Joint Effects of PON1 Polymorphisms and Vegetable Intake on Ischemic Stroke: A Family-Based Case Control Study

Juan, Juan; Jiang, Xia; Tang, Xun; Wu, Yiqun; Sun, Kexin; Xiao, Xiang; Tian, Yaohua; Wu, Tao; Sun, Qi; Kraft, Peter; Hu, Yonghua

doi:10.3390/ijms18122652

Cited by 12 publications

(13 citation statements)

References 56 publications

(68 reference statements)

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“…We applied EPISFA/EPISFA‐LD to a real dataset of 105 SNP variants in 1,001 ischemic stroke families (2,348 individuals) obtained from FISSC. Detailed information on FISSIC is documented elsewhere (Juan et al, 2017; Tang et al, 2007). FISSIC collected its participants' genetic information of 105 SNPs that were reported to be associated with ischemic stroke in either previously published GWAS/GWAS meta, or from candidate gene studies of ischemic stroke in Chinese populations.…”

Section: Resultsmentioning

confidence: 99%

Exploring gene–gene interaction in family‐based data with an unsupervised machine learning method: EPISFA

Xiao

Wang

Liu

et al. 2020

Genetic Epidemiology

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Gene–gene interaction (G × G) is thought to fill the gap between the estimated heritability of complex diseases and the limited genetic proportion explained by identified single‐nucleotide polymorphisms. The current tools for exploring G × G were often developed for case‐control designs with less considerations for their applications in families. Family‐based studies are robust against bias led from population stratification in genetic studies and helpful in understanding G × G. We proposed a new algorithm epistasis sparse factor analysis (EPISFA) and epistasis sparse factor analysis for linkage disequilibrium (EPISFA‐LD) based on unsupervised machine learning to screen G × G. Extensive simulations were performed to compare EPISFA/EPISFA‐LD with a classical family‐based algorithm FAM‐MDR (family‐based multifactor dimensionality reduction). The results showed that EPISFA/EPISFA‐LD is a tool of both high power and computational efficiency that could be applied in family designs and is applicable within high‐dimensionality datasets. Finally, we applied EPISFA/EPISFA‐LD to a real dataset drawn from the Fangshan/family‐based Ischemic Stroke Study in China. Five pairs of G × G were discovered by EPISFA/EPISFA‐LD, including three pairs verified by other algorithms (FAM‐MDR and logistic), and an additional two pairs uniquely identified by EPISFA/EPISFA‐LD only. The results from EPISFA might offer new insights for understanding the genetic etiology of complex diseases. EPISFA/EPISFA‐LD was implemented in R. All relevant source code as well as simulated data could be freely downloaded from https://github.com/doublexism/episfa.

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Section: Resultsmentioning

confidence: 99%

Exploring gene–gene interaction in family‐based data with an unsupervised machine learning method: EPISFA

Xiao

Wang

Liu

et al. 2020

Genetic Epidemiology

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“…Human MSCs from Wharton’s jelly could improve survival and increase the production of prostaglandin 2 and IL-10 in LPS-injected mice [ 30 ]. Human menstrual MSCs administered to LPS mice could decrease lung edema, decrease BALF IL-1β, and enhance lung repair [ 31 ]. Rats that had 100% O 2 for 48 h and cecal ligation puncture also were observed to have improved survival with the early administration of human umbilical cord MSCs [ 32 ].…”

Section: Discussionmentioning

confidence: 99%

Studies on the effects of bone marrow stem cells on mitochondrial function and the alleviation of ARDS

et al. 2020

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Mesenchymal stem cells (MSCs) can alleviate acute respiratory distress syndrome (ARDS), but the mechanisms involved are unclear, especially about their specific effects on cellular mitochondrial respiratory function. Thirty mice were allocated into the Control, LPS, and LPS + Bone marrow mesenchymal stem cell (BMSC) group (n = 10/group). Mouse alveolar epithelial cells (MLE-12) and macrophage cells (RAW264.7) were divided into the same groups. Pathological variation, inflammationrelated factors, reactive oxygen species (ROS), ATP levels, and oxygen consumption rate (OCR) were analyzed. Pathologic features of ARDS were observed in the LPS group and were significantly alleviated by BMSCs. The trend in inflammationrelated factors among the three groups was the LPS group > LPS + BMSC group > Control group. In the MLE-12 co-culture system, IL-6 was increased in the LPS group but not significantly reduced in the LPS + BMSC group. In the RAW264.7 co-culture system, IL-1β, TNF-α, and IL-10 levels were all increased in the LPS group, IL-1β and TNF-α levels were reduced by BMSCs, while IL-10 level kept increasing. ROS and ATP levels were increased and decreased respectively in both MLE-12 and RAW264.7 cells in the LPS groups but reversed by BMSCs. Basal OCR, ATP-linked OCR, and maximal OCR were lower in the LPS groups. Impaired basal OCR and ATP-linked OCR in MLE-12 cells were partially restored by BMSCs, while impaired basal OCR and maximal OCR in RAW264.7 cells were restored by BMSCs. BMSCs improved the mitochondrial respiration dysfunction of macrophages and alveolar epithelial cells induced by LPS, alleviated lung tissue injury, and inflammatory response in a mouse model of ARDS.

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“…Eligible parents and biological siblings of the probands were recruited by the proband-initiated contact method [ 22 ]. Self-reported IS cases were confirmed through medical records’ review and head imaging by computed tomography and/or magnetic resonance imaging according to the criteria of National Survey of Stroke [ 23 , 24 ]. In addition, IS cases were classified into five subtypes of large-artery atherosclerosis (LAA), small-vessel occlusion (SVO), cardioembolism, stroke of other determined etiology, and stroke of undetermined etiology based on the Trial of Org 10172 in acute stroke treatment (TOAST) [ 25 ].…”

Section: Methodsmentioning

confidence: 99%

Carotid Intima-Media Thickness, Genetic Risk, and Ischemic Stroke: A Family-Based Study in Rural China

Wang

et al. 2020

IJERPH

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Background: Carotid intima-media thickness (cIMT) has been associated with an elevated risk of ischemic stroke (IS) in several studies, but the results are inconsistent. We investigated whether the association between cIMT and IS varied across different IS subtypes, and further assessed gene–cIMT interactions’ association with IS risk. Methods: A total of 1048 IS cases (795 large-artery atherosclerosis (LAA) cases, 103 small-vessel occlusion (SVO) cases, and 150 other subtypes) and 2696 IS-free controls across 2179 families were included in the analysis. Self-reported IS cases were confirmed through medical records’ review and head imaging by computed tomography and/or magnetic resonance imaging. The mean values of the common cIMT obtained in bilateral distal and proximal carotid artery segments were used. The genotype information of rs2910164 polymorphism in microRNA-146a (miR-146a) was also collected. Results: We found that cIMT was significantly associated with a higher risk of IS and LAA subtype but not SVO subtype in the multivariate-adjusted models. The odds ratio (OR) and 95% confidence interval (CI) in the highest quartile versus the lowest quartile of cIMT was 2.48 (1.92–3.20) for IS and 2.75 (2.08–3.64) for LAA (both p trend <0.001). The results also showed that there was a significant interaction between cIMT and rs2910164 genotype with the risk of IS (p interaction = 0.03) and LAA (p interaction = 0.02). The associations of cIMT with IS and LAA were strengthened among participants carried rs2910164_GG genotype compared with those with rs2910164_CC genotype. Conclusions: Our results indicate that higher cIMT levels were significantly associated with IS and LAA subtype but not SVO subtype, and the relations were modified by rs2910164 polymorphism in miR-146a.

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Joint Effects of PON1 Polymorphisms and Vegetable Intake on Ischemic Stroke: A Family-Based Case Control Study

Cited by 12 publications

References 56 publications

Exploring gene–gene interaction in family‐based data with an unsupervised machine learning method: EPISFA

Exploring gene–gene interaction in family‐based data with an unsupervised machine learning method: EPISFA

Studies on the effects of bone marrow stem cells on mitochondrial function and the alleviation of ARDS

Carotid Intima-Media Thickness, Genetic Risk, and Ischemic Stroke: A Family-Based Study in Rural China

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