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研究生：	杜瓊莊 Do, Quynh-Trang
論文名稱：	以組學與液相層析串聯質譜技術解析兒茶酚雌激素誘發的內源性基因毒性 Deciphering Endogenous Genotoxicity Induced by Catechol Estrogens Using Omics and LC-MS/MS Techniques
指導教授：	陳淑慧 Chen, Shu-Hui
學位類別：	博士 Doctor
系所名稱：	理學院 - 化學系 Department of Chemistry
論文出版年：	2025
畢業學年度：	113
語文別：	英文
論文頁數：	157
中文關鍵詞：	兒茶酚雌激素、點擊探針測序、液相色譜-串聯質譜、點擊化學、定量蛋白質組學、兒茶酚雌激素誘導的去氧核糖核酸損傷、兒茶酚雌激素誘導的蛋白質加成物、脫嘌呤去氧核糖核酸加成物、穩定去氧核糖核酸加合物
外文關鍵詞：	Catechol Estrogens, Click Probe-Seq, LC-MS/MS, click chemistry, quantitative proteomics, CE- induced DNA damage, CE- induced protein adducts, depurinating DNA adducts, stable DNA adducts
ORCID：	https://orcid.org/0000-0003-2567-598X
ResearchGate：	https://www.researchgate.net/profile/Trang-Do-Quynh-2?ev=hdr_xprf
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雌激素的反應性代謝物兒茶酚雌激素在加成於去氧核糖核酸或蛋白質上後會具有基因毒性，影響基因組的穩定性。儘管了解兒茶酚雌激素加成後會產生毒性，但加成物誘發基因損傷的機制及其對細胞轉化的影響仍然知之甚少。為了解明上述問題，我們運用先進組學與液相色譜-串聯質譜來研究蛋白質和去氧核糖核酸的兒茶酚雌激素加合物。
在第二章中我們開發了一種專門針對兒茶酚雌激素-蛋白質加成物的濃縮工作流程，其中運用了點擊化學並結合定量蛋白質組學，能提高專一性同時抑制背景訊號。我們透過此方法識別並定量了兒茶酚雌激素加成的蛋白質及其加成位點，總共有310個蛋白質和40個兒茶酚雌激素加成位點被識別出來。結果顯示經兒茶酚雌激素處理後細胞中抗壓蛋白量會隨之減少，表明兒茶酚雌激素在促進細胞生存和惡性轉化方面起著雙重作用。
在第三章及第四章中，將用於兒茶酚雌激素-蛋白質加成物的濃縮工作流程運用在研究兒茶酚雌激素-去氧核糖核酸加成物上。我們先透過點擊探針測序進行全基因組圖譜繪製以鑑定兒茶酚雌激素誘導的去氧核糖核酸損傷，並使用液相色譜-串聯質譜和序列分析評估了染色質可及性對兒茶酚雌激素-去氧核糖核酸加成物生成的影響。由全基因組圖譜繪製的結果顯示，兒茶酚雌激素誘導的去氧核糖核酸損傷優先發生在轉錄活躍區域，這些區域對雌激素受體調節的基因調控至關重要。另外還發現了暴露於兒茶酚雌激素下會抑制了去氧核糖核酸修復基因 (如BRCA1和RAD51C) 的轉錄，影響雙鏈斷裂修復同時導致了基因組的不穩定性。染色質的結構被證明可以保護去氧核糖核酸免受兒茶酚雌激素加成，其中鳥嘌呤加成物占大宗而沒有腺嘌呤加合物，表明了組蛋白的包裹限制兒茶酚雌激素對去氧核糖核酸的可及性。
本研究開發的方法為研究兒茶酚雌激素誘導的蛋白質與去氧核糖核酸加合物提供了強而有力的工具，顯著提高了我們對雌激素相關癌症及其基本機制的理解。此外，這些方法還提供了一個平台來研究其他內源性化合物的基因毒性，為內源代謝物誘導的損傷及其對疾病影響的分子機制提供了更廣泛的見解。

Catechol estrogen (CEs), reactive metabolites of estrogen, induce genotoxicity through DNA and protein adduction, leading to genomic instability and impaired cellular processes. Despite the known reactivity of CEs, the mechanism of CE-induced damage and its implications for cellular transformation remain poorly understood. To address these gaps, we employed advanced omics and LC-MS/MS techniques to comprehensively investigate CE-induced protein and DNA adducts.
In the first topic (chapter 2), a click chemistry-based enrichment workflow coupled quantitative proteomics was developed and optimized for targeting CE-protein adducts, achieving enhanced specificity and reduced background noise. The catechol estrogen- adducted proteins and its adducted sites were identified and quantified. A total of 310 protein targets with 40 CE-adducted sites were identified. The results revealed that CE treatment induce downregulated stress-resistant proteins, indicating a dual role of CEs in promoting both cell survival and malignant transformation.
In the second and third topic (chapter 3 and 4), the click chemistry-based enrichment workflow was extended to study CE-induced DNA adducts. A genome-wide mapping approach using click probe-seq was employed to identify CE-induced DNA damage. The effect of chromatin accessibility to CE-DNA adduct formation was also assessed using liquid chromatography- tandem mass spectrometry (LC-MS/MS) and sequence analysis. Genome-wide mapping showed that CE-induced DNA damage preferentially occurs at transcriptional active regions, which are critical for estrogen receptor-mediated gene regulation. CE exposure was also found to suppress the transcription of key DNA repair genes, such as BRCA1 and RAD51C, impairing double-strand break (DSB) repair and leading to genomic instability. Chromatin structure was shown to protect DNA from CE adduction, with guanine adducts being predominant and adenine adducts absent, suggesting that histone wrapping limits DNA accessibility to CEs.
In addition, the methodology developed in this study provide powerful tools for studying catechol estrogens induced protein and DNA adducts, thus significantly improve our understanding of estrogen-related cancers and their underlying mechanisms. Furthermore, these approaches offer a platform to investigate the genotoxicity of other endogenous compounds, giving a way for broader insights into molecular mechanisms of endogenous metabolite-induced damage and its implications for disease.

ABSTRACT	I
摘要	III
ACKNOWLEDGEMENTS	V
TABLE OF CONTENTS	VII
LIST OF TABLES	X
LIST OF FIGURES	XI
LIST OF APPENDIX	XV
ABBREVIATIONS	XVI
CHAPTER 1:	INTRODUCTION	1
1.	Breast Cancer	1
2.	Catechol Estrogen Metabolism and Adduct Formation	2
3.	Catechol Estrogen Protein Adducts	6
4.	Characterization Methods for CE-induced protein Adducts	7
5.	Catechol Estrogen-DNA Adducts	9
6.	Characterization Methods for Catechol Estrogen DNA Adducts	11
6.1.	HPLC-ECD	11
6.2.	32P-Postlabeling	12
6.3.	Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)	12
6.4.	Immunodetection Using Biotin-Labeled Estradiol	13
6.5.	Chromatin Immunoprecipitation Sequencing (ChIP-seq)	13
6.6.	Chemical Affinity Capture and Sequencing (Chem-Seq)	14
6.7.	Integrated LC-MS/MS and Immunoprecipitation-Sequencing	14
7.	Challenges in Studying Genotoxicity of Catechol Estrogen	15
8.	Objectives of the Study	16
9.	Introduction to key techniques	17
9.1.	Liquid chromatography- Tandem Mass spectrometry (LC-MS/MS)	17
9.2.	LC-MS/MS based bottom-up quantitative proteomics	23
9.3.	Click Chemistry coupled Affinity Purification	26
9.4.	Next generation sequencing (NGS)	28
CHAPTER 2:	QUANTIFICATION OF PROTEIN ADDUCTS USING QUANTITATIVE PROTEOMICS AND CLICK PROBE	34
1. Experimental section	34
1.1. Reagents	34
1.2. Instruments	35
2. Methods	36
2.1. Culture procedure of MCF-7 cells	36
2.2. 4OHEE2 treated MCF-7 cells	36
2.3. Cytosolic protein extraction	37
2.3. Cellular Viability	37
2.4. Adduct and non-Adducted Protein Standard Mixture	38
2.5. Click Chemistry-Based Enrichment	38
2.6. Dimethyl Labeling	41
2.7. Fractionation of with HILIC column	41
2.8. nano-UPLC System Coupled with LTQ-Orbitrap XL MS	42
2.9. nano-UPLC System Coupled with Q Exactive Mass spectrometer	43
2.10. Automatic Database Search	43
2.11. Relative quantitative proteomics analysis	44
3. Results	45
3.1. Validation of the Click Chemistry-Based Enrichment Workflow	45
3.2. Identification CE protein adducts	49
3.3. Quantification of protein targets	51
3.4. Identification of adducts sites	56
4. Discussion	59
5. Conclusion	60
CHAPTER 3:	GENOME-WIDE MAPPING OF DNA ADDUCTS USING CLICK PROBE-SEQ	61
1. Experimental section	61
1.1. Materials	61
1.2. Study design	63
1.2. Cell Culture and Chromatin Isolation	64
1.3. In-situ generation of CE quinone and DNA Adducts in Chromatin	65
1.4. Click Probe-Seq: Combining Click Chemistry with Sequencing	66
1.5. NGS and DHS Correlation	67
1.6. Cell Viability	68
1.7. Immunofluorescence Staining	68
1.8. RT-PCR	69
2. Results	70
2.1. Click Probe-seq and Genome Wide-Mapping of DNA Damage	70
2.2. Chromatin Accessibility and CE-DNA adduct Formation	76
2.4. GC Content and Genomic Element Distribution of Enriched peaks	77
2.5. Functional Annotation of Genes Affected by CE-Induced DNA Damage	81
2.6. Transcriptional Impact of 4OHE2/4OHEE2 compared to E2	82
2.7. Comparative Analysis of DNA Damage and Repair Mechanisms	84
2.8. Comparative Studies of Cell Viability	87
3. Discussion	88
4.   Conclusion	91
CHAPTER 4:	QUANTIFICATION OF CATECHOL ESTROGEN DNA ADDUCTS USING LC-MS/MS	92
1. Experimental Section	92
1.1. Materials	92
1.2. In-situ generation of CE quinone	92
1.3. Adduct formation	93
1.4. DNA digestion	94
1.5. Capillary-flow LC-MRM and data analysis	94
1.6. Total non-modified nucleobase quantification	95
2. Results	96
2.2. Quantification of non-adduct nucleosides	100
2.2. Quantification of Stable and Depurinating adducts	101
3. Discussion	106
4. Conclusion	107
CHAPTER 5:	SUMMARY	109
CHAPTER 6:	REFERENCES	111
CHAPTER 7:	APPENDICES	121
                                    

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