Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images.
Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images.
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DOI：
10.1093/bioinformatics/btq398
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发表时间：
2010-09-15
期刊：
影响因子：
--
通讯作者：
König R
中科院分区：
文献类型：
--
作者：
Suratanee A;Rebhan I;Matula P;Kumar A;Kaderali L;Rohr K;Bartenschlager R;Eils R;König R
动机：现代高通量RNAi筛选技术有助于检测参与病毒进入和复制的人类蛋白质。然而，来自不同实验室的袭击名单几乎没有一致性。这可能不仅是由于实验差异造成的，也可能是由于没有充分探索数据分析的可能性。我们希望通过将感染细胞的群体分析与已建立的染料强度读数相结合来提高这种筛选的可靠性。结果如下：病毒感染主要通过细胞-细胞接触传播，并且在原位和体内感染传播期间可以观察到感染细胞的聚集。我们采用这种聚类特征来定义对人类丙型肝炎病毒的病毒感染效率造成损害的敲除。用已建立的点模式分析方法（Ripley’s K-函数）分析719个人激酶基因的敲低细胞的图像，以检测其中病毒感染的细胞未显示任何聚集并因此阻碍其感染扩散到其邻近细胞的敲低。将结果与使用表达GFP的病毒的共同强度读数的统计分析进行比较，并基于内切酶的二次筛选产生五个有希望的宿主因子，这些因子可能适合作为药物治疗的潜在靶点。结论：我们报告的高通量成像方法的替代方法，以检测宿主因子相关的病毒感染效率。该方法是通用的，并有可能被用于各种不同的病毒和治疗正在筛选的成像技术。联系方式：r. dkfz.de; r. dkfz.de补充信息：补充数据可在生物信息学在线获得。
Motivation: Detecting human proteins that are involved in virus entry and replication is facilitated by modern high-throughput RNAi screening technology. However, hit lists from different laboratories have shown only little consistency. This may be caused by not only experimental discrepancies, but also not fully explored possibilities of the data analysis. We wanted to improve reliability of such screens by combining a population analysis of infected cells with an established dye intensity readout. Results: Viral infection is mainly spread by cell–cell contacts and clustering of infected cells can be observed during spreading of the infection in situ and in vivo. We employed this clustering feature to define knockdowns which harm viral infection efficiency of human Hepatitis C Virus. Images of knocked down cells for 719 human kinase genes were analyzed with an established point pattern analysis method (Ripley's K-function) to detect knockdowns in which virally infected cells did not show any clustering and therefore were hindered to spread their infection to their neighboring cells. The results were compared with a statistical analysis using a common intensity readout of the GFP-expressing viruses and a luciferase-based secondary screen yielding five promising host factors which may suit as potential targets for drug therapy. Conclusion: We report of an alternative method for high-throughput imaging methods to detect host factors being relevant for the infection efficiency of viruses. The method is generic and has the potential to be used for a large variety of different viruses and treatments being screened by imaging techniques. Contact: r.eils@dkfz.de; r.koenig@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
12.3
作者：
Boutros M;Brás LP;Huber W
通讯作者：
Huber W
影响因子：
--
作者：
Erfle, Holger;Neumann, Beate;Pepperkok, Rainer
通讯作者：
Pepperkok, Rainer
DOI：
10.1006/bbrc.1999.0460
发表时间：
1999-04-21
影响因子：
3.1
作者：
Kim, J;Lee, D;Choe, J
通讯作者：
Choe, J
DOI：
10.1073/pnas.0912090107
发表时间：
2010-02-16
影响因子：
11.1
作者：
Peng, Tao;Bonamy, Ghislain M. C.;Murphy, Robert F.
通讯作者：
Murphy, Robert F.
影响因子：
7.8
作者：
Prior, Ian A;Muncke, Cornelia;Parton, Robert G;Hancock, John F
通讯作者：
Hancock, John F