1
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Singh M, Kumar S. Effect of single nucleotide polymorphisms on the structure of long noncoding RNAs and their interaction with RNA binding proteins. Biosystems 2023; 233:105021. [PMID: 37703988 DOI: 10.1016/j.biosystems.2023.105021] [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: 02/21/2023] [Revised: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
Long non-coding RNAs (lncRNA) are emerging as a new class of regulatory RNAs with remarkable potential to be utilized as therapeutic targets against many human diseases. Several genome-wide association studies (GWAS) have catalogued Single Nucleotide Polymorphisms (SNPs) present in the noncoding regions of the genome from where lncRNAs originate. In this study, we have selected 67 lncRNAs with GWAS-tagged SNPs and have also investigated their role in affecting the local secondary structures. Majority of the SNPs lead to changes in the secondary structure of lncRNAs to a different extent by altering the base pairing patterns. These structural changes in lncRNA are also manifested in form of alteration in the binding site for RNA binding proteins (RBPs) along with affecting their binding efficacies. Ultimately, these structural modifications may influence the transcriptional and post-transcriptional pathways of these RNAs, leading to the causation of diseases. Hence, it is important to understand the possible underlying mechanism of RBPs in association with GWAS-tagged SNPs in human diseases.
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Affiliation(s)
- Mandakini Singh
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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2
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Zeng Q, Zou D, Zeng Q, Chen X, Wei Y, Guo R. Association Between Insulin-like Growth Factor-1 rs35767 Polymorphism and Type 2 Diabetes Mellitus Susceptibility: A Meta-Analysis. Front Genet 2021; 12:774489. [PMID: 34880907 PMCID: PMC8646032 DOI: 10.3389/fgene.2021.774489] [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] [Received: 09/12/2021] [Accepted: 10/25/2021] [Indexed: 12/17/2022] Open
Abstract
Background: Insulin-like growth factor-1 (IGF-1) has been demonstrated to increase fatty acid β oxidation during fasting, and play an important role in regulating lipid metabolism and type 2 diabetes mellitus (T2DM). The rs35767 (T > C) polymorphism, a functional SNP was found in IGF-1 promoter, which may directly affect IGF-1 expression. However, the inconsistent findings showed on the IGF-1 rs35767 polymorphism and T2DM risk. Methods: We performed a comprehensive meta-analysis to estimate the association between the IGF-1 rs35767 and T2DM risk among four genetic models (the allele, additive, recessive and dominant models). Results: A total 49,587 T2DM cases and 97,906 NDM controls were included in the allele model, a total 2256 T2DM cases and 2228 NDM controls were included in the other three genetic models (the additive; recessive and dominant models). In overall analysis, the IGF-1 rs35767 was shown to be significantly associated with increased T2DM risk for the allele model (T vs. C: OR = 1.251, 95% CI: 1.082–1.447, p = 0.002), additive model (homozygote comparisons: TT vs. CC: OR = 2.433, 95% CI: 1.095–5.405, p = 0.029; heterozygote comparisons: TC vs. CC: OR = 1.623, 95% CI: 1.055–2.495, p = 0.027) and dominant model (TT + CT vs. CC: OR = 1.934, 95% CI: 1.148–3.257, p = 0.013) with random effects model. After omitting Gouda’s study could reduce the heterogeneity, especially in the recessive model (TT vs. CC + CT: I2 = 38.7%, p = 0.163), the fixed effects model for recessive effect of the T allele (TT vs. CC + CT) produce results that were of borderline statistical significance (OR = 1.206, 95% CI: 1.004–1.448, p = 0.045). And increasing the risk of T2DM in Uyghur population of subgroup for the allele model. Conclusion: The initial analyses that included all studies showed statistically significant associations between the rs35767 SNP and type 2 diabetes, but after removing the Gouda et al. study produced results that were mostly not statistically significant. Therefore, there is not enough evidence from the results of the meta-analysis to indicate that the rs35767 SNP has a statistically significant association with type 2 diabetes.
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Affiliation(s)
- Qiaoli Zeng
- Department of Internal Medicine, Shunde Women and Children's Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China.,Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China.,Shunde Women and Children's Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Matenal and Child Research Institute, Guangdong Medical University, Foshan, China
| | - Dehua Zou
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China.,Shunde Women and Children's Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Matenal and Child Research Institute, Guangdong Medical University, Foshan, China.,State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau (SAR) China
| | - Qiaodi Zeng
- Department of Clinical Laboratory, People's Hospital of Haiyuan County, Zhongwei, China
| | - Xiaoming Chen
- Department of Endocrinology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yue Wei
- Department of Ultrasound, Shunde Women and Children's Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China
| | - Runmin Guo
- Department of Internal Medicine, Shunde Women and Children's Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, China.,Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China.,Shunde Women and Children's Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Matenal and Child Research Institute, Guangdong Medical University, Foshan, China.,Department of Endocrinology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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3
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Lu L, Yao QY, Ruan SS, Hu JW, Long WJ, Dai WZ, Ma T, Zhu XC. Explore the role of CR1 genetic variants in late-onset Alzheimer's disease susceptibility. Psychiatr Genet 2021; 31:216-229. [PMID: 34347684 DOI: 10.1097/ypg.0000000000000291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Complement component (3b/4b) receptor 1 (CR1) is an interesting candidate gene which has a close connection with Alzheimer's disease, and its polymorphisms have been reported to link to the late-onset Alzheimer's disease (LOAD) susceptibility. However, the findings of these related studies are inconsistent. Objective To explore the effect of CR1 genetic variants in LOAD susceptibility. MethodsWe searched relevant studies for the period up to 1 November 2020. And odds ratios (ORs) and their 95% confidence intervals (CIs) were utilized to assess the strength of the association. In addition, we carried out a case-control association study to assess their genetic association. RESULTS Finally, a total of 30 articles with 30108 LOAD cases and 37895 controls were included. Significant allele frequency between LOAD patients and controls was observed in rs3818361 and rs6656401 (rs3818361, T vs. C: OR,1.18; 95% CI, 1.13-1.23; rs6656401, A vs. G: OR, 1.23; 95% CI, 1.10-1.36). Moreover, these results remain significant in subgroup of rs3818361 in Asia or America (OR,1.26; 95% CI,1.06-1.45; OR, 1.18; 95% CI, 1.13-1.24, respectively) and rs6656401 in Europe (OR = 1.26; 95% CI, 1.09-1.42). In addition, the two single nucleotide polymorphisms were proved to significantly increase LOAD risk in the overall population under the dominant model (OR = 1.12; 95% CI, 1.02-1.21; OR = 1.18, 95% CI, 1.15-1.22, respectively). Our case-control study showed that the distribution of rs6656401 genotype was significant (P = 0.000; OR, 6.889; 95% CI, 2.709-17.520), suggesting the A allele of rs6656401 is the risk allele. CONCLUSION These available data indicate that rs6656401 in CR1 is significant to increase LOAD risk.
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Affiliation(s)
- Liu Lu
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Qing-Yu Yao
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Sha-Sha Ruan
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Jia-Wei Hu
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Wen-Jun Long
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Wen-Zhuo Dai
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
| | - Tao Ma
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
- Department of Neurology, The WuXi NO.2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
| | - Xi-Chen Zhu
- Department of Neurology, The Affiliated WuXi NO.2 People's Hospital of Nanjing Medical University
- Department of Neurology, The WuXi NO.2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
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4
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Zeng Q, Ning F, Gu S, Zeng Q, Chen R, Peng L, Zou D, Ma G, Wang Y. The 10-Repeat 3'-UTR VNTR Polymorphism in the SLC6A3 Gene May Confer Protection Against Parkinson's Disease: A Meta-analysis. Front Genet 2021; 12:757601. [PMID: 34646314 PMCID: PMC8502797 DOI: 10.3389/fgene.2021.757601] [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: 08/12/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
The dopamine transporter (DAT) is encoded by the SLC6A3 gene and plays an important role in the regulation of the neurotransmitter dopamine. The SLC6A3 gene contains several repetition alleles (3-11 repeats) of a 40-base pair variable number of tandem repeats (VNTR) in the 3'-untranslated region (3'-UTR), which may affect DAT expression levels. The 10-repeat (10R) allele could play a protective role against PD. However, inconsistent findings have been reported. Methods: A comprehensive meta-analysis was performed to accurately estimate the association between the 10R allele of the 3'-UTR VNTR in SLC6A3 and PD among four different genetic models. Results: This meta-analysis included a total of 3,142 patients and 3,496 controls. We observed a significant difference between patients and controls for the allele model (10R vs. all others: OR = 0.860, 95% CI: 0.771-0.958, P = 0.006), pseudodominant model (10R/10R + 10R/9R vs. all others: OR = 0.781, 95% CI: 0.641-0.952, P = 0.014) and pseudorecessive model (10R/10R vs. all others: OR = 0.858, 95% CI: 0.760-0.969, P = 0.013) using a fixed effects model. No significant differences were observed under the pseudocodominant model (10R/9R vs. all others: OR = 1.079, 95% CI: 0.945-1.233, P = 0.262). By subgroup analysis, the 10R, 10R/10R and 10R/9R genotypes were found to be significantly different from PD in Asian populations. Conclusion: Our findings suggest that the SLC6A3 10R may be a protective factor in susceptibility to PD.
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Affiliation(s)
- Qiaoli Zeng
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
| | - Fan Ning
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
- Institute of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Shanshan Gu
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
- Institute of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Qiaodi Zeng
- Department of Clinical Laboratory, People’s Hospital of Haiyuan County, Zhongwei, China
| | - Riling Chen
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
- Department of Pediatrics, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
| | - Liuquan Peng
- Department of Pediatrics, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
| | - Dehua Zou
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
| | - Guoda Ma
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
| | - Yajun Wang
- Institute of Respiratory, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
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5
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Zeng Q, Chen Q, Zou D, Guo R, Xiao D, Jiang S, Chen R, Wang Y, Ma G. Different Associations Between the IREB2 Variants and Chronic Obstructive Pulmonary Disease Susceptibility. Front Genet 2020; 11:598053. [PMID: 33304392 PMCID: PMC7701307 DOI: 10.3389/fgene.2020.598053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/20/2020] [Indexed: 01/14/2023] Open
Abstract
Background: Iron responsive element binding protein 2 (IREB2) variants may be involved in the pathogenesis of chronic obstructive pulmonary disease (COPD). Recently, many studies have been performed on IREB2 susceptibility variants, including rs2568494, rs2656069, rs10851906, rs12593229, and rs13180, associated with COPD. However, inconsistent findings have been reported. The aim of our research was to determine the association of IREB2 SNPs with COPD. Methods: A comprehensive meta-analysis was performed to accurately estimate the association between IREB2 variants and COPD among four different genetic models. Results: This meta-analysis included a total of 4,096 patients and 5,870 controls. Here, we investigated the 5 IREB2 variants to identify COPD risk. Our results indicate that rs2568494 was associated with an increased risk of COPD for the dominant model (AA+GA vs. GG: OR = 1.150, 95% CI: 1.5–1.304, P = 0.029); rs2656069 was associated with a decreased risk of COPD for the recessive model (GG vs. AA+AG: OR = 0.589, 95% CI: 0.440–0.789; P = 0.000), additive model (GG vs. AA: OR =0.641, 95% CI: 0.441–0.931; P = 0.020), and allele model (G vs. A: OR = 0.812, 95% CI: 0.668–0.988; P = 0.037); and rs10851906 was associated with a decreased risk of COPD for the recessive model (GG vs. AA+AG: OR = 0.732, 95% CI: 0.560–0.958; P = 0.023) and additive model (GG vs. AA: OR = 0.777, 95% CI: 0.637–0.947; P = 0.012). Conclusion: Our findings suggest that the IREB2 rs2568494 minor alleles A may be a genetic factor in susceptibility to COPD. In addition, the minor alleles G of rs2656069 and rs10851906 appear to have a protective effect.
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Affiliation(s)
- Qiaoli Zeng
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Qikang Chen
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Dehua Zou
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Runmin Guo
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China.,Department of Medicine, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Dawei Xiao
- Department of Medicine, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Shaohu Jiang
- Department of Pediatrics, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Riling Chen
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China.,Department of Pediatrics, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Yajun Wang
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China.,Department of Medicine, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Guoda Ma
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
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6
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Taxonomy dimension reduction for colorectal cancer prediction. Comput Biol Chem 2019; 83:107160. [DOI: 10.1016/j.compbiolchem.2019.107160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 02/01/2023]
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7
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Zhao T, Wang D, Hu Y, Zhang N, Zang T, Wang Y. Identifying Alzheimer’s Disease-related miRNA Based on Semi-clustering. Curr Gene Ther 2019; 19:216-223. [DOI: 10.2174/1566523219666190924113737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 01/14/2023]
Abstract
Background:
More and more scholars are trying to use it as a specific biomarker for Alzheimer’s
Disease (AD) and mild cognitive impairment (MCI). Multiple studies have indicated that
miRNAs are associated with poor axonal growth and loss of synaptic structures, both of which are early
events in AD. The overall loss of miRNA may be associated with aging, increasing the incidence of
AD, and may also be involved in the disease through some specific molecular mechanisms.
Objective:
Identifying Alzheimer’s disease-related miRNA can help us find new drug targets, early
diagnosis.
Materials and Methods:
We used genes as a bridge to connect AD and miRNAs. Firstly, proteinprotein
interaction network is used to find more AD-related genes by known AD-related genes. Then,
each miRNA’s correlation with these genes is obtained by miRNA-gene interaction. Finally, each
miRNA could get a feature vector representing its correlation with AD. Unlike other studies, we do not
generate negative samples randomly with using classification method to identify AD-related miRNAs.
Here we use a semi-clustering method ‘one-class SVM’. AD-related miRNAs are considered as outliers
and our aim is to identify the miRNAs that are similar to known AD-related miRNAs (outliers).
Results and Conclusion:
We identified 257 novel AD-related miRNAs and compare our method with
SVM which is applied by generating negative samples. The AUC of our method is much higher than
SVM and we did case studies to prove that our results are reliable.
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Affiliation(s)
- Tianyi Zhao
- Department of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Donghua Wang
- Department of General Surgery, General Hospital of Heilongjiang Province Land Reclamation Bureau, Harbin, China
| | - Yang Hu
- School of life Science and Tenchnology, Harbin Institute of Technology, Harbin, China
| | - Ningyi Zhang
- Department of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianyi Zang
- Department of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yadong Wang
- Department of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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8
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Han Z, Hua J, Xue W, Zhu F. Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. Front Genet 2019; 10:1136. [PMID: 31781177 PMCID: PMC6861379 DOI: 10.3389/fgene.2019.01136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/18/2019] [Indexed: 12/19/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic fatal central nervous system (CNS) disease involving in complex immunity dysfunction. Recently, long noncoding RNAs (lncRNAs) were discovered as the important regulatory factors for the pathogenesis of MS. However, these findings often cannot be repeated and confirmed by the subsequent studies. We considered that the small-scale samples or the heterogeneity among various tissues may result in the divergence of the results. Currently, RNA-seq has become a powerful approach to quantify the abundances of lncRNA transcripts. Therefore, we comprehensively collected the MS-related RNA-seq data from a variety of previous studies, and integrated these data using an expression-based meta-analysis to identify the differentially expressed lncRNA between MS patients and controls in whole samples and subgroups. Then, we performed the Jensen-Shannon (JS) divergence and cluster analysis to explore the heterogeneity and expression specificity among various tissues. Finally, we investigated the potential function of identified lncRNAs for MS using weighted gene co-expression network analysis (WGCNA) and gene set enrichment analysis (GSEA), and 5,420 MS-related lncRNAs specifically expressed in the brain tissue were identified. The subgroup analysis found a small heterogeneity of the lncRNA expression profiles between brain and blood tissues. The results of WGCNA and GSEA showed that a potential important function of lncRNAs in MS may be involved in the regulation of ribonucleoproteins and tumor necrosis factor cytokines receptors. In summary, this study provided a strategy to explore disease-related lncRNAs on genome-wide scale, and our findings will be benefit to improve the understanding of MS pathogenesis.
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Affiliation(s)
- Zhijie Han
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Jiao Hua
- School of Mathematics, Harbin Institute of Technology, Harbin, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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9
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Yang Y, Wang X, Ju W, Sun L, Zhang H. Genetic and Expression Analysis of COPI Genes and Alzheimer's Disease Susceptibility. Front Genet 2019; 10:866. [PMID: 31608112 PMCID: PMC6761859 DOI: 10.3389/fgene.2019.00866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease in the elderly and the leading cause of dementia in humans. Evidence shows that cellular trafficking and recycling machineries are associated with AD risk. A recent study found that the coat protein complex I (COPI)-dependent trafficking in vivo could significantly reduce amyloid plaques in the cortex and hippocampus of neurological in the AD mouse models and identified 12 single-nucleotide polymorphisms in COPI genes to be significantly associated with increased AD risk using 6,795 samples. Here, we used a large-scale GWAS dataset to investigate the potential association between the COPI genes and AD susceptibility by both SNP and gene-based tests. The results showed that only rs9898218 was associated with AD risk with P = 0.017. We further conducted an expression quantitative trait loci (eQTLs) analysis and found that rs9898218 G allele was associated with increased COPZ2 expression in cerebellar cortex with P = 0.0184. Importantly, the eQTLs analysis in whole blood further indicated that 11 of these 12 genetic variants could significantly regulate the expression of COPI genes. Hence, these findings may contribute to understand the association between COPI genes and AD susceptibility.
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Affiliation(s)
- Yu Yang
- Department of Neurology and Neuroscience Center, First Hospital of Jilin University, Changchun, China
| | - Xu Wang
- Department of Neurology and Neuroscience Center, First Hospital of Jilin University, Changchun, China
| | - Weina Ju
- Department of Neurology and Neuroscience Center, First Hospital of Jilin University, Changchun, China
| | - Li Sun
- Department of Neurology and Neuroscience Center, First Hospital of Jilin University, Changchun, China
| | - Haining Zhang
- Department of Neurology and Neuroscience Center, First Hospital of Jilin University, Changchun, China
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10
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Liu G, Zhang Y, Wang L, Xu J, Chen X, Bao Y, Hu Y, Jin S, Tian R, Bai W, Zhou W, Wang T, Han Z, Zong J, Jiang Q. Alzheimer's Disease rs11767557 Variant Regulates EPHA1 Gene Expression Specifically in Human Whole Blood. J Alzheimers Dis 2019; 61:1077-1088. [PMID: 29332039 DOI: 10.3233/jad-170468] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Large-scale genome-wide association studies have reported EPHA1 rs11767557 variant to be associated with Alzheimer's disease (AD) risk in the European population. However, it is still unclear how this variant functionally contributes to the underlying disease pathogenesis. The rs11767557 variant is located approximately 3 kb upstream of EPHA1 gene. We think that rs11767557 may modify the expression of nearby genes such as EPHA1 and further cause AD risk. Until now, the potential association between rs11767557 and the expression of nearby genes has not been reported in previous studies. Here, we evaluate the potential expression association between rs11767557 and EPHA1 using multiple large-scale eQTLs datasets in human brain tissues and the whole blood. The results show that rs11767557 variant could significantly regulate EPHA1 gene expression specifically in human whole blood. These findings may further provide important supplementary information about the regulating mechanisms of rs11767557 variant in AD risk.
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Affiliation(s)
- Guiyou Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yan Zhang
- Department of Pathology, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Longcai Wang
- Department of Anesthesiology, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jianyong Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Xiaoyun Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Yunjuan Bao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Yang Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Shuilin Jin
- Department of Mathematics, Harbin Institute of Technology, Harbin, China
| | - Rui Tian
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Weiyang Bai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tao Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhifa Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jian Zong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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11
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Sun JY, Hou YJ, Zhang Y, Wang L, Liu L, Sun BL, Yuan H. Genetic Variants Associated With Neurodegenerative Diseases Regulate Gene Expression in Immune Cell CD14+ Monocytes. Front Genet 2018; 9:666. [PMID: 30619483 PMCID: PMC6305550 DOI: 10.3389/fgene.2018.00666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
Until now, large-scale genome-wide association studies have identified 94 genes associated with Alzheimer's disease, Parkinson's disease, and multiple sclerosis. Expression quantitative trait locus (eQTL) analysis showed that six genetic variants around six of these 94 genes could drive both disease susceptibility and altered expression of six nearby genes including CD33 (rs3865444), PILRB (rs1476679), NUP160 (rs10838725), LRRK2 (rs76904798), RGS1 (rs1323292), and METTL21B (rs701006). However, two of these six genetic variants rs1476679 and rs76904798 variants could regulate the expression of PILRB and LRRK2 only in the human monocyte-derived microglia-like (MDMi) cells, but not in human peripheral blood monocytes. Here, we aim to verify these findings using another two eQTL datasets in human peripheral blood immune cell CD14+ monocytes. The results that showed that rs1476679 and rs76904798 variants or their proxy variants could significantly regulate the expression of PILRB and LRRK2 in immune cell CD14+ monocytes and human peripheral blood. We believe that these findings provide important supplementary information about the regulatory mechanisms by which both variants influence PILRB and LRRK2 gene expression and neurodegenerative disease risk.
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Affiliation(s)
- Jing-Yi Sun
- Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, South Korea
| | - Ya-Jun Hou
- Key Laboratory of Cerebral Microcirculation, Department of Neurology, Affiliated Hospital of Taishan Medical University, Universities of Shandong, Taian, China
| | - Yan Zhang
- Department of Pathology, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Longcai Wang
- Department of Anesthesiology, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Lidong Liu
- Brain Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Bao-Liang Sun
- Key Laboratory of Cerebral Microcirculation, Department of Neurology, Affiliated Hospital of Taishan Medical University, Universities of Shandong, Taian, China
| | - Hui Yuan
- Key Laboratory of Cerebral Microcirculation, Department of Neurology, Affiliated Hospital of Taishan Medical University, Universities of Shandong, Taian, China
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12
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Shi Z, Yu H, Wu Y, Ford M, Perschon C, Wang C, Zheng SL, Xu J. Genetic risk score modifies the effect of APOE on risk and age onset of Alzheimer's disease. Clin Genet 2018; 95:302-309. [PMID: 30460685 DOI: 10.1111/cge.13479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 01/08/2023]
Abstract
Single nucleotide polymorphism (SNP)-based genetic risk score (GRS) and APOE genotype are both important in risk prediction of Alzheimer's disease (AD); however, the interaction between GRS and APOE has not been extensively investigated. Our objective was to determine whether GRS modifies the APOE effect on AD risk and age at onset (AAO). The study included 774 AD cases and 767 controls of European descent. Population standardized GRS was calculated based on 17 previously implicated AD risk-associated SNPs. Association was analyzed using logistic regression, Cox proportional hazards model and Kaplan-Meier curve. We found that GRS was significantly associated with AD risk and the association was stronger among APOE ε4 carriers. Compared to ε4 non-carriers, the Odds Ratio (OR) for AD was 8.09 (95% Confidence Interval [CI]: 4.98-13.63) for ε4 carriers with high-GRS (≥1.5). In contrast, the OR was 2.55 (95% CI: 1.46-4.49) for ε4 carriers with low-GRS (<0.6). In conclusion, these results suggest SNP-based GRS may supplement APOE for better assessment of inherited risk and age of onset of AD.
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Affiliation(s)
- Zhuqing Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Yishuo Wu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Madison Ford
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chihsiung Wang
- Center for Biomedical Research Informatics, NorthShore University Health System, Evanston, Illinois
| | - Siqun L Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
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13
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Huang WH, Chen W, Jiang LY, Yang YX, Yao LF, Li KS. Influence of ADAM10 Polymorphisms on Plasma Level of Soluble Receptor for Advanced Glycation End Products and The Association With Alzheimer's Disease Risk. Front Genet 2018; 9:540. [PMID: 30555509 PMCID: PMC6282062 DOI: 10.3389/fgene.2018.00540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022] Open
Abstract
To determine the role of A disintegrin and metalloproteinase 10 (ADAM10) in genetic susceptibility to Alzheimer's disease (AD) in a representative Chinese sample, we genotyped 362 AD patients and 370 healthy controls for the rs514049A/C and rs653765C/T polymorphisms in the ADAM10 promoter using the SNaPshot technique. We also examined the potential impact of these polymorphisms on the plasma level of soluble receptor for advanced glycation end products (sRAGE), a decoy receptor whose reduction has been associated with a higher risk of AD. Additionally, a meta-analysis was performed using the present study and the largest GWAS from the International Genomics of Alzheimer's Project (IGAP). No significant differences were found in the distributions of genotypes or alleles between AD patients and control subjects. However, age-at-onset stratification analysis revealed that there were significant differences in the genotypes (P = 0.015) and alleles (P = 0.006) of the rs653765 SNP. Furthermore, patients with the rs653765 CC genotype showed a lower ADAM10 level and a faster cognitive deterioration than those in patients with the CT/TT genotype in late-onset AD (LOAD), and the rs653765 CC polymorphism was able to regulate the production of the ADAM10 substrate sRAGE. In contrast, the rs514049 polymorphism was not statistically associated with AD. In the meta-analysis, we observed that both rs514049 (A allele vs. C allele, P = 0.002) and rs653765 (C allele vs. T allele, P = 0.004) were associated with AD risk. The present study indicated that the rs653765 polymorphism might be associated with the risk and development of LOAD; in particular, the risk genotype, CC, may decrease the expression of ADAM10, influencing the plasma levels of sRAGE, and thus may be correlated with the clinical progression of AD.
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Affiliation(s)
- Wen-Hui Huang
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Clinical Neuroscience Institute of Jinan University, Guangzhou, China
| | - Wei Chen
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Clinical Neuroscience Institute of Jinan University, Guangzhou, China
| | - Lian-Ying Jiang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Yi-Xia Yang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical College, Zhanjiang, China
| | - Li-Fen Yao
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ke-Shen Li
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Clinical Neuroscience Institute of Jinan University, Guangzhou, China
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14
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Cai Q, Xin Z, Zuo L, Li F, Liu B. Alzheimer's Disease and Rheumatoid Arthritis: A Mendelian Randomization Study. Front Neurosci 2018; 12:627. [PMID: 30258348 PMCID: PMC6143656 DOI: 10.3389/fnins.2018.00627] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/21/2018] [Indexed: 01/08/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disease. In recent years, multiple pathway analyses of AD genome-wide association studies (GWAS) have been conducted, and provided strong support for immune pathways in AD. Rheumatoid arthritis (RA) is a chronic autoimmune disease. It is reported that antirheumatic drugs had protective effect on dementia in RA patients. However, observational studies have reported a controversial inverse relationship between AD and RA. In addition, Mendelian randomization studies have also been performed to evaluate the association of RA with AD. However, these studies reported inconsistent association of RA with AD. Until now, it is still unclear that AD is a causally associated with RA. Here, we performed a Mendelian randomization study to investigate the causal association of AD with RA. We analyzed the large-scale AD GWAS dataset (74,046 individuals) and RA GWAS dataset (58,284 individuals) from the European descent. However, we did not identify any significant association of AD with RA using inverse-variance weighted meta-analysis (IVW), weighted median regression and MR-Egger regression.
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Affiliation(s)
- Qixuan Cai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Zhuoyuan Xin
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Lin Zuo
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Fan Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Bin Liu
- Center of Cardiovascular Disease, The First Hospital of Jilin University, Changchun, China
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15
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Cui P, Ma X, Li H, Lang W, Hao J. Shared Biological Pathways Between Alzheimer's Disease and Ischemic Stroke. Front Neurosci 2018; 12:605. [PMID: 30245614 PMCID: PMC6137293 DOI: 10.3389/fnins.2018.00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022] Open
Abstract
Alzheimer's disease (AD) and ischemic stroke (IS) are an immense socioeconomic burden worldwide. There is a possibility that shared genetic factors lead to their links at epidemiological and pathophysiological levels. Although recent genome-wide association studies (GWAS) have provided profound insights into the genetics of AD and IS, no shared genetic variants have been identified to date. This prompted us to initiate this study, which sought to identify shared pathways linking AD and IS. We took advantage of large-scale GWAS summary data of AD (17,008 AD cases and 37,154 controls) and IS (10,307 cases and 19,326 controls) to conduct pathway analyses using genetic pathways from multiple well-studied databases, including GO, KEGG, PANTHER, Reactome, and Wikipathways. Collectively, we discovered that AD and IS shared 179 GO categories (56 biological processes, 95 cellular components, and 28 molecular functions); and the following pathways: six KEGG pathways; two PANTHER pathways; four Reactome pathways; and one in Wikipathways pathway. The more fine-grained GO terms were mainly summarized into different functional categories: transcriptional and post-transcriptional regulation, synapse, endocytic membrane traffic through the endosomal system, signaling transduction, immune process, multi-organism process, protein catabolic metabolism, and cell adhesion. The shared pathways were roughly classified into three categories: immune system; cancer (NSCLC and glioma); and signal transduction pathways involving the cadherin signaling pathway, Wnt signaling pathway, G-protein signaling and downstream signaling mediated by phosphoinositides (PIPs). The majority of these common pathways linked to both AD and IS were supported by convincing evidence from the literature. In conclusion, our findings contribute to a better understanding of common biological mechanisms underlying AD and IS and serve as a guide to direct future research.
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Affiliation(s)
- Pan Cui
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Ministry of Education and Tianjin City, Tianjin, China
| | - Xiaofeng Ma
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Ministry of Education and Tianjin City, Tianjin, China
| | - He Li
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Ministry of Education and Tianjin City, Tianjin, China
| | - Wenjing Lang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Ministry of Education and Tianjin City, Tianjin, China
| | - Junwei Hao
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Ministry of Education and Tianjin City, Tianjin, China
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16
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Liu G, Zhao Y, Jin S, Hu Y, Wang T, Tian R, Han Z, Xu D, Jiang Q. Circulating vitamin E levels and Alzheimer's disease: a Mendelian randomization study. Neurobiol Aging 2018; 72:189.e1-189.e9. [PMID: 30174138 DOI: 10.1016/j.neurobiolaging.2018.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 08/04/2018] [Accepted: 08/05/2018] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease (AD) is the leading cause of dementia in older adults. It is more than 50 years since vitamin E was recognized as critical for optimal neurological health. Clinical studies have yielded inconsistent findings on the effect of vitamin E on AD risk. Thus, it remains unclear whether vitamin E levels are genetically associated with AD risk. We performed a Mendelian randomization study to investigate association of circulating vitamin E levels with AD using large-scale vitamin E genome-wide association study data set (N = 7781 individuals of European descent) and AD genome-wide association study data set (N = 54,162 individuals [including 17,008 AD cases and 37,154 controls of European descent]). Mendelian randomization-Egger intercept test showed no significant pleiotropy (β = -0.113; p = 0.296). Inverse-variance weighted (odds ratio = 0.96, 95% confidence interval: 0.47-1.94, p = 0.936) and weighted median analyses (odds ratio = 1.13, 95% confidence interval: 0.35-3.69, p = 0.836) showed no significant association between vitamin E and AD. Together with previous literature, this suggests that vitamin E supplementation may not forestall AD in the general population.
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Affiliation(s)
- Guiyou Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yi Zhao
- Affiliated Hospital, Taishan Medical University, Taian, Shandong, China
| | - Shuilin Jin
- Department of Mathematics, Harbin Institute of Technology, Harbin, China
| | - Yang Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tao Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Rui Tian
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhifa Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Dandan Xu
- Department of Biology, Faculty of Sciences, Harbin University, Harbin, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
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17
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Han P, Liu G, Lu X, Cao M, Yan Y, Zou J, Li X, Wang G. CDH1 rs9929218 variant at 16q22.1 contributes to colorectal cancer susceptibility. Oncotarget 2018; 7:47278-47286. [PMID: 27259261 PMCID: PMC5216941 DOI: 10.18632/oncotarget.9758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/08/2016] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer. Large-scale genome-wide association studies (GWAS) have been performed and reported some novel CRC susceptibility variants in European ancestry including the CDH1 rs9929218. Following GWAS and candidate studies evaluated the association between the CDH1 rs9929218 polymorphism and CRC in European, Asian and American populations. However, these studies reported inconsistent associations. Evidence shows that rs9929218 may regulate different gene expressions in different human tissues. Here, we reevaluated this association using large-scale samples from 16 studies (n=131768) using a meta-analysis method. In heterogeneity test, we did not identify significant heterogeneity among these studies. Meta-analysis using fixed effect model showed significant association between rs9929218 and CRC (P=6.16E-21, odds ratio (OR) =0.92, 95% confidence interval (CI) 0.91-0.94). In order to validate the effect of rs9929218 variant on CDH1 expression, we further performed a functional analysis using two large-scale expression datasets. We identified significant regulation relation between rs9929218 variant and the expression of CDH1, ZFP90, RP11-354M1.2 and MCOLN2 by both cis-effect and trans-effect. In summary, our analysis highlights significant association between rs9929218 polymorphism and CRC susceptibility.
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Affiliation(s)
- Peng Han
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150040, China
| | - Guiyou Liu
- Genome Analysis Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xin Lu
- Department of Gastroenterology, The First Hospital of Harbin, Harbin, 150001, China
| | - Minmin Cao
- Department of Endocrinology, The First Hospital of Harbin, Harbin, 150001, China
| | - Youling Yan
- Department of Gastroenterology, The First Hospital of Harbin, Harbin, 150001, China
| | - Jing Zou
- Department of Hematology, The First Hospital of Harbin, Harbin, 150001, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Guangyu Wang
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, 150040, China
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18
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Mukhamedyarov MA, Rizvanov AA, Yakupov EZ, Zefirov AL, Kiyasov AP, Reis HJ, Teixeira AL, Vieira LB, Lima LM, Salafutdinov II, Petukhova EO, Khaiboullina SF, Schlauch KA, Lombardi VC, Palotás A. Transcriptional Analysis of Blood Lymphocytes and Skin Fibroblasts, Keratinocytes, and Endothelial Cells as a Potential Biomarker for Alzheimer's Disease. J Alzheimers Dis 2018; 54:1373-1383. [PMID: 27589530 DOI: 10.3233/jad-160457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alzheimer's disease (AD) is a devastating and progressive form of dementia that is typically associated with a build-up of amyloid-β plaques and hyperphosphorylated and misfolded tau protein in the brain. Presently, there is no single test that confirms AD; therefore, a definitive diagnosis is only made after a comprehensive medical evaluation, which includes medical history, cognitive tests, and a neurological examination and/or brain imaging. Additionally, the protracted prodromal phase of the disease makes selection of control subjects for clinical trials challenging. In this study we have utilized a gene-expression array to screen blood and skin punch biopsy (fibroblasts, keratinocytes, and endothelial cells) for transcriptional differences that may lead to a greater understanding of AD as well as identify potential biomarkers. Our analysis identified 129 differentially expressed genes from blood of dementia cases when compared to healthy individuals, and four differentially expressed punch biopsy genes between AD subjects and controls. Additionally, we identified a set of genes in both tissue compartments that showed transcriptional variation in AD but were largely stable in controls. The translational products of these variable genes are involved in the maintenance of the Golgi structure, regulation of lipid metabolism, DNA repair, and chromatin remodeling. Our analysis potentially identifies specific genes in both tissue compartments that may ultimately lead to useful biomarkers and may provide new insight into the pathophysiology of AD.
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Affiliation(s)
| | | | | | | | | | - Helton J Reis
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | | | | | - Svetlana F Khaiboullina
- Kazan Federal University, Kazan, Russia.,Nevada Center for Biomedical Research, Reno, NV, USA
| | | | - Vincent C Lombardi
- University of Nevada, Reno, NV, USA.,Nevada Center for Biomedical Research, Reno, NV, USA
| | - András Palotás
- Kazan Federal University, Kazan, Russia.,Asklepios-Med (private medical practice and research center), Szeged, Hungary
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19
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GLRB variants regulate nearby gene expression in human brain tissues. Sci Rep 2017; 7:13326. [PMID: 29042589 PMCID: PMC5645380 DOI: 10.1038/s41598-017-13702-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/25/2017] [Indexed: 12/02/2022] Open
Abstract
A recent genome-wide association study (GWAS) identified four genetic variants rs78726293, rs191260602, rs17035816 and rs7688285 in GLRB gene to be associated with panic disorder (PD) risk. In fact, GWAS is an important first step to investigate the genetics of human complex diseases. In order to translate into opportunities for new diagnostics and therapies, we must identify the genes perturbed by these four variants, and understand how these variant functionally contributes to the underlying disease pathogenesis. Here, we investigated the effect of these four genetic variants and the expression of three nearby genes including PDGFC, GLRB and GRIA2 in human brain tissues using the GTEx (version 6) and Braineac eQTLs datasets. In GTEx (version 6) dataset, the results showed that both rs17035816 and rs7688285 variants could significantly regulate PDGFC and GLRB gene expression. In Braineac dataset, the results showed that rs17035816 variant could significantly regulate GLRB and GRIA2 gene expression. We believe that these findings further provide important supplementary information about the regulating mechanisms of rs17035816 and rs7688285 variants in PD risk.
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20
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Wu QJ, Sun SY, Yan CJ, Cheng ZC, Yang MF, Li ZF, Cheng HW, Fang TK. EXOC3L2 rs597668 variant contributes to Alzheimer's disease susceptibility in Asian population. Oncotarget 2017; 8:20086-20091. [PMID: 28423615 PMCID: PMC5386745 DOI: 10.18632/oncotarget.15380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/11/2017] [Indexed: 12/12/2022] Open
Abstract
Recent genome-wide association studies have established the association between EXOC3L2 rs597668 variant and Alzheimer's disease (AD) in European population. However, recent studies reported inconsistent results in Asian population. Here, we performed a systematic review and meta-analysis to evaluate the impact of rs597668 on AD risk in Asian population using a total of 8686 samples including 2855 cases and 5831 controls. Meanwhile, we selected 17,008 AD cases and 37,154 controls in European population to evaluate the potential heterogeneity between East Asian and European populations. In East Asian population, we identified no potential heterogeneity with P=0.31 and I2 = 15.8%. By meta-analysis, we identified positive association between rs597668 and AD risk with P=0.023, OR=0.93, 95% CI 0.87-0.99. We further found significant heterogeneity in pooled Asian and European populations with P<0.0001 and I2 = 87.7%. The meta-analysis indicated negative association with P=0.66, OR=0.97, 95% CI 0.85-1.11. In summary, all these findings indicate that rs597668 C allele is a risk factor for AD in European population with OR=1.18 and P=2.49E-13. However the rs597668 C allele played a protective role in AD with OR=0.93 and P=0.023 in East Asian population.
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Affiliation(s)
- Qing-Jian Wu
- Department of Emergency, Jining No. 1 People's Hospital, Jining, Shandong, 272011, China.,Department of Neurology, Shandong University School of Medicine, Jinan, Shandong, 250012, China.,Key Lab of Cerebral Microcirculation in Universities of Shandong, Taishan Medical University, Taian, Shandong, 271000, China
| | - Shu-Yin Sun
- Department of Emergency, Jining No. 1 People's Hospital, Jining, Shandong, 272011, China
| | - Cheng-Jun Yan
- Department of Emergency, Jining No. 1 People's Hospital, Jining, Shandong, 272011, China
| | - Zi-Cui Cheng
- Department of Encephalopathy Rehabiliation Center, Taian Traditional Chinese Medical Hospital, Taian, Shandong, 271000, China
| | - Ming-Feng Yang
- Key Lab of Cerebral Microcirculation in Universities of Shandong, Taishan Medical University, Taian, Shandong, 271000, China
| | - Zi-Fei Li
- Department of Emergency, Jining No. 1 People's Hospital, Jining, Shandong, 272011, China
| | - Hou-Wen Cheng
- Key Lab of Cerebral Microcirculation in Universities of Shandong, Taishan Medical University, Taian, Shandong, 271000, China
| | - Ti-Kun Fang
- Department of Emergency, Jining No. 1 People's Hospital, Jining, Shandong, 272011, China
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21
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Zhang C, Li X, Zhang W, Wang Y, Fan G, Wang W, Chen S, Qin H, Zhang X. Common genetic variant rs3802842 in 11q23 contributes to colorectal cancer risk in Chinese population. Oncotarget 2017; 8:72227-72234. [PMID: 29069782 PMCID: PMC5641125 DOI: 10.18632/oncotarget.19702] [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: 04/18/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022] Open
Abstract
A genome-wide association study identified a common genetic variant rs3802842 at 11q23 to be associated with CRC risk with OR=1.1 and P = 5.80E-10 in European population. In Chinese population, several genetic association studies have investigated the association between rs3802842 variant and CRC risk. However these studies reported both positive and negative association results. It is still necessary to evaluate a specific variant in a specific population, which would be informative to reveal the disease mechanism. Until recently, there is no a systemic study to evaluate the potential association between rs3802842 and CRC risk in Chinese population by a meta-analysis method. Here, we aim to evaluate this association in Chinese population by a meta-analysis method using 12077 samples including 5816 CRC cases and 6261 controls. We identified the T allele of rs3802842 to be significantly related with an increase CRC risk (P=2.22E-05, OR=1.14, 95% CI 1.07-1.21) in Chinese population.
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Affiliation(s)
- Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Xichuan Li
- Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Weihua Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Yijia Wang
- Department of Pathology, Tianjin Union Medical Center, Tianjin 300121, China
| | - Guanwei Fan
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.,State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Wenhong Wang
- Department of Imaging, Tianjin Union Medical Center, Tianjin 300121, China
| | - Shuo Chen
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Hai Qin
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Xipeng Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
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22
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Liu G, Sun JY, Xu M, Yang XY, Sun BL. SORL1 Variants Show Different Association with Early-Onset and Late-Onset Alzheimer’s Disease Risk. J Alzheimers Dis 2017; 58:1121-1128. [PMID: 28527213 DOI: 10.3233/jad-170005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Guiyou Liu
- Department of Neurology, Affiliated Hospital of Taishan Medical College, Key Laboratory of Cerebral Microcirculation in Universities of Shandong, Taian, Shandong, China
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jing-yi Sun
- Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Gangwon, Korea
| | - Meiling Xu
- Department of Neurology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xiao-yi Yang
- Department of Neurology, Affiliated Hospital of Taishan Medical College, Key Laboratory of Cerebral Microcirculation in Universities of Shandong, Taian, Shandong, China
| | - Bao-liang Sun
- Department of Neurology, Affiliated Hospital of Taishan Medical College, Key Laboratory of Cerebral Microcirculation in Universities of Shandong, Taian, Shandong, China
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23
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Zhang C, Li X, Fu W, Wang Y, Wang T, Wang W, Chen S, Qin H, Zhang X. SMAD7 rs4939827 variant contributes to colorectal cancer risk in Chinese population. Oncotarget 2017; 8:41125-41131. [PMID: 28467803 PMCID: PMC5522279 DOI: 10.18632/oncotarget.17065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/11/2017] [Indexed: 01/10/2023] Open
Abstract
A genome-wide association study identified a common genetic variant rs4939827 at 18q21 in SMAD7 to be related with colorectal cancer (CRC) risk with OR=1.2 and P =7.80E-28. Until recently, several meta-analysis studies have been conducted, and reported significant association between rs4939827 and CRC risk. However none of these studies evaluated the potential association between rs4939827 and CRC risk in Chinese population. In this study, we evaluated this association by a meta-analysis using 12077 samples including 5816 CRC cases and 6261 controls. In the end, we identified the T allele of rs4939827 to be significantly related with an increase CRC risk (P=2.22E-05, OR=1.14, 95% CI 1.07-1.21) in Chinese population.
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Affiliation(s)
- Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Xichuan Li
- Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Wenzheng Fu
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Yijia Wang
- Department of Pathology, Tianjin Union Medical Center, Tianjin 300121, China
| | - Tao Wang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Wenhong Wang
- Department of Imaging, Tianjin Union Medical Center, Tianjin 300121, China
| | - Shuo Chen
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Hai Qin
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Xipeng Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
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24
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Rs4878104 contributes to Alzheimer’s disease risk and regulates DAPK1 gene expression. Neurol Sci 2017; 38:1255-1262. [DOI: 10.1007/s10072-017-2959-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/07/2017] [Indexed: 01/03/2023]
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25
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Liu S, Wu Y, Liu X, Zhou J, Wang Z, He Z, Huang Z. Lack of association between MTHFR A1298C variant and Alzheimer's disease: evidence from a systematic review and cumulative meta-analysis. Neurol Res 2017; 39:426-434. [PMID: 28281392 DOI: 10.1080/01616412.2017.1297340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Previous studies have investigated the association between MTHFR A1298C (rs1801131) polymorphism and susceptibility to Alzheimer's disease (AD). Nevertheless, an ultimate conclusion remains obscure. We then executed this meta-analysis to estimate this association more precisely. METHODS Related studies were systematically searched on PubMed, Embase, China National Knowledge Infrastructure, Google scholar, and AlzGene databases. The association was evaluated by reviewing the odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Publication bias, sensitivity analysis, and cumulative meta-analysis were performed to help draw a more definite conclusion. RESULTS Ten eligible studies were finally enrolled in this meta-analysis. Lack of association between MTHFR A1298C polymorphism and AD risk was observed in five genetic models (allelic: OR = 1.17, 95% CI: 0.88-1.56; homozygous: OR = 1.15, 95% CI: 0.87-1.53; heterozygous: OR = 1.19, 95% CI: 0.76-1.86; dominant: OR = 1.23, 95% CI: 0.81-1.87; recessive: OR = 1.16, 95% CI: 0.89-1.52). The result of cumulative meta-analysis sorted by publication year was also detected a dynamic tendency of no correlation between MTHFR A1298C polymorphism and AD. CONCLUSION This meta-analysis reveals that MTHFR A1298C polymorphism may not be associated with AD risk.
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Affiliation(s)
- Shumin Liu
- a China-America Cancer Research Institute , Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University , Dongguan , China.,b Department of Pathophysiology , Guangdong Medical University , Dongguan , China
| | - Yongfu Wu
- c Department of Pharmacy , Yuebei People's Hospital , Shaoguan , China
| | - Xu Liu
- d The Second School of Clinical Medicine , Guangdong Medical University , Dongguan , China
| | - Jiahui Zhou
- a China-America Cancer Research Institute , Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University , Dongguan , China.,b Department of Pathophysiology , Guangdong Medical University , Dongguan , China
| | - Ziyou Wang
- a China-America Cancer Research Institute , Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University , Dongguan , China.,b Department of Pathophysiology , Guangdong Medical University , Dongguan , China
| | - Zhiwei He
- a China-America Cancer Research Institute , Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University , Dongguan , China.,b Department of Pathophysiology , Guangdong Medical University , Dongguan , China
| | - Zunnan Huang
- a China-America Cancer Research Institute , Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University , Dongguan , China.,b Department of Pathophysiology , Guangdong Medical University , Dongguan , China
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26
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Su F, Shu H, Ye Q, Xie C, Yuan B, Zhang Z, Bai F. Integration of Multilocus Genetic Risk into the Default Mode Network Longitudinal Trajectory during the Alzheimer’s Disease Process. J Alzheimers Dis 2017; 56:491-507. [PMID: 28035927 DOI: 10.3233/jad-160787] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fan Su
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Hao Shu
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Qing Ye
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Chunming Xie
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Baoyu Yuan
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Zhijun Zhang
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Feng Bai
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
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27
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Hu Y, Zheng L, Cheng L, Zhang Y, Bai W, Zhou W, Wang T, Han Z, Zong J, Jin S, Zhang J, Liu G, Jiang Q. GAB2 rs2373115 variant contributes to Alzheimer's disease risk specifically in European population. J Neurol Sci 2017; 375:18-22. [PMID: 28320126 DOI: 10.1016/j.jns.2017.01.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/02/2017] [Accepted: 01/09/2017] [Indexed: 01/01/2023]
Abstract
A genome-wide association study identified GAB2 rs2373115 to be associated with Alzheimer's disease (AD) risk in European population. However, inconsistent results are reported in East Asian population. Here, we performed an updated analysis using 65,704 samples including 20,982 AD cases and 44,722 controls. First, we investigated the GAB2 rs2373115 variant in Asian population using 3974 AD cases and 7568 controls. To further evaluate the effect of rs2373115 in different populations, we selected 17,008 AD cases and 37,154 controls in European population. We used three genetic models, and found no significant heterogeneity in Asian population. A fixed effect model analysis showed no significant association between rs2373115 and AD in Asian population. There was no significant heterogeneity in the pooled East Asian and European populations. The fixed effect model analysis again showed no significant association between rs2373115 and AD in these pooled populations. Taken together, these findings suggest that GAB2 rs2373115 may contribute to AD susceptibility only in European population but not in East Asian population.
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Affiliation(s)
- Yang Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Likun Zheng
- School of Computer and Information Engineering, Harbin University of Commerce, Harbin, China
| | - Liang Cheng
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Ying Zhang
- Department of pharmacy, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Weiyang Bai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tao Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhifa Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jian Zong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Shuilin Jin
- Department of Mathematics, Harbin Institute of Technology, Harbin, China
| | - Jun Zhang
- Department of pharmacy, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China.
| | - Guiyou Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
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28
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Inflammatory Cytokines and Alzheimer's Disease: A Review from the Perspective of Genetic Polymorphisms. Neurosci Bull 2016; 32:469-80. [PMID: 27568024 DOI: 10.1007/s12264-016-0055-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/03/2016] [Indexed: 12/30/2022] Open
Abstract
Neuroinflammatory processes are a central feature of Alzheimer's disease (AD) in which microglia are over-activated, resulting in the increased production of pro-inflammatory cytokines. Moreover, deficiencies in the anti-inflammatory system may also contribute to neuroinflammation. Recently, advanced methods for the analysis of genetic polymorphisms have further supported the relationship between neuroinflammatory factors and AD risk because a series of polymorphisms in inflammation-related genes have been shown to be associated with AD. In this review, we summarize the polymorphisms of both pro- and anti-inflammatory cytokines related to AD, primarily interleukin-1 (IL-1), IL-6, tumor necrosis factor alpha, IL-4, IL-10, and transforming growth factor beta, as well as their functional activity in AD pathology. Exploration of the relationship between inflammatory cytokine polymorphisms and AD risk may facilitate our understanding of AD pathogenesis and contribute to improved treatment strategies.
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29
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Obtaining Human Ischemic Stroke Gene Expression Biomarkers from Animal Models: A Cross-species Validation Study. Sci Rep 2016; 6:29693. [PMID: 27407070 PMCID: PMC4942769 DOI: 10.1038/srep29693] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/21/2016] [Indexed: 02/06/2023] Open
Abstract
Recent studies have revealed the systematic altering of gene expression in human peripheral blood during the early stages of ischemic stroke, which suggests a new potential approach for the rapid diagnosis or prediction of stroke onset. Nevertheless, due to the difficulties of collecting human samples during proper disease stages, related studies are rather restricted. Many studies have instead been performed on manipulated animal models for investigating the regulation patterns of biomarkers during different stroke stages. An important inquiry is how well the findings of animal models can be replicated in human cases. Here, a method is proposed based on PageRank scores of miRNA-mRNA interaction network to select ischemic stroke biomarkers derived from rat brain samples, and biomarkers are validated with two human peripheral blood gene expression datasets. Hierarchical clustering results revealed that the achieved biomarkers clearly separate the blood gene expression of stroke patients and healthy people. Literature searches and functional analyses further validated the biological significance of these biomarkers. Compared to the traditional methods, such as differential expression, the proposed approach is more stable and accurate in detecting cross-species biomarkers with biological relevance, thereby suggesting an efficient approach of re-using gene biomarkers obtained from animal-model studies for human diseases.
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30
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Association of single nucleotide polymorphism rs3803662 with the risk of breast cancer. Sci Rep 2016; 6:29008. [PMID: 27350156 PMCID: PMC4924094 DOI: 10.1038/srep29008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/09/2016] [Indexed: 02/02/2023] Open
Abstract
Large scale association studies have identified the single nucleotide polymorphism rs3803662 associated with breast cancer risk. However, the sample size of most studies is too small. Here, we performed this meta-analysis to make the result more convincing. Relevant articles published up to 2016 were identified by searching the PubMed database. 13 studies, involving a total of 29405 participants, were included in the meta-analysis. Odds Ratios (ORs) with 95% confidence intervals (CIs) was calculated with random or fixed effects model. All data analyses were analyzed by Review Manger 5.3 software. In Caucasian subgroup: Dominant model (TT + CT vs CC): OR = 1.17 (1.06, 1.29), Recessive model (TT vs CT + CC): OR = 1.25 (1.13, 1.39) and Allele frequency (T vs C): OR = 1.15 (1.08, 1.22). The present meta-analysis suggests that rs3803662 polymorphism is significantly associated with breast cancer risk in Caucasian women, and we did not find the association in Asian women.
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31
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Jiang Q, Jin S, Jiang Y, Liao M, Feng R, Zhang L, Liu G, Hao J. Alzheimer’s Disease Variants with the Genome-Wide Significance are Significantly Enriched in Immune Pathways and Active in Immune Cells. Mol Neurobiol 2016; 54:594-600. [DOI: 10.1007/s12035-015-9670-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
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