Name: integration of bioinformatics approaches and experimental validations to understand the role of notch signaling in ovarian cancer
Uploaded: 2020-01-12T14:00:00
Description: Watch this Scientific Journal Video about Integration of Bioinformatics Approaches and Experimental Validations to Understand the Role of Notch Signaling in Ovarian Cancer at JoVE.com

这项工作得到了来自佐治亚南方大学的启动基金、科学和数学研究基金、夏季研究会议奖和研究种子资助奖的支持。

1. 基因组谱的临床结果预测
注：PRECOG门户（precog.stanford.edu）访问来自165个癌症表达数据集的公开数据，包括基因表达水平和患者临床结果17。它特别提供 Meta_u2012Z 分析，该分析包含大型数据集，在 39 种癌症类型中提供不同基因的 Z_u2012 分数，以指示患者的总体存活率。差和好存活率分别由正数和负 Z_u2012 分数值表示。
<ol><li>使用学术附属电子邮件创建帐?...

<ol>
	<li>Bocchicchio, S., Tesone, M., Irusta, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Convergence+of+Wnt+and+Notch+signaling+controls+ovarian+cancer+cell+survival.">Convergence of Wnt and Notch signaling controls ovarian cancer cell survival.</a> Journal of Cellular Physiology. , (2019).</li><li>Hibdon, E. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notch+and+mTOR+Signaling+Pathways+Promote+Human+Gastric+Cancer+Cell+Proliferation.">Notch and mTOR Signaling Pathways Promote Human Gastric Cancer Cell Proliferation.</a> Neoplasia. 21 (7), 702-712 (2019).</li><li>Kucukkose, C., Yalcin Ozuysal, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+Notch+signalling+on+the+expression+of+SEMA3C,+HMGA2,+CXCL14,+CXCR7,+and+CCL20+in+breast+cancer.">Effects of Notch signalling on the expression of SEMA3C, HMGA2, CXCL14, CXCR7, and CCL20 in breast cancer.</a> Turkish Journal of Biology. 43 (1), 70-76 (2019).</li><li>Lan, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notch+pathway+is+involved+in+the+suppression+of+colorectal+cancer+by+embryonic+stem+cell+microenvironment.">Notch pathway is involved in the suppression of colorectal cancer by embryonic stem cell microenvironment.</a> OncoTargets and Therapy. 12, 2869-2878 (2019).</li><li>Lian, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notch+signaling+promotes+serrated+neoplasia+pathway+in+colorectal+cancer+through+epigenetic+modification+of+EPHB2+and+EPHB4.">Notch signaling promotes serrated neoplasia pathway in colorectal cancer through epigenetic modification of EPHB2 and EPHB4.</a> Cancer Management and Research. 10, 6129-6141 (2018).</li><li>Salazar, J. L., Yamamoto, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integration+of+Drosophila+and+Human+Genetics+to+Understand+Notch+Signaling+Related+Diseases.">Integration of Drosophila and Human Genetics to Understand Notch Signaling Related Diseases.</a> Advances in Experimental Medicine and Biology. 1066, 141-185 (2018).</li><li>Bray, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notch+signalling+in+context.">Notch signalling in context.</a> Nature Reviews Molecular Cell Biology. 17 (11), 722-735 (2016).</li><li>Andersson, E. R., Sandberg, R., Lendahl, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notch+signaling:+simplicity+in+design,+versatility+in+function.">Notch signaling: simplicity in design, versatility in function.</a> Development. 138 (17), 3593-3612 (2011).</li><li>Brou, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+proteolytic+cleavage+involved+in+Notch+signaling:+the+role+of+the+disintegrin-metalloprotease+TACE.">A novel proteolytic cleavage involved in Notch signaling: the role of the disintegrin-metalloprotease TACE.</a> Molecular Cell. 5 (2), 207-216 (2000).</li><li>Oswald, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=p300+acts+as+a+transcriptional+coactivator+for+mammalian+Notch-1.">p300 acts as a transcriptional coactivator for mammalian Notch-1.</a> Molecular and Cellular Biology. 21 (22), 7761-7774 (2001).</li><li>Xiu, M. X., Liu, Y. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+oncogenic+Notch2+signaling+in+cancer:+a+novel+therapeutic+target.">The role of oncogenic Notch2 signaling in cancer: a novel therapeutic target.</a> American Journal of Cancer Research. 9 (5), 837-854 (2019).</li><li>Allenspach, E. J., Maillard, I., Aster, J. C., Pear, W. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notch+signaling+in+cancer.">Notch signaling in cancer.</a> Cancer Biololgy &amp; Therapy. 1 (5), 466-476 (2002).</li><li>Jia, D., Underwood, J., Xu, Q., Xie, Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NOTCH2/NOTCH3/DLL3/MAML1/ADAM17+signaling+network+is+associated+with+ovarian+cancer.">NOTCH2/NOTCH3/DLL3/MAML1/ADAM17 signaling network is associated with ovarian cancer.</a> Oncology Letters. 17 (6), 4914-4920 (2019).</li><li>Weng, J. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+bioinformatics+approaches+for+analysis+of+high-throughput+biological+data.">Novel bioinformatics approaches for analysis of high-throughput biological data.</a> Biomed Research International. 2014, 814092 (2014).</li><li>Readhead, B., Dudley, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Translational+Bioinformatics+Approaches+to+Drug+Development.">Translational Bioinformatics Approaches to Drug Development.</a> Advances in Wound Care (New Rochelle). 2 (9), 470-489 (2013).</li><li>Bayat, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Science,+medicine,+and+the+future:+Bioinformatics.">Science, medicine, and the future: Bioinformatics.</a> BMJ. 324 (7344), 1018-1022 (2002).</li><li>Gentles, A. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+prognostic+landscape+of+genes+and+infiltrating+immune+cells+across+human+cancers.">The prognostic landscape of genes and infiltrating immune cells across human cancers.</a> Nature Medicine. 21 (8), 938-945 (2015).</li><li>Tan, T. Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CSIOVDB:+a+microarray+gene+expression+database+of+epithelial+ovarian+cancer+subtype.">CSIOVDB: a microarray gene expression database of epithelial ovarian cancer subtype.</a> Oncotarget. 6 (41), 43843-43852 (2015).</li><li>Shin, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GENT:+gene+expression+database+of+normal+and+tumor+tissues.">GENT: gene expression database of normal and tumor tissues.</a> Cancer Informatics. 10, 149-157 (2011).</li><li>Barretina, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cancer+Cell+Line+Encyclopedia+enables+predictive+modelling+of+anticancer+drug+sensitivity.">The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.</a> Nature. 483 (7391), 603-607 (2012).</li><li>Gao, J. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integrative+Analysis+of+Complex+Cancer+Genomics+and+Clinical+Profiles+Using+the+cBioPortal.">Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal.</a> Science Signaling. 6 (269), (2013).</li><li>Cerami, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cBio+Cancer+Genomics+Portal:+An+Open+Platform+for+Exploring+Multidimensional+Cancer+Genomics+Data.">The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data.</a> Cancer Discovery. 2 (5), 401-404 (2012).</li><li>McGuire, S. E., Mao, Z., Davis, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatiotemporal+gene+expression+targeting+with+the+TARGET+and+gene-switch+systems+in+Drosophila.">Spatiotemporal gene expression targeting with the TARGET and gene-switch systems in Drosophila.</a> Science's STKE. 2004 (220), 6 (2004).</li><li>Jia, D., Huang, Y. C., Deng, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+Cell+Cycle+Switches+in+Drosophila+Oogenesis.">Analysis of Cell Cycle Switches in Drosophila Oogenesis.</a> Methods in Molecular Biology. 1328, 207-216 (2015).</li><li>Lo, P. K., Huang, Y. C., Corcoran, D., Jiao, R., Deng, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inhibition+of+Notch+signaling+by+the+p105+and+p180+subunits+of+Drosophila+chromatin+assembly+factor+1+is+required+for+follicle+cell+proliferation.">Inhibition of Notch signaling by the p105 and p180 subunits of Drosophila chromatin assembly factor 1 is required for follicle cell proliferation.</a> Journal of Cell Science. 132 (2), (2019).</li><li>Keller Larkin, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+Notch+pathway+in+terminal+follicle+cell+differentiation+during+Drosophila+oogenesis.">Role of Notch pathway in terminal follicle cell differentiation during Drosophila oogenesis.</a> Development Genes and Evolution. 209 (5), 301-311 (1999).</li><li>Sun, J., Deng, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notch-dependent+downregulation+of+the+homeodomain+gene+cut+is+required+for+the+mitotic+cycle/endocycle+switch+and+cell+differentiation+in+Drosophila+follicle+cells.">Notch-dependent downregulation of the homeodomain gene cut is required for the mitotic cycle/endocycle switch and cell differentiation in Drosophila follicle cells.</a> Development. 132 (19), 4299-4308 (2005).</li><li>Jia, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+large-scale+in+vivo+RNAi+screen+to+identify+genes+involved+in+Notch-mediated+follicle+cell+differentiation+and+cell+cycle+switches.">A large-scale in vivo RNAi screen to identify genes involved in Notch-mediated follicle cell differentiation and cell cycle switches.</a> Scientific Reports. 5, 12328 (2015).</li><li>Shcherbata, H. R., Althauser, C., Findley, S. D., Ruohola-Baker, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mitotic-to-endocycle+switch+in+Drosophila+follicle+cells+is+executed+by+Notch-dependent+regulation+of+G1/S,+G2/M+and+M/G1+cell-cycle+transitions.">The mitotic-to-endocycle switch in Drosophila follicle cells is executed by Notch-dependent regulation of G1/S, G2/M and M/G1 cell-cycle transitions.</a> Development. 131 (13), 3169-3181 (2004).</li></ol>

由于利用生物信息学的方法和方法不计其数，因此有许多数据库可在线供公众使用。可以从每个数据库中提取大量信息，但有些数据库最适合特定目的，例如根据某些输入评估患者存活率。对从不同数据库检索到的数据进行系统分析，可以令人信服地产生重要的科学发现。
目前的分析侧重于Notch信号在卵巢癌中的作用，通过生物信息学方法的利用。例如，PRECOG门户数据库上的...

Notch 信号通路是高度保守的途径，对生物体内的许多发育过程非常重要。Notch信号在细胞增殖和自我更新中起着重要作用，Notch信号通路的缺陷可导致多种癌症1、2、3、4、5、6。在某些情况下，Notch信号通路与组织生长和癌症以及细胞死亡和肿瘤抑制7相关联。多个 Notch 受体 （NOTCH 1⁄4） 和 co_u2012 活化剂主谋 （MAML 1⁄3）， 所有功能各不相同，增加了额外的复杂性级别。虽然Notch信号通路在功能方面是复杂的，但其核心通路在分子基础8上是简单的。Notch受体充当由细胞外和细胞内区域组成的跨膜蛋白9。与Notch受体细胞外区域结合的配体促进蛋白溶性裂解，使Notch细胞内域（NICD）被释放到细胞核中。然后，NICD 绑定到 co_u2012 活化剂主谋以激活下游基因表达10。
近年来，Notch信号显示，在不同物种6、11的几种癌症的起始和进展中，Notch信号扮演着各种角色。例如，Notch信号与涉及人类NOTCH1基因12的肿瘤发生有关。最近，NOTCH2、NOTCH3、类似三角洲的3（DLL3）、Mastermind_u2012样蛋白1（MAML1）以及含有蛋白17（ADAM17）的脱粒蛋白和金属蛋白酶域被证明与卵巢癌有强烈关联，特别是与患者13的整体存活率较差有关。
随着实验和患者相关数据量的不断增加，对可用数据的分析需求也不断增加。现有数据分散在出版物中，它们可能提供不一致甚至相互矛盾的结论。随着近几十年来新技术（如下一代测序）的发展，可用数据量呈指数级增长。虽然这代表了科学的快速发展和继续生物学研究的机会，但评估公开数据对解决研究问题的意义是一个巨大的挑战。我们相信生物信息学是从大规模数据集中提取较小信息片段的有用方法。通过实施各种生物信息学方法，研究人员可以快速、可靠、高效地解释这些大型数据集，从而获得有见地的发现。这些发现可能从确定潜在的新药物治疗靶点或疾病生物标志物，到个性化患者治疗15、16。
生物信息学本身正在迅速发展，随着技术进步席卷医学和生物科学，方法也在不断变化。目前，常见的生物信息学方法包括利用可公开访问的数据库和软件程序来分析DNA或蛋白质序列，识别具有特殊相关性或重要性的基因，并通过功能基因组学确定基因和基因产物的相关性。虽然生物信息学领域当然不限于这些方法，但这些对于帮助临床医生和研究人员管理生物数据以造福于整个患者具有重要意义。
本研究旨在突出几个重要的数据库及其用于研究Notch信号通路。NOTCH2，NOTCH3，及其co_u2012活化剂MAML1被用作数据库研究的例子。这些基因的使用，因为Notch信号通路在卵巢癌的重要性已经得到证实。对检索到的数据的系统分析证实了Notch信号在卵巢癌中的重要性。此外，由于Notch信号在物种间保存良好，因此证实果蝇黑色素素和主脑的过度表达可以诱发果蝇卵巢中的肿瘤，支持数据库发现和Notch信号在卵巢癌中的重要和保守作用。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>DAPI (4&#39;,6-Diamidino-2-Phenylindole, Dihydrochloride)</td>
			<td>Invitrogen</td>
			<td>D1306</td>
			<td>1:1000 Dilution</td>
		</tr>
		<tr>
			<td>PBS, Phosphate Buffered Saline, 10X Powder, pH 7.4</td>
			<td>ThermoFisher</td>
			<td>FLBP6651</td>
			<td>Dissolved with ddH2O to make 1X PBS</td>
		</tr>
		<tr>
			<td>Goat serum</td>
			<td>Gibco</td>
			<td>16210064</td>
			<td>Serum</td>
		</tr>
		<tr>
			<td>Embryo dish</td>
			<td>Electron Microscopy Sciences</td>
			<td>70543-45</td>
			<td>Dissection Dish</td>
		</tr>
		<tr>
			<td>Nutating mixers</td>
			<td>Fisherbrand</td>
			<td>88861041</td>
			<td>Nutator</td>
		</tr>
		<tr>
			<td>tj-Gal4, Gal80ts/ CyO; UAS-NICD-GFP/ TM6B</td>
			<td>Dr. Wu-Min Deng at Florida State University</td>
			<td>N/A</td>
			<td>Fly stock</td>
		</tr>
		<tr>
			<td>w*; UAS-mam.A</td>
			<td>Bloomington Drosophila Stock Center</td>
			<td>#27743</td>
			<td>Fly stock</td>
		</tr>
		<tr>
			<td>w[1118]</td>
			<td>Bloomington Drosophila Stock Center</td>
			<td>#5905</td>
			<td>Fly stock</td>
		</tr>
		<tr>
			<td>The PRECOG portal</td>
			<td>Stanford University</td>
			<td>precog.stanford.edu</td>
			<td>Publicly accessible database of cancer expression datasets</td>
		</tr>
		<tr>
			<td>CSIOVDB</td>
			<td>Cancer Science Institute of Singapore</td>
			<td>csibio.nus.edu.sg/CSIOVDB/CSIOVDB.html</td>
			<td>Microarray database used to study ovarian cancer</td>
		</tr>
		<tr>
			<td>The Gene Expression across Normal and Tumor tissue (GENT) Portal</td>
			<td>Korea Research Institute of Bioscience and Biotechnology (KRIBB)</td>
			<td>medical&#8211;genome.kribb.re.kr/GENT</td>
			<td>Publicly accessible database of gene expression data across diverse tissues, divided into tumor and normal tissues.</td>
		</tr>
		<tr>
			<td>Broad Institute Cancer Cell Line Encyclopedia (CCLE)</td>
			<td>Broad Institute and The Novartis Institutes for BioMedical Research</td>
			<td>portals.broadinstitute.org/ccle</td>
			<td>Provides genomic profiles and mutations of human cancer cell lines</td>
		</tr>
		<tr>
			<td>cBioPortal</td>
			<td>Memorial Sloan Kettering Cancer Center (MSK)</td>
			<td>cioportal.org</td>
			<td>Portal that allows researchers to search for genetic alterations and signaling networks</td>
		</tr>
		<tr>
			<td>Zeiss 710 Inverted confocal microscope</td>
			<td>Carl Zeiss</td>
			<td>ID #M 210491</td>
			<td>Examination and image collection of fluorescently labeled specimens</td>
		</tr>
	</tbody>
</table>

integration of bioinformatics approaches and experimental validations to understand the role of notch signaling in ovarian cancer

槽口信令是一种高度保守的调节途径，涉及许多细胞过程。这种信号通路调节不良通常会导致对适当发育的干扰，甚至在某些情况下可能导致癌症的启动或进展。由于该通路具有复杂和通用的功能，因此可以通过许多不同的方法进行广泛的研究。其中，生物信息学提供了一种无可否认的成本效益、平易近人和用户友好的研究方法。生物信息学是从大规模数据集中提取较小信息片段的有用方法。通过实施各种生物信息学方法，研究人员可以快速、可靠、高效地解释这些大型数据集，从而产生有见地的应用和科学发现。在这里，提出了一个协议，用于整合生物信息学方法，以研究Notch信号在卵巢癌中的作用。此外，生物信息学的发现通过实验验证。

使用 PRECOG 门户的步骤 1 中提及的程序，在卵巢癌中获得了NOTCH2、NOTCH3和MAML1的 Z 得分（分别为 1.3、2.32、1.62）。 负Z\u2012分值表明三个基因表达水平高的患者总体存活率较差。使用电子表格软件的条件格式，Z\u2012score 值如图1中的彩色条形图所示。
CSIOVDB数据库被用来确认这些发现。使用步骤2、NOTCH2、NOTCH3和MAML...

Watch this Scientific Journal Video about Integration of Bioinformatics Approaches and Experimental Validations to Understand the Role of Notch Signaling in Ovarian Cancer at JoVE.com

Integration of Bioinformatics Approaches and Experimental Validations to Understand the Role of Notch Signaling in Ovarian Cancer

生物信息学是处理大规模数据集的有用方法。通过实施生物信息学方法，研究人员可以快速、可靠、高效地获得有见地的应用和科学发现。本文介绍了生物信息学在卵巢癌研究中的运用。它还通过实验成功验证了生物信息学的发现。

生物信息学方法与实验验证的集成，了解诺奇信号在卵巢癌中的作用

Notch signaling is a highly conserved regulatory pathway involved in many cellular processes. Dysregulation of this signaling pathway often leads to ...

生物信息学是从数据中提取信息的有用方法。实验对于验证同样重要。我们结合这两种方法来研究凹口信号在卵巢癌中的作用。该技术的主要优点是，研究人员可以利用生物信息学数据库的信息，在进行实验之前规划他们的研究方向。随着人类疾病的生物信息学数据的积累，科学家不再被蒙上眼睛。实验可以进行，以验证特定的发现，这可能导致改善的疗法或疾病诊断。要对感兴趣的基因与特定类型的癌症的关联进行分析，请创建一个包含学术附属电子邮件地址的帐户以访问 PRECOG 数据库，并在登录终端中输入与该帐户关联的电子邮件地址和密码。单击"查看详细信息"，将感兴趣的基因输入搜索栏。然后使用滚动条获取特定癌症类型的兴趣生存 Z 得分。要调查基因表达水平和卵巢癌阶段之间的关联，请导航到CSIOVDB网页，并在搜索栏中输入感兴趣的基因的名称。然后单击"生存"选项卡。要评估不同、正常和肿瘤组织中的基因表达数据，请导航到 GENT 门户，然后单击"搜索"选项卡。在关键字部分中，从下拉菜单中选择术语的基因符号，输入感兴趣的基因的基因符号，然后选择"组织"的类型选项。单击"搜索"按钮。将显示基于U133A和U122Plus2平台的不同癌症类型的正常和肿瘤组织中的基因表达摘要。然后单击结果数据下载链接，访问有关基因表达值、组织类型和数据源的详细信息。要搜索基因改变和信号网络，请打开CBIO门户网页，并使用着陆页上的查询，单击"选择研究"部分下感兴趣的器官或组织，选择感兴趣的特定研究，然后单击按基因查询。在"选择基因组配置文件"部分中，选择突变、GISTIC 中的指定拷贝编号更改或 mRNA 表达选项。从"选择患者/案例集"菜单中选择相应的数据，并在"输入基因"查询框中输入目标基因符号。单击"提交查询"按钮，然后打开"网络"选项卡以检索所需的基因网络。然后单击"文件"选项卡，然后选择"保存为图像 PNG 以下载网络图像"。要创建具有NICD或NICD和妈妈过度表达的苍蝇，准备适当的苍蝇种群，并应用时态和区域基因表达靶向技术，根据标准协议控制时空基因表达。将苍蝇在18摄氏度下升起，直到成年，然后用酵母将苍蝇温度提升至29摄氏度，长达48小时。在29摄氏度的孵育结束时，在胚胎收集盘中加入三毫升PBS，用二氧化碳垫麻醉苍蝇培养。使用解剖显微镜识别麻醉性雌性苍蝇，并使用一对解剖钳子小心地抓住苍蝇的下胸。将苍蝇淹没在胚胎收集盘中的PBS中，用第二对钳子捏下腹部，轻轻拉扯释放内脏。定位和分离一对卵巢从苍蝇的身体，并打破肌肉护套，位于卵巢的后端，以分离卵巢。然后将分离的卵巢放在1.5毫升离心管中，在冰上含有500微升PBS。收集所有卵巢后，用 500 微升 4%甲醛代替 PBS，将管子放在螺母器上 10 分钟。在孵育结束时，丢弃固定物，每次洗涤一毫升 PBT，用三次15分钟的冲洗冲洗来清洗卵巢。上次洗涤后，在螺母上用 150 微升（每毫升 DAPI 10 微克）标记卵巢 10-15 分钟。在孵育结束时，用1毫升PBT清洗卵巢10分钟，然后用PBS清洗两次10分钟。第二次洗涤后，除最后300微升的PBS外，全部取出，并使用200微升移液器尖端数次三叶酸三酯，以释放蛋室。接下来，在微离心中快速旋转，轻轻沉淀卵巢组织，在不干扰卵巢颗粒的情况下去除尽可能多的PBS。使用 1，000 微升移液器尖端，将大约三滴安装溶液转移到管中，并使用 200 微升移液器尖端，从末端修剪约 0.33 毫米，将整个 120 微升含卵巢安装溶液转移到玻璃显微镜幻灯片上。轻轻地将盖玻片玻璃放在安装溶液上，用透明指甲油密封边缘。然后使用 10 倍放大率和 0.8 孔径的共体显微镜获取染色和安装的卵巢的图像。如所证明，使用 PRECOG 门户，可以获得卵巢癌中 NOTCH2、NOTCH3 和 MAML1 的 Z 得分。负Z-评分值表明三个基因表达水平高的患者整体存活率较差。使用 CSIOVD 数据库确认这些发现，进一步表明 NOTCH2、NOTCH3 和 MAML1 的高表达与整体生存率差和无病性相关。进一步的置换测试表明，NOTCH2、NOTCH3和MAML1在肿瘤组织中表达强烈。基于这三个核心基因，可以创建一个信号网络，以提供50个最常改变的相邻基因，这些基因也位于同一通路，突变率最高。感兴趣的是，仅NICD就过度表达果蝇等效型的STCH）基因不会诱发果蝇的肿瘤。而NICD和妈妈的过度表达一起诱发果蝇的肿瘤，如存在多个上皮层和累积细胞。进一步的实验验证可以为确定潜在的新药物治疗靶点、疾病生物标志物和个性化治疗铺平道路。

Research

JoVE Journal

Cancer Research

Murine Experimental Model of Original Tumor Development and Peritoneal Metastasis via Orthotopic Inoculation with Ovarian Carcinoma Cells

Murine Experimental Model of Original Tumor Development and Peritoneal Metastasis via Orthotopic Inoculation with Ovarian Carcinoma Cells

原发肿瘤发展小鼠实验模型和腹膜转移<em&gt;通过</em&gt;原位接种卵巢癌细胞

Epithelial ovarian carcinoma (EOC) is associated with a poor prognosis because it shows peritoneal dissemination. To improve the prognosis, it is ...

科研

癌症研究

Evaluating the Role of Mitochondrial Function in Cancer-related Fatigue

线粒体功能在癌症相关疲劳中的作用评价

Fatigue is a common and debilitating condition that affects most cancer patients. To date, fatigue remains poorly characterized with no diagnostic test to ...

Methods for Evaluating the Role of c-Fos and Dusp1 in Oncogene Dependence

c-fos 和 dusp1 在癌基因依赖性中的作用评价方法

The demonstration of tyrosine kinase inhibitors (TKIs) in treating chronic myeloid leukemia (CML) has heralded a new era in cancer therapeutics. However, ...

Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods

使用一套实用可行的方法,描述英国皇家空军家族激酶与疾病相关的突变体

The rapidly accelerated fibrosarcoma (RAF) family kinases play a central role in cell biology and their dysfunction leads to cancers and developmental ...

Characterization and Functional Prediction of Bacteria in Ovarian Tissues

卵巢组织细菌的特征和功能预测

The theory of a "sterile" female upper reproductive tract has been encountering increasing opposition due to advancements in bacterial detection. However, ...

A Mouse Model to Investigate the Role of Cancer-Associated Fibroblasts in Tumor Growth

研究癌症相关成纤维细胞在肿瘤生长中的作用的小鼠模型

Cancer-associated fibroblasts (CAFs) can play an important role in tumor growth by creating a tumor-promoting microenvironment. Models to study the role ...

Generation and Culturing of High-Grade Serous Ovarian Cancer Patient-Derived Organoids

高级别浆液性卵巢癌患者来源类器官的生成和培养

Organoids are 3D dynamic tumor models that can be grown successfully from patient-derived ovarian tumor tissue, ascites, or pleural fluid and aid in the ...

Visualizing DNA Damage Repair Proteins in Patient-Derived Ovarian Cancer Organoids via Immunofluorescence Assays

Visualizing DNA Damage Repair Proteins in Patient-Derived Ovarian Cancer Organoids via Immunofluorescence Assays

通过免疫荧光测定 可视化 患者来源的卵巢癌类器官中的 DNA 损伤修复蛋白

Immunofluorescence is one of the most widely used techniques to visualize target antigens with high sensitivity and specificity, allowing for the accurate ...

Quantifying Telomere Length Using Non-Radioactive Chemiluminescence Detection

Optimization of Performance Parameters of the TAGGG Telomere Length Assay

Optimization of Performance Parameters of the TAGGG Telomere Length Assay (Video) | JoVE 

TAGGG端粒长度测定性能参数优化

Telomeres are repetitive sequences which are present at chromosomal ends; their shortening is a characteristic feature of human somatic cells. Shortening ...

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Pharmacological Targeting of Ion Channels to Treat Solid Tumors

Screening Ion Channels in Cancer Cells

Exploring the Role of Ion Channels in Cancer: Characterization and Potential Treatment Approaches (Video) | JoVE

筛选癌细胞中的离子通道

Ion channels are critical for cell development and maintaining cell homeostasis. The perturbation of ion channel function contributes to the development ...