臺灣博碩士論文加值系統

近年來，生物標記分子被廣泛應用於臨床疾病診斷、術後追蹤及輔助治療方式的選擇等等，然而，因缺乏可信分析方法、方法開發的高成本與高難度大大降低了驗證大量候選的生物標記分子的可能性，進而阻礙了這類分子於臨床使用上的發展。本篇論文中，我們建立一個新的定量分析方法並探討其後轉譯修飾的變異程度，藉由此一方法於非侵入性樣本尋找與驗證蛋白質生物標記分子。首先，我們設計界面劑包覆的單分散磁性奈米探針來提升其測量的靈敏度(MNP@IGEPAL)，並以固化定向抗體提升其專一性與免疫活性。我們發現，MNP@IGEPAL於溶劑中分散性與萃取效率皆優於傳統共沉澱法合成之磁性奈米探針(MNPcp)。 接著，我們將MNP@IGEPAL的萃取方法串聯多重反應監測質譜術(MRM-MS)，同時定量血清中低豐度的生物標記分子：甲種胎兒蛋白(AFP)與高爾基體膜蛋白1(GOLM1)，此一方法提供高靈敏度、優化的分析品質(平均準確度與精密度皆於15%以內)與寬動態範圍的分析條件。此外，我們基於此方法分析定量肝病病患血清中的生物標記分子，結果顯示，甲種胎兒蛋白與高爾基體膜蛋白1對肝癌具有相似的診斷準確度，更重要的是，近七成低濃度甲種胎兒蛋白(<20 ng/mL)病患中，高爾基體膜蛋白1的量增加，因此我們認為這兩個蛋白質於疾病診斷上有互補性。除了檢測蛋白質濃度外，我們希望藉由蛋白質上的後轉譯修飾輔助疾病的診斷，因此，我們設計了一鍋化雙功能奈米探針搭配質譜分析技術，以期同時定量蛋白質與定性其後轉譯修飾的分布。藉由分析AFP與血紅素結合蛋白 (Hp) 證實我們能以少量樣品於短時間內完成高靈敏度的蛋白質定量並鑑定其醣型分布。個人化分析肝癌病患除提供其標的蛋白的生物特徵外，更於甲種胎兒蛋白中鑑定了59個醣型，其中12種醣型是於此一蛋白中首次被辨認。最終，我們期許此一方法的建立能促進疾病診斷便利性，並應用於其他癌症與疾病的大規模生物標記分子的篩選、定量與後轉譯修飾的分布。

Disease biomarker development is plagued by lack of acceptable analytical methods, difficulty and cost for method development, overwhelming need for validation on a large population and the poor performance of biomarkers under development. In this dissertation, we introduce alternative methods for protein biomarker discovery and validation that encompasses quantification and post-translational modification (PTM) profiling in non-invasive specimens. We first designed surfactant-coated monodisperse magnetic nanoprobes to improve detection sensitivity (MNP@IGEPAL). Following oriented antibody immobilization for increased specificity and immuno-activity, the MNP@IGEPAL were found to be superior in solvent dispersibility and enrichment efficiency compared to nanoprobes obtained by conventional co-precipitation method (MNPCP). We then coupled the MNP@IGEPAL-based enrichment to multiple reaction monitoring mass spectrometry (MRM-MS) for multiplexed quantification of alpha-fetoprotein (AFP) and golgi membrane protein 1 (GOLM1), which are low-abundant biomarkers in human serum. The method was found to be sensitive, have good analytical merits (average precision and accuracy of 15%) and wide dynamic range. This method was applied to qualify the biomarkers in serum of liver disease patients, where we found that AFP and GOLM1 had similar diagnostic accuracy for hepatocellular carcinoma (HCC), although AFP has a higher false negative rate (sensitivity = 22%). More importantly, we found complementarity between AFP and GOLM1, where GOLM1 was found to be elevated in 69% of patients with low AFP concentration (<20 ng/mL). To supplement disease diagnoses based on protein concentration, we designed a one-pot dual nanoprobe-based mass spectrometry method to simultaneously quantify the protein and profile its post-translational modification (PTM). Using AFP and another clinically-relevant protein, haptoglobin (Hp), we were able to quantify the protein and profile its glycoforms with superior speed and sensitivity and minimal amount of sample. In addition to obtaining individual biosignatures of AFP in HCC patients, we were able to identify a total of 59 glycoforms, 12 of which were identified on AFP for the first time. Ultimately, we were able to develop methods that can improve disease diagnosis, which can be applied to other cancers and diseases for large-scale biomarker triaging, qualification and PTM profiling.

T口試委員會審定書 i
ACKNOWLEDGMENTS iii
中文摘要 v
ABSTRACT vii
LIST OF FIGURES xv
LIST OF TABLES xxiii
LIST OF ABBREVIATIONS xxv
CHAPTER 1 1
1.1 Cancer Biomarker Research: Discovery, Verification and Validation 1
1.1.1 Biomarker discovery 2
1.1.2 Biomarker verification and validation 3
1.1.3 Glycosylation 4
1.1.3.1 N-linked glycosylation 4
1.1.3.2 Correlation with diseases, including cancer 5
1.2 Mass spectrometry and sample preparation methods for protein biomarker quantification 6
1.2.1 Multiple reaction monitoring mass spectrometry for protein quantification 7
1.2.2 Sample pre-concentration strategies for protein quantification from human plasma or serum 11
1.2.3 Magnetic nanoparticles (MNPs) for Bioseparation Applications 13
1.3 Methods for Glycosylation Profiling 15
1.3.1 Sample preparation strategies 15
1.3.2 Mass spectrometry-based methods 18
1.4 Hepatocellular carcinoma 19
1.4.1 Risk Factors 19
1.4.2 Early Detection 20
1.5 Objectives and outline of the dissertation 22
CHAPTER 2 31
2.1 Introduction 31
2.2 Materials and Methods 34
2.2.1 Materials 34
2.2.2 Human serum samples and ELISA 35
2.2.3 Synthesis of NH2-MNP@IGEPAL 36
2.2.4 Synthesis of NH2-MNPCP 37
2.2.5 Fabrication of boronic acid-oriented antibody-conjugated nanoprobe (anti-CRP-MNP@IGEPAL or anti-CRP-MNPCP) 37
2.2.6 Synthesis of Protein G-oriented antibody-conjugated dispersed magnetic nanoparticles (anti-AFP-MNP@IGEPAL and anti-GOLM1-MNP@IGEPAL) 38
2.2.7 Antibody density 38
2.2.8 Aggregation and Sedimentation Experiment 39
2.2.9 Characterization 39
2.2.10 Immunoaffinity extraction using Boronic acid-oriented antibody-conjugated MNPs 40
2.2.11 MALDI-TOF Analysis 40
2.2.12 Immunoaffinity extraction using protein G-oriented nanoprobes, digestion, dimethyl labeling and desalting 41
2.2.13 Multiple reaction monitoring (MRM) Analysis 42
2.2.14 Method validation 43
2.3 Results and Discussion 44
2.3.1 Synthesis of biocompatible monodisperse MNPs 44
2.3.2 Enrichment of Protein Biomarker from Human Serum 47
2.3.3 Examination of physico-chemical factors that influence enrichment efficiency 48
2.3.4 Elimination of non-specific binding by monodisperse MNPs 51
2.3.5 Application of monodisperse MNPs for Multiplexed Protein Enrichment 53
2.3.6 Development of MRM-MS method for multiplexed detection and quantification 54
2.3.7 Validation of the Nanoprobe-based MRM Method multiplexed quantification 61
2.3.8 ELISA Validation and analysis of Clinical samples 63
2.4 Conclusion 64
CHAPTER 3 83
3.1 Introduction 83
3.2 Materials and Methods 86
3.2.1 Materials 86
3.2.2 Human serum samples and ELISA 87
3.2.3 Synthesis of Amine-modified silica nanoparticles (NH2-SiO2 NPs) 87
3.2.4 Synthesis of anti-AFP antibody-conjugated silica nanoparticles (anti-AFP-SiO2) 88
3.2.5 Synthesis of Concanavalin A-conjugated magnetic nanoparticles (ConA-MNP) 88
3.2.6 One-pot enrichment and on-particle digestion 89
3.2.6.1 One-pot enrichment by hybrid titanium dioxide-coated MNP (MNP@TiO2) 90
3.2.7 Stable isotope dimethyl labeling for protein quantification 90
3.2.8 Glycosylation analysis by Liquid chromatography-mass spectrometry (LC-MS/MS) 91
3.2.9 Protein quantification by Multiple reaction monitoring (MRM) 92
3.3 Results and Discussion 92
3.3.1 Experimental Design and Workflow 92
3.3.2 Specificity of Protein Level Enrichment 93
3.3.3 Identification of Glycopeptides 95
3.3.4 Comparison to non-one pot method 96
3.3.5 Protein level quantification 97
3.3.6 Versatility of one-pot method towards targeted glycosylation analysis. 98
3.4 Conclusion 99
CHAPTER 4 111
4.1 Introduction 111
4.2 Materials and Methods 113
4.2.1 Manual Literature Search 113
4.2.2 Serum samples 114
4.2.3 Nanoprobe-based MRM and ELISA analysis of top 3 biomarker candidates 114
4.2.4 Glycosylation profiling of alpha-fetoprotein 114
4.2.4.1 Protein and glycopeptide enrichment 114
4.2.4.2 LC-MS/MS analysis for Glycosylation profiling 115
4.2.4.3 Data processing and Database search 116
4.3 Results and Discussion 117
4.3.1 Biomedical literature mining 117
4.3.2 Qualification of HCC biomarker candidates by ELISA 119
4.3.3 Qualification of HCC biomarker candidates by nanoprobe-MRM assay 124
4.3.4 Glycosylation Profiling of Alpha-fetoprotein by Sequential Antibody-conjugated Nanoprobe and HILIC 127
4.3.5 Clinical application of one-pot method to HCC patient samples 132
4.4 Conclusion 134
CHAPTER 5 161
REFERENCES 165

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