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研究生: 林芳逵
Lin, Fang-Kuei
論文名稱: 以單細胞RNA定序分析口腔癌癌化關鍵
Single-cell RNA sequencing analysis of carcinogenesis crux of oral cancer
指導教授: 黃則達
Huang, Tze-Ta
學位類別: 碩士
Master
系所名稱: 醫學院 - 口腔醫學研究所
Institute of Oral Medicine
論文出版年: 2021
畢業學年度: 109
語文別: 中文
論文頁數: 82
中文關鍵詞: 口腔鱗狀細胞癌 、單細胞RNA測序 、白色念珠菌
外文關鍵詞: Oral Squamous cell carcinoma, Single-cell RNA sequencing, Candidiasis albicans
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  • 根據台灣衛生福利部的統計,口腔癌在台灣癌症死亡人數位居第五位。口腔癌的發生主要與吸菸、檳榔食用和飲酒有關,另外還有一些其他的危險因素,包括不良的口腔衛生習慣、念珠菌、病毒感染和口腔長期創傷等。藉由單細胞RNA測序技術(Single-cell RNA sequencing)分析口腔癌癌變過程中的生物標記物(Biomarker),可以以檢測不同的腫瘤細胞群之間的消長來分析腫瘤癌化、侵襲和轉移的關係。白色念珠菌時常在口腔鱗狀細胞癌(Oral Squamous Cell Carcinoma)及口腔癌前病變(OPMD;Oral Premalignant Disorder)患者的口腔發生,WHO分類已經將「慢性念珠菌病」列為口腔癌前病變,因此本研究將臨床取得之口腔癌及口腔癌前病患之黏膜檢體,檢測病患的念珠菌感染情況,個別取得口腔癌、口腔癌前病患病灶及正常口腔黏膜之組織檢體進一步進行單細胞RNA測序分析,測定基因表達差異,併一同檢視念珠菌對口腔癌細胞所造成之差異。研究結果顯示整體細胞共分成24個族群,6群為癌症相關細胞群、18群為免疫細胞群,癌症相關細胞群又可以細分為13個次族群、免疫細胞群可分為15個次族群,腫瘤癌化族群及念珠菌相關表達的細胞可以看出細胞族群的消長,以上結果揭示口腔腫瘤演化、次族群細胞及念珠菌與癌症癌化過程間之相關消長資訊,此資訊可為口腔癌精準醫療之治療生物標記。

    According to the Ministry of Health and Welfare in Taiwan, oral cancer is the fifth cancer deaths in Taiwan. Oral cancers are mainly associated with the usage of tobacco, betel nuts and alcohol consumption. Other risk factors include poor oral hygiene, candidiasis, viral infection, and chronic oral mucosa trauma.
    With the technologies of Single-cell RNA sequencing, tumor cell invasion and metastasis between different tumor cell groups can be detected in oral cancer carcinogenesis. The clinical specimens were used to investigate the carcinogenesis crux in oral cancer and precancer lesion. In addition, Candida Albicans is frequently presence in oral cavity of cancer and precancerous lesion. The WHO classification lists “Chronic candidiasis” as an Oral Premalignant Disorder (OPMD). The clinical mucosal specimens from normal oral mucosa, oral cancer and oral precancerous patients were collected and candida infection was detected. Single-cell RNA sequencing analysis were performed. The differences in oral mucosa carcinogenesis and between candida infection or not were analyzed.
    The total cells can be distinguished into 24 cell clusters, 6 cell clusters are cancer related cells, and 18 cell cluster are immune cell cluster. The gain or loss of the cell cluster, and gene expression difference can be observed in oral mucosa carcinogenesis, and between Candida infection. The above results can be utilized to investigate the carcinogenesis of oral tumors and subcluster cells concerning to Candida infection. These results can be utilized as treatment biomarker of precision medicine.

    中文摘要 I Abstract III 致謝 XV 目錄 XVII 圖目錄 XX 表目錄 XXI 第一章 緒論 1 一、口腔鱗狀細胞癌(Oral Squamous Cell Carcinoma;OSCC)與口腔癌前病變(Oral Premalignant Disorder;OPMD) 1 二、致癌潛在因素(Potential carcinogenic factors) 5 三、單細胞基因測序(Single-Cell RNA Sequencing) 8 四、研究動機 10 第二章 實驗材料和方法 11 一、臨床病患檢體之蒐集(Clinical patient specimens collection) 11 二、念珠菌檢測(Detection of candidiasis) 11 三、口腔黏膜組織分離(Dissociation of oral mucosa tissue) 11 1. 酵素製備(Preparation of enzyme) 11 (1) 製備Dispase type II 12 (2) 製備Collagenase type IV 12 2. 組織分解(Tissue dissociation) 12 四、10x Genomics platform 14 1. GEM油滴微珠包覆以及細胞條碼標示(GEM generation and barcoding) 14 (1) 製備Master mix 15 (2) 製備Chromium Next GEM Chip G 15 (3) Transfer GEM 16 (4) GEM-RT incubation 16 2. Post GEM-RT Clean-up and cDNA amplification 17 (1) Post GEM-RT Cleanup-Dynabeads 17 (2) cDNA Amplification 19 (3) cDNA Cleanup SPRIselect 20 (4) cDNA QC & Qualification 20 3. 3’ Gene Expression Library Construction 20 (1) Fragmentation, End Repair & A-tailing 21 (2) Post Fragmentation End Repair & A-tailing Double Sided Size Selection -SPRIselect 22 (3) Adaptor Ligation 23 (4) Post Ligation Cleanup SPRIselect 24 (5) Sample Index PCR 24 (6) Post Sample Index PCR Double Sided Size Selection-SPRIselect 25 (7) Post Library Construction QC 26 五、次世代測序 (NGS;Next Generation Sequencing) 26 第三章 實驗結果 27 一、念珠菌篩檢符合之臨床病例 27 二、臨床檢體取得 27 三、單細胞基因檢測分析臨床病例檢體 27 四、臨床檢體檢視癌化過程參與的調控途徑 30 五、K-ras signaling downregulation及E2F targets途徑相關之基因在所有癌症相關細胞群的表現程度 31 第四章 討論 33 第五章 結論 39 參考文獻 40 圖表 47 補充資料 78

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