以全基因組與轉錄組分探討人類疾病與治療的生理藥理生物標記

Taipei Medical University Institutional Repository > 藥學院 > 藥學系 > 博碩士論文 > Item 987654321/58525

jsp.display-item.identifier=請使用永久網址來引用或連結此文件: http://libir.tmu.edu.tw/handle/987654321/58525

题名:	以全基因組與轉錄組分探討人類疾病與治療的生理藥理生物標記 Large-scale genomic and transcriptomic approaches revealing biology and pharmacology in human diseases
作者:	黃順清 Ching, Henry Wong Sung
贡献者:	藥學系(碩博士班) 張偉嶠
关键词:	生物資訊學;計算生物學;統計遺傳學;全基因體關聯分析;免疫球蛋白;川崎病;末期腎臟病;紅血球生成素;T細胞組庫;細胞因子組;TCGA;mRNA定序;體細胞拷貝數變異 Bioinformatics;computational biology;statistical genetics;genome-wide association study;intravenous immunoglobulin;Kawasaki disease;end-stage renal disease;erythropoietin;T cell receptor repertoire;cytokinome landscape;the cancer genome atlas;mRNA-sequencing;somatic copy number alteration
日期:	2018-12-28
上传时间:	2020-01-21 11:56:11 (UTC+8)
摘要:	計算生物學是一個跨領域學科，是利用數學建模技術來回答與生物學，疾病病理學和藥理學相關的問題。這些基於數學建模的工具不僅促進了我們對人類疾病的病理與生理學的理解，並促進了新治療目標的發現和新藥的開發。高通量技術的進步，包括微陣列和定序，已經產生了大量具有前所未有的價值的數據。計算生物學可以幫助我們剖析疾病相關的信息傳導網絡或細胞內途徑，揭示疾病相關的生理過程之間的相互關係，並提供系統生物學水平的疾病病理與生理學的縱觀圖。另一方面，計算生物學的工具推動了治療方法的進展。在精準醫學時代，計算生物學，生物信息學和高通量技術三者使得利用分子標籤制定醫療處置計劃這件事變得可行。本論文涵蓋了四個不同的主題，包括全基因組關聯研究（GWAS），TCR組庫定序，細胞因子等基因的泛癌表達圖譜和細胞因子等基因的泛癌體細胞拷貝數改變（SCNA）圖譜。靜脈注射免疫球蛋白（IVIG）是川崎病（KD）的第一線治療方法。IVIG用於預防與KD相關的心血管並發症。然而，一部分KD患者在IVIG治療後持續發熱，並被定義為IVIG抗藥。為了開發基於遺傳標記的風險評分系統來預測KD患者的IVIG反應性，本研究招募了總共150名KD患者（126名IVIG反應者和24名IVIG無反應者）。我們進行全基因組關聯分析並鑑定IVIG抗性的風險等位基因。加權遺傳風險評分通過勝算比的自然對數乘以風險等位基因的數量來計算。通過全基因組關聯研究，我們鑑定了11個單核苷酸多態性。KD患者根據其計算的加權遺傳風險評分分為3組。結果表明加權遺傳風險評分（第3組和第4組與第1組）和對IVIG的反應之間存在顯著相關性。這是第一個基於KD全基因組關聯研究的加權遺傳風險評分研究。預測模型整合了所有11種單核苷酸多態性的相加效應，以預測對IVIG的反應性。貧血在接受血液透析的終末期腎病（ESRD）患者中很常見。紅細胞（RBC）計數的總減少與這些患者的不良預後相關。雖然促紅細胞生成素（EPO）已被用作治療貧血的ESRD患者的有效治療，但是大量患者仍然對EPO治療反應差。我們測量了T細胞受體測序譜，包括互補性 - 檢測區域3（CDR3）的長度，組內和組間（EPO抗性與響應性）克隆型多樣性，V（D）J使用譜和來自ESRD患者的VJ組合。並研究這些特徵與EPO治療效果之間的相關性。我們的結果揭示了兩組中Vβ/Jβ最高的3~15個關節分佈的統計學意義，表明V或J基因利用在ESRD患者的EPO反應中的重要性。總之，我們提供了證據，解決了ESRD患者免疫譜與EPO反應之間的潛在相關性。複雜的腫瘤內免疫反應是由細胞因子（包括趨化因子）的表現與交互作用網絡決定，然而細胞因子體如何影響腫瘤尚未被系統性地研究。利用多維度的癌症標本數據，我們探索了19種腫瘤類型中局部細胞因子的轉錄表現量，生物標誌物潛力和對預後的影響。我們發現大多數細胞因子有顯著表現量上升或下降，揭示了癌症發展過程中局部細胞因子的表現量模式。此外，我們注意到CCL14和CXCL12分別在9種和10種癌症類型中顯著下調，這意味著它們在腫瘤發病機制中起著至關重要的作用。我們還發現細胞因子與原發腫瘤標本中的其他蛋白質編碼基因（PCGs）相比顯示出顯著更高的特異性，表明在考慮癌症細胞因子時，周邊腫瘤微環境是需要被同時檢視的。最後，我們將局部細胞因子的表現量與患者存活率進行關聯分析。因此，我們的結果提供了泛癌細胞因子的全景圖，突出了癌症相關細胞因子的腫瘤類型特異性及其對疾病預後的影響。細胞因子（包括趨化因子）之間錯綜複雜的關係塑造了腫瘤微環境（TME）並反映了惡性細胞與來自TME的其他細胞之間的細胞，即細胞-細胞相互作用。儘管我們之前的研究表明了19種癌症類型中細胞因子的轉錄（表現量）情況，但尚未系統地研究體細胞拷貝數（SCN）改變和細胞因子的臨床相關性。在這裡，我們揭示了細胞因子基因的負選擇。我們還將細胞因子基因的SCN損失與影響癌症進展和患者預後的免疫浸潤量進行分析。本研究也證實並驗證了帶有細胞因子的基因座的SCN改變與藥物敏感性之間的相關性。綜上所述，我們的研究結果表明惡性細胞中細胞因子的基因組丟失是癌症進展，惡性細胞-TME相互作用和治療的關鍵。 Computational biology is an interdisciplinary field that adopt computational modeling techniques to answer the questions relating to biology, disease pathology and pharmacology. The emerged tools based on mathematical modeling has boost our understanding of human diseases’ pathophysiology, and leading to discovering of new therapeutic targets and development of new drugs. The advances in high-throughput technologies, including microarray and sequencing, has resulted in tremendous amount of data with unprecedented depth of value. The utilization of computational biology may help us to dissect the disease-related signaling networks or intracellular pathways, reveal the inter-relationship between disease-related biology processes and provide panoramic view of disease pathophysiology on system biology levels. In other aspect, the tools of computational biology have fueled the progress in optimizing therapies. Together, computational biology, bioinformatics and high-throughput technologies makes customization of healthcare with using molecular signature(s) become feasible in the precision medicine era. Four different subjects have been covered in this thesis, including genome-wide association study (GWAS), TCR repertoire sequencing, pan-cancer expression landscape of cytokine genes, and pan-cancer somatic copy number alteration (SCNA) landscape of cytokine genes. Intravenous immunoglobulin (IVIG) is the treatment of choice in Kawasaki disease (KD). IVIG is used to prevent cardiovascular complications related to KD. However, a proportion of KD patients have persistent fever after IVIG treatment and are defined as IVIG resistant. To develop a risk scoring system based on genetic markers to predict IVIG responsiveness in KD patients, a total of 150 KD patients (126 IVIG responders and 24 IVIG nonresponders) were recruited for this study. A genome-wide association analysis was performed to compare the 2 groups and identify risk alleles for IVIG resistance. A weighted genetic risk score was calculated by the natural log of the odds ratio multiplied by the number of risk alleles. Eleven single-nucleotide polymorphisms were identified by genome-wide association study. The KD patients were categorized into 3 groups based on their calculated weighted genetic risk score. Results indicated a significant association between weighted genetic risk score (groups 3 and 4 versus group 1) and the response to IVIG (Fisher’s exact P value 4.518×10−3 and 8.224×10−10, respectively). This is the first weighted genetic risk score study based on a genome-wide association study in KD. The predictive model integrated the additive effects of all 11 single-nucleotide polymorphisms to provide a prediction of the responsiveness to IVIG. Anemia is common among end-stage renal disease (ESRD) patients who undergone hemodialysis. The total reduction of red blood cell (RBC) count is associated with poor prognosis in these patients. Although erythropoietin (EPO) has been used as an effective treatment for ESRD patients with anemia, a large number of patients still present poor responses to EPO treatment. We measured T-cell receptor sequencing profiles, including length of complementarity-deteremining region 3 (CDR3), intra- and inter-group (EPO resistant vs. responsive) clonotype diversity, V(D)J usage profiles and V-J combinations from ESRD patients and to investigate the correlation between these features and EPO treatment efficacy. Our results revealed statistical significance in the top 3~15 most abundant joint distributions of Vβ/Jβ among the two groups, suggesting the importance of V or J gene utilization in the EPO response of ESRD patients. In summary, we provided evidence addressing the potential correlation between the immune repertoire and EPO response in ESRD patients. Dysfunctional intratumoral immune reactions are shaped by complex networks of cytokines (including chemokines), and how the cytokinome landscape coordinates with tumors has not been systematically investigated. Using high-dimensional datasets of cancer specimens, we explored the transcript abundance, biomarker potential, and prognostic impact of local cytokines across 19 tumor types. We found that most cytokines are highly locally dysregulated (p = 0.024), revealing spatiotemporal pattern of local cytokines in the development of cancers. In addition, we noted the significant downregulation of CCL14 and CXCL12 in 9 and 10 cancer types, respectively, implying their crucial roles in tumor pathogenesis. We also found that cytokines showed significantly higher specificity properties compared to other protein-coding genes (PCGs) in primary tumor specimens (p << 0.001), indicating that tissue context remains an issue when considering cancer cytokinomes. Finally, we linked concentrations of local cytokines to patient survival. Our results thus provide a panoramic view of pan-cancer cytokinomes, which highlights tumor type specificity of cancer-related cytokines and their impacts on disease prognosis. Intricate relationships among cytokines (including chemokines) shape the tumor microenvironment (TME) and reflect cell-cell interactions between malignant cells and other cells from the TME. Although our previous study indicated the transcriptional landscape of cytokines in 19 cancer types, the global pattern somatic copy number (SCN) alterations and the clinical relevance of cytokines have not been systematically investigated. Here, we reported a significant negative selection on cytokine genes. We also linked the SCN losses of cytokine genes to the abundance of immune infiltrates which affects cancer progression and patient prognoses. We also demonstrated and validated the correlations between SCN alterations of cytokine-containing loci and drug sensitivity. The results indicated the genomic loss of cytokines in malignant cells as a crucial theme for interrogating cancer progression, malignant cell-TME interactions, and therapeutics.
描述:	博士指導教授：張偉嶠委員：張文昌委員：沈志陽委員：吳麥斯委員：陳炳焜
数据类型:	thesis
显示于类别:	[藥學系] 博碩士論文

文件中的档案:

档案	描述	大小	格式	浏览次数
index.html		0Kb	HTML	79	检视/开启

检视Licence

在TMUIR中所有的数据项都受到原著作权保护.

TAIR相关文章

数据加载中.....