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Chis AF, Râjnoveanu RM, Man MA, Todea DA, Chis BA, Stancu B, Arghir IA, Alexescu TG, Pop CM. Increased Vascular Endothelial Growth Factor Serum Level and the Role of +936C/T Gene Polymorphism in Chronic Obstructive Pulmonary Disease. Medicina (B Aires) 2021; 57:medicina57121351. [PMID: 34946296 PMCID: PMC8707840 DOI: 10.3390/medicina57121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/30/2021] [Accepted: 12/05/2021] [Indexed: 11/16/2022] Open
Abstract
Background and Objectives: Chronic obstructive pulmonary disease (COPD) represents a debilitating disease, with rising morbidity and mortality. Vascular endothelial growth factor (VEGF) plays a major role in angiogenesis, vascular permeability, and airway remodeling. The purpose of this study was to investigate the relationship between VEGF serum levels and VEGF +936 C/T gene polymorphism (rs3025039) with COPD, for the first time in a Romanian population. Materials and Methods: In total, 120 participants from Transylvania were included in this case-control study. Serum levels of VEGF were determined using an enzyme-linked immune-sorbent assay and rs3025039 was investigated by high molecular weight genomic deoxyribonucleic acid (DNA). Spirometric values, arterial blood gas analysis, and the Six Minute Walk Test (6MWT) outcome were also determined. Results: The serum level of VEGF was higher in the COPD group versus controls (p < 0.001), with a positive correlation with the 6MWT outcome. No significant difference was observed in the VEGF serum levels between VEGF +936C/T genotypes. There was no difference in the VEGF +936C/T genotype between COPD patients and healthy subjects (chi2 test p = 0.92, OR = 1.04, 95%CI = 0.41–2.62), but the presence of the T allele was significantly linked to the presence of COPD (chi2 test p = 0.02, OR = 2.36, 95%CI = 1.12–4.97). Conclusions: Higher VEGF serum levels were found in moderate and severe COPD and were positively correlated with the distance in the 6MWT. No significant difference was found between CC, CT, and TT genotypes of rs3025039 and the presence of COPD. The presence of the T allele was found to be linked to COPD and also to the degree of airway obstruction.
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Affiliation(s)
- Ana Florica Chis
- Department of Pneumology, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 8th Victor Babeș Street, 400012 Cluj, Romania; (A.F.C.); (R.-M.R.); (M.A.M.); (D.A.T.); (C.M.P.)
- “Leon Daniello” Clinical Hospital of Pneumology, 6th Bogdan Petriceicu Hașdeu Street, 400332 Cluj, Romania
| | - Ruxandra-Mioara Râjnoveanu
- Department of Pneumology, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 8th Victor Babeș Street, 400012 Cluj, Romania; (A.F.C.); (R.-M.R.); (M.A.M.); (D.A.T.); (C.M.P.)
- “Leon Daniello” Clinical Hospital of Pneumology, 6th Bogdan Petriceicu Hașdeu Street, 400332 Cluj, Romania
| | - Milena Adina Man
- Department of Pneumology, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 8th Victor Babeș Street, 400012 Cluj, Romania; (A.F.C.); (R.-M.R.); (M.A.M.); (D.A.T.); (C.M.P.)
- “Leon Daniello” Clinical Hospital of Pneumology, 6th Bogdan Petriceicu Hașdeu Street, 400332 Cluj, Romania
| | - Doina Adina Todea
- Department of Pneumology, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 8th Victor Babeș Street, 400012 Cluj, Romania; (A.F.C.); (R.-M.R.); (M.A.M.); (D.A.T.); (C.M.P.)
- “Leon Daniello” Clinical Hospital of Pneumology, 6th Bogdan Petriceicu Hașdeu Street, 400332 Cluj, Romania
| | - Bogdan Augustin Chis
- 2nd Department of Internal Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8th Victor Babeș Street, 400012 Cluj, Romania
- Correspondence: ; Tel.: +40-740047253
| | - Bogdan Stancu
- 2nd Department of General Surgery, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8th Victor Babeș Street, 400012 Cluj, Romania;
| | - Ioan Anton Arghir
- 4th Department of Clinical Medical Disciplines II, “Ovidius” University of Medicine and Pharmacy, Mamaia Boulevard, No. 124, 900527 Constanța, Romania;
| | - Teodora Gabriela Alexescu
- 5th Departament Internal Medicine, 4th Medical Clinic, University of Medicine and Pharmacy, 400015 Cluj, Romania;
| | - Carmen Monica Pop
- Department of Pneumology, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 8th Victor Babeș Street, 400012 Cluj, Romania; (A.F.C.); (R.-M.R.); (M.A.M.); (D.A.T.); (C.M.P.)
- “Leon Daniello” Clinical Hospital of Pneumology, 6th Bogdan Petriceicu Hașdeu Street, 400332 Cluj, Romania
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Gao X, Wang X, Jiao N, Chen J, Sun D. Association of VEGFA polymorphisms with chronic obstructive pulmonary disease in Chinese Han and Mongolian populations. Exp Physiol 2021; 106:1839-1848. [PMID: 34081380 DOI: 10.1113/ep089523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/19/2021] [Indexed: 12/19/2022]
Abstract
NEW FINDINGS What is the central question of this study? Vascular endothelial growth factor A (VEGFA) is an important growth factor involved in changes in the bronchial microvascular and airway inflammation in chronic obstructive pulmonary disease (COPD) progression. What is the association of single nucleotide polymorphisms (SNPs) in VEGFA with the risk of COPD in the Chinese Han and Mongolian populations? What is the main finding and its importance? The effect of five SNPs in the VEGFA gene was analysed and compared between the Chinese Han and Mongolian populations. A contribution of risk alleles rs833068, rs833070 and rs3024997 to COPD was detected in the Chinese Mongolian population only. The study provided data from different populations to validate the role of VEGFA polymorphisms in COPD and provided reliable SNPs to predict the risk of COPD. ABSTRACT We attempted to define the associations between single nucleotide polymorphisms (SNPs) in the vascular endothelial growth factor A (VEGFA) gene and chronic obstructive pulmonary disease (COPD) in Chinese Han and Mongolian cohorts. Five SNPs were genotyped in cohorts of 684 COPD patients (350 Mongolian and 334 Han) and 784 healthy controls (350 Mongolian and 434 Han) using SNPscan multiplex PCR. SNP frequencies, genetic models and haplotypes were analysed using the chi-square test. The associations of SNPs with COPD and linkage disequilibrium were analysed using logistic regression and HaploView, respectively. We found that only rs833068G>A, rs833070T>C and rs3024997G>A were significantly associated with the risk of COPD in the Mongolian population (rs833068: P < 0.001, rs833070: P < 0.001, rs3024997: P = 0.002). In the analysis of genotype distributions, the A/A and G/A genotypes in rs833068 (A/A: odds ratio (OR) = 0.313, P < 0.001; G/A: OR = 0.724, P < 0.001) and rs3024997 (A/A: OR = 0.513, P = 0.008; G/A: OR = 0.671, P = 0.008) and the C/C and T/C genotypes in rs833070 (C/C: OR = 0.435, P = 0.007; T/C: OR = 0.593, P = 0.007) were associated with protection against COPD in the Mongolian population. The haplotype frequencies of GCCAT and GTCGC were significantly different between the patients and controls (GCCAT: P = 0.001; GTCGC: P < 0.001) in the Mongolian population. Our findings indicate that five SNPs in the VEGFA gene play divergent roles in the Han and Mongolian populations. rs833068A, rs833070C and rs3024997A were observed to be associated with the risk of COPD in the Mongolian population.
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Affiliation(s)
- Xiaoyu Gao
- Key Laboratory of National Health Commission for the Diagnosis & Treatment of COPD, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China
| | - Xin Wang
- Key Laboratory of National Health Commission for the Diagnosis & Treatment of COPD, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China.,Health care institution, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China
| | - Na Jiao
- Key Laboratory of National Health Commission for the Diagnosis & Treatment of COPD, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China
| | - Jiyuan Chen
- Key Laboratory of National Health Commission for the Diagnosis & Treatment of COPD, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China
| | - Dejun Sun
- Key Laboratory of National Health Commission for the Diagnosis & Treatment of COPD, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China
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Gorenjak V, Vance DR, Dade S, Stathopoulou MG, Doherty L, Xie T, Murray H, Masson C, Lamont J, Fitzgerald P, Visvikis-Siest S. Epigenome-wide association study in healthy individuals identifies significant associations with DNA methylation and PBMC extract VEGF-A concentration. Clin Epigenetics 2020; 12:79. [PMID: 32503626 PMCID: PMC7273671 DOI: 10.1186/s13148-020-00874-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/26/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Vascular endothelial growth factor A (VEGF-A) is a chemokine that induces proliferation and migration of vascular endothelial cells and is essential for both physiological and pathological angiogenesis. It is known for its high heritability (> 60%) and involvement in most common morbidities, which makes it a potentially interesting biomarker. Large GWAS studies have already assessed polymorphisms related to VEGF-A. However, no previous research has provided epigenome-wide insight in regulation of VEGF-A. METHODS VEGF-A concentrations of healthy participants from the STANISLAS Family Study (n = 201) were comprehensively assessed for association with DNA methylation. Genome-wide DNA methylation profiles were determined in whole blood DNA using the 450K Infinium BeadChip Array (Illumina). VEGF-A concentration in PBMC extracts was detected using a high-sensitivity multiplex Cytokine Array (Randox Laboratories, UK). RESULTS Epigenome-wide association analysis identified 41 methylation sites significantly associated with VEGF-A concentrations derived from PBMC extracts. Twenty CpG sites within 13 chromosomes reached Holm-Bonferroni significance. Significant values ranged from P = 1.08 × 10-7 to P = 5.64 × 10-15. CONCLUSION This study exposed twenty significant CpG sites linking DNA methylation to VEGF-A concentration. Methylation detected in promoter regions, such as TPX2 and HAS-1, could explain previously reported associations with the VEGFA gene. Methylation may also help in the understanding of the regulatory mechanisms of other genes located in the vicinity of detected CpG sites.
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Affiliation(s)
- Vesna Gorenjak
- IGE-PCV, Inserm, Université de Lorraine, F-54000, Nancy, France
| | - Dwaine R Vance
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, UK
| | - Sébastien Dade
- IGE-PCV, Inserm, Université de Lorraine, F-54000, Nancy, France
| | | | - Lauren Doherty
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, UK
| | - Ting Xie
- IGE-PCV, Inserm, Université de Lorraine, F-54000, Nancy, France
| | - Helena Murray
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, UK
| | | | - John Lamont
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, UK
| | - Peter Fitzgerald
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, UK
| | - Sophie Visvikis-Siest
- IGE-PCV, Inserm, Université de Lorraine, F-54000, Nancy, France.
- Department of Internal Medicine and Geriatrics, CHU Technopôle Nancy-Brabois, Rue du Morvan, F-54511, Vandoeuvre-lès-, Nancy, France.
- INSERM UMR U1122, IGE-PCV, Faculté de Pharmacie-Université de Lorraine, 30 rue Lionnois, 54000, Nancy, France.
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Ma X, Wu Y, Zhang L, Yuan W, Yan L, Fan S, Lian Y, Zhu X, Gao J, Zhao J, Zhang P, Tang H, Jia W. Comparison and development of machine learning tools for the prediction of chronic obstructive pulmonary disease in the Chinese population. J Transl Med 2020; 18:146. [PMID: 32234053 PMCID: PMC7110698 DOI: 10.1186/s12967-020-02312-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 03/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a major public health problem and cause of mortality worldwide. However, COPD in the early stage is usually not recognized and diagnosed. It is necessary to establish a risk model to predict COPD development. Methods A total of 441 COPD patients and 192 control subjects were recruited, and 101 single-nucleotide polymorphisms (SNPs) were determined using the MassArray assay. With 5 clinical features as well as SNPs, 6 predictive models were established and evaluated in the training set and test set by the confusion matrix AU-ROC, AU-PRC, sensitivity (recall), specificity, accuracy, F1 score, MCC, PPV (precision) and NPV. The selected features were ranked. Results Nine SNPs were significantly associated with COPD. Among them, 6 SNPs (rs1007052, OR = 1.671, P = 0.010; rs2910164, OR = 1.416, P < 0.037; rs473892, OR = 1.473, P < 0.044; rs161976, OR = 1.594, P < 0.044; rs159497, OR = 1.445, P < 0.045; and rs9296092, OR = 1.832, P < 0.045) were risk factors for COPD, while 3 SNPs (rs8192288, OR = 0.593, P < 0.015; rs20541, OR = 0.669, P < 0.018; and rs12922394, OR = 0.651, P < 0.022) were protective factors for COPD development. In the training set, KNN, LR, SVM, DT and XGboost obtained AU-ROC values above 0.82 and AU-PRC values above 0.92. Among these models, XGboost obtained the highest AU-ROC (0.94), AU-PRC (0.97), accuracy (0.91), precision (0.95), F1 score (0.94), MCC (0.77) and specificity (0.85), while MLP obtained the highest sensitivity (recall) (0.99) and NPV (0.87). In the validation set, KNN, LR and XGboost obtained AU-ROC and AU-PRC values above 0.80 and 0.85, respectively. KNN had the highest precision (0.82), both KNN and LR obtained the same highest accuracy (0.81), and KNN and LR had the same highest F1 score (0.86). Both DT and MLP obtained sensitivity (recall) and NPV values above 0.94 and 0.84, respectively. In the feature importance analyses, we identified that AQCI, age, and BMI had the greatest impact on the predictive abilities of the models, while SNPs, sex and smoking were less important. Conclusions The KNN, LR and XGboost models showed excellent overall predictive power, and the use of machine learning tools combining both clinical and SNP features was suitable for predicting the risk of COPD development.
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Affiliation(s)
- Xia Ma
- Department of Pulmonary and Critical Care Medicine, General Hospital of Datong Coal Mine Group Co., Ltd., Datong, 037000, China.,Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Yanping Wu
- Department of Respiratory, General Hospital of Tisco (Sixth Hospital of Shanxi Medical University), 2 Yingxin Street, Jiancaoping District, Taiyuan, 030008, Shanxi Province, China
| | - Ling Zhang
- Department of Respiratory, Linfen People's Hospital, Linfen, 041000, China
| | - Weilan Yuan
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China
| | - Li Yan
- Department of Respiratory Medicine, Hebei General Hospital, Shijiazhuang, 050000, China
| | - Sha Fan
- Department of Respiratory Medicine, Heji Hospital Affiliated with Changzhi Medical College, Changzhi, 046011, China
| | - Yunzhi Lian
- Department of Clinical Laboratory, JinCheng People's Hospital, Jincheng, 048000, China
| | - Xia Zhu
- Department of Respiratory, General Hospital of Tisco (Sixth Hospital of Shanxi Medical University), 2 Yingxin Street, Jiancaoping District, Taiyuan, 030008, Shanxi Province, China
| | - Junhui Gao
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China
| | - Ping Zhang
- Department of Clinical Laboratory, Linfen People's Hospital, West of Rainbow Bridge, West Binhe Road, Yaodu District, Linfen, 041000, Shanxi Province, China.
| | - Hui Tang
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China. .,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China.
| | - Weihua Jia
- Department of Respiratory, General Hospital of Tisco (Sixth Hospital of Shanxi Medical University), 2 Yingxin Street, Jiancaoping District, Taiyuan, 030008, Shanxi Province, China.
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KDR (VEGFR2) Genetic Variants and Serum Levels in Patients with Rheumatoid Arthritis. Biomolecules 2019; 9:biom9080355. [PMID: 31405022 PMCID: PMC6727087 DOI: 10.3390/biom9080355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 12/17/2022] Open
Abstract
We investigated kinase insert domain-containing receptor (KDR) polymorphisms and protein levels in relation to susceptibility to and severity of Rheumatoid Arthritis (RA). 641 RA patients and 340 controls (HC) were examined for the rs1870377 KDR variant by the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method and for rs2305948 and rs2071559 KDR single nucleotide polymorphisms (SNPs) by TaqMan SNP genotyping assay. KDR serum levels were determined by enzyme-linked immunosorbent assay (ELISA). The rs1870377 KDR variant has shown association with RA under the codominant (p = 0.02, OR = 1.76, 95% CI = 1.09–2.85) and recessive models (p = 0.019, OR = 1.53, 95% CI = 1.07–2.20). KDR rs2305948 was associated with RA under the dominant model (p = 0.005, OR = 1.38, 95% CI = 1.10–1.73). Under the codominant model, the frequency of the rs2071559 TC and GG genotypes were lower in RA patients than in controls (p < 0.001, OR = 0.51, 95% CI = 0.37–0.69, and p = 0.002, OR = 0.57, 95% CI = 0.39–0.81). KDR rs2071559 T and rs2305948 A alleles were associated with RA (p = 0.001, OR = 0.60, 95% CI = 0.45–0.81 and p = 0.008, OR = 1.71, CI = 1.15–2.54). KDR rs2305948SNP was associated with Disease Activity Score (DAS)-28 score (p < 0.001), Visual Analog Scale (VAS) score (p < 0.001), number of swollen joints (p < 0.001), mean value of CRP (p < 0.001). A higher KDR serum level was found in RA patients than in HC (8018 pg/mL versus 7381 pg/mL, p = 0.002). Present results shed light on the role of KDR genetic variants in the severity of RA.
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