3C2A could serve as a potential biomarker to predict risk of AMI.
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Affiliation(s)
- Buchuan Tan
- China-Japan Union Hospital of Jilin University
| | - Miao Liu
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yushuang Yang
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
| | - Long Liu
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
| | - Fanbo Meng
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
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Skeletal Muscle-specific PGC-1α Overexpression Suppresses Atherosclerosis in Apolipoprotein E-Knockout Mice. Sci Rep 2019; 9:4077. [PMID: 30858489 PMCID: PMC6411944 DOI: 10.1038/s41598-019-40643-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/21/2019] [Indexed: 12/12/2022] Open
Abstract
Endurance exercise training prevents atherosclerosis. Peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) increases myokine secretion from the skeletal muscle, and these myokines have been shown to affect the function of multiple organs. Since endurance exercise training increases PGC-1α expression in skeletal muscles, we investigated whether skeletal muscle-specific PGC-1α overexpression suppresses atherosclerosis. Apolipoprotein E-knockout (ApoE-KO)/PGC-1α mice, which overexpress PGC-1α in the skeletal muscle of ApoE-KO mice, were sacrificed, and the atherosclerotic plaque area, spontaneous activity, plasma lipid profile, and aortic gene expression were measured. Immunohistochemical analyses were also performed. The atherosclerotic lesions in ApoE-KO/PGC-1α mice were 40% smaller than those in ApoE-KO mice, concomitant with the reduction in vascular cell adhesion molecule-1 (VCAM-1) and monocyte chemoattractant protein-1 (MCP-1) mRNA and protein levels in the aorta. Spontaneous activity and plasma lipid profiles were not changed by the overexpression of PGC-1α in the skeletal muscle. In human umbilical vein endothelial cells, Irisin and β-aminoisobutyric acid (BAIBA), PGC-1α-dependent myokines, inhibited the tumor necrosis factor α-induced VCAM-1 gene and protein expression. BAIBA also inhibited TNFα-induced MCP-1 gene expression. These results showed that the skeletal muscle-specific overexpression of PGC-1α suppresses atherosclerosis and that PGC-1α-dependent myokines may be involved in the preventive effects observed.
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Tan B, Liu Q, Yang L, Yang Y, Liu D, Liu L, Meng F. Low expression of PRMT5 in peripheral blood may serve as a potential independent risk factor in assessments of the risk of stable CAD and AMI. BMC Cardiovasc Disord 2019; 19:31. [PMID: 30704408 PMCID: PMC6357489 DOI: 10.1186/s12872-019-1008-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 01/23/2019] [Indexed: 01/03/2023] Open
Abstract
Background Protein arginine methyltransferases (PRMTs) can catalyse the methylation of arginine and participate in many important cellular reaction processes. The purpose of this research is to determine whether the expression levels of the PRMT5 gene in peripheral blood can be used as a biomarker for predicting the risk of Acute Myocardial Infarction (AMI). Methods In this research, peripheral blood was collected from 91 patients with AMI and 87 patients with stable coronary artery disease (CAD). Real-time fluorescent quantitative PCR was performed to measure the expression levels of the PRMT5 gene at the mRNA level, and a western blot analysis was performed to measure the expression levels of the PRMT5 gene at the protein level. Results The results indicate that at both the RNA and protein levels, the expression levels of the PRMT5 gene in peripheral blood from patients with AMI are significantly lower than those in peripheral blood from patients with stable CAD (Z = − 4.813, P = 0.000). The low expression of the PRMT5 gene is relevant to the Gensini score of the coronary artery (rs = − 0.205, P = 0.015) but is irrelevant to the serum level of blood lipids, level of cardiac troponin (rs = − 0.125, P = 0.413) and time intervals of occurrence (rs = − 0.146, P = 0.211). Patients who have a low PRMT5 expression in the peripheral blood are 5.472 times more likely to suffer from AMI than other patients. Conclusion Compared to stable CAD patients, AMI patients have a lower expression of the PRMT5 gene in their peripheral blood. Patients who have low PRMT5 gene expression in the peripheral blood are more likely to suffer from AMI than those with stable CAD. A low expression of the PRMT5 gene serves as an independent risk factor for the occurrence of AMI.
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Affiliation(s)
- Buchuan Tan
- China-Japan Union Hospital of Jilin University, Changchun, China
| | - Qian Liu
- First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Liping Yang
- Peking University Shenzhen Hospital, Shenzhen, China
| | - Yushuang Yang
- Cardiology Department of the China-Japan Union Hospital of Jilin University, 126, Xiantai Street, Changchun City, 130033, NO, China
| | - Dongna Liu
- Cardiology Department of the China-Japan Union Hospital of Jilin University, 126, Xiantai Street, Changchun City, 130033, NO, China
| | - Long Liu
- Cardiology Department of the China-Japan Union Hospital of Jilin University, 126, Xiantai Street, Changchun City, 130033, NO, China
| | - Fanbo Meng
- Cardiology Department of the China-Japan Union Hospital of Jilin University, 126, Xiantai Street, Changchun City, 130033, NO, China.
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Tutino VM, Poppenberg KE, Li L, Shallwani H, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H. Biomarkers from circulating neutrophil transcriptomes have potential to detect unruptured intracranial aneurysms. J Transl Med 2018; 16:373. [PMID: 30593281 PMCID: PMC6310942 DOI: 10.1186/s12967-018-1749-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/17/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Intracranial aneurysms (IAs) are dangerous because of their potential to rupture and cause deadly subarachnoid hemorrhages. Previously, we found significant RNA expression differences in circulating neutrophils between patients with unruptured IAs and aneurysm-free controls. Searching for circulating biomarkers for unruptured IAs, we tested the feasibility of developing classification algorithms that use neutrophil RNA expression levels from blood samples to predict the presence of an IA. METHODS Neutrophil RNA extracted from blood samples from 40 patients (20 with angiography-confirmed unruptured IA, 20 angiography-confirmed IA-free controls) was subjected to next-generation RNA sequencing to obtain neutrophil transcriptomes. In a randomly-selected training cohort of 30 of the 40 samples (15 with IA, 15 controls), we performed differential expression analysis. Significantly differentially expressed transcripts (false discovery rate < 0.05, fold change ≥ 1.5) were used to construct prediction models for IA using four well-known supervised machine-learning approaches (diagonal linear discriminant analysis, cosine nearest neighbors, nearest shrunken centroids, and support vector machines). These models were tested in a testing cohort of the remaining 10 neutrophil samples from the 40 patients (5 with IA, 5 controls), and model performance was assessed by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (PCR) was used to corroborate expression differences of a subset of model transcripts in neutrophil samples from a new, separate validation cohort of 10 patients (5 with IA, 5 controls). RESULTS The training cohort yielded 26 highly significantly differentially expressed neutrophil transcripts. Models using these transcripts identified IA patients in the testing cohort with accuracy ranging from 0.60 to 0.90. The best performing model was the diagonal linear discriminant analysis classifier (area under the ROC curve = 0.80 and accuracy = 0.90). Six of seven differentially expressed genes we tested were confirmed by quantitative PCR using isolated neutrophils from the separate validation cohort. CONCLUSIONS Our findings demonstrate the potential of machine-learning methods to classify IA cases and create predictive models for unruptured IAs using circulating neutrophil transcriptome data. Future studies are needed to replicate these findings in larger cohorts.
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Affiliation(s)
- Vincent M. Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY USA
| | - Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY USA
| | - Lu Li
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, NY USA
| | - Hussain Shallwani
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY USA
| | - James N. Jarvis
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY USA
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY USA
| | - Kenneth V. Snyder
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Elad I. Levy
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - John Kolega
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Hui Meng
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY USA
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Liu M, Jiang S, Ma Y, Ma J, Hassan W, Shang J. Peripheral-blood gene expression profiling studies for coronary artery disease and its severity in Xinjiang population in China. Lipids Health Dis 2018; 17:154. [PMID: 30021655 PMCID: PMC6052538 DOI: 10.1186/s12944-018-0798-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/11/2018] [Indexed: 12/19/2022] Open
Abstract
Background Alterations in gene expression in peripheral blood cells play a curtail role in the presence and extent of coronary artery disease (CAD), but its severity reflected by gene expression alterations in peripheral blood cells is still unknown in Xinjiang population in China. Methods Global gene expression profiling in peripheral blood was used to explore differentially expressed genes in coronary artery stenosis patients. RNA was extracted from peripheral blood of 9 controls without coronary stenosis and 21 cases with angiographically CAD. The extent of CAD severity was categorized angiographically as no CAD, mild CAD (20 to 50% luminal diameter stenosis [LDS]), moderate CAD (50 to 75% LDS) and severe CAD (≥75% LDS). Differentially expressed genes related with CAD severity from peripheral blood cells were screened by linear mixed effects analysis using the lme4 package in R. Then the differentially expressed genes that gradually up-regulated or down-regulated were enriched by Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Results The most significantly enrichments were toll-like receptor signaling pathway, immune responses, translational processes, cellular growth, inflammation and metabolic processes. Combined with NCBI-GeneRIF and PubMed analysis, we focused on the 12 genes associated with toll-like receptor signaling pathway in the extent of coronary artery stenosis patients. Receiver operating characteristic (ROC) analysis of 12 genes associated with toll-receptor signaling pathway in the 236 CAD patients from GEO database demonstrated that 12 genes expression could predict severe CAD with an area under the curve of 0.67, sensitivity of 77.65% and specificity of 51.52%. Conclusion These results suggest that 12 genes associated with toll-like receptor signaling pathway in peripheral-blood cells reflect the presence and extent of CAD severity in Xinjiang population in China. Electronic supplementary material The online version of this article (10.1186/s12944-018-0798-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng Liu
- Cancer Prevention and Research Institute, The affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Shubin Jiang
- Department of Coronary Care Unit, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, 830000, Xinjiang, China
| | - Yu Ma
- Department of Clinical Laboratory, The Fourth People' Hospital of Urumqi, Urumqi, 830002, Xinjiang, China
| | - Jun Ma
- Department of Coronary Care Unit, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, 830000, Xinjiang, China
| | - Waseem Hassan
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Jing Shang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China. .,Jiangsu Key Laboratory of TCM Evaluation and Translational Research, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
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Reynés B, Priego T, Cifre M, Oliver P, Palou A. Peripheral Blood Cells, a Transcriptomic Tool in Nutrigenomic and Obesity Studies: Current State of the Art. Compr Rev Food Sci Food Saf 2018; 17:1006-1020. [DOI: 10.1111/1541-4337.12363] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Bàrbara Reynés
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
| | - Teresa Priego
- Dept. of Physiology, Faculty of Medicine; Univ. Complutense de Madrid; Madrid Spain
| | - Margalida Cifre
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
| | - Paula Oliver
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
| | - Andreu Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
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D’Amore S, Härdfeldt J, Cariello M, Graziano G, Copetti M, Di Tullio G, Piglionica M, Scialpi N, Sabbà C, Palasciano G, Vacca M, Moschetta A. Identification of miR-9-5p as direct regulator of ABCA1 and HDL-driven reverse cholesterol transport in circulating CD14+ cells of patients with metabolic syndrome. Cardiovasc Res 2018; 114:1154-1164. [DOI: 10.1093/cvr/cvy077] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/22/2018] [Indexed: 01/01/2023] Open
Abstract
Abstract
Aims
Metabolic syndrome (MS) is a cluster of cardio-metabolic risk factors associated with atherosclerosis and low-grade inflammation. Using unbiased expression screenings in peripheral blood mononuclear cells, we depict here a novel expression chart of 678 genes and 84 microRNAs (miRNAs) controlling inflammatory, immune and metabolic responses. In order to further elucidate the link between inflammation and the HDL cholesterol pathway in MS, we focussed on the regulation of the ATP-binding cassette transporter A1 (ABCA1), a key player in cholesterol efflux (CE).
Methods and results
ABCA1 mRNA levels are suppressed in CD14+ cells of MS patients and are negatively correlated to body mass index (BMI), insulin-resistance (HOMA-IR) and cardiovascular risk, and positively to HDL cholesterol and CE. miRNA target in silico prediction identified a putative modulatory role of ABCA1 for the nuclear factor kappa-light-chain-enhancer of activated B cell (NF-κB) target miR-9-5p, whose expression pattern was up-regulated in CD14+ cells of MS patients, positively correlated to BMI, HOMA-IR, and triglycerides, and negatively to ABCA1 mRNA levels, HDL cholesterol and CE. Ectopic gain and loss of miR-9-5p function in macrophages modulated ABCA1 mRNA and protein levels, ABCA1 miRNA 3’-untranslated region target sequence reporter assay, and CE into HDL, thus confirming ABCA1 as a target of miR-9-5p.
Conclusions
We identified the NF-κB target miR-9-5p as a negative regulator of ABCA1 adding a novel target pathway in the relationship between inflammation and HDL-driven reverse cholesterol transport for prevention or treatment of atherosclerosis in MS.
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Affiliation(s)
- Simona D’Amore
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
- National Cancer Research Center, IRCCS Istituto Tumori ‘Giovanni Paolo II’, Viale Orazio Flacco, 65, 70124 Bari, Italy
| | - Jennifer Härdfeldt
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
- INBB, National Institute for Biostructures and Biosystems, Viale delle Medaglie d'Oro 305, 00136 Rome, Italy
| | - Marica Cariello
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
- INBB, National Institute for Biostructures and Biosystems, Viale delle Medaglie d'Oro 305, 00136 Rome, Italy
| | - Giusi Graziano
- National Cancer Research Center, IRCCS Istituto Tumori ‘Giovanni Paolo II’, Viale Orazio Flacco, 65, 70124 Bari, Italy
| | - Massimiliano Copetti
- Unit of Biostatistics IRCCS ‘Casa Sollievo della Sofferenza’, Viale Cappuccini 1, 71013 San Giovanni Rotondo (FG), Italy
| | - Giuseppe Di Tullio
- De Matteis Laboratory, Telethon Institute of Genetics and Medicine, Piazza Aldo Moro 34, 80078 Pozzuoli (NA), Italy
| | - Marilidia Piglionica
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Natasha Scialpi
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Carlo Sabbà
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Giuseppe Palasciano
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Michele Vacca
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Antonio Moschetta
- Department of Medicine, Aldo Moro University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy
- National Cancer Research Center, IRCCS Istituto Tumori ‘Giovanni Paolo II’, Viale Orazio Flacco, 65, 70124 Bari, Italy
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Su Y, Li L, Zhao S, Yue Y, Yang S. The long noncoding RNA expression profiles of paroxysmal atrial fibrillation identified by microarray analysis. Gene 2018; 642:125-134. [DOI: 10.1016/j.gene.2017.11.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/28/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
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Křivohlavá R, Grobárová V, Neuhöferová E, Fišerová A, Benson V. Interaction of colon cancer cells with glycoconjugates triggers complex changes in gene expression, glucose transporters and cell invasion. Mol Med Rep 2018; 17:5508-5517. [PMID: 29393416 DOI: 10.3892/mmr.2018.8490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/15/2017] [Indexed: 11/06/2022] Open
Abstract
Glycan metabolism balance is critical for cell prosperity, and macromolecule glycosylation is essential for cell communication, signaling and survival. Thus, glycotherapy may be a potential cancer treatment. The aim of the present study was to determine whether combined synthetic glycoconjugates (GCs) induce changes in gene expression that alter the survival of colon cancer cells. The current study evaluated the effect of the GCs N‑acetyl‑D‑glucosamine modified polyamidoamine dendrimer and calix[4]arene scaffold on cancer cell proliferation, apoptosis, invasion and sensitivity to immune cell‑mediated killing. Using reverse transcription‑quantitative polymerase chain reaction, the expression of genes involved in the aforementioned processes was measured. It was determined that GCs reduce the expression of the glucosaminyltransferases Mgat3 and Mgat5 responsible for surface glycosylation and employed components of the Wnt signaling pathway Wnt2B and Wnt9B. In addition, the calix[4]arene‑based GC reduced cell colony formation; this was accompanied by the downregulation of the metalloproteinase Mmp3. By contrast, the dendrimer‑based GC affected the expression of the glucose transporter components Sglt1 and Egfr1. Therefore, to the best of our knowledge, the present study is the first to reveal that N‑acetyl‑D‑glucosamine‑dendrimer/calix[4]arene GCs alter mRNA expression in a comprehensive way, resulting in the reduced malignant phenotype of the colon cancer cell line HT‑29.
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Affiliation(s)
- Romana Křivohlavá
- Laboratory of Molecular Biology and Immunology, Department of Immunology, Institute of Microbiology, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
| | - Valika Grobárová
- Laboratory of Molecular Biology and Immunology, Department of Immunology, Institute of Microbiology, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
| | - Eva Neuhöferová
- Laboratory of Molecular Biology and Immunology, Department of Immunology, Institute of Microbiology, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
| | - Anna Fišerová
- Laboratory of Molecular Biology and Immunology, Department of Immunology, Institute of Microbiology, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
| | - Veronika Benson
- Laboratory of Molecular Biology and Immunology, Department of Immunology, Institute of Microbiology, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
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Tan B, Liu L, Yang Y, Liu Q, Yang L, Meng F. Low CPNE3 expression is associated with risk of acute myocardial infarction: A feasible genetic marker of acute myocardial infarction in patients with stable coronary artery disease. Cardiol J 2018; 26:186-193. [PMID: 29297177 DOI: 10.5603/cj.a2017.0155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/28/2017] [Accepted: 12/15/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Gene COPINE III may be related to a phosphoprotein with intrinsic kinase activity and belongs to an unconventional kinase family. The CPNE3 gene may be used as a biomarker for assess- ment of occurrence and prognosis of various tumors. METHODS Peripheral blood was collected from 87 stable coronary artery disease (CAD) patients and 91 acute myocardial infarction (AMI) patients. Real-time quantitative polymerase chain reaction test and the western blot method were adopted to measure expression quantity of CPNE3 gene at the mRNA level and the protein level. RESULTS The expression of the CPNE3 gene in peripheral blood of AMI patients was significantly lower than those in peripheral blood of stable CAD patients. Low expression of CPNE3 gene was found to be unrelated to level of fasting blood glucose and serum blood lipid of patients, quantity of cardiac troponin and time of onset but was found to be correlated to the Gensini score for coronary artery. When the ex- pression of CPNE3 gene at the mRNA level in peripheral blood was used as the criterion for diagnosing AMI, its sensitivity, specificity, positive predictive value and negative predictive value were 69%, 64.8%, 68.6% and 65.2%, respectively. CONCLUSIONS Compared to stable CAD patients, AMI patients have a lower expression of CPNE3 gene in their peripheral blood. Patients who have low CPNE3 expression in peripheral blood are more likely to suffer from AMI than those with stable CAD. Low expression of CPNE3 gene serves as an potential independent risk factor of AMI.
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Affiliation(s)
- Buchuan Tan
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
| | - Long Liu
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yushuang Yang
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
| | - Qian Liu
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liping Yang
- Peking University Shenzhen Hospital, Shenzhen, China
| | - Fanbo Meng
- Cardiology Department of the China-Japan Union Hospital of Jilin University, Changchun, China.
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Early Right Ventricular Apical Pacing-Induced Gene Expression Alterations Are Associated with Deterioration of Left Ventricular Systolic Function. DISEASE MARKERS 2017; 2017:8405196. [PMID: 28928601 PMCID: PMC5591927 DOI: 10.1155/2017/8405196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/04/2017] [Indexed: 01/05/2023]
Abstract
The chronic high-dose right ventricular apical (RVA) pacing may have deleterious effects on left ventricular (LV) systolic function. We hypothesized that the expression changes of genes regulating cardiomyocyte energy metabolism and contractility were associated with deterioration of LV function in patients who underwent chronic RVA pacing. Sixty patients with complete atrioventricular block and preserved ejection fraction (EF) who underwent pacemaker implantation were randomly assigned to either RVA pacing (n = 30) group or right ventricular outflow tract (RVOT) pacing (n = 30) group. The mRNA levels of OPA1 and SERCA2a were significantly lower in the RVA pacing group at 1 month's follow-up (both p < 0.001). Early changes in the expression of selected genes OPA1 and SERCA2a were associated with deterioration in global longitudinal strain (GLS) that became apparent months later (p = 0.002 and p = 0.026, resp.) The altered expressions of genes that regulate cardiomyocyte energy metabolism and contractility measured in the peripheral blood at one month following pacemaker implantation were associated with subsequent deterioration in LV dyssynchrony and function in patients with preserved LVEF, who underwent RVA pacing.
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Gong R, Chen M, Zhang C, Chen M, Li H. A comparison of gene expression profiles in patients with coronary artery disease, type 2 diabetes, and their coexisting conditions. Diagn Pathol 2017; 12:44. [PMID: 28595632 PMCID: PMC5465468 DOI: 10.1186/s13000-017-0630-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 05/01/2017] [Indexed: 02/07/2023] Open
Abstract
Background To support a hypothesis that there is an intrinsic interplay between coronary artery disease (CAD) and type 2 diabetes (T2D), we used RNA-seq to identify unique gene expression signatures of CAD, T2D, and coexisting conditions. Methods After transcriptome sequencing, differential expression analysis was performed between each disordered state and normal control group. By comparing gene expression profiles of CAD, T2D, and coexisting conditions, common and specific patterns of each disordered state were displayed. To verify the specific gene expression patterns of CAD or T2D, the gene expression data of GSE23561 was extracted. Results A strong overlap of 191 genes across CAD, T2D and coexisting conditions, were mainly involved in a viral infectious cycle, anti-apoptosis, endocrine pancreas development, innate immune response, and blood coagulation. In T2D-specific PPI networks involving 64 genes, TCF7L2 (Degree = 169) was identified as a key gene in T2D development, while in CAD-specific PPI networks involving 64 genes, HIF1A (Degree = 124), SMAD1 (Degree = 112) and SKIL (Degree = 94) were identified as key genes in the CAD development. Interestingly, with the provided expression data from GSE23561, the three genes were all up-regulated in CAD, and SMAD1 and SKIL were specifically differentially expressed in CAD, while HIF1A was differentially expressed in both CAD and T2D, but with opposite trends. Conclusions This study provides some evidences in transcript level to uncover the association of T2D, CAD and coexisting conditions, and may provide novel drug targets and biomarkers for these diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13000-017-0630-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rui Gong
- Department of gerontology, The Third Municipal Hospital of Shijiazhuang City, Shijiazhuang, Hebei province, 050011, China
| | - Menghui Chen
- Department of cardiothoracic surgery, The Third Municipal Hospital of Shijiazhuang City, Shijiazhuang, Hebei province, 050011, China
| | - Cuizhao Zhang
- Medical laboratory technology, The Third Municipal Hospital of Shijiazhuang City, Shijiazhuang, Hebei province, 050011, China
| | - Manli Chen
- Department of gerontology, The Third Municipal Hospital of Shijiazhuang City, Shijiazhuang, Hebei province, 050011, China
| | - Haibin Li
- Department of Cardiology, The Third Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei province, 050051, China.
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Ribalta J, Alipour A, Sánchez-Cabo F, Vallvé JC, Njo T, Álvarez R, Janssen H, Liem A, Dopazo A, Castro-Cabezas M. Differential leucocyte RNA expression in the coronary arteries compared to systemic circulation discriminates between patients with and those without coronary artery disease. CLINICA E INVESTIGACION EN ARTERIOSCLEROSIS 2017; 29:60-66. [PMID: 28188023 DOI: 10.1016/j.arteri.2016.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/17/2022]
Abstract
AIMS To test the hypothesis that the pattern of gene expression in circulating leukocytes may differ between vascular compartments, depending on the presence or absence of atherosclerosis, we evaluated the regional vascular differences in patterns of inflammatory cell activation. METHODS Patients (n=8) with angiographically-established coronary artery disease (CAD+) and 8 without (CAD-) had blood samples taken from a peripheral vein as well as from left and right coronary arteries. Samples were pooled resulting in 4 CAD+ samples versus 4 CAD- samples and hybridised to a Whole Human Genome Microarray 4×44K. RESULTS CAD- patients had a similar gene expression profile across the different sites. CAD+ patients had statistically significant different gene expression patterns in venous vs. right and left coronary artery compartments. The expression pattern observed in the right coronary was where the most differences in gene expression were observed in CAD+ vs. CAD- patients. Overall, 1964 genes were differentially expressed between CAD+ and CAD-. Of these, 1052 were less expressed in CAD+ and 912 were more expressed in CAD+. Up to 12 of the 20 most differentially expressed genes appeared to reflect different phases of the atherosclerosis process: endothelial dysfunction, lipid accumulation, and smooth muscle cell proliferation. CONCLUSIONS Gene expression of circulating leukocytes differentiates CAD+ from CAD- patients. Gene expression is significantly different between coronary arteries and the systemic circulation in CAD+ patients, but not in CAD- patients. Gene expression is significantly different between CAD+ and CAD- subjects, and appears to reflect the atherosclerosis process. These intra-individual differences may be an additional feature of established coronary artery disease.
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Affiliation(s)
- Josep Ribalta
- Unitat de Recerca en Lípids i Arteriosclerosi, Facultat de Medicina, Hospital Universitari de Sant Joan de Reus, Universitat Rovira i Virgili, Institut d'Investigació Sanitària Pere Virgili, CIBERDEM, Reus, Spain.
| | - Arash Alipour
- Department of Internal Medicine, Centre for Diabetes and Vascular Medicine, St Franciscus Gasthuis, Rotterdam, The Netherlands
| | - Fátima Sánchez-Cabo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Joan-Carles Vallvé
- Unitat de Recerca en Lípids i Arteriosclerosi, Facultat de Medicina, Hospital Universitari de Sant Joan de Reus, Universitat Rovira i Virgili, Institut d'Investigació Sanitària Pere Virgili, CIBERDEM, Reus, Spain
| | - Tjin Njo
- Department of Clinical Chemistry, St Franciscus Gasthuis, Rotterdam, The Netherlands
| | - Rebeca Álvarez
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Hans Janssen
- Department of Clinical Chemistry, St Franciscus Gasthuis, Rotterdam, The Netherlands
| | - Anho Liem
- Department of Cardiology, St. Franciscus Gasthuis, Rotterdam, The Netherlands
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Manuel Castro-Cabezas
- Department of Internal Medicine, Centre for Diabetes and Vascular Medicine, St Franciscus Gasthuis, Rotterdam, The Netherlands
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Infante T, Forte E, Aiello M, Salvatore M, Cavaliere C. In Vivo and In Vitro Analysis in Coronary Artery Disease Related to Type 2 Diabetes. Front Endocrinol (Lausanne) 2017; 8:209. [PMID: 28871240 PMCID: PMC5566996 DOI: 10.3389/fendo.2017.00209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022] Open
Abstract
AIM The leading cause of morbidity and mortality in patients with type 2 diabetes mellitus (DM) is coronary artery disease (CAD), a condition often asymptomatic but severe in these patients. Although glucose metabolism impairment and oxidative stress are known actors in the endothelial dysfunction/remodeling that occurs in diabetic patients, the relationship between cardiovascular disorders and DM is not fully understood. We have performed both an in vivo imaging and in vitro molecular analysis to investigate diabetic-specific CAD alterations. METHODS Computed tomography coronary angiography (CTCA) was performed in a group of 20 diabetic patients with CAD (DM+CAD+), 20 non-diabetic with CAD (DM-CAD+), 10 diabetic non-CAD patients (DM+CAD-), and 20 non-diabetic healthy subjects (HS). Imaging quantitative parameters such as calcium score (Cascore), calcified plaque volume (CPV), non-calcified plaque volume (NCPV), total plaque volume (TPV), remodeling index (RI), and plaque burden were extracted for each CAD subject. Moreover, the expression levels of superoxide dismutase 2 (SOD2) and liver X receptor alpha (LXRα) genes were analyzed in the peripheral blood mononuclear cells, whereas hyaluronan (HA) concentrations were evaluated in the plasma of each subject. RESULTS Imaging parameters, such as Cascore, CPV, RI, and plaque burden, were significantly higher in DM+CAD+ group, compared to DM-CAD+ (P = 0.019; P = 0.014; P < 0.001, P < 0.001, respectively). SOD2 mRNA was downregulated, while LXRα gene expression was upregulated in DM+CAD-, DM+CAD+, and DM-CAD+ groups compared to HS (P = 0.001, P = 0.03, and P = 0.001 for SOD2 and P = 0.006, P = 0.008, and P < 0.001 for LXRα, respectively). Plasmatic levels of HA were higher in DM-CAD+, DM+CAD-, and DM+CAD+ groups, compared to HS (P = 0.001 for the three groups). When compared to DM-CAD+, HA concentration was higher in DM+CAD- (P = 0.008) and DM+CAD+ (P < 0.001) with a significant difference between the two diabetic groups (P = 0.003). Moreover, HA showed a significant association with diabetes (P = 0.01) in the study population, and the correlation between HA levels and glycemia was statistically significant (ρ = 0.73, P < 0.001). CONCLUSION In our population, imaging parameters highlight a greater severity of CAD in diabetic patients. Among molecular parameters, HA is modulated by diabetic CAD-related alterations while SOD2 and LXRα are found to be more associated with CAD but do not discriminate between diabetic and non-diabetic subgroups.
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Affiliation(s)
| | - Ernesto Forte
- IRCCS SDN, Naples, Italy
- *Correspondence: Ernesto Forte,
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Hartmann K, Seweryn M, Handleman SK, Rempała GA, Sadee W. Non-linear interactions between candidate genes of myocardial infarction revealed in mRNA expression profiles. BMC Genomics 2016; 17:738. [PMID: 27640124 PMCID: PMC5027110 DOI: 10.1186/s12864-016-3075-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alterations in gene expression are key events in disease etiology and risk. Poor reproducibility in detecting differentially expressed genes across studies suggests individual genes may not be sufficiently informative for complex diseases, such as myocardial infarction (MI). Rather, dysregulation of the 'molecular network' may be critical for pathogenic processes. Such a dynamic network can be built from pairwise non-linear interactions. RESULTS We investigate non-linear interactions represented in mRNA expression profiles that integrate genetic background and environmental factors. Using logistic regression, we test the association of individual GWAS-based candidate genes and non-linear interaction terms (between these mRNA expression levels) with MI. Based on microarray data in CATHGEN (CATHeterization in GENetics) and FHS (Framingham Heart Study), we find individual genes and pairs of mRNAs, encoded by 41 MI candidate genes, with significant interaction terms in the logistic regression model. Two pairs replicate between CATHGEN and FHS (CNNM2|GUCY1A3 and CNNM2|ZEB2). Analysis of RNAseq data from GTEx (Genotype-Tissue Expression) shows that 20 % of these disease-associated RNA pairs are co-expressed, further prioritizing significant interactions. Because edges in sparse co-expression networks formed solely by the 41 candidate genes are unlikely to represent direct physical interactions, we identify additional RNAs as links between network pairs of candidate genes. This approach reveals additional mRNAs and interaction terms significant in the context of MI, for example, the path CNNM2|ACSL5|SCARF1|GUCY1A3, characterized by the common themes of magnesium and lipid processing. CONCLUSIONS The results of this study support a role for non-linear interactions between genes in MI and provide a basis for further study of MI systems biology. mRNA expression profiles encoded by a limited number of candidate genes yield sparse networks of MI-relevant interactions that can be expanded to include additional candidates by co-expression analysis. The non-linear interactions observed here inform our understanding of the clinical relevance of gene-gene interactions in the pathophysiology of MI, while providing a new strategy in developing clinical biomarker panels.
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Affiliation(s)
- Katherine Hartmann
- College of Medicine Center for Pharmacogenomics, The Ohio State University Wexner Medical Center, Biomedical Research Tower, 460 W 12th Avenue, Columbus, OH USA
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Biomedical Research Tower, 460 W 12th Avenue, Columbus, OH USA
| | - Michał Seweryn
- Faculty of Mathematics and Computer Science, University of Łodz, Łodz, Poland
- Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH USA
| | - Samuel K. Handleman
- College of Medicine Center for Pharmacogenomics, The Ohio State University Wexner Medical Center, Biomedical Research Tower, 460 W 12th Avenue, Columbus, OH USA
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Biomedical Research Tower, 460 W 12th Avenue, Columbus, OH USA
| | - Grzegorz A. Rempała
- Division of Biostatistics, College of Public Health, The Ohio State University, 250 Cunz Hall, 1841 Neil Avenue, Columbus, OH USA
- Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH USA
| | - Wolfgang Sadee
- College of Medicine Center for Pharmacogenomics, The Ohio State University Wexner Medical Center, Biomedical Research Tower, 460 W 12th Avenue, Columbus, OH USA
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Biomedical Research Tower, 460 W 12th Avenue, Columbus, OH USA
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Altered mitochondrial expression genes in patients receiving right ventricular apical pacing. Exp Mol Pathol 2016; 100:469-75. [DOI: 10.1016/j.yexmp.2016.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/09/2016] [Accepted: 05/09/2016] [Indexed: 11/22/2022]
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Park HJ, Noh JH, Eun JW, Koh YS, Seo SM, Park WS, Lee JY, Chang K, Seung KB, Kim PJ, Nam SW. Assessment and diagnostic relevance of novel serum biomarkers for early decision of ST-elevation myocardial infarction. Oncotarget 2016; 6:12970-83. [PMID: 26025919 PMCID: PMC4536992 DOI: 10.18632/oncotarget.4001] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/04/2015] [Indexed: 11/25/2022] Open
Abstract
Blood transcriptome reflects the status of diseases, and characteristic molecular signature provides a novel window on gene expression preceding acute coronary events. We aim to determine blood transcriptome-based molecular signature of acute coronary syndrome (ACS), and to identify novel serum biomarkers for early stage ST-segment-elevation myocardial infarction (STEMI). We obtained peripheral blood from the patients with ACS who visited emergency department within 4 hours after the onset of chest pain: STEMI (n = 10), Non-ST-segment-elevation MI (NSTEMI, n = 10) and unstable angina (UA, n = 11). Blood transcriptome scans revealed that a characteristic gene expression change exists in STEMI, resulting in 531 outlier genes as STEMI molecular signature (Welch's t test, P < 0.05). Another analysis with a set of blood samples of patients with STEMI (n = 7) before and 7 days after the primary percutaneous coronary intervention (n = 7) and normal control (n = 10) evidenced that STEMI molecular signature directly reflects the onset of STEMI pathogenesis. From the two sets of transcriptome-based STEMI signatures, we identified 10 genes encoding transmembrane or secretory proteins that are highly expressed in STEMI. We validated blood protein expression levels of these 10 putative biomarkers in 40 STEMI and 32 healthy subjects by ELISA. Data suggested that PGLYRP1, IRAK3 and VNN3 are more specific and sensitive diagnostic biomarkers for STEMI than traditional CK-MB or troponin. Blood transcriptome scans of ACS evidenced early stage molecular markers for STEMI. Here, we report novel biomarkers to diagnose STEMI at emergency department in hospitals by a simple ELISA method.
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Affiliation(s)
- Hun-Jun Park
- Department of Cardiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ji Heon Noh
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Functional RNomics Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Woo Eun
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Functional RNomics Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon-Seok Koh
- Department of Cardiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Suk Min Seo
- Department of Cardiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Won Sang Park
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Young Lee
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kiyuk Chang
- Department of Cardiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki Bae Seung
- Department of Cardiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Pum-Joon Kim
- Department of Cardiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Suk Woo Nam
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Functional RNomics Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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van ’t Hof FNG, Ruigrok YM, Medic J, Sanjabi B, van der Vlies P, Rinkel GJE, Veldink JH. Whole Blood Gene Expression Profiles of Patients with a Past Aneurysmal Subarachnoid Hemorrhage. PLoS One 2015; 10:e0139352. [PMID: 26439625 PMCID: PMC4595144 DOI: 10.1371/journal.pone.0139352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/11/2015] [Indexed: 11/19/2022] Open
Abstract
Background The pathogenesis of development and rupture of intracranial aneurysms (IA) is largely unknown. Also, screening for IA to prevent aneurysmal subarachnoid hemorrhage (aSAH) is inefficient, as disease markers are lacking. We investigated gene expression profiles in blood of previous aSAH patients, who are still at risk for future IA, aiming to gain insight into the pathogenesis of IA and aSAH, and to make a first step towards improvement of aSAH risk prediction. Methods and Results We collected peripheral blood of 119 patients with aSAH at least two years prior, and 118 controls. We determined gene expression profiles using Illumina HumanHT-12v4 BeadChips. After quality control, we divided the dataset in a discovery (2/3) and replication set (1/3), identified differentially expressed genes, and applied (co-)differential co-expression to identify disease-related gene networks. No genes with a significant (false-discovery rate <5%) differential expression were observed. We detected one gene network with significant differential co-expression, but did not find biologically meaningful gene networks related to a history of aSAH. Next, we applied prediction analysis of microarrays to find a gene set that optimally predicts absence or presence of a history of aSAH. We found no gene sets with a correct disease state prediction higher than 40%. Conclusions No gene expression differences were present in blood of previous aSAH patients compared to controls, besides one differentially co-expressed gene network without a clear relevant biological function. Our findings suggest that gene expression profiles, as detected in blood of previous aSAH patients, do not reveal the pathogenesis of IA and aSAH, and cannot be used for aSAH risk prediction.
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Affiliation(s)
- Femke N. G. van ’t Hof
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
| | - Ynte M. Ruigrok
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jelena Medic
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bahram Sanjabi
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Pieter van der Vlies
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Gabriel J. E. Rinkel
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan H. Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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