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研究生: 羅芳宜
Fang-Yi Lo
論文名稱: 以微矩陣比較基因體雜合方法偵測東西方肺癌族群新穎致癌基因及其機制與臨床探討
Identification and characterization of novel cancer-related genes in lung cancer by array-comparative genomic hybridization, clinical correlation, and functional studies
指導教授: 王憶卿
Wang, Yi-Ching
李桂楨
Lee, Guey-Jen
學位類別: 博士
Doctor
系所名稱: 生命科學系
Department of Life Science
論文出版年: 2011
畢業學年度: 99
語文別: 英文
論文頁數: 151
中文關鍵詞: 肺癌微矩陣比較基因體雜合方法DNA 套數變異亞洲人白種人致癌基因抑癌基因
英文關鍵詞: lung cancer, array-comparative genomic hybridization, DNA copy number alteration, Asian, Caucasian, oncogene, tumor suppressor gene
論文種類: 學術論文
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  • 近年研究顯示,腫瘤形成基因於不同種族之間存在差異性。因
    此,鑑別各人種族群之間共通及具有差異性的基因群,是近代研究腫
    瘤形成的重要課題。為了進一步探究腫瘤形成相關基因的分子機制,
    本研究收集了40 對來自於臺灣肺癌病人(由台北榮民總醫院胸腔外
    科許瀚水醫師提供檢體)及20 對來自於美國白種肺癌病人(由美國
    芝加哥大學附設醫院胸腔外科Dr. Ravi Salgia 醫師提供檢體)的東西
    方肺癌族群樣本,對其進行微矩陣比較基因體(array-comparative
    genomic hybridization, array-CGH) 的圖譜分析。本研究發現,於東方肺癌群族偵測到17 段染色體變異區域,涵蓋註解基因數為476;並
    於西方肺癌群族偵測到20 段染色體變異區域,涵蓋註解基因數為
    459。進一步針對本研究室先前分析出的expression array 基因群進行
    一致性比對,篩選214 個於肺癌族群中基因結構變異及基因表現異常
    趨勢相符的候選基因,並對候選基因進行基因已知功能的資料庫搜
    尋。這些候選基因包含位於6p22.1 參與MAPK 路徑的 ZNF322A 基
    因、位於10q24.1 參與Rho GTPase 路徑的 ARHGAP19 基因、位於
    10q24.1 參與Wnt 路徑的 FRAT2 基因、以及位於17p13.3 功能與
    motility 相關的 PAFAH1B1 基因。本研究對這四個極具潛力的候選
    基因進行即時定量聚合酶鏈鎖反應系統、chromogenic in situ
    hybridization 方法、反轉錄即時定量聚合酶鏈鎖反應系統及免疫組織
    染色法,確認候選候選基因於臨床肺癌樣本及肺癌細胞株中的基因變
    異情形,其結果顯示候選候選基因其基因體套數及其 mRNA 表現量
    皆於肺癌組織中高於正常組織 (P<0.001~P=0.06)。本研究亦利用反轉
    錄即時定量聚合酶鏈鎖反應 及免疫組織染色法對101 位肺癌族群檢
    測 PAFAH1B1 基因其 mRNA 及蛋白層次變異情形。結果發現
    PAFAH1B1 基因於 mRNA 層次的過度表現頻率為62.4%,於蛋白層
    次過度表現頻率為57.4%,且此基因於mRNA 及蛋白層次的過度表
    現皆與病人的晚期具有相關性 (mRNA:P=0.008,蛋白層:P=0.008),
    且屬於腺細胞癌 (P=0.020) 及男性 (P=0.049) 的病人於蛋白層次的
    過度表現具有較差的預後,顯示PAFAH1B1 基因於肺癌族群具有過
    度表達的變異;細胞及動物實驗顯示過度表達PAFAH1B1 且可能促
    進肺癌細胞轉移能力。本研究提供了第一個東西方肺癌族群新穎基因
    變異資料庫,並以細胞、動物及臨床模式探討基因變異之致癌機轉。

    Cancer-related genes show racial differences. Therefore,
    identification and characterization of DNA copy number alteration regions in different racial groups help to dissect the mechanism of tumorigenesis. Here, DNA copy number alteration profile was analyzed by array-comparative genomic hybridization (array-CGH) for 40 Asian
    and 20 Caucasian lung cancer patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Among the genes identified, the ion transport and chromatin remodeling are the two main
    common biological processes altered in both Asia and Caucasian populations. Interestingly, genes involved in Wnt receptor signaling pathway were unique in Asian lung cancer, whereas Caucasian lung cancer was addictive to cell surface receptor linked signal transduction and G-protein coupled receptor protein signaling pathways. Genes
    residing within the chromosomal imbalance regions were integrated with gene expression databases to identify 214 potential cancer-related genes.
    Four racial-specific candidate oncogenes were validated in 164 patients using quantitative polymerase chain reaction (q-PCR), chromogenic in situ hybridization (CISH), reverse transcriptase-q-PCR, and immunohistochemistry. These four genes were ARHGAP19 (10q24.1)
    functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were
    significantly higher than the corresponding normal tissues
    (P<0.001~P=0.06). PAFAH1B1 which showed amplification and
    overexpression in both Asian and Caucasian lung cancer patients was further characterized in cell, animal, and clinical models. The PAFAH1B1 mRNA and protein overexpression frequency were 62.4% (63/101) and
    57.4% (58/101) in 101 lung cancer patients. The results indicated that mRNA and protein overexpression level of PAFAH1B1 was significantly associated with late stage (mRNA: P=0.008, protein: P=0.008) and poor survival in lung adenocarcinoma (P=0.020) and male patients (P=0.049).
    Collectively, our study provides the first database revealing common and differential chromosomal imbalance regions among lung cancer from Asians and Caucasians. Four validation methods in a large patient cohort
    confirm our database. The cell and animal studies verify a novel metastasis-promoting oncogene, PAFAH1B1.

    Chinese abstract ------------------------------------------------------------ 1 English abstract ------------------------------------------------------------- 3 Study rationale -------------------------------------------------------------- 5 Literature review ----------------------------------------------------------- 7 I. Lung cancer ---------------------------------------------------------------- 7 II. Genomic DNA copy number aberrations in tumorigenesis --------- 8 III. Molecular methods for detecting genomic DNA copy number aberrations ---------------------------------------------------------------- 8 IV. Array-CGH in recent lung cancer research -------------------------- 11 V. PAFAH1B1---------------------------------------------------------------- 12 Specific aims ---------------------------------------------------------------- 14 Materials and Methods ------------------------------------------------- 16 Results ------------------------------------------------------------------------- 27 Discussion ------------------------------------------------------------------- 37 References ------------------------------------------------------------------- 45 Tables-------------------------------------------------------------------------- 52 Figures ------------------------------------------------------------------------ 95 Appendices ---------------------------------------------------------------- 116

    Albertson, D.G. (2006). Gene amplification in cancer. Trends Genet 22,
    447-455.
    Albertson, D.G., and Pinkel, D. (2003). Genomic microarrays in human
    genetic disease and cancer. Hum Mol Genet 12 Spec No 2, R145-152.
    Aumais, J.P., Tunstead, J.R., McNeil, R.S., Schaar, B.T., McConnell,
    S.K., Lin, S.H., Clark, G.D., and Yu-Lee, L.Y. (2001). NudC associates
    with Lis1 and the dynein motor at the leading pole of neurons. J
    Neurosci 21, RC187.
    Broet, P., Dalmasso, C., Tan, E.H., Alifano, M., Zhang, S., Wu, J., Lee,
    M.H., Regnard, J.F., Lim, D., Koong, H.N., Agasthian, T., Miller, L.D.,
    Lim, E., Camilleri-Broet, S., and Tan, P. (2011). Genomic profiles
    specific to patient ethnicity in lung adenocarcinoma. Clin Cancer Res 17,
    3542-3550.
    Cardoso, C., Leventer, R.J., Matsumoto, N., Kuc, J.A., Ramocki, M.B.,
    Mewborn, S.K., Dudlicek, L.L., May, L.F., Mills, P.L., Das, S., Pilz,
    D.T., Dobyns, W.B., and Ledbetter, D.H. (2000). The location and type
    of mutation predict malformation severity in isolated lissencephaly
    caused by abnormalities within the LIS1 gene. Hum Mol Genet. 9,
    3019-3028.
    Caspi, M., Atlas, R., Kantor, A., Sapir, T., and Reiner, O. (2000).
    Interaction between LIS1 and doublecortin, two lissencephaly gene
    products. Hum Mol Genet. 9, 2205-2213.
    Chang, J.W., Liu, H.P., Hsieh, M.H., Fang, Y.F., Hsieh, M.S., Hsieh, J.J.,
    Chiu, Y.T., Tsai, H.Y., Chen, Y.H., Chen, Y.T., Hsu, H.Y., Chen, Y.T.,
    Tsai, S.F., Chen, Y.R., Hsi, B.L., and Huang, S.F. (2008). Increased
    epidermal growth factor receptor (EGFR) gene copy number is strongly
    associated with EGFR mutations and adenocarcinoma in non-small cell
    lung cancers: a chromogenic in situ hybridization study of 182 patients.
    Lung cancer 61, 328-339.
    Chen, X., Jorgenson, E., and Cheung, S.T. (2009). New tools for
    functional genomic analysis. Drug discovery today 14, 754-760.
    Cheng, H.C., Abdel-Ghany, M., and Pauli, B.U. (2003). A novel
    consensus motif in fibronectin mediates dipeptidyl peptidase IV
    adhesion and metastasis. The Journal of biological chemistry 278,
    24600-24607.
    Davies, J.J., Wilson, I.M., and Lam, W.L. (2005). Array CGH
    technologies and their applications to cancer genomes. Chromosome
    Res 13, 237-248.
    Dennis, G., Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane,
    H.C., and Lempicki, R.A. (2003). DAVID: Database for Annotation,
    Visualization, and Integrated Discovery. Genome Biol. 4, P3.
    Ford, N.L., Graham, K.C., Groom, A.C., Macdonald, I.C., Chambers,
    A.F., and Holdsworth, D.W. (2006). Time-course characterization of the
    computed tomography contrast enhancement of an iodinated blood-pool
    contrast agent in mice using a volumetric flat-panel equipped computed
    tomography scanner. Invest Radiol. 41, 384-390.
    Govindan, R., Page, N., Morgensztern, D., Read, W., Tierney, R.,
    Vlahiotis, A., Spitznagel, E.L., and Piccirillo, J. (2006). Changing
    epidemiology of small-cell lung cancer in the United States over the last
    30 years: analysis of the surveillance, epidemiologic, and end results
    database. J Clin Oncol 24, 4539-4544.
    Hattori, M., Adachi, H., Tsujimoto, M., Arai, H., and Inoue, K. (1994).
    Miller-Dieker lissencephaly gene encodes a subunit of brain
    platelet-activating factor acetylhydrolase. Nature 370, 216-218.
    Hayami, S., Kelly, J.D., Cho, H.S., Yoshimatsu, M., Unoki, M., Tsunoda,
    T., Field, H.I., Neal, D.E., Yamaue, H., Ponder, B.A., Nakamura, Y., and
    Hamamoto, R. (2010). Overexpression of LSD1 contributes to human
    carcinogenesis through chromatin regulation in various cancers. Int J
    Cancer 128, 574-586.
    Hirotsune, S., Fleck, M.W., Gambello, M.J., Bix, G.J., Chen, A., Clark,
    G.D., Ledbetter, D.H., McBain, C.J., and Wynshaw-Boris, A. (1998).
    Graded reduction of Pafah1b1 (Lis1) activity results in neuronal
    migration defects and early embryonic lethality. Nat Genet 19, 333-339.
    Hou, Q., Wu, Y.H., Grabsch, H., Zhu, Y., Leong, S.H., Ganesan, K.,
    Cross, D., Tan, L.K., Tao, J., Gopalakrishnan, V., Tang, B.L., Kon, O.L.,
    and Tan, P. (2008). Integrative genomics identifies RAB23 as an invasion mediator gene in diffuse-type gastric cancer. Cancer Res 68,
    4623-4630.
    Kallioniemi, A. (2008). CGH microarrays and cancer. Curr Opin
    Biotechnol 19, 36-40.
    Kallioniemi, A., Kallioniemi, O.P., Sudar, D., Rutovitz, D., Gray, J.W.,
    Waldman, F., and Pinkel, D. (1992). Comparative genomic hybridization
    for molecular cytogenetic analysis of solid tumors. Science 258,
    818-821.
    Kang, J.U., Koo, S.H., Kwon, K.C., and Park, J.W. (2010). Frequent
    silence of chromosome 9p, homozygous DOCK8, DMRT1 and DMRT3
    deletion at 9p24.3 in squamous cell carcinoma of the lung. Int J Oncol
    37, 327-335.
    Kang, J.U., Koo, S.H., Kwon, K.C., Park, J.W., and Kim, J.M. (2008).
    Gain at chromosomal region 5p15.33, containing TERT, is the most
    frequent genetic event in early stages of non-small cell lung cancer.
    Cancer Genet Cytogenet 182, 1-11.
    Katoh, Y., and Katoh, M. (2004). Identification and characterization of
    ARHGAP27 gene in silico. Int J Mol Med 14, 943-947.
    Kim, Y.H., Kwei, K.A., Girard, L., Salari, K., Kao, J.,
    Pacyna-Gengelbach, M., Wang, P., Hernandez-Boussard, T., Gazdar,
    A.F., Petersen, I., Minna, J.D., and Pollack, J.R. (2010). Genomic and
    functional analysis identifies CRKL as an oncogene amplified in lung
    cancer. Oncogene 29, 1421-1430.
    Kresse, S.H., Skarn, M., Ohnstad, H.O., Namlos, H.M., Bjerkehagen, B.,
    Myklebost, O., and Meza-Zepeda, L.A. (2008). DNA copy number
    changes in high-grade malignant peripheral nerve sheath tumors by
    array CGH. Mol Cancer 7, 48.
    Lambros, M.B., Natrajan, R., and Reis-Filho, J.S. (2007). Chromogenic
    and fluorescent in situ hybridization in breast cancer. Hum Pathol 38,
    1105-1122.
    Ledbetter, S.A., Kuwano, A., Dobyns, W.B., and Ledbetter, D.H. (1992).
    Microdeletions of chromosome 17p13 as a cause of isolated
    lissencephaly. Am J Hum Genet. 50, 182-189.
    Lee, L.N., Shew, J.Y., Sheu, J.C., Lee, Y.C., Lee, W.C., Fang, M.T.,Chang, H.F., Yu, C.J., Yang, P.C., and Luh, K.T. (1994). Exon 8
    mutation of p53 gene associated with nodal metastasis in non-small-cell
    lung cancer. Am J Respir Crit Care Med 150, 1667-1671.
    Li, Y., Wang, Y., Zhang, C., Yuan, W., Wang, J., Zhu, C., Chen, L.,
    Huang, W., Zeng, W., Wu, X., and Liu, M. (2004). ZNF322, a novel
    human C2H2 Kruppel-like zinc-finger protein, regulates transcriptional
    activation in MAPK signaling pathways. Biochem Biophys Res
    Commun 325, 1383-1392.
    Lo Nigro, C., Chong, C.S., Smith, A.C., Dobyns, W.B., Carrozzo, R.,
    and Ledbetter, D.H. (1997). Point mutations and an intragenic deletion
    in LIS1, the lissencephaly causative gene in isolated lissencephaly
    sequence and Miller-Dieker syndrome. Hum Mol Genet. 6, 157-164.
    Lockwood, W.W., Chari, R., Chi, B., and Lam, W.L. (2006). Recent
    advances in array comparative genomic hybridization technologies and
    their applications in human genetics. Eur J Hum Genet 14, 139-148.
    Lv, L., Xu, J., Zhao, S., Chen, C., Zhao, X., Gu, S., Ji, C., Xie, Y., and
    Mao, Y. (2007). Sequence analysis of a human RhoGAP
    domain-containing gene and characterization of its expression in human
    multiple tissues. DNA Seq 18, 184-189.
    Mantripragada, K.K., Buckley, P.G., de Stahl, T.D., and Dumanski, J.P.
    (2004). Genomic microarrays in the spotlight. Trends Genet 20, 87-94.
    Messi, E., Florian, M.C., Caccia, C., Zanisi, M., and Maggi, R. (2008).
    Retinoic acid reduces human neuroblastoma cell migration and
    invasiveness: effects on DCX, LIS1, neurofilaments-68 and vimentin
    expression. BMC cancer 8, 30.
    Nam, J.M., Onodera, Y., Bissell, M.J., and Park, C.C. (2010). Breast
    cancer cells in three-dimensional culture display an enhanced
    radioresponse after coordinate targeting of integrin alpha5beta1 and
    fibronectin. Cancer Res. 70, 5238-5248.
    Parkin, D.M., Bray, F.I., and Devesa, S.S. (2001). Cancer burden in the
    year 2000. The global picture. Eur J Cancer 37 Suppl 8, S4-66.
    Phan, V.H., Moore, M.M., McLachlan, A.J., Piquette-Miller, M., Xu, H.,
    and Clarke, S.J. (2009). Ethnic differences in drug metabolism and
    toxicity from chemotherapy. Expert Opin Drug Metab Toxicol 5,243-257.
    Pinkel, D., and Albertson, D.G. (2005). Array comparative genomic
    hybridization and its applications in cancer. Nat Genet 37 Suppl, S11-17.
    Reiner, O., Carrozzo, R., Shen, Y., Wehnert, M., Faustinella, F., Dobyns,
    W.B., Caskey, C.T., and Ledbetter, D.H. (1993). Isolation of a
    Miller-Dieker lissencephaly gene containing G protein beta-subunit-like
    repeats. Nature 364, 717-721.
    Saitoh, T., and Katoh, M. (2001). FRAT1 and FRAT2, clustered in
    human chromosome 10q24.1 region, are up-regulated in gastric cancer.
    Int J Oncol 19, 311-315.
    Saitoh, T., Moriwaki, J., Koike, J., Takagi, A., Miwa, T., Shiokawa, K.,
    and Katoh, M. (2001). Molecular cloning and characterization of
    FRAT2, encoding a positive regulator of the WNT signaling pathway.
    Biochem Biophys Res Commun 281, 815-820.
    Schneider, K.U., Dietrich, D., Fleischhacker, M., Leschber, G., Merk, J.,
    Schaper, F., Stapert, H.R., Vossenaar, E.R., Weickmann, S., Liebenberg,
    V., Kneip, C., Seegebarth, A., Erdogan, F., Rappold, G., and Schmidt, B.
    (2011). Correlation of SHOX2 Gene Amplification and DNA
    Methylation in Lung Cancer Tumors. BMC cancer 11, 102.
    Schwab, M. (1999). Oncogene amplification in solid tumors. Semin
    Cancer Biol. 9, 319-325.
    Sharma, R.K., Rogojina, A.T., and Chalam, K.V. (2009). Multiplex
    immunoassay analysis of biomarkers in clinically accessible quantities
    of human aqueous humor. Mol Vis. 15, 60-69.
    Smith, D.S., Niethammer, M., Ayala, R., Zhou, Y., Gambello, M.J.,
    Wynshaw-Boris, A., and Tsai, L.H. (2000). Regulation of cytoplasmic
    dynein behaviour and microtubule organization by mammalian Lis1.
    Nat Cell Biol. 2, 767-775.
    Soukoulis, V., Reddy, S., Pooley, R.D., Feng, Y., Walsh, C.A., and Bader,
    D.M. (2005). Cytoplasmic LEK1 is a regulator of microtubule function
    through its interaction with the LIS1 pathway. Proc Natl Acad Sci U S A
    102, 8549-8554.
    Subramanyam, D., Lamouille, S., Judson, R.L., Liu, J.Y., Bucay, N.,
    Derynck, R., and Blelloch, R. (2011). Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced
    pluripotent stem cells. Nat Biotechnol. 29, 443-448.
    Suzuki, S.O., McKenney, R.J., Mawatari, S.Y., Mizuguchi, M., Mikami,
    A., Iwaki, T., Goldman, J.E., Canoll, P., and Vallee, R.B. (2007).
    Expression patterns of LIS1, dynein and their interaction partners
    dynactin, NudE, NudEL and NudC in human gliomas suggest roles in
    invasion and proliferation. Acta Neuropathol 113, 591-599.
    Tian, Y., Zhang, Y., Hurd, L., Hannenhalli, S., Liu, F., Lu, M.M., and
    Morrisey, E.E. (2011). Regulation of lung endoderm progenitor cell
    behavior by miR302/367. Development 138, 1235-1245.
    Tomlinson, I.P., Lambros, M.B., and Roylance, R.R. (2002). Loss of
    heterozygosity analysis: practically and conceptually flawed? Genes
    Chromosomes Cancer 34, 349-353.
    Tseng, R.C., Chang, J.W., Hsien, F.J., Chang, Y.H., Hsiao, C.F., Chen,
    J.T., Chen, C.Y., Jou, Y.S., and Wang, Y.C. (2005). Genomewide loss of
    heterozygosity and its clinical associations in non small cell lung cancer.
    Int J Cancer 117, 241-247.
    Tseng, R.C., Lin, R.K., Wen, C.K., Tseng, C., Hsu, H.S., Hsu, W.H., and
    Wang, Y.C. (2008). Epigenetic silencing of AXIN2/betaTrCP and
    deregulation of p53-mediated control lead to wild-type beta-catenin
    nuclear accumulation in lung tumorigenesis. Oncogene 27, 4488-4496.
    Uchida, M., Tsukamoto, Y., Uchida, T., Ishikawa, Y., Nagai, T., Hijiya,
    N., Nguyen, L.T., Nakada, C., Kuroda, A., Okimoto, T., Kodama, M.,
    Murakami, K., Noguchi, T., Matsuura, K., Tanigawa, M., Seto, M., Ito,
    H., Fujioka, T., Takeuchi, I., and Moriyama, M. (2010). Genomic
    profiling of gastric carcinoma in situ and adenomas by array-based
    comparative genomic hybridization. J Pathol 221, 96-105.
    Wang, T., Li, J., Chen, F., Zhao, Y., He, X., Wan, D., and Gu, J. (2007).
    Choline transporters in human lung adenocarcinoma: expression and
    functional implications. Acta biochimica et biophysica Sinica 39,
    668-674.
    Wen, C.C., Wu, Y.J., Huang, Y.H., Chen, W.C., Liu, S.C., Jiang, S.S.,
    Juang, J.L., Lin, C.Y., Fang, W.T., Hsiung, C.A., and Chang, I.S. (2006).
    A Bayes regression approach to array-CGH data. Stat Appl Genet Mol
    Biol 5, Article3.
    Wynshaw-Boris, A. (2007). Lissencephaly and LIS1: insights into the
    molecular mechanisms of neuronal migration and development. Clin
    Genet. 72, 296-304.
    Xing, Z., Tang, X., Gao, Y., Da, L., Song, H., Wang, S., Tiollais, P., Li,
    T., and Zhao, M. (2011). The human LIS1 is downregulated in
    hepatocellular carcinoma and plays a tumor suppressor function.
    Biochem Biophys Res Commun. 409, 193-199.
    Zhang, L., and Rosin, M.P. (2001). Loss of heterozygosity: a potential
    tool in management of oral premalignant lesions? J Oral Pathol Med 30,
    513-520.

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