A Bioinformatic Profile of Gene Expression of Colorectal Carcinoma Derived Organoids.
A Bioinformatic Profile of Gene Expression of Colorectal Carcinoma Derived Organoids.
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DOI：
10.1155/2018/2594076
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发表时间：
2018
影响因子：
--
通讯作者：
Yang J
中科院分区：
文献类型：
--
作者：
A P;Xu X;Wang C;Ye L;Yang J
结直肠癌是人类常见的癌症之一。在理解结直肠癌的分子特征方面，体外癌细胞系是否足以再现原始肿瘤一直存在激烈争论。类器官作为一种新型的体外3D培养系统因其具有复兴原始组织的能力而在结直肠癌研究中应运而生。本研究的目的是分析 CRC 类器官的基因表达。基因表达GSE64392来自GEO数据库，包含20个患者的37个类器官样本，其中包括22个结直肠肿瘤类器官样本和15个配对的健康样本。应用基因本体论（GO）和京都基因和基因组百科全书（KEGG）对差异表达基因（DEG）进行分类。通过相互作用基因检索搜索工具 (STRING) 和 Cytoscape 软件分析 DEG 之间的蛋白质相互作用。总共鉴定了 853 个基因序列。 GO分析表明DEGs广泛参与多种生物过程（BP），如增殖、细胞周期和生物合成。 KEEG 通路分析显示 WNT、MAPK、TGF-β、SHH、ECM-受体相互作用和 FGF 通路发生改变。与蛋白质相互作用鉴定的 DEG 是细胞外基质组织和 GPCR 途径的主要反应。总之，我们的研究分析了 CRC 类器官中的 DEG，并促进了我们对 CRC 类器官作为结直肠癌研究新模型的理解。
Colorectal carcinoma is one of the common cancers in human. It has been intensely debated whether the in vitro cancer cell lines are closely enough for recapitulating the original tumor in understanding the molecular characteristic of CRC. Organoid as a new in vitro 3D culture system has sprang out in CRC study for the capability in reviving the original tissue. The aim of this study is to profile the gene expression of CRC organoid. The gene expression GSE64392 was from GEO database contained 20-patients-derived 37 organoid samples, including 22 colorectal tumor organoid samples and 15 paired healthy samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied for classifying differentially expressed genes (DEGs). Protein interaction among DEGs was analyzed by Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. In total, 853 gene sequences were identified. GO analysis revealed that DEGs were extensively involved in various biological process (BP), like proliferation, cell cycle, and biosynthesis. KEEG pathway analysis showed that WNT, MAPK, TGF-β, SHH, ECM-receptor interaction, and FGF pathways were altered. DEGs which were identified with protein interactions were major response for extracellular matrix organization and the GPCR pathway. In conclusion, our study profiled the DEGs in CRC organoids and promotes our understanding of the CRC organoids as a new model for colorectal cancer research.
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正常细胞的基因组测序揭示了发育谱系和突变过程。
影响因子：
64.8
作者：
Behjati, Sam;Huch, Meritxell;van Boxtel, Ruben;Karthaus, Wouter;Wedge, David C.;Tamuri, Asif U.;Martincorena, Inigo;Petljak, Mia;Alexandrov, Ludmil B.;Gundem, Gunes;Tarpey, Patrick S.;Roerink, Sophie;Blokker, Joyce;Maddison, Mark;Mudie, Laura;Robinson, Ben;Nik-Zainal, Serena;Campbell, Peter;Goldman, Nick;van de Wetering, Marc;Cuppen, Edwin;Clevers, Hans;Stratton, Michael R.
通讯作者：
Stratton, Michael R.
DOI：
10.1126/science.aao3130
发表时间：
2017-10-13
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Drost J;van Boxtel R;Blokzijl F;Mizutani T;Sasaki N;Sasselli V;de Ligt J;Behjati S;Grolleman JE;van Wezel T;Nik-Zainal S;Kuiper RP;Cuppen E;Clevers H
通讯作者：
Clevers H
影响因子：
46.9
作者：
Roper J;Tammela T;Cetinbas NM;Akkad A;Roghanian A;Rickelt S;Almeqdadi M;Wu K;Oberli MA;Sánchez-Rivera FJ;Park YK;Liang X;Eng G;Taylor MS;Azimi R;Kedrin D;Neupane R;Beyaz S;Sicinska ET;Suarez Y;Yoo J;Chen L;Zukerberg L;Katajisto P;Deshpande V;Bass AJ;Tsichlis PN;Lees J;Langer R;Hynes RO;Chen J;Bhutkar A;Jacks T;Yilmaz ÖH
通讯作者：
Yilmaz ÖH
影响因子：
64.5
作者：
van de Wetering M;Francies HE;Francis JM;Bounova G;Iorio F;Pronk A;van Houdt W;van Gorp J;Taylor-Weiner A;Kester L;McLaren-Douglas A;Blokker J;Jaksani S;Bartfeld S;Volckman R;van Sluis P;Li VS;Seepo S;Sekhar Pedamallu C;Cibulskis K;Carter SL;McKenna A;Lawrence MS;Lichtenstein L;Stewart C;Koster J;Versteeg R;van Oudenaarden A;Saez-Rodriguez J;Vries RG;Getz G;Wessels L;Stratton MR;McDermott U;Meyerson M;Garnett MJ;Clevers H
通讯作者：
Clevers H
影响因子：
12.3
作者：
Sandberg, R;Ernberg, I
通讯作者：
Ernberg, I