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对暴露于放线菌素D和Nutlin-3a的癌细胞系进行转录组学和蛋白质组学研究,揭示了众多新的p53调控基因候选者。

Transcriptomic and proteomic study of cancer cell lines exposed to actinomycin D and nutlin-3a reveals numerous, novel candidates for p53-regulated genes.

作者信息

Łasut-Szyszka Barbara, Gdowicz-Kłosok Agnieszka, Małachowska Beata, Krześniak Małgorzata, Będzińska Agnieszka, Gawin Marta, Pietrowska Monika, Rusin Marek

机构信息

Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-101, Gliwice, Poland.

Department of Radiation Oncology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY, 10461, USA.

出版信息

Chem Biol Interact. 2024 Apr 1;392:110946. doi: 10.1016/j.cbi.2024.110946. Epub 2024 Mar 7.

Abstract

Transcriptomic analyses have revealed hundreds of p53-regulated genes; however, these studies used a limited number of cell lines and p53-activating agents. Therefore, we searched for candidate p53-target genes by employing stress factors and cell lines never before used in a high-throughput search for p53-regulated genes. We performed RNA-Seq on A549 cells exposed to camptothecin, actinomycin D, nutlin-3a, as well as a combination of actinomycin D and nutlin-3a (A + N). The latter two substances synergise upon the activation of selected p53-target genes. A similar analysis was performed on other cell lines (U-2 OS, NCI-H460, A375) exposed to A + N. To identify proteins in cell lysates or those secreted into a medium of A549 cells in control conditions or treated with A + N, we employed mass spectrometry. The expression of selected genes strongly upregulated by A + N or camptothecin was examined by RT-PCR in p53-deficient cells and their controls. We found that p53 participates in the upregulation of: ACP5, APOL3, CDH3, CIBAR2, CRABP2, CTHRC1, CTSH, FAM13C, FBXO2, FRMD8, FRZB, GAST, ICOSLG, KANK3, KCNK6, KLRG2, MAFB, MR1, NDRG4, PTAFR, RETSAT, TMEM52, TNFRSF14, TRANK1, TYSND1, WFDC2, WFDC5, WNT4 genes. Twelve of these proteins were detected in the secretome and/or proteome of treated cells. Our data generated new hypotheses concerning the functioning of p53. Many genes activated by A + N or camptothecin are also activated by interferons, indicating a noticeable overlap between transcriptional programs of p53 and these antiviral cytokines. Moreover, several identified genes code for antagonists of WNT/β-catenin signalling pathways, which suggests new connections between these two cancer-related signalling systems. One of these antagonists is DRAXIN. Previously, we found that its gene is activated by p53. In this study, using mass spectrometry and Western blotting, we detected expression of DRAXIN in a medium of A549 cells exposed to A + N. Thus, this protein functions not only in the development of the nervous system, but it may also have a new cancer-related function.

摘要

转录组分析已揭示了数百个p53调控基因;然而,这些研究使用的细胞系和p53激活剂数量有限。因此,我们通过采用应激因素和从未用于高通量搜索p53调控基因的细胞系来寻找候选p53靶基因。我们对暴露于喜树碱、放线菌素D、nutlin-3a以及放线菌素D和nutlin-3a组合(A + N)的A549细胞进行了RNA测序。后两种物质在激活选定的p53靶基因时具有协同作用。对暴露于A + N的其他细胞系(U-2 OS、NCI-H460、A375)进行了类似分析。为了鉴定对照条件下或用A + N处理的A549细胞裂解物中或分泌到培养基中的蛋白质,我们采用了质谱分析法。通过RT-PCR在p53缺陷细胞及其对照中检测了被A + N或喜树碱强烈上调的选定基因的表达。我们发现p53参与以下基因的上调:ACP5、APOL3、CDH3、CIBAR2、CRABP2、CTHRC1、CTSH、FAM13C、FBXO2、FRMD8、FRZB、GAST、ICOSLG、KANK3、KCNK6、KLRG2、MAFB、MR1、NDRG4、PTAFR、RETSAT、TMEM52、TNFRSF14、TRANK1、TYSND1、WFDC2、WFDC5、WNT4基因。在处理过的细胞的分泌蛋白质组和/或蛋白质组中检测到了其中12种蛋白质。我们的数据产生了关于p53功能的新假设。许多被A + N或喜树碱激活的基因也被干扰素激活,这表明p53的转录程序与这些抗病毒细胞因子之间存在明显重叠。此外,几个已鉴定的基因编码WNT/β-连环蛋白信号通路的拮抗剂,这表明这两个与癌症相关的信号系统之间有新的联系。其中一种拮抗剂是DRAXIN。此前,我们发现其基因被p53激活。在本研究中,我们使用质谱分析法和蛋白质免疫印迹法在暴露于A + N的A549细胞培养基中检测到了DRAXIN的表达。因此,这种蛋白质不仅在神经系统发育中起作用,而且可能还具有与癌症相关的新功能。

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