跳到主要內容

簡易檢索 / 詳目顯示

研究生: 許鈞亮
Chun-Liang Hsu
論文名稱: VHL剔除模型之轉錄體差異以及台灣透明細胞腎細胞癌族群之特定基因體變異之研究
The study of transcriptome differentiation in VHL knockout model and specific genomic variations in Taiwanese ccRCC population
指導教授: 徐沺
Tien Hsu
口試委員:
學位類別: 碩士
Master
系所名稱: 生醫理工學院 - 系統生物與生物資訊研究所
Graduate Institute of Systems Biology and Bioinformatics
論文出版年: 2019
畢業學年度: 107
語文別: 英文
論文頁數: 84
中文關鍵詞: 透明細胞腎細胞癌
相關次數: 點閱:16下載:0
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報
  • 透明細胞腎細胞癌佔據約60%腎臟惡性腫瘤,其中70%以上的透明細胞腎細胞
    癌源自於VHL 腫瘤抑制基因的失能,VHL 基因的失能導致低氧誘導轉錄因子的累積,使
    低氧誘導因子活化低氧反應基因,如:血管內皮生長因子,其能促進血管增生。低氧誘
    導因子也能於低氧環境下調節代謝適應基因。先前的研究中,我們已經發現VHL 剔除腎
    臟的差異基因表達與細胞增生、細胞分化、免疫反應以及細胞代謝有關。此外我們連結
    發炎反應與VHL 失能誘導的內質網壓力的關係。然而,腎小管上皮細胞的基因表達特異
    性仍屬於未知,我們也注意到一個鈣離子通道ITPR2 基因活性在透明細胞腎細胞癌中常
    有增加現象,我們也懷疑其功能是否能誘導內質網壓力的惡化。因此,這篇研究中,我
    們利用腎小管上皮細胞作為模型,利用RNA 定序來分析其轉錄體的變化,以及利用DN
    A定序分析基因體的突變。我們發現部份上調表現的基因,如:Cxcl12、Vegfa、Tgfa、
    Cldn8、Cldn9 以及Vasp 能夠促進腫瘤前期的生成。另外,Egln3、Peg3os、Cd82、Scnn1b
    以及Sulf1 卻能夠抑制腫瘤生成。有些下調的基因能促進腫瘤的形成,如:Adam9;調
    節異常的代謝,如Cbs 以及Kcnma1;或是抑制腫瘤生長,如:Sptan1。這提供我們許多
    有關腫瘤形成前轉錄體的轉變訊息。我們也發現台灣透明細胞腎細胞癌患者帶有VHL 突
    變的比例與世界是一致的,且我們也找到ITPR2 單核甘酸多樣性能夠增強VHL 失能造成
    的內質網壓力的反應。這提供我們ITPR2 與透明細胞腎細胞癌生成間的關係。


    Clear-cell renal cell carcinoma (ccRCC) constitutes 60% renal malignancy and up to 70%
    of ccRCC cases result from loss function of the von Hippel-Lindau (VHL) tumor suppressor
    gene. Loss-of-function of VHL gene causes accumulation of hypoxia inducible factor 1 alpha
    (HIF1-α) transcription factor, then HIF1-α can activate hypoxia-responsive genes such as
    vascular endothelial growth factor (VEGF) gene that promotes angiogenesis. HIF transcription
    factor also regulates other genes involved in metabolic adaption to the hypoxia condition
    (Warburg effect). In previous research, we have found that the differentially expressed genes in
    Vhlh (mouse allele of the VHL gene) conditional knockout kidney were mostly involved in cell
    proliferation, cell differentiation, immune response, and cell metabolism. In addition, we also
    linked the inflammatory response with ER-stress induced by VHL inactivation. However, gene
    expression patterns specific to renal tubular epithelial cells are still unclear. We are also
    interesting in whether deterioration of ER-stress can be induced by the activity of a calcium
    channel genes ITPR2, the amplification of which has been shown to correlate with the risk of
    developing ccRCC. Therefore, in this research, we used the primary renal proximal tubular
    epithelial cells as a model and analyzed the differential transcriptome by RNA sequencing, and
    analyzed genomic mutation by DNA sequencing. We found that some upregulated genes such
    as Cxcl12, Vegfa, Tgfa, Cldn8, Cldn9 and Vasp may promote cancer formation, but some genes
    such as Egln3, Peg3os, Cd82, Scnn1b, and Sulf1 may inhibit tumorigenesis. The downregulated
    genes may promote cancer formation such as Adam9, lead to aberrant metabolism such as Cbs
    and Kcnma1, or inhibit cell growth such as Sptan1. The global gene expression profile of Vhlh
    loss-of-function kidney tubule cells provided us with information about the transformation that
    promote cancer formation. In addition, we found the proportion of VHL dysfunction in ccRCC
    patients in Taiwan was consistent with prevalence in the world. And, we also found that single
    nucleotide polymorphism for ITPR2 may enhance ER-stress response induced by VHL
    dysfunction. This provided us with more information to link ITPR2 and ccRCC formation

    摘要 ..............................................................................i Abstract ..........................................................................ii 誌謝 ..............................................................................iii Table of Contents .................................................................iv List of Figures ...................................................................v List of Tables ....................................................................vii Chapter 1 Introduction ............................................................1 1-1 Renal cell carcinoma and von Hippel-Lindau gene dysfunction ...................1 1-2 The prevalence of renal cell carcinoma in Taiwan ..............................3 1-2-1 Urothelial carcinoma and its prevalence .....................................3 1-2-2 The change of DNA sequence in ccRCC .........................................5 Chapter 2 Material and Methods ....................................................7 2-1 Animal ........................................................................7 2-2 Mouse renal tubule isolation ..................................................7 2-3 RNA extraction and RNA sequencing ............................................ 9 2-4 Reverse transcription PCR (RT-PCR) and quantitative real-time PCR (QRT-PCR) .. 10 2-5 Patient samples ...............................................................12 2-6 DNA extraction ................................................................12 2-7 DNA sequencing and bioinformatics .............................................13 2-8 Statistical analysis ..........................................................13 Chapter 3 Results .................................................................14 3-1 Renal cell carcinoma and von Hippel-Lindau gene dysfunction ...................14 3-2 The prevalence of renal cell carcinoma in Taiwan ..............................24 Chapter 4 Conclusion and Discussion ...............................................30 Chapter 5 Reference ...............................................................43 Appendix ..........................................................................51

    1. Hsieh, J.J., et al., Renal cell carcinoma. Nature Reviews Disease Primers, 2017. 3: p.17009.
    2. Cohen, H.T. and F.J. McGovern, Renal-cell carcinoma. New England Journal of Medicine, 2005. 353(23): p. 2477-2490.
    3. Network, C.G.A.R., Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature, 2013. 499(7456): p. 43.
    4. Peña-Llopis, S., et al., BAP1 loss defines a new class of renal cell carcinoma. Nature genetics, 2012. 44(7): p. 751.
    5. Ricketts, C.J., et al., Genome-wide CpG island methylation analysis implicates novel genes in the pathogenesis of renal cell carcinoma. Epigenetics, 2012. 7(3): p. 278-290.
    6. Pritchett, T.L., et al., Conditional inactivation of the mouse von Hippel-Lindau tumor suppressor gene results in wide-spread hyperplastic, inflammatory and fibrotic lesions in the kidney. Oncogene, 2015. 34(20): p. 2631-9.
    7. Hagiwara, Yuki, Study of the association between inflammation and the initiation of renal cell carcinoma: microarray-based gene profiling analysis. National Central
    Unoversity, Master Thesis, 2016.
    8. Czerniak, B., C. Dinney, and D. McConkey, Origins of Bladder Cancer. Annu Rev Pathol, 2016. 11: p. 149-74.
    9. Roupret, M., et al., European Association of Urology Guidelines on Upper Urinary Tract Urothelial Cell Carcinoma: 2015 Update. Eur Urol, 2015. 68(5): p. 868-79.
    10. Sjodahl, G., et al., A molecular taxonomy for urothelial carcinoma. Clin Cancer Res, 2012. 18(12): p. 3377-86.
    11. Van Batavia, J., et al., Bladder cancers arise from distinct urothelial sub-populations. Nat Cell Biol, 2014. 16(10): p. 982-91, 1-5.
    12. Chen, C.H., et al., Aristolochic acid-associated urothelial cancer in Taiwan. Proc Natl Acad Sci U S A, 2012. 109(21): p. 8241-6.
    13. Turesky, R.J., et al., Aristolochic acid exposure in Romania and implications for renal cell carcinoma. British journal of cancer, 2016. 114(1): p. 76.
    14. Hoang, M.L., et al., Aristolochic acid in the etiology of renal cell carcinoma. Cancer Epidemiology and Prevention Biomarkers, 2016.
    15. Feldman, D.E., et al., Formation of the VHL–elongin BC tumor suppressor complex is mediated by the chaperonin TRiC. Molecular cell, 1999. 4(6): p. 1051-1061.
    16. Zhang, J., et al., VHL substrate transcription factor ZHX2 as an oncogenic driver in clear cell renal cell carcinoma. Science, 2018. 361(6399): p. 290-295.
    17. Kuo, C.Y., C.H. Lin, and T. Hsu, VHL Inactivation in Precancerous Kidney Cells Induces an Inflammatory Response via ER Stress-Activated IRE1alpha Signaling.
    Cancer Res, 2017. 77(13): p. 3406-3416.
    18. Butler, M.R., et al., Endoplasmic reticulum (ER) Ca(2+)-channel activity contributes to ER stress and cone death in cyclic nucleotide-gated channel deficiency. J Biol Chem, 2017. 292(27): p. 11189-11205.
    19. Wu, X., et al., A genome-wide association study identifies a novel susceptibility locus for renal cell carcinoma on 12p11.23. Hum Mol Genet, 2012. 21(2): p. 456-62.
    20. Nowak, G., P.M. Price, and R.G. Schnellmann, Lack of a functional p21 WAF1/CIP1 gene accelerates caspase-independent apoptosis induced by cisplatin in renal cells.
    American Journal of Physiology-Renal Physiology, 2003. 285(3): p. F440-F450.
    21. Klagsbrun, M. and A. Eichmann, A role for axon guidance receptors and ligands in blood vessel development and tumor angiogenesis. Cytokine Growth Factor Rev,
    2005. 16(4-5): p. 535-48.
    22. Biankin, A.V., et al., Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature, 2012. 491(7424): p. 399-405.
    23. Basile, J.R., et al., Semaphorin 4D provides a link between axon guidance processes and tumor-induced angiogenesis. Proceedings of the National Academy of Sciences,
    2006. 103(24): p. 9017-9022.
    24. Van Buul, J.D. and P.L. Hordijk, Signaling in leukocyte transendothelial migration. Arteriosclerosis, thrombosis, and vascular biology, 2004. 24(5): p. 824-833.
    25. Cook‐Mills, J.M. and T.L. Deem, Active participation of endothelial cells in inflammation. Journal of leukocyte biology, 2005. 77(4): p. 487-495.
    26. Imhof, B.A. and M. Aurrand-Lions, Adhesion mechanisms regulating the migration of monocytes. Nature Reviews Immunology, 2004. 4(6): p. 432.
    27. Polyak, S.J., Hepatitis C virus–cell interactions and their role in pathogenesis. Clinics in liver disease, 2003. 7(1): p. 67-88.
    28. Gale Jr, M. and E.M. Foy, Evasion of intracellular host defence by hepatitis C virus. Nature, 2005. 436(7053): p. 939.
    29. Kountouras, J., C. Zavos, and D. Chatzopoulos, Apoptosis in hepatitis C. Journal of viral hepatitis, 2003. 10(5): p. 335-342.
    30. Pieperhoff, S., Gene Mutations Resulting in the Development of ARVC/D Could Affect Cells of the Cardiac Conduction System. Front Physiol, 2012. 3: p. 22.
    31. Zhang, M., et al., PKP2 Mutations in Sudden Death From Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) and Sudden Unexpected Death With Negative
    Autopsy (SUDNA). Circulation Journal, 2012. 76(1): p. 189-194.
    32. Fatkin, D. and R.M. Graham, Molecular mechanisms of inherited cardiomyopathies. Physiological reviews, 2002. 82(4): p. 945-980.
    33. Shapiro-Shelef, M. and K. Calame, Regulation of plasma-cell development. Nature Reviews Immunology, 2005. 5(3): p. 230.
    34. Radtke, F., et al., Notch regulation of lymphocyte development and function. Nature immunology, 2004. 5(3): p. 247.
    35. Zihni, C., et al., Tight junctions: from simple barriers to multifunctional molecular gates. Nature reviews Molecular cell biology, 2016. 17(9): p. 564.
    36. Martin-Belmonte, F. and M. Perez-Moreno, Epithelial cell polarity, stem cells and cancer. Nature Reviews Cancer, 2012. 12(1): p. 23.
    37. Takimoto, E., Cyclic GMP-dependent signaling in cardiac myocytes. Circulation Journal, 2012. 76(8): p. 1819-1825.
    38. Murthy, K.S., Signaling for contraction and relaxation in smooth muscle of the gut. Annu. Rev. Physiol., 2006. 68: p. 345-374.
    39. Li, N., et al., Sulindac selectively inhibits colon tumor cell growth by activating the cGMP/PKG pathway to suppress Wnt/β-catenin signaling. Molecular cancer
    therapeutics, 2013: p. molcanther. 0048.2013.
    40. Montoya, M.C., et al., Cell adhesion and polarity during immune interactions. Immunological reviews, 2002. 186(1): p. 68-82.
    41. Yamagata, M., J.R. Sanes, and J.A. Weiner, Synaptic adhesion molecules. Current opinion in cell biology, 2003. 15(5): p. 621-632.
    42. Dejana, E., Endothelial cell–cell junctions: happy together. Nature reviews Molecular cell biology, 2004. 5(4): p. 261.
    43. Tahara, M., et al., RhoA/Rho-kinase cascade is involved in oxytocin-induced rat uterine contraction. Endocrinology, 2002. 143(3): p. 920-929.
    44. Gutkowska, J., et al., Oxytocin releases atrial natriuretic peptide by combining with oxytocin receptors in the heart. Proceedings of the National Academy of Sciences, 1997. 94(21): p. 11704-11709.
    45. Cassoni, P., et al., Oxytocin inhibits the proliferation of MDA‐MB231 human breastcancer cells via cyclic adenosine monophosphate and protein kinase A. International journal of cancer, 1997. 72(2): p. 340-344.
    46. del Peso, L., et al., The von Hippel Lindau/hypoxia-inducible factor (HIF) pathway regulates the transcription of the HIF-proline hydroxylase genes in response to low oxygen. J Biol Chem, 2003. 278(49): p. 48690-5.
    47. Lee, S., et al., Neuronal apoptosis linked to EglN3 prolyl hydroxylase and familial pheochromocytoma genes: developmental culling and cancer. Cancer Cell, 2005. 8(2):p. 155-67.
    48. Fu, J., et al., EGLN3 prolyl hydroxylase regulates skeletal muscle differentiation and myogenin protein stability. J Biol Chem, 2007. 282(17): p. 12410-8.
    49. Melo, R.C.C., et al., CXCR7 is highly expressed in acute lymphoblastic leukemia and potentiates CXCR4 response to CXCL12. PLoS One, 2014. 9(1): p. e85926.
    50. Guo, F., et al., CXCL12/CXCR4: a symbiotic bridge linking cancer cells and their stromal neighbors in oncogenic communication networks. Oncogene, 2016. 35(7): p.
    816-26.
    51. Collins, P.J., et al., Epithelial chemokine CXCL14 synergizes with CXCL12 via allosteric modulation of CXCR4. FASEB J, 2017. 31(7): p. 3084-3097.
    52. Kanter, J.A., et al., Decreased CXCL12 is associated with impaired alveolar epithelial cell migration and poor lung healing after lung resection. Surgery, 2015. 158(4): p. 1073-80; discussion 1080-2.
    53. Yang, S.M., et al., Joint Effect of Urinary Total Arsenic Level and VEGF-A Genetic Polymorphisms on the Recurrence of Renal Cell Carcinoma. PLoS One, 2015. 10(12):
    p. e0145410.
    54. Claesson‐Welsh, L. and M. Welsh, VEGFA and tumour angiogenesis. Journal of internal medicine, 2013. 273(2): p. 114-127.
    55. Brito, M.J., et al., Association of transforming growth factor alpha (TGFA) and its precursors with malignant change in Barrett's epithelium: biological and clinical variables. International journal of cancer, 1995. 60(1): p. 27-32.
    56. Degl'Innocenti, D., et al., Integrated ligand-receptor bioinformatic and in vitro functional analysis identifies active TGFA/EGFR signaling loop in papillary thyroid carcinomas. PLoS One, 2010. 5(9): p. e12701.
    57. Siveke, J.T., et al., Concomitant pancreatic activation of Kras(G12D) and Tgfa results in cystic papillary neoplasms reminiscent of human IPMN. Cancer Cell, 2007. 12(3):p. 266-79.
    58. Yamasaki, T., et al., Tumor-suppressive microRNA-1291 directly regulates glucose transporter 1 in renal cell carcinoma. Cancer Sci, 2013. 104(11): p. 1411-9.
    59. Chan, D.A., et al., Targeting GLUT1 and the Warburg effect in renal cell carcinoma by chemical synthetic lethality. Sci Transl Med, 2011. 3(94): p. 94ra70.
    60. Xu, J., et al., Claudin 8 Contributes to Malignant Proliferation in Human Osteosarcoma U2OS Cells. Cancer Biother Radiopharm, 2015. 30(9): p. 400-4.
    61. Angelow, S., E.E. Schneeberger, and A.S. Yu, Claudin-8 expression in renal epithelial cells augments the paracellular barrier by replacing endogenous claudin-2. J Membr Biol, 2007. 215(2-3): p. 147-59.
    62. Ashikari, D., et al., CLDN8, an androgen-regulated gene, promotes prostate cancer cell proliferation and migration. Cancer Sci, 2017. 108(7): p. 1386-1393.
    63. Zavala-Zendejas, V.E., et al., Claudin-6, 7, or 9 overexpression in the human gastric adenocarcinoma cell line AGS increases its invasiveness, migration, and proliferation rate. Cancer investigation, 2011. 29(1): p. 1-11.
    64. Park, S.K., et al., Innate immunity and non-Hodgkin's lymphoma (NHL) related genes in a nested case-control study for gastric cancer risk. PLoS One, 2012. 7(9): p.
    e45274.
    65. Loboda, A., et al., EMT is the dominant program in human colon cancer. BMC medical genomics, 2011. 4(1): p. 9.
    66. Zhang, J.W., et al., Matrine inhibits the adhesion and migration of BCG823 gastric cancer cells by affecting the structure and function of the vasodilator-stimulated phosphoprotein (VASP). Acta Pharmacol Sin, 2013. 34(8): p. 1084-92.
    67. Su, Z.-Z., et al., PEG-3, a nontransforming cancer progression gene, is a positive regulator of cancer aggressiveness and angiogenesis. Proceedings of the National
    Academy of Sciences, 1999. 96(26): p. 15115-15120.
    68. Kwon, H.J., et al., Expression of CD9 and CD82 in clear cell renal cell carcinoma and its clinical significance. Pathol Res Pract, 2014. 210(5): p. 285-90.
    69. Yang, C.H., et al., EGFR over-expression in non-small cell lung cancers harboring EGFR mutations is associated with marked down-regulation of CD82. Biochim
    Biophys Acta, 2015. 1852(7): p. 1540-9.
    70. Yusenko, M.V., D. Zubakov, and G. Kovacs, Gene expression profiling of chromophobe renal cell carcinomas and renal oncocytomas by Affymetrix GeneChip
    using pooled and individual tumours. International journal of biological sciences, 2009. 5(6): p. 517.
    71. Liao, C., W. Chen, and J. Wang, MicroRNA-20a Regulates Glioma Cell Proliferation, Invasion, and Apoptosis by Targeting CUGBP Elav-Like Family Member 2. World
    Neurosurg, 2018.
    72. Deckers, I.A., et al., Promoter CpG island methylation in ion transport mechanisms and associated dietary intakes jointly influence the risk of clear-cell renal cell cancer. Int J Epidemiol, 2017. 46(2): p. 622-631.
    73. Qian, Y., et al., Sodium Channel Subunit SCNN1B Suppresses Gastric Cancer Growth and Metastasis via GRP78 Degradation. Cancer Res, 2017. 77(8): p. 1968-1982.
    74. Dardiotis, E., et al., Genetic variations in the SULF1 gene alter the risk of cervical cancer and precancerous lesions. Oncol Lett, 2018. 16(3): p. 3833-3841.
    75. Lai, J.P., et al., The tumor suppressor function of human sulfatase 1 (SULF1) in carcinogenesis. J Gastrointest Cancer, 2008. 39(1-4): p. 149-58.
    76. Lin, C.Y., et al., ADAM9 promotes lung cancer metastases to brain by a plasminogen activator-based pathway. Cancer Res, 2014. 74(18): p. 5229-43.
    77. Erin, N., et al., Changes in expressions of ADAM9, 10, and 17 as well as alphasecretase activity in renal cell carcinoma. Urol Oncol, 2017. 35(1): p. 36 e15-36 e22.
    78. Cuadros, T., et al., HAVCR/KIM-1 activates the IL-6/STAT-3 pathway in clear cell renal cell carcinoma and determines tumor progression and patient outcome. Cancer
    Res, 2014. 74(5): p. 1416-28.
    79. Bhattacharyya, S., et al., Cystathionine beta-synthase (CBS) contributes to advanced ovarian cancer progression and drug resistance. PLoS One, 2013. 8(11): p. e79167.
    80. Szabo, C., et al., Tumor-derived hydrogen sulfide, produced by cystathionine-betasynthase, stimulates bioenergetics, cell proliferation, and angiogenesis in colon
    cancer. Proc Natl Acad Sci U S A, 2013. 110(30): p. 12474-9.
    81. Hinrichsen, I., et al., Reduced migration of MLH1 deficient colon cancer cells depends on SPTAN1. Molecular cancer, 2014. 13(1): p. 11.
    82. Bloch, M., et al., KCNMA1 gene amplification promotes tumor cell proliferation in human prostate cancer. Oncogene, 2007. 26(17): p. 2525-34.
    83. Oeggerli, M., et al., Role of KCNMA1 in breast cancer. PLoS One, 2012. 7(8): p.e41664.
    84. Khaitan, D., et al., Role of KCNMA1 gene in breast cancer invasion and metastasis to brain. BMC Cancer, 2009. 9: p. 258.

    QR CODE
    :::