Association of CALM1 rs3179089 Polymorphism with Ischemic Stroke in Chinese Han Population

DDCM: A Computational Strategy for Drug Repositioning Based on Support-Vector Regression Algorithm

Computational drug-repositioning technology is an effective tool for speeding up drug development. As biological data resources continue to grow, it becomes more important to find effective methods to identify potential therapeutic drugs for diseases. The effective use of valuable data has become a more rational and efficient approach to drug repositioning. The disease-drug correlation method (DDCM) proposed in this study is a novel approach that integrates data from multiple sources and different levels to predict potential treatments for diseases, utilizing support-vector regression (SVR). The DDCM approach resulted in potential therapeutic drugs for neoplasms and cardiovascular diseases by constructing a correlation hybrid matrix containing the respective similarities of drugs and diseases, implementing the SVR algorithm to predict the correlation scores, and undergoing a randomized perturbation and stepwise screening pipeline. Some potential therapeutic drugs were predicted by this approach. The potential therapeutic ability of these drugs has been well-validated in terms of the literature, function, drug target, and survival-essential genes. The method's feasibility was confirmed by comparing the predicted results with the classical method and conducting a co-drug analysis of the sub-branch. Our method challenges the conventional approach to studying disease-drug correlations and presents a fresh perspective for understanding the pathogenesis of diseases.

Association of MMP3, MMP14, and MMP25 gene polymorphisms with cerebral stroke risk: a case-control study

BACKGROUND

Cerebral stroke (CS) is the leading cause of death in China, and a complex disease caused by both alterable risk factors and genetic factors. This study intended to investigate the association of MMP3, MMP14, and MMP25 single nucleotide polymorphisms (SNPs) with CS risk in a Chinese Han population.

METHODS

A total of 1,348 Han Chinese were recruited in this case-control study. Four candidate loci including rs520540 A/G and rs679620 T/C of MMP3, rs2236302 G/C of MMP14, and rs10431961 T/C of MMP25 were successfully screened. The correlation between the four SNPs and CS risk was assessed by logistic regression analysis. The results were analyzed by false-positive report probability (FPRP) for chance or significance. The interactions between four SNPs associated with CS risk were assessed by multifactor dimensionality reduction (MDR).

RESULTS

rs520540 A/G and rs679620 C/T SNP in MMP3 were associated with risk of CS in allele, codominant, dominant and log-additive models. Ischemic stroke risk were significantly lower in carriers with rs520540-A allele and rs679620-T allele than those with G/G or C/C genotypes. However, rs520540-A allele and rs679620-T allele were associated with higher risk of hemorrhagic stroke. Stratified analysis showed that these two SNPs were associated with reduced risk of CS in aged < 55 years, non-smoking and non-drinking participants, and rs679620 SNP also reduced CS risk in male participants. The levels of uric acid, high-density lipoprotein cholesterol, and eosinophil were different among patients with different genotypes of rs520540 and rs679620. No statistically significant association was found between MMP14 rs2236302 G/C or MMP25 rs10431961 T/C with CS even after stratification by stroke subtypes, age, gender as well as smoking and drinking conditions in all the genetic models.

CONCLUSION

MMP3 rs520540 A/G and rs679620 C/T polymorphisms were associated with CS risk in the Chinese Han population, which provides useful information for the prevention and diagnosis of CS.

Influence of ZFHX3 Polymorphisms on the Risk of Ischemic Stroke in Chinese Han Population

The association of ZFHX3 gene polymorphisms with ischemia stroke (IS) susceptibility has been clarified in Europeans, but not in the Chinese Han population. To assess the effect of ZFHX3 polymorphisms on IS risk, rs7193343, rs879324, and rs12932445 were selected and genotyped using the Agena MassARRAY platform in 694 patients and 687 healthy controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression model adjusted for age, sex, smoking, and drinking status. The potentially influential factors for IS risk were analyzed using multifactor dimension reduction (MDR) software v3.0.2 and least absolute shrinkage and selection operator (LASSO) logistic regression. Our results displayed that rs879324 (p = 0.011, OR = 0.81) and rs12932445 (p = 0.012, OR = 0.81) were protective factors for IS in the Chinese Han population. Specifically, rs879324 had a lower susceptibility to IS in subjects aged ≤ 64 years, non-smokers, and non-drinkers (p < 0.05). Furthermore, rs12932445 was associated with a reduced risk of IS in people aged > 64 years, females, non-smokers, and non-drinkers (p < 0.05). MDR and LASSO analyses revealed that rs879324 was the most influential factor for IS risk. These findings suggested that ZFHX3 variants may be biomarkers in IS occurrence in the Chinese Han population, which may provide a new insight into the etiology of IS.

CYP11B1 gene polymorphisms and susceptibility to ischemic stroke in a Chinese Han population

Objectives

Ischemic stroke (IS) is the major cause of death and disability. While previous studies confirmed that CYP11B1 is closely associated with IS, the present study aimed to analyze the impact of CYP11B1 gene polymorphisms on the IS susceptibility.

Methods

The present study genotyped six single nucleotide polymorphisms (SNPs) (including rs4736312, rs5017238, rs5301, rs5283, rs6410, and rs4534) of CYP11B1 in peripheral blood samples from IS and control populations. Logistic regression analysis was used to analyze the association between the SNPs and IS risk. The multifactor dimensionality reduction (MDR) method was used to determine the roles of SNP–SNP interactions in IS.

Results

The present study showed that rs5283 was associated with an increased susceptibility to IS [odds ratio (OR) 1.81, p = 0.012]. On the contrary, rs6410 had a protective influence on IS risk (OR 0.56, p = 0.020). Stratified analyses indicated that rs5283 could enhance the risk of IS in subjects aged &gt;63 years (OR 2.41, p = 0.011), of female gender (OR 3.31, p = 0.001), that do not smoke (OR 1.64, p = 0.005), and with hypertension (OR 2.07, p = 0.003). Whereas, rs6410 was related to a lower susceptibility to IS in subjects aged &gt;63 years (OR 0.43, p = 0.032), of female gender (OR 0.30, p = 0.006), do not smoke (OR 0.42, p = 0.017), and with hypertension (OR 0.52, p = 0.022). Besides, rs4736312 reduced the IS susceptibility in non-smokers (OR 0.69, p = 0.031). Rs4534 had a risk-decreasing impact on IS in non-drinking (OR 0.54, p = 0.016). Moreover, the results of the MDR analysis corroborate that the best prediction model for IS was rs5283.

Conclusion

This study revealed that CYP11B1 gene polymorphisms strongly correlated with IS in the Chinese Han population.

The roles of MMP8/MMP10 polymorphisms in ischemic stroke susceptibility

BACKGROUND

Ischemic stroke (IS), a multifactorial and polygenic disease, is the most common cause of death. This study aimed to determine the roles of MMP8/MMP10 polymorphisms in IS susceptibility in the Chinese Han population.

METHODS

MMP8 rs1940475 and rs3765620, and MMP10 rs17860949 from 700 IS patients and 700 controls were genotyped by the MassARRAY iPLEX platform. The impact of polymorphisms on IS risk was evaluated by logistic regression analysis.

RESULTS

Our study indicated that rs17860949 in MMP10 was significantly associated with a reduced risk of IS (OR = 0.632, p = .002). Precisely, stratification analysis showed that rs17860949 was relate to a decreased susceptibility to IS in patients aged > 55 years (OR = 0.472, p < .001), males (OR = 0.632, p = .012), nonsmokers (OR = 0.610, p = .017), and nondrinkers (OR = 0.559, p = .006). All these significant findings were verified by false-positive report probability test. Furthermore, GG genotype and AG genotype in MMP8 rs3765620 polymorphism were related to a reduced triglycerides concentration (p = .018).

CONCLUSION

Our study suggests that rs17860949 in MMP10 may play a protective role in IS in the Chinese Han population.

LncRNA SERPINB9P1 expression and polymorphisms are associated with ischemic stroke in a Chinese Han population

Long noncoding RNAs (lncRNAs) were reported to play important roles in the pathogenesis of ischemic stroke (IS). Our study aimed to investigate the role of lncRNA SERPINB9P1 expression in ischemic stroke and the association between SERPINB9P1 polymorphisms and IS risk, as well as examine the correlation of SERPINB9P1 expression and variants with clinical parameters of IS. The SERPINB9P1 levels in human participants and oxygen-glucose deprivation (OGD)-treated human A172 cells were measured by qRT-PCR. The SERPINB9P1 polymorphisms (rs375556 and rs318429) were genotyped by the MassARRAY platform. We found that the SERPINB9P1 expression was significantly downregulated in patients with IS compared with that in healthy controls. On the 14th day in the hospital, the SERPINB9P1 level in patients with moderate and severe stroke was significantly downregulated compared with the normal group. After stratification by gender, the rs375556 polymorphism was significantly associated with susceptibility to female IS in the recessive model, and the significant association remained after adjusting for age. After adjusting for gender and age, rs318429 was significantly associated with FPG and D-D levels, and rs375556 was significantly associated with INR and PTA levels in IS cases. Besides, the lncRNA SERPINB9P1 expressed downregulated in OGD/reoxygenation-treated human A172 cells. In conclusion, the lncRNA SERPINB9P1 may protect against cerebral ischemia-reperfusion injury and neurological impairment after IS. The SERPINB9P1 rs375556 polymorphism was associated with susceptibility to female IS, and SERPINB9P1 polymorphisms may influence the metabolism of blood glucose and regulation of coagulation function in patients with IS.

Exploring the Potential Mechanism of Shennao Fuyuan Tang for Ischemic Stroke Based on Network Pharmacology and Molecular Docking

Methods

Screen the biologically active components and potential targets of SNFYT through Traditional Chinese Medicine Systems Pharmacology (TCMSP), Traditional Chinese Medicines Integrated Database (TCMID), and related literature. In addition, DrugBank, OMIM, DisGeNET, and the Therapeutic Target Database were searched to explore the therapeutic targets of IS. The cross-targets of SNFYT potential targets and IS treatment targets were taken as candidate gene targets, and GO and KEGG enrichment analyses were performed on the candidate targets. On this basis, the SNFYT-component-target network and protein-protein interaction (PPI) network were constructed using Cytoscape 3.7.2. Finally, AutoDock was used to verify the molecular docking of core components and core targets.

Results

We screened out 95 potentially active components and 143 candidate targets. SNFYT-component-target network, PPI network, and Cytoscape analysis identified four core active ingredients and 14 core targets. GO enrichment analyzed 2333 biological processes, 79 cell components, and 149 molecular functions. There are 170 KEGG-related signal pathways (P < 0.05), including the IL-17 signal pathway, TNF signal pathway, and HIF-1 signal pathway. The molecular docking results of the core components and the core targets showed good binding power.

Conclusions

SNFYT may achieve the effect of treating ischemic stroke through its anti-inflammatory effect through a signal pathway with core targets as the core.

CALM1 rs3179089 polymorphism might contribute to coronary artery disease susceptibility in Chinese male: a case-control study

BACKGROUND

Calmodulin 1 (CALM1) mutations are involved in the development of coronary artery disease (CAD). However, the relationship of CALM1 rs3179089 polymorphism with CAD is unknown.

OBJECTIVE

This study aimed to identify the relationship of CALM1 rs3179089 polymorphism with CAD susceptibility, CALM1 expression, blood pressure, blood glucose, blood coagulation and serum lipid levels of CAD patients.

METHODS

550 CAD patients and 550 control subjects were genotyped for CALM1 using Sequenom MassARRAY technology. CALM1 expression level was measured by quantitative real time polymerase chain reaction (qRT-PCR).

RESULTS

CALM1 mRNA expression was higher in CAD patients than that in control subjects (P < 0.001). CAD patients with CC genotype had higher CALM1 mRNA expression level than control subjects with CC genotype (P = 0.006). Genotypic frequency of rs3179089 was different between male patients of CAD and control subjects (P = 0.045). Rs3179089 polymorphism was related to CAD risk of males in recessive model (P = 0.039). Moreover, rs3179089 polymorphism was associated with systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting plasma glucose (FPG), and D-Dimer (D-D) level of patients with CAD in recessive model (P = 0.013 for SBP; P = 0.034 for DBP; P = 0.004 for FPG; P = 0.046 for D-D). In addition, rs3179089 polymorphism was correlated with low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) serum levels of patients with CAD in both addictive (P = 0.025 for LDL-C; P = 0.001 for TC) and recessive models (P = 0.001 for LDL-C; P = 0.001 for TC).

CONCLUSION

CALM1 expression is associated with development of CAD. CALM1 rs3179089 polymorphism affects CAD susceptibility in males, and blood pressure, blood glucose, blood coagulation and serum lipid of CAD patients.

Mechanism of Radix Rhei Et Rhizome Intervention in Cerebral Infarction: A Research Based on Chemoinformatics and Systematic Pharmacology

OBJECTIVE

To explore the therapeutic targets, network modules, and coexpressed genes of Radix Rhei Et Rhizome intervention in cerebral infarction (CI), and to predict significant biological processes and pathways through network pharmacology. To explore the differential proteins of Radix Rhei Et Rhizome intervention in CI, conduct bioinformatics verification, and initially explain the possible therapeutic mechanism of Radix Rhei Et Rhizome intervention in CI through proteomics.

METHODS

The TCM database was used to predict the potential compounds of Radix Rhei Et Rhizome, and the PharmMapper was used to predict its potential targets. GeneCards and OMIM were used to search for CI-related genes. Cytoscape was used to construct a protein-protein interaction (PPI) network and to screen out core genes and detection network modules. Then, DAVID and Metascape were used for enrichment analysis. After that, in-depth analysis of the proteomics data was carried out to further explore the mechanism of Radix Rhei Et Rhizome intervention in CI.

RESULTS

(1) A total of 14 Radix Rhei Et Rhizome potential components and 425 potential targets were obtained. The core components include sennoside A, palmidin A, emodin, toralactone, and so on. The potential targets were combined with 297 CI genes to construct a PPI network. The targets shared by Radix Rhei Et Rhizome and CI include ALB, AKT1, MMP9, IGF1, CASP3, etc. The biological processes that Radix Rhei Et Rhizome may treat CI include platelet degranulation, cell migration, fibrinolysis, platelet activation, hypoxia, angiogenesis, endothelial cell apoptosis, coagulation, and neuronal apoptosis. The signaling pathways include Ras, PI3K-Akt, TNF, FoxO, HIF-1, and Rap1 signaling pathways. (2) Proteomics shows that the top 20 proteins in the differential protein PPI network were Syp, Syn1, Mbp, Gap43, Aif1, Camk2a, Syt1, Calm1, Calb1, Nsf, Nefl, Hspa5, Nefh, Ncam1, Dcx, Unc13a, Mapk1, Syt2, Dnm1, and Cltc. Differential protein enrichment results show that these proteins may be related to synaptic vesicle cycle, vesicle-mediated transport in synapse, presynaptic endocytosis, synaptic vesicle endocytosis, axon guidance, calcium signaling pathway, and so on.

CONCLUSION

This study combined network pharmacology and proteomics to explore the main material basis of Radix Rhei Et Rhizome for the treatment of CI such as sennoside A, palmidin A, emodin, and toralactone. The mechanism may be related to the regulation of biological processes (such as synaptic vesicle cycle, vesicle-mediated transport in synapse, presynaptic endocytosis, and synaptic vesicle endocytosis) and signaling pathways (such as Ras, PI3K-Akt, TNF, FoxO, HIF-1, Rap1, and axon guidance).

Gene polymorphisms in calcium-calmodulin pathway: Focus on cardiovascular disease

Cardiovascular disease is the leading cause of death in industrialized countries and affects an increasing number of people. Several risk factors play an important role in the etiology of this disease, such as an unhealthy lifestyle. It is increasingly clear that genetic factors influencing the molecular basis of excitation-contraction mechanisms in the heart could contribute to modify the individual's risk. Thanks to the progress that has been made in understanding calcium signaling in the heart, it is assumed that calmodulin can play a crucial role in the excitation-contraction coupling. In fact, calmodulin (CaM) binds calcium and consequently regulates calcium channels. Several works show how some polymorphic variants can be considered predisposing factors to complex pathologies. Therefore, we hypothesize that the identification of polymorphic variants of proteins involved in the CaM pathway could be important for understanding how genetic traits can influence predisposition to myocardial infarction. This review considers each pathway of the three different isoforms of calmodulin (CaM1; CaM2; CaM3) and focuses on some common proteins involved in the three pathways, with the aim of analyzing the polymorphisms studied in the literature and understanding if they are associated with cardiovascular disease.

Association between a functional interleukin 6 receptor genetic variant and the risk and functional outcome of large artery atherosclerotic stroke

Purpose: To investigate whether the Asp358Ala of interleukin 6 receptor related to the risk and outcome of large artery atherosclerotic (LAA) stroke in Han Chinese.Materials and methods: A prospective cohort study was conducted on 768 patients with LAA stroke and 686 non-stroke controls. The genotypes of Asp358Ala polymorphism were determined using SNPscan technology. Associations between genotypes and the risk of LAA stroke were analyzed with logistic regression model.Results: CC genotype (P < 0.001) and AC genotype (P = 0.023) decreased the risk of LAA stroke compared with AA genotype. Multivariate logistic regression analysis revealed that CC genotype was significantly associated with the risk of LAA stroke (P = 0.002). In the subgroup analyses, polymorphisms of Asp358Ala were significantly associated with the risk of LAA stroke in additive model, dominant model and recessive model (P = 0.009, P = 0.017, P = 0.012, respectively) for male, but not for female. Further regression analysis showed that compared with participants with AA genotype and obesity, participants with CC genotype and non-obesity were less likely to suffer LAA stroke (P = 0.003). For male participants, these associations were still existed (additive model, P = 0.022). After 3-month follow-up, patients with C allele had good functional prognosis compared with patients with A allele (P = 0.009).Conclusion: The study demonstrated that the Asp358Ala polymorphism might be associated with susceptibility to the development and outcome of LAA stroke in Han Chines.