博碩士論文 109826007 詳細資訊




以作者查詢圖書館館藏 以作者查詢臺灣博碩士 以作者查詢全國書目 勘誤回報 、線上人數:85 、訪客IP:3.135.208.236
姓名 劉明翰(Ming-Han Liu)  查詢紙本館藏   畢業系所 系統生物與生物資訊研究所
論文名稱 尼曼匹克症轉錄體學研究
(Transcriptomics research of Niemann-Pick disease)
相關論文
★ 整合深度學習方法預測年齡以及衰老基因之研究★ 運用深度學習方法預測阿茲海默症惡化與腦中風手術存活
★ 運用深度學習方法預測癌症種類及存活死亡與治癒復發★ 基於檢驗數值的糖尿病腎病變預測模型
★ 機械循環拉伸對肺癌細胞功能的影響之研究★ 整合多種基因組型態資料預測肺腺癌患者存活之研究
★ 以系統生物學策略探討臍帶血來源之造血幹細胞分子調控網路★ TP53突變對具有EGFR突變的非小細胞肺癌患者帶來的影響
★ 以系統生物學方法探討肺腺癌抗藥性成因★ 機械循環拉伸力對3D培養肺癌細胞之影響
★ PM2.5對人類心肺細胞的影響★ 體外仿生肺肝纖維化3D模型研究
★ 肝纖維化細胞與動物模型以轉錄體資料分析比較★ 基於深度學習之皮膚病兆切割之研究
★ 體外仿生心臟衰竭三維模型研究★ 在大腸桿菌與酵母菌蛋白質體晶片中量化其蛋白質的濃度
檔案 [Endnote RIS 格式]    [Bibtex 格式]    [相關文章]   [文章引用]   [完整記錄]   [館藏目錄]   至系統瀏覽論文 ( 永不開放)
摘要(中) 尼曼匹克症C型是基因突變所導致的罕見疾病,它會使次級內體及溶酶體中的膽固醇及鞘糖脂過度累積,導致患者引發神經或精神上的症狀。尼曼匹克症C型與其他疾病相比,尼曼匹克症C型的研究相對少很多,而運用轉錄組來瞭解這種疾病的研究更是屈指可數。在這份研究中,我們從患者的周邊血液中取得轉錄組需要的樣本,透過次世代定序取得RNA的表現量,這些基因表現量透過顯著檢定與差異倍數篩選出顯著的基因,我們使用這些基因進行後續的生物途徑分析。我們也將這些尼曼匹克症C型的患者進行不同表徵的分組,並在分析後進行討論。透過生物途徑的分析,我們從尼曼匹克症C型的患者的差異表達基因中發現了與神經退化疾病相關的生物途徑,也找出與尼曼匹克症C型相關的PIK3CG及PIK3CD兩個基因和磷酸肌醇的代謝路徑。
摘要(英) Niemann-Pick disease type C is a rare disease caused by gene mutations that cause excessive accumulation of cholesterol and glycosphingolipids in late endosomes and lysosomes, resulting in neurological or psychiatric symptoms. The research of Niemann-Pick disease type C is relatively understudied compared to other diseases, and it is rare that use transcriptomes to understand this disease. In this study, we obtained the samples needed for the transcriptome from the peripheral blood of patients, and we got RNA expressions through next-generation sequencing. The expressions of these genes were filtered by significance testing and foldchange. After the analysis, we also grouped these Niemann-Pick disease type C patients with different characteristics and discussed them. Through the analysis of biological pathways, we found some pathways related to neurodegenerative diseases from the differentially expressed genes of patients with Niemann-Pick disease type C. We also identified that PIK3CG, PIK3CD, and the inositol phosphate metabolism pathway are associated with Niemann-Pick disease type C.
關鍵字(中) ★ 尼曼匹克症C型
★ 罕見疾病
★ 次世代定序
★ 轉錄組
關鍵字(英) ★ Niemann-Pick disease type C
★ rare disease
★ next generation sequence
★ transcriptome
論文目次 中文摘要 i
Abstract ii
目錄 iii
圖目錄 vi
表目錄 vii
一、緒論 1
1-1尼曼匹克症C型 1
1-2尼曼匹克症C型治療方法 2
1-3 尼曼匹克症C型的淋巴細胞 2
1-4次世代定序 3
1-5基因表現量、差異表達基因 3
1-6研究動機與目的 4
二、材料與方法 5
2-1資料來源 5
2-2研究方法 7
2-2-1開發環境 7
2-2-2 RNA-Sequencing 8
2-2-3資料預處理 8
2-2-4基因集富集分析 9
2-2-5 Ingenuity Pathways Analysis 9
2-2-6 CIBERSORT 10
2-2-7 Kyoto Encyclopedia of Genes and Genomes 10
2-2-8 Gene Ontology 11
三、實驗流程 12
四、結果 13
4-1 NPC患者與一般人的RNA表達差異 13
4-1-1 CIBERSORT分析 13
4-1-2主成分分析 14
4-1-3基因集富集分析 16
4-1-4基因篩選 17
4-1-5 IPA 18
4-1-6 KEGG 途徑分析 20
4-1-7 GO功能分析 21
4-2在NPC患者之間分組的RNA表達差異 23
4-2-1使用HPβCD治療的NPC患者與使用Miglustat治療的NPC患者 24
4-2-1-1基因集富集分析 24
4-2-1-2基因篩選 25
4-2-1-3 IPA 27
4-2-1-4 KEGG 途徑分析 29
4-2-1-5 GO功能分析 30
4-2-2 NPC1基因有兩個突變點的NPC患者與單一突變點的NPC患者 32
4-2-2-1基因篩選 32
4-2-2-2 IPA 34
4-2-2-3 KEGG 途徑分析 36
4-2-2-4 GO功能分析 37
4-2-3發病年齡小於6歲的NPC患者與大於6歲的NPC患者 39
4-2-3-1基因篩選 39
4-2-3-2 IPA 41
4-2-3-3 KEGG 途徑分析 43
4-2-4男性NPC患者與女性NPC患者 44
4-2-4-1基因篩選 44
4-2-4-2 IPA 46
4-2-4-3 KEGG 途徑分析 48
4-3 各組別分析結果當中的重要基因 49
五、討論與結論 51
5-1 NPC患者與一般人的差異表達基因分析 51
5-2 PI3K/AKT與mTOR訊號通路 52
5-3 NPC患者之間分組的差異表達基因分析 53
5-4 NPC患者的免疫系統 54
5-5結論 55
參考文獻 56
參考文獻 1. Vanier, M.T., Niemann-Pick disease type C. Orphanet J Rare Dis, 2010. 5: p. 16.
2. Vanier, M.T., Complex lipid trafficking in Niemann-Pick disease type C. J Inherit Metab Dis, 2015. 38(1): p. 187-99.
3. Sevin, M., et al., The adult form of Niemann-Pick disease type C. Brain, 2007. 130(Pt 1): p. 120-33.
4. Zervas, M., et al., Critical role for glycosphingolipids in Niemann-Pick disease type C. Curr Biol, 2001. 11(16): p. 1283-7.
5. Patterson, M., Niemann-Pick Disease Type C, in GeneReviews((R)), M.P. Adam, et al., Editors. 1993: Seattle (WA).
6. Patterson, M.C., et al., Recommendations for the diagnosis and management of Niemann-Pick disease type C: an update. Mol Genet Metab, 2012. 106(3): p. 330-44.
7. Walterfang, M., et al., Dysphagia as a risk factor for mortality in Niemann-Pick disease type C: systematic literature review and evidence from studies with miglustat. Orphanet J Rare Dis, 2012. 7: p. 76.
8. Yanjanin, N.M., et al., Linear clinical progression, independent of age of onset, in Niemann-Pick disease, type C. Am J Med Genet B Neuropsychiatr Genet, 2010. 153B(1): p. 132-40.
9. Mengel, E., et al., Differences in Niemann-Pick disease Type C symptomatology observed in patients of different ages. Mol Genet Metab, 2017. 120(3): p. 180-189.
10. Vanier, M.T. and G. Millat, Niemann-Pick disease type C. Clin Genet, 2003. 64(4): p. 269-81.
11. Camargo, F., et al., Cyclodextrins in the treatment of a mouse model of Niemann-Pick C disease. Life Sci, 2001. 70(2): p. 131-42.
12. Davidson, C.D., et al., Chronic cyclodextrin treatment of murine Niemann-Pick C disease ameliorates neuronal cholesterol and glycosphingolipid storage and disease progression. PLoS One, 2009. 4(9): p. e6951.
13. Peake, K.B. and J.E. Vance, Normalization of cholesterol homeostasis by 2-hydroxypropyl-beta-cyclodextrin in neurons and glia from Niemann-Pick C1 (NPC1)-deficient mice. J Biol Chem, 2012. 287(12): p. 9290-8.
14. Ory, D.S., et al., Intrathecal 2-hydroxypropyl-beta-cyclodextrin decreases neurological disease progression in Niemann-Pick disease, type C1: a non-randomised, open-label, phase 1-2 trial. Lancet, 2017. 390(10104): p. 1758-1768.
15. Taconet, S., et al., Finding vacuolated lymphocytes in fetal effusions improves the prenatal diagnosis of lysosomal storage diseases. Prenat Diagn, 2020. 40(5): p. 605-611.
16. Parisi, D., et al., Vacuolated PAS-Positive Lymphocytes on Blood Smear: An Easy Screening Tool and a Possible Biomarker for Monitoring Therapeutic Responses in Late Onset Pompe Disease (LOPD). Front Neurol, 2018. 9: p. 880.
17. Vasei, M., M. Abolhasani, and M. Safavi, Vacuolated Lymphocytes as a Clue for Diagnosis of Lysosomal Storage Disease like GM1 Gangliosidosis. Indian J Hematol Blood Transfus, 2018. 34(4): p. 749-750.
18. Anderson, G., et al., Blood film examination for vacuolated lymphocytes in the diagnosis of metabolic disorders; retrospective experience of more than 2,500 cases from a single centre. J Clin Pathol, 2005. 58(12): p. 1305-10.
19. Slatko, B.E., A.F. Gardner, and F.M. Ausubel, Overview of Next-Generation Sequencing Technologies. Curr Protoc Mol Biol, 2018. 122(1): p. e59.
20. Levy, S.E. and R.M. Myers, Advancements in Next-Generation Sequencing. Annu Rev Genomics Hum Genet, 2016. 17: p. 95-115.
21. Burghel, G.J., et al., Towards a Next-Generation Sequencing Diagnostic Service for Tumour Genotyping: A Comparison of Panels and Platforms. Biomed Res Int, 2015. 2015: p. 478017.
22. Behjati, S. and P.S. Tarpey, What is next generation sequencing? Arch Dis Child Educ Pract Ed, 2013. 98(6): p. 236-8.
23. Shen, T., et al., Clinical applications of next generation sequencing in cancer: from panels, to exomes, to genomes. Front Genet, 2015. 6: p. 215.
24. Dawson, S.J., et al., Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med, 2013. 368(13): p. 1199-209.
25. Ley, T.J., et al., A pilot study of high-throughput, sequence-based mutational profiling of primary human acute myeloid leukemia cell genomes. Proc Natl Acad Sci U S A, 2003. 100(24): p. 14275-80.
26. Fremond, M.L., et al., Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis. J Pediatric Infect Dis Soc, 2015. 4(3): p. e53-7.
27. Chiu, R.W., et al., Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A, 2008. 105(51): p. 20458-63.
28. Zhang, X., I. Jonassen, and A. Goksoyr, Machine Learning Approaches for Biomarker Discovery Using Gene Expression Data, in Bioinformatics, I.N. Helder, Editor. 2021: Brisbane (AU).
29. Lovf, M., et al., Multifocal Primary Prostate Cancer Exhibits High Degree of Genomic Heterogeneity. Eur Urol, 2019. 75(3): p. 498-505.
30. Zhang, Y., et al., Differential expression profiles of microRNAs as potential biomarkers for the early diagnosis of lung cancer. Oncol Rep, 2017. 37(6): p. 3543-3553.
31. Yu, G., et al., clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS, 2012. 16(5): p. 284-7.
32. Subramanian, A., et al., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A, 2005. 102(43): p. 15545-50.
33. Chen, C., et al., Ingenuity pathway analysis of human facet joint tissues: Insight into facet joint osteoarthritis. Exp Ther Med, 2020. 19(4): p. 2997-3008.
34. Hwang, J.W., S.K. Jang, and D.J. Lee, Genomic analysis of pancreatic cancer reveals 3 molecular subtypes with different clinical outcomes. Medicine (Baltimore), 2021. 100(14): p. e24969.
35. Kawada, J.I., et al., Immune cell infiltration landscapes in pediatric acute myocarditis analyzed by CIBERSORT. J Cardiol, 2021. 77(2): p. 174-178.
36. Craven, K.E., Y. Gokmen-Polar, and S.S. Badve, CIBERSORT analysis of TCGA and METABRIC identifies subgroups with better outcomes in triple negative breast cancer. Sci Rep, 2021. 11(1): p. 4691.
37. Kanehisa, M. and S. Goto, KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 2000. 28(1): p. 27-30.
38. Ogata, H., et al., KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res, 1999. 27(1): p. 29-34.
39. Green, R., I. Esparza, and R. Schreiber, Iron inhibits the nonspecific tumoricidal activity of macrophages. A possible contributory mechanism for neoplasia in hemochromatosis. Ann N Y Acad Sci, 1988. 526: p. 301-9.
40. Gene Ontology, C., Gene Ontology Consortium: going forward. Nucleic Acids Res, 2015. 43(Database issue): p. D1049-56.
41. Ashburner, M., et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000. 25(1): p. 25-9.
42. Geberhiwot, T., et al., Consensus clinical management guidelines for Niemann-Pick disease type C. Orphanet J Rare Dis, 2018. 13(1): p. 50.
43. Ediriweera, M.K., K.H. Tennekoon, and S.R. Samarakoon, Role of the PI3K/AKT/mTOR signaling pathway in ovarian cancer: Biological and therapeutic significance. Semin Cancer Biol, 2019. 59: p. 147-160.
44. Davis, O.B., et al., NPC1-mTORC1 Signaling Couples Cholesterol Sensing to Organelle Homeostasis and Is a Targetable Pathway in Niemann-Pick Type C. Dev Cell, 2021. 56(3): p. 260-276 e7.
45. Johnston, P.A. and J.R. Grandis, STAT3 signaling: anticancer strategies and challenges. Mol Interv, 2011. 11(1): p. 18-26.
46. Chen, F., et al., Case Report: Be Aware of "New" Features of Niemann-Pick Disease: Insights From Two Pediatric Cases. Front Genet, 2022. 13: p. 845246.
指導教授 許藝瓊(Yi-Chiung Hsu) 審核日期 2022-9-16
推文 facebook   plurk   twitter   funp   google   live   udn   HD   myshare   reddit   netvibes   friend   youpush   delicious   baidu   
網路書籤 Google bookmarks   del.icio.us   hemidemi   myshare   

若有論文相關問題,請聯絡國立中央大學圖書館推廣服務組 TEL:(03)422-7151轉57407,或E-mail聯絡  - 隱私權政策聲明