High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response.
High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response.
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DOI：
10.1128/msystems.01466-21
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发表时间：
2022-04-26
期刊：
影响因子：
6.4
通讯作者：
中科院分区：
文献类型：
--
作者：
宿主先天免疫应答的抑制是病毒复制的关键方面。一旦感染，病毒可能会引入一种或多种抑制关键免疫途径（如I型干扰素途径）的蛋白质。然而，预测和评估靶向途径上的病毒蛋白生物活性的能力仍然具有挑战性，并且通常在单病毒或单基因基础上进行。在这里，我们提出了一个中等通量高含量的细胞为基础的测定，以揭示病毒蛋白的免疫抑制作用。为了测试我们的方法的预测能力，我们开发了一个包含800个编码已知、预测和未表征的人类病毒基因的基因库。我们发现，以前已知的免疫抑制剂从许多病毒家族，如小核糖核酸病毒科和黄病毒科记录阳性反应。这些包括许多病毒蛋白酶，我们进一步证实了先天免疫抑制取决于蛋白酶活性。由弹状病毒编码的一类预测抑制剂被证明可以阻断核转运，并且来自未培养病毒的几种先前未表征的蛋白质被证明可以抑制转录因子NF-κB和干扰素调节因子3（IRF 3）的核转运。我们建议，这种基于途径的测定，连同早期测序，基因合成，和病毒感染的研究，可以部分地作为新的病毒蛋白质的快速体外表征的基础。重要性由病毒病原体引起的传染病加重了卫生保健和经济负担。许多病毒生物分子抑制人类先天免疫系统，使病毒能够逃避宿主的免疫反应。尽管我们目前了解病毒复制和免疫逃避，但新的病毒蛋白，包括未培养病毒或新出现病毒编码的蛋白，正在从大规模测序和监测项目中快速挖掘出来。使用中通量和高通量功能测定来表征病毒蛋白的免疫抑制功能可以促进我们对病毒复制和可能的感染治疗的理解。在这项研究中，我们组装了一个来自不同病毒家族的大型病毒基因库，并开发了一种高含量的检测方法来检测先天免疫途径的抑制作用。我们的工作扩展了可以快速连接序列和蛋白质功能的工具，代表了对新兴和未充分研究的病毒进行早期评估的实际步骤。
Suppression of the host innate immune response is a critical aspect of viral replication. Upon infection, viruses may introduce one or more proteins that inhibit key immune pathways, such as the type I interferon pathway. However, the ability to predict and evaluate viral protein bioactivity on targeted pathways remains challenging and is typically done on a single-virus or -gene basis. Here, we present a medium-throughput high-content cell-based assay to reveal the immunosuppressive effects of viral proteins. To test the predictive power of our approach, we developed a library of 800 genes encoding known, predicted, and uncharacterized human virus genes. We found that previously known immune suppressors from numerous viral families such as Picornaviridae and Flaviviridae recorded positive responses. These include a number of viral proteases for which we further confirmed that innate immune suppression depends on protease activity. A class of predicted inhibitors encoded by Rhabdoviridae viruses was demonstrated to block nuclear transport, and several previously uncharacterized proteins from uncultivated viruses were shown to inhibit nuclear transport of the transcription factors NF-κB and interferon regulatory factor 3 (IRF3). We propose that this pathway-based assay, together with early sequencing, gene synthesis, and viral infection studies, could partly serve as the basis for rapid in vitro characterization of novel viral proteins. IMPORTANCE Infectious diseases caused by viral pathogens exacerbate health care and economic burdens. Numerous viral biomolecules suppress the human innate immune system, enabling viruses to evade an immune response from the host. Despite our current understanding of viral replications and immune evasion, new viral proteins, including those encoded by uncultivated viruses or emerging viruses, are being unearthed at a rapid pace from large-scale sequencing and surveillance projects. The use of medium- and high-throughput functional assays to characterize immunosuppressive functions of viral proteins can advance our understanding of viral replication and possibly treatment of infections. In this study, we assembled a large viral-gene library from diverse viral families and developed a high-content assay to test for inhibition of innate immunity pathways. Our work expands the tools that can rapidly link sequence and protein function, representing a practical step toward early-stage evaluation of emerging and understudied viruses.
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影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
30.3
作者：
Arze, Cesar A.;Springer, Simeon;Yozwiak, Nathan L.
通讯作者：
Yozwiak, Nathan L.
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
5
作者：
Greninger AL
通讯作者：
Greninger AL
影响因子：
6.4
作者：
Addetia A;Lieberman NAP;Phung Q;Hsiang TY;Xie H;Roychoudhury P;Shrestha L;Loprieno MA;Huang ML;Gale M Jr;Jerome KR;Greninger AL
通讯作者：
Greninger AL