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研究生: 廖唯甄
Liao, Wei-Chen
論文名稱: 台灣人體生物資料庫於臨床應用:連結基因變異位點與多重維生素補充對癲癇的影響
From Taiwan Biobank to clinical application: linking the effects of genetic loci to multi-vitamins supplementation against epilepsy
指導教授: 張惠華
Chang, Hui Hua
學位類別: 碩士
Master
系所名稱: 醫學院 - 臨床藥學與藥物科技研究所
Institute of Clinical Pharmacy and Pharmaceutical sciences
論文出版年: 2020
畢業學年度: 108
語文別: 英文
論文頁數: 474
中文關鍵詞: 全基因組關聯研究癲癇難治性癲癇維生素色氨酸基因多型性
外文關鍵詞: Genome-wide association study, GWAS, Epilepsy, Drug-resistant epilepsy (DRE), Vitamins, Tryptophan, Polymorphism
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  • 研究背景
    癲癇是由大腦神經細胞功能異常所引起的神經系統疾病,該疾病會影響個人的健康狀況和生活質量,尤其是在耐藥性的難治型患者中更為明顯。考慮到藥物治療反應和新陳代謝會因個體差異和種族而異,因此我們需要探索針對個體化藥物的潛在標靶。本研究的首要目的是探討台灣人群基因多型性與癲癇之間的關係。其次是評估接受多種維生素補充劑對於難治型癲癇患者的臨床療效。最後,第三個目標是探討耐藥性癲癇(DRE)患者中維生素相關的基因多型性與治療效果之間的關係。

    研究方法
    全基因組關聯研究(GWAS)和後續分析
    本次的全基因組關聯研究選用台灣人體生物資料庫的癲癇個案和其對應的非癲癇患者。我們在Golden Helix上進行樣本和基因位點(SNP)的品質控制(QC),並使用邏輯回歸進行關聯性分析。基因型的插補使用Beagle 4.1軟體進行,並且基於千人基因組計劃(1000 Genome project)。我們後續利用基因型-組織表達研究聯盟(GTEx)第八版數據庫進行差異表達分析,並在STRING上進行基因間的關聯網分析,接著通過人類表型本體(HPO)註釋基因群相對應的表型。路徑分析基於KEGG GENOME和REACTOME數據庫。功能豐富度註釋是基於基因本體論(GO)。藥物基因相互作用數據庫(DGIdb)則主要用於搜索基因與藥物之間的相互作用。
    臨床耐藥性難治型癲癇受試者
    這項研究已經由國立成功大學醫院的機構審查委員會批准,所有受試者將簽署知情同意書。受試者為被診斷為難治型癲癇(年齡20歲以上)並接受多種維生素補充(B6,B9,D,E,Q10)。
    臨床評估
    疾病嚴重程度以癲癇發作次數和治療反應來評估。受試者會被採集空腹血樣以檢測代謝指標、色氨酸代謝產物和多種維生素的血清濃度。使用Axiom TWB 2.0 array檢測受試者的全基因組基因型,以進行後續臨床驗證以及探討維生素相關的基因多型性。

    結果與討論
    由台灣人體生物資料庫中,最後共有332名癲癇患者和986名對照受試者通過了品質管控標準。在進行關聯分析後,我們發現了幾個與疾病有關的基因座,例如CMTM7、DNAH11、CARS2、ADCY7等。在這些基因座的組織差異表達分析中,我們發現SH3GL2、GRIK2和SNX10在腦部相關區域中高表達,並且顯示在大腦皮層,杏仁核,海馬迴,基底神經節等中有顯著差異表達(P < 10-3)。在機轉路徑及GO豐富度的分析中以下幾個項目較為顯著,包含「神經遞質受體和突觸後信號傳遞」、「PKA激活」及「白介素信號傳導」等。後續我們在耐藥性難治型癲癇門診患者(n = 32)中驗證了上述基因座的連鎖不平衡區域中的位點,並發現了幾個潛在與癲癇相關的位點。另外,在臨床維生素補充的試驗中,我們觀察到這些患者在維生素補充前癲癇發作控制不良(癲癇發作每月次數= 6.6±15.7次),並且已平均接受了3種以上的抗癲癇藥物。在接受多重維生素補充後,患者們的平均癲癇發作頻率降低到每月1.9±3.6次,並在治療6個月後,約有75%的患者被定義為對治療有反應。經過這段時間的維生素補充,維生素B9和D的平均血中含量顯著增加,而B6、E和Q10含量則下降。最後,在與維生素攝取和代謝有關的基因變異中發現,在介入前維生素血中濃度及介入後有顯著影響,而介入後的發作頻率也有觀察到不同基因型間的差異。例如,在葉酸相關的基因SLC19A1中,rs1051266、rs12659、rs2838956、rs914232擁有相似的基因型分布,在補充維生素前可以觀察到野生型比起變異型擁有較高的葉酸濃度,補充後也觀察到其維生素濃度的變化及發作次數的變化在不同基因型間有顯著差異。在維生素D相關的基因中,rs4646537 (CYP27B1), rs2296241 (CYP24A1)等與維生素D濃度有關,也與介入後的發作次數相關。另外,過去文獻中提到與Q10濃度相關的基因中,我們發現在rs41313321 (SWI5)及rs7412 (APOE)中,不同的基因型濃度變化的趨勢相反。

    結論
    根據上述結果,癲癇患者罹患精神和心血管疾病的風險更高。並且我們通過GWAS結果,發現了與癲癇相關的基因座,並由基因集中豐富的表型、機轉路徑和功能為臨床發現和開發新型的潛在癲癇生物標誌物提供了可能的研究方向。此外,在維生素補充和基因變異之間對癲癇發作頻率和維生素濃度變化的相互作用揭示了個體化醫療的重要性。

    INTRODUCTION
    Epilepsy, a neurological disorder caused by malfunctioning nerve cell activity in the brain, affects individuals’ health status and life quality, especially in anti-epilepsy drugs (AEDs) resistant patients. Considered that pharmacotherapy response and metabolism varied in individual differences and ethnicity, the exploration of potential targeting markers for personalized medicine were needed. The first objective of the current study was to investigate the association between genetic polymorphisms and epilepsy in Taiwanese population. The secondary objective was to evaluate the clinical effectiveness in AED-resistance patients receiving multivitamins supplementation. Finally, the third objective was to explore the associations between vitamin related polymorphisms and the treatment outcomes in drug-resistant epilepsy (DRE) patients.

    MATERIALS AND METHODS
    Genome-wide association study (GWAS) and post-GWAS
    GWAS was performed on epilepsy and non-epilepsy individuals from Taiwan Biobank. Quality control (QC) and logistic association analysis were performed on Golden Helix. Genotype imputation was based on the 1000 genome project using Beagle 4.1. The gene-set differential expression was operated utilizing Genotype-Tissue Expression project (GTEx) v8 database. The network analysis was performed on STRING and the phenotypes were annotated by the Human Phenotype Ontology (HPO). Pathway analyses were based on KEGG GENOME and REACTOME database. The functional enrichment annotation and network analysis were based on Gene Ontology (GO). The Drug Gene Interaction database (DGIdb) were mainly used for searching interaction between genes and drugs.
    AED-resistance Subjects
    This study was approved by the institutional review boards at the National Cheng Kung University Hospital. All subjects will sign the informed consent. Patients (aged  20 years) who are diagnosed refractory epilepsy were enrolled and received multi-vitamins (B6, B9, D, E, Q10).
    Measurements
    Disease severity were assessed by seizure frequency and treatment response rate. Fasting blood samples were collected to detect metabolic indices (include lipid profiles and sugar profiles), tryptophan metabolites and multi-vitamins concentration. After genotyping the whole genome profiles using Axiom TWB 2.0 array, we further performed clinical validation on GWAS results and determined the vitamin-related genetic polymorphisms.
    RESULTS AND DISCUSSION
    332 epilepsy and 986 control subjects passed the quality criteria. After the association test, we found several genetic loci, such as CMTM7, DNAH11, CARS2, ADCY7, etc. In the tissue expression analysis for those top loci, we found SH3GL2, GRIK2, and SNX10 highly expressed in brain-related regions, and shown significant differential expressed (P < 10-3) in brain cortex, amygdala, hippocampus, basal ganglia, etc. Further pathway and GO term enrichment analysis highlighted in “Neurotransmitter receptors and postsynaptic signal transmission”, “PKA activation”, “Interleukin signaling”, etc. Then, we validated regions in the top loci’s linkage disequilibrium blocks with drug-resistant epilepsy outpatients (n = 32) and found several targeted SNPs. At first, these drug-resistant patients were averagely received more than 3 kinds of AEDs and observed to have bad seizure control (seizure number = 6.6±15.7 per month). However, after receiving multi-vitamins supplementation, their average seizure frequency reduced to 1.9±3.6 per month, and about 75% of patients were defined as responder after 6-month treatment. What’s more, vitamin levels had significant increase in B9 and D, and decreased in B6, E and Q10. Finally, the investigation on genetic variants related to vitamin uptake and metabolism found significant results on both baseline vitamin level and after intervention. For example, among the folate-related genes SLC19A1, rs1051266, rs12659, rs2838956, and rs914232 have similar genotype distributions. The wild type group in these four SNPs had a higher folate concentration than the mutant type before vitamin supplementation, and we also observed the difference between changes in vitamin concentration and seizure frequency after receiving vitamins. Among the genes related to vitamin D, rs4646537 (CYP27B1), rs2296241 (CYP24A1), etc. were related to the concentration of vitamin D, as well as the seizure frequency after intervention. Additionally, in genes related to Q10 which were mentioned in the past literature, we found that the trend of Q10 concentration during the six months were different by genotypes in rs41313321 (SWI5) and rs7412 (APOE).

    CONCLUSION
    Our findings indicated the higher risk of mental and cardiovascular disease in epilepsy. Through the GWAS results, loci associated with epilepsy was found, and the corresponding phenotypes, pathways and functions enriched in the gene set gave possible insights to explain clinical findings, and to develop novel potential biomarker in epilepsy. Additionally, the interaction effects found between vitamin supplements and genetic variants on changes of seizure frequency and vitamin levels revealed the importance of personalized medicine.

    中文摘要 I Abstract III 誌謝 V Contents VII List of Tables XI List of Figures XVI List of Supplementary Appendices XIX List of Supplementary Appendix Tables XX List of Supplementary Appendix Figures XXV Abbreviations XXVI Chapter 1 Introduction 1 1.1 Epilepsy 1 1.1.1 Clinical influence and epidemiology of epilepsy 1 1.1.2 Drug-resistant epilepsy (DRE) 1 1.1.3 Pathogenesis of epilepsy: focusing on oxidative stress 3 1.2 Micronutrients hypothesis in epilepsy 6 1.2.1 Ketogenic diets (KD) and its limitation 6 1.2.2 Roles of vitamins supplementations in seizures 6 1.3 Genetic-based hypothesis in epilepsy 10 1.3.1 Genome-wide association study in epilepsy 10 1.3.2 Genetic impacts on multi-vitamin supplementation 12 Chapter 2 Objective of current study 15 Chapter 3 Materials and methods 16 3.1 Study design 16 3.2 Population data collection 16 3.2.1 Subjects in Taiwan Biobank 16 3.2.2 Health-related information survey 16 3.2.3 Whole genome genotype and genotyping quality control 17 3.3 Bioinformatics of population-based genetic study 17 3.3.1 Genome-wide association study (GWAS) 18 3.3.2 Computational post-GWAS 19 3.4 Subjects in clinical study 21 3.4.1 Physical measurements 21 3.4.2 Blood sample measurements 22 3.4.3 Genotype profiles 25 3.4.4 Questionnaire and surveys 26 3.5 Statistics 27 3.5.1 Clinical analysis 27 3.5.2 Genetic analysis 27 Chapter 4 Results 28 4.1 Genome-wide association study of epilepsy in Taiwan 28 4.1.1 Characteristic and model selection of epilepsy patients and non-epilepsy subjects in Taiwan Biobank 28 4.1.2 Genome-wide association analysis 31 4.2 Post genome-wide analysis of epilepsy in Taiwan 34 4.2.1 Gene association analysis 34 4.2.2 Gene expression and co-expression 34 4.2.3 Functional pathway and Enrichment analysis 35 4.2.4 Gene-drug interaction analysis 35 4.3 Validation of population-based epilepsy genetic polymorphisms on clinical drug-resistant epilepsy outpatients 36 4.3.1 Genetic variants validated in drug-resistant epilepsy outpatients 36 4.3.2 Characteristics of drug-resistant epilepsy outpatients carrying different alleles of the validated genetic variants 37 4.4 Clinical features of drug-resistant epilepsy outpatients 40 4.4.1 Seizure severity of drug-resistant epilepsy (DRE) 40 4.4.2 Difference in clinical indices between drug-resistant epilepsy and controls 41 4.4.3 Correlations of clinical indices in drug-resistant epilepsy before the intervention 42 4.5 The effects of multi-vitamins supplementation against drug-resistant epilepsy 47 4.5.1 Compliance of receiving multi-vitamins supplementation and prescribed medication in drug-resistant epilepsy patients 47 4.5.2 Change of seizure severity 48 4.5.3 Changes of clinical indices 48 4.5.4 Correlations of changes in clinical indices of drug-resistant epilepsy after the intervention 50 4.5.5 Correlations of clinical indices in drug-resistant epilepsy (per-person time) 52 4.6 Comparisons between patients in different conditions 56 4.6.1 Comparisons between patients with poor response and with good response to multi-vitamin intervention 56 4.6.2 Effects of compliance about receiving the multi-vitamins supplementation on changes of seizure frequency and vitamin levels 56 4.6.3 Effects of drug on vitamin levels and vitamin treatment response 57 4.6.4 Seizure severity after completed the trial (not receiving vitamins) 59 4.7 Effects of vitamin-related genetic variants in disease and vitamin treatment response on drug-resistant epilepsy 60 4.7.1 Difference between drug-resistant epilepsy and controls in vitamin-related genetic polymorphism 60 4.7.2 Relationship between vitamin-related genetic polymorphism and baseline vitamin level 60 4.7.3 The interaction effects of vitamin-related gene polymorphisms and multi-vitamins supplementation 61 Chapter 5 Discussion 307 5.1 Discovery from population database to clinical practice 307 5.1.1 Comorbidity issues in Taiwan biobank epilepsy to clinical epilepsy patients 307 5.1.2 Variants observed in the GWAS results and validated on clinical outpatients 308 5.1.3 Importance of serotonin and postsynaptic signal transmission found in epilepsy 309 5.1.4 Protein kinase A activation and sugar profiles in epilepsy and drug-resistant epilepsy 312 5.1.5 Association between interleukin and epilepsy 312 5.2 Effects of vitamins on drug-resistant epilepsy 313 5.2.1 Previous studies of effects on vitamin supplementation in epilepsy 313 5.2.2 Trends of vitamin levels after intervention and interaction between vitamins 313 5.2.3 Roles of tryptophan metabolites in seizure severity and in vitamin levels 315 5.2.4 Physiological phenomena accompanied by elevated creatine phosphokinase in drug-resistant epilepsy 316 5.2.5 Possible role of Q10 / Cholesterol ratio in epilepsy 316 5.2.6 Association between anti-epileptic drugs and vitamin levels 316 5.3 Effects of vitamin related gene polymorphisms and multi-vitamins supplementation 318 5.3.1 The role of ALDH7A1 and PNPO on drug-resistant epilepsy patients receiving multiple vitamins 318 5.3.2 The role of FOLR1 and SLC19A1 on drug-resistant epilepsy patients receiving multiple vitamins 318 5.3.3 The role of CYP27B1, CYP24A1, and VDR on drug-resistant epilepsy patients receiving multiple vitamins 319 5.3.4 The role of COQ family on drug-resistant epilepsy patients receiving multiple vitamins 319 5.3.5 The role of SWI5 and APOE on drug-resistant epilepsy patients receiving multiple vitamins 320 5.4 Clinical implication of this study 321 5.5 Limitation 322 Chapter 6 Conclusion 323 Chapter 7 Reference 324 Appendix 342

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