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Zheng PF, Zou QC, Chen LZ, Liu P, Liu ZY, Pan HW. Identifying patterns of immune related cells and genes in the peripheral blood of acute myocardial infarction patients using a small cohort. J Transl Med 2022; 20:321. [PMID: 35864510 PMCID: PMC9306178 DOI: 10.1186/s12967-022-03517-1] [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] [Received: 03/23/2022] [Accepted: 07/04/2022] [Indexed: 12/31/2022] Open
Abstract
Background The immune system plays a vital role in the pathophysiology of acute myocardial infarction (AMI). However, the exact immune related mechanism is still unclear. This research study aimed to identify key immune-related genes involved in AMI. Methods CIBERSORT, a deconvolution algorithm, was used to determine the proportions of 22 subsets of immune cells in blood samples. The weighted gene co-expression network analysis (WGCNA) was used to identify key modules that are significantly associated with AMI. Then, CIBERSORT combined with WGCNA were used to identify key immune-modules. The protein–protein interaction (PPI) network was constructed and Molecular Complex Detection (MCODE) combined with cytoHubba plugins were used to identify key immune-related genes that may play an important role in the occurrence and progression of AMI. Results The CIBERSORT results suggested that there was a decrease in the infiltration of CD8 + T cells, gamma delta (γδ) T cells, and resting mast cells, along with an increase in the infiltration of neutrophils and M0 macrophages in AMI patients. Then, two modules (midnightblue and lightyellow) that were significantly correlated with AMI were identified, and the salmon module was found to be significantly associated with memory B cells. Gene enrichment analysis indicated that the 1,171 genes included in the salmon module are mainly involved in immune-related biological processes. MCODE analysis was used to identify four different MCODE complexes in the salmon module, while four hub genes (EEF1B2, RAC2, SPI1, and ITGAM) were found to be significantly correlated with AMI. The correlation analysis between the key genes and infiltrating immune cells showed that SPI1 and ITGAM were positively associated with neutrophils and M0 macrophages, while they were negatively associated with CD8 + T cells, γδ T cells, regulatory T cells (Tregs), and resting mast cells. The RT-qPCR validation results found that the expression of the ITGAM and SPI1 genes were significantly elevated in the AMI samples compared with the samples from healthy individuals, and the ROC curve analysis showed that ITGAM and SPI1 had a high diagnostic efficiency for the recognition of AMI. Conclusions Immune cell infiltration plays a crucial role in the occurrence and development of AMI. ITGAM and SPI1 are key immune-related genes that are potential novel targets for the prevention and treatment of AMI. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03517-1.
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Affiliation(s)
- Peng-Fei Zheng
- Cardiology Department, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China.,Clinical Research Center for Heart Failure in Hunan Province, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China.,Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
| | - Qiong-Chao Zou
- Cardiology Department, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China.,Clinical Research Center for Heart Failure in Hunan Province, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China.,Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
| | - Lu-Zhu Chen
- Department of Cardiology, The Central Hospital of ShaoYang, No.36 QianYuan lane, Daxiang District, Shaoyang, 422000, Hunan, China
| | - Peng Liu
- Department of Cardiology, The Central Hospital of ShaoYang, No.36 QianYuan lane, Daxiang District, Shaoyang, 422000, Hunan, China
| | - Zheng-Yu Liu
- Cardiology Department, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China. .,Clinical Research Center for Heart Failure in Hunan Province, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China. .,Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China.
| | - Hong-Wei Pan
- Cardiology Department, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China. .,Clinical Research Center for Heart Failure in Hunan Province, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China. .,Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, No.61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China.
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Zheng PF, Chen LZ, Pan HW, Liu P, Zheng ZF. Effects of USF1 SNPs and SNP–Environment Interactions on Serum Lipid Profiles and the Risk of Early-Onset Coronary Artery Disease in the Chinese Population. Front Cardiovasc Med 2022; 9:882728. [PMID: 35783856 PMCID: PMC9240353 DOI: 10.3389/fcvm.2022.882728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundUpstream transcription factor 1 (USF1) single-nucleotide polymorphisms (SNPs) are significantly associated with serum lipid levels in several different ethnic groups or populations, but their association with lipid levels and the risk of early-onset coronary artery disease (EOCAD) has not been reported in Han populations of southern China.MethodsSix USF1 SNPs (rs3737787, rs2774276, rs2516839, rs2516838, rs1556259, and rs2516837) were genotyped by next-generation sequencing (NGS) techniques in 686 control subjects and 728 patients with EOCAD.ResultsThe genotypic and allelic frequencies of the USF1 rs3737787 SNP were significantly different between the control and EOCAD groups. The subgroup analysis identified that the rs3737787T allele was related to a decreased risk of EOCAD, whereas the rs3737787C–rs2774276G–rs2516839A and rs3737787C–rs2774276G–rs2516839G haplotypes were related to an increased risk of EOCAD in men, and the rs3737787C–rs2774276G–rs2516839A and rs3737787T–rs2774276C–rs2516839A haplotypes were correlated with an increased risk of EOCAD in women (p < 0.05–0.01). Male rs3737787T allele carriers had lower low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglyceride (TG) concentrations than the rs3737787T allele non-carriers (p < 0.01). The interactions of rs3737787 with alcohol consumption and rs2516839 with smoking affected serum TC and LDL-C levels in men, whereas the interaction of rs3737787 with alcohol consumption affected serum high-density lipoprotein cholesterol (HDL-C) levels and the rs2516839-smoking interaction affected serum TC levels in women (pI < 0.001). The expression levels of the USF1 mRNA, interleukin 1β (IL-1β), tumor necrosis factor-α (TNF-α), and interleukin 6 (IL-6) were significantly lower in controls than in patients with EOCAD, and rs3737787T allele carriers displayed lower IL-1β, TNF-α, IL-6, and USF1 mRNA expression levels than the rs3737787T allele non-carriers. In addition, IL-1β, TNF-α, and IL-6 expression levels were significantly positively correlated with USF1 mRNA levels (p < 0.01).ConclusionSex-specific correlations were identified between the USF1 rs3737787T allele with blood lipid levels and the risk of EOCAD. The USF1 rs3737787T allele affects the risk of EOCAD by modulating serum lipid levels and the expression of inflammatory factors, including IL-1β, TNF-α, and IL-6.
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Affiliation(s)
- Peng-Fei Zheng
- Cardiology Department, Hunan Provincial People's Hospital, Changsha, China
- Clinical Research Center for Heart Failure in Hunan Province, Changsha, China
- Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, Changsha, China
| | - Lu-Zhu Chen
- Department of Cardiology, The Central Hospital of ShaoYang, Shaoyang, China
| | - Hong-Wei Pan
- Cardiology Department, Hunan Provincial People's Hospital, Changsha, China
- Clinical Research Center for Heart Failure in Hunan Province, Changsha, China
- Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, Changsha, China
| | - Peng Liu
- Department of Cardiology, The Central Hospital of ShaoYang, Shaoyang, China
- *Correspondence: Peng Liu
| | - Zhao-Fen Zheng
- Cardiology Department, Hunan Provincial People's Hospital, Changsha, China
- Clinical Research Center for Heart Failure in Hunan Province, Changsha, China
- Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, Changsha, China
- Zhao-Fen Zheng
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Zheng PF, Chen LZ, Liu P, Pan HW. A novel lncRNA-miRNA-mRNA triple network identifies lncRNA XIST as a biomarker for acute myocardial infarction. Aging (Albany NY) 2022; 14:4085-4106. [PMID: 35537778 PMCID: PMC9134965 DOI: 10.18632/aging.204075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/16/2022] [Indexed: 11/25/2022]
Abstract
Despite the well-established role of long non-coding RNAs (lncRNAs) across various biological processes, their mechanisms in acute myocardial infarction (AMI) are not fully elucidated. The GSE34198 dataset from the Gene Expression Omnibus (GEO) database, which comprised 49 specimens from individuals with AMI and 47 specimens from controls, was extracted and analysed using the weighted gene co-expression network analysis (WGCNA) package. Twenty-seven key genes were identified through a combination of the degree and gene significance (GS) values, and the CDC42 (degree = 64), JAK2 (degree = 41), and CHUK (degree = 30) genes were identified as having the top three-degree values among the 27 genes. Potential interactions between lncRNA, miRNAs and mRNAs were predicted using the starBase V3.0 database, and a lncRNA-miRNA-mRNA triple network containing the lncRNA XIST, twenty-one miRNAs and three hub genes (CDC42, JAK2 and CHUK) was identified. RT-qPCR validation showed that the expression of the JAK2 and CDC42 genes and the lncRNA XIST was noticeably increased in samples from patients with AMI compared to normal samples. Pearson's correlation analysis also proved that JAK2 and CDC42 expression levels correlated positively with lncRNA XIST expression levels. The area under ROC curve (AUC) of lncRNA XIST was 0.886, and the diagnostic efficacy of the lncRNA XIST was significantly better than that of JAK2 and CDC42. The results suggested that the lncRNA XIST appears to be a risk factor for AMI likely through its ability to regulate JAK2 and CDC42 gene expressions, and it is expected to be a novel and reliable biomarker for the diagnosis of AMI.
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Affiliation(s)
- Peng-Fei Zheng
- Cardiology Department, Hunan Provincial People's Hospital, Furong District, Changsha 410000, Hunan, China.,Clinical Research Center for Heart Failure in Hunan Province, Furong District, Changsha 410000, Hunan, China.,Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, Furong District, Changsha 410000, Hunan, China
| | - Lu-Zhu Chen
- Department of Cardiology, The Central Hospital of ShaoYang, Daxiang District, Shaoyang 422000, Hunan, China
| | - Peng Liu
- Department of Cardiology, The Central Hospital of ShaoYang, Daxiang District, Shaoyang 422000, Hunan, China
| | - Hong-Wei Pan
- Cardiology Department, Hunan Provincial People's Hospital, Furong District, Changsha 410000, Hunan, China.,Clinical Research Center for Heart Failure in Hunan Province, Furong District, Changsha 410000, Hunan, China.,Institute of Cardiovascular Epidemiology, Hunan Provincial People's Hospital, Furong District, Changsha 410000, Hunan, China
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4
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Wai Yeung M, Wang S, van de Vegte YJ, Borisov O, van Setten J, Snieder H, Verweij N, Said MA, van der Harst P. Twenty-Five Novel Loci for Carotid Intima-Media Thickness: A Genome-Wide Association Study in >45 000 Individuals and Meta-Analysis of >100 000 Individuals. Arterioscler Thromb Vasc Biol 2021; 42:484-501. [PMID: 34852643 PMCID: PMC8939707 DOI: 10.1161/atvbaha.121.317007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE Carotid artery intima-media thickness (cIMT) is a widely accepted marker of subclinical atherosclerosis. Twenty susceptibility loci for cIMT were previously identified and the identification of additional susceptibility loci furthers our knowledge on the genetic architecture underlying atherosclerosis. Approach and Results: We performed 3 genome-wide association studies in 45 185 participants from the UK Biobank study who underwent cIMT measurements and had data on minimum, mean, and maximum thickness. We replicated 15 known loci and identified 20 novel loci associated with cIMT at P<5×10-8. Seven novel loci (ZNF385D, ADAMTS9, EDNRA, HAND2, MYOCD, ITCH/EDEM2/matrix metalloproteinase [MMP]24, and MRTFA) were identified in all 3 phenotypes. An additional new locus (LOXL1) was identified in the meta-analysis of the 3 phenotypes. Sex interaction analysis revealed sex differences in 7 loci including a novel locus (SYNE3) in males. Meta-analysis of UK Biobank data with a previous meta-analysis led to identification of three novel loci (APOB, FIP1L1, and LOXL4). Transcriptome-wide association analyses implicated additional genes ARHGAP42, NDRG4, and KANK2. Gene set analysis showed an enrichment in extracellular organization and the PDGF (platelet-derived growth factor) signaling pathway. We found positive genetic correlations of cIMT with coronary artery disease rg=0.21 (P=1.4×10-7), peripheral artery disease rg=0.45 (P=5.3×10-5), and systolic blood pressure rg=0.30 (P=4.0×10-18). A negative genetic correlation between average of maximum cIMT and high-density lipoprotein was found rg=-0.12 (P=7.0×10-4). CONCLUSIONS Genome-wide association meta-analyses in >100 000 individuals identified 25 novel loci associated with cIMT providing insights into genes and tissue-specific regulatory mechanisms of proatherosclerotic processes. We found evidence for shared biological mechanisms with cardiovascular diseases.
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Affiliation(s)
- Ming Wai Yeung
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.)
| | - Siqi Wang
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.).,Department of Epidemiology, University of Groningen, University Medical Center Groningen, the Netherlands. (S.W., H.S.)
| | - Yordi J van de Vegte
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.)
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Germany (O.B.)
| | - Jessica van Setten
- Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, the Netherlands. (S.W., H.S.)
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.)
| | - M Abdullah Said
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.).,Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands. (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.).,Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
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Zheng PF, Yin RX, Cao XL, Chen WX, Wu JZ, Huang F. Effect of SYTL3- SLC22A3 Variants, Their Haplotypes, and G × E Interactions on Serum Lipid Levels and the Risk of Coronary Artery Disease and Ischaemic Stroke. Front Cardiovasc Med 2021; 8:713068. [PMID: 34458338 PMCID: PMC8387813 DOI: 10.3389/fcvm.2021.713068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/21/2021] [Indexed: 11/18/2022] Open
Abstract
Background: The current study aimed to investigate the effects of synaptotagmin-like 3 (SYTL3) and solute carrier family 22 member 3 (SLC22A3) single nucleotide polymorphisms (SNPs) and gene-environment (G × E) interactions on blood lipid levels as well as the risk of coronary artery disease (CAD) and ischaemic stroke (IS) in the Southern Chinese Han population. Methods: The genetic makeup of 6 SYTL3-SLC22A3 SNPs in 2269 unrelated participants (controls, 755; CAD, 758 and IS, 756) of Chinese Han ethnicity was detected by the next-generation sequencing techniques. Results: The allele and genotype frequencies of the SYTL3 rs2129209 and SLC22A3 rs539298 SNPs were significantly different between the case and control groups. The SLC22A3 rs539298 SNP was correlated with total cholesterol (TC) levels in controls, the rs539298G allele carriers maintained lower TC levels than the rs539298G allele non-carriers. At the same time, the SLC22A3 rs539298 SNP interacted with alcohol consumption reduced the risk of CAD and IS. The SYTL3-SLC22A3 A-C-A-A-A-A, G-T-C-G-C-A and A-T-A-A-C-A haplotypes increased and the A-C-A-A-C-G haplotype reduced the risk of CAD, whereas the SYTL3-SLC22A3 A-C-A-A-A-A, G-T-C-G-A-G and A-T-A-A-C-A haplotypes increased and the A-C-A-A-A-G and A-C-A-A-C-G haplotypes reduced the risk of IS. In addition, several SNPs interacted with alcohol consumption, body mass index ≥ 24 kg/m2 and cigarette smoking to affect serum lipid parameters such as triglyceride, high-density lipoprotein cholesterol, TC, and apolipoprotein A1 levels. Conclusions: Several SYTL3-SLC22A3 variants, especially the rs539298 SNP, several haplotypes, and G × E interactions, were related to blood lipid parameters and the risk of CAD and IS in the Southern Chinese Han population.
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Affiliation(s)
- Peng-Fei Zheng
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Xiao-Li Cao
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Wu-Xian Chen
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Jin-Zhen Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Feng Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
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Abudureyimu S, Abulaiti P, Li H, Xing Z, Liu S, Li W, Gao Y. Roles of endothelial lipase gene related single nucleotide polymorphisms in patients with coronary artery disease. Gene 2021; 788:145669. [PMID: 33882321 DOI: 10.1016/j.gene.2021.145669] [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: 01/18/2021] [Revised: 03/23/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
The current work focused on evaluating the roles of endothelial lipase gene (LIPG) related single nucleotide polymorphisms (SNPs) in patients with coronary artery disease (CAD). This study involved 1,883 subjects with 959 CAD patients and 924 healthy controls. Data were harvested to assess the association of LIPG related SNPs including rs3744841, rs3744843, rs3813082 and rs2000813 with the risk of CAD. The CC + AC genotype in rs3813082 played a protective role for CAD [odds ratio (OR) = 0.709, P = 0.039]. Differences existed in apolipoprotein-A1 (Apo-A1) and high-density lipoprotein-cholesterol (HDL-C) levels in rs3744843 variant between control and CAD groups. The rs3744841 variant increased the levels of total cholesterol (TC), HDL-C, low-density lipoprotein cholesterol (LDL-C), Apo-A1 and Lipoprotein a (LPa) in the CAD group and TC, LDL-C, HDL-C, Apo-B, Apo-A1 in the control group. The triglyceride (TG) level was lower in rs2000813 variant in the CAD group and elevated in the control group. The rs2000813 variant decreased the number of vascular stenosis while rs3744843 and rs3744841 variants increased the number of vascular stenosis in CAD patients. This study explored the roles of LIPG related SNPs in CAD, showing that CC + AC genotype in rs3813082 was a protective factor for CAD. The rs3744843, rs3744841 and rs2000813 variants were associated with the levels of lipid parameters in CAD patients. The rs3744843, rs3744841 and rs2000813 variants influenced the number of vascular stenosis in CAD patients. The results of our study might be a promising reference for preventing CAD.
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Affiliation(s)
- Shajidan Abudureyimu
- Department of Comprehensive Internal Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011 China
| | - Palida Abulaiti
- Department of Comprehensive Internal Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011 China
| | - Hui Li
- Department of Comprehensive Internal Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011 China
| | - Zhi Xing
- Department of Comprehensive Internal Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011 China
| | - Shasha Liu
- Department of Comprehensive Internal Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011 China
| | - Wen Li
- Department of Comprehensive Internal Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011 China
| | - Ying Gao
- Department of Comprehensive Internal Medicine, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011 China.
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Discrimination of alcohol dependence based on the convolutional neural network. PLoS One 2020; 15:e0241268. [PMID: 33108388 PMCID: PMC7591038 DOI: 10.1371/journal.pone.0241268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/13/2020] [Indexed: 11/19/2022] Open
Abstract
In this paper, a total of 20 sites of single nucleotide polymorphisms (SNPs) on the serotonin 3 receptor A gene (HTR3A) and B gene (HTR3B) are used for feature fusion with age, education and marital status information, and the grid search-support vector machine (GS-SVM), the convolutional neural network (CNN) and the convolutional neural network combined with long and short-term memory (CNN-LSTM) are used to classify and discriminate between alcohol-dependent patients (AD) and the non-alcohol-dependent control group. The results show that 19 SNPs combined with academic qualifications have the best discrimination effect. In the GS-SVM, the area under the receiver operating characteristic (ROC) curve (AUC) is 0.87, the AUC of CNN-LSTM is 0.88, and the performance of the CNN model is the best, with an AUC of 0.92. This study shows that the CNN model can more accurately discriminate AD than the SVM to treat patients in time.
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8
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Improvements and deficits progression among ischemic stroke patients with pre-stroke depression and thrombolytic therapy. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.npbr.2020.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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9
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Liu CX, Yin RX, Shi ZH, Deng GX, Zheng PF, Wei BL, Guan YZ. EHBP1 SNPs, Their Haplotypes, and Gene-Environment Interactive Effects on Serum Lipid Levels. ACS OMEGA 2020; 5:7158-7169. [PMID: 32280856 PMCID: PMC7143410 DOI: 10.1021/acsomega.9b03522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/18/2020] [Indexed: 05/03/2023]
Abstract
The associations between single nucleotide polymorphisms (SNPs) rs2710642 and rs10496099 and their effect on the EH domain-binding protein 1 (EHBP1) gene and serum lipid profiles remain uncertain. This study was performed to investigate the two EHBP1 SNPs in Han and Maonan populations, including their association, haplotypes, and effects on serum lipid levels. Two EHBP1 SNPs in 564 Han and 796 Maonan participants were genotyped by high-throughput sequencing, and then the genotype and haplotype distributions of two EHBP1 SNPs were analyzed. Moreover, risk factors and their effects on serum lipid levels were analyzed using multivariable linear regression and logistic regression analyses. In Han and Maonan populations, a significant difference was found in the allelic and genotypic frequencies of the EHBP1 rs2710642 and rs10496099 SNPs and the alternate alleles of rs2710642A and rs10496099C might be potentially beneficial for healthy lipid levels. Medium linkage disequilibrium between the two SNPs was noted in each ethnic group, and four main haplotypes were detected. The rs2710642G-rs10496099C haplotype was associated with high triglycerides (TGs) and low high-density lipoprotein cholesterol, and the rs2710642A-rs10496099C haplotype was associated with low TGs and high apolipoprotein A1. The rs2710642G-rs10496099C haplotype was a high-risk factor for hyperlipidemia, and it interacted with smoking, fasting blood glucose, and hypertension to increase but with the female factor to decrease the prevalence of hyperlipidemia in Han individuals. The EHBP1 rs2710642 and rs10496099 SNPs and gene-environment interactions were associated with serum lipid profiles and hyperlipidemia, which is of ethnic specificity to our study populations.
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Affiliation(s)
- Chun-Xiao Liu
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
| | - Rui-Xing Yin
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
- Guangxi
Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular
Disease Control and Prevention, Nanning 530021, Guangxi, People’s Republic of China
- Guangxi
Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning 530021, Guangxi, People’s Republic
of China
| | - Zong-Hu Shi
- Department
of Prevention and Health Care, The Fourth Affiliated Hospital, Guangxi Medical University, Liuzhou 545005, Guangxi, People’s Republic
of China
| | - Guo-Xiong Deng
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
| | - Peng-Fei Zheng
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
| | - Bi-Liu Wei
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
| | - Yao-Zong Guan
- Department
of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated
Hospital, Guangxi Medical University, Nanning 530021, Guangxi, People’s Republic
of China
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Li KG, Yin RX, Huang F, Chen WX, Wu JZ, Cao XL. XKR6 rs7014968 SNP Increases Serum Total Cholesterol Levels and the Risk of Coronary Heart Disease and Ischemic Stroke. Clin Appl Thromb Hemost 2020; 26:1076029620902844. [PMID: 32024373 PMCID: PMC7288804 DOI: 10.1177/1076029620902844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The X Kell blood group complex subunit-related family member 6
(XKR6) gene single-nucleotide polymorphisms (SNPs) have
been associated with serum lipid profiles and the risk of coronary heart disease
(CHD) and ischemic stroke (IS) in several previous studies, but the association
between the XKR6 rs7014968 SNP and serum lipid levels and the
risk of CHD and IS has not been detected previously. This study aims to explore
the association between the XKR6 rs7014968 SNP and serum lipid
traits and the susceptibility to CHD and IS in the Guangxi Han Chinese
population. Snapshot technology was used to determine the genotypes of the
XKR6 rs7014968 SNP in 624 controls, 588 patients with CHD,
and 544 patients with IS. The XKR6 rs7014968C allele carriers
in the control group had higher serum total cholesterol (TC) levels than the C
allele noncarriers (P = .025). The XKR6
rs7014968C allele carriers also had an increased risk of CHD and IS
(P < .05-.01). Stratified analysis showed that the
patients with the rs7014968C allele in the female, age >60 years, body mass
index (BMI) >24 kg/m2, and hypertension subgroups had a higher
risk of CHD than those in the subgroup counterparts. The patients with the
rs7014968C allele in the male, BMI > 24 kg/m2, smoker, and
hypertension subgroups also had a higher risk of IS than those in the subgroup
counterparts. These results suggest that the XKR6 rs7014968 SNP
is likely to increase the risk of CHD and IS by increasing serum TC levels in
our study populations.
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Affiliation(s)
- Kai-Guang Li
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, Nanning, Guangxi, People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, People's Republic of China
| | - Feng Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, Nanning, Guangxi, People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, People's Republic of China
| | - Wu-Xian Chen
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Jin-Zhen Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiao-Li Cao
- Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, Nanning, Guangxi, People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, People's Republic of China.,Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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