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药物机制富集分析可提高重新定位治疗药物的优先级。

Drug mechanism enrichment analysis improves prioritization of therapeutics for repurposing.

机构信息

Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 3710 McClintock Ave., RTH 509, Los Angeles, CA, 90089, USA.

Nautilus Biotechnology, San Carlos, CA, USA.

出版信息

BMC Bioinformatics. 2023 May 24;24(1):215. doi: 10.1186/s12859-023-05343-8.


DOI:10.1186/s12859-023-05343-8
PMID:37226094
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10207828/
Abstract

BACKGROUND: There is a pressing need for improved methods to identify effective therapeutics for diseases. Many computational approaches have been developed to repurpose existing drugs to meet this need. However, these tools often output long lists of candidate drugs that are difficult to interpret, and individual drug candidates may suffer from unknown off-target effects. We reasoned that an approach which aggregates information from multiple drugs that share a common mechanism of action (MOA) would increase on-target signal compared to evaluating drugs on an individual basis. In this study, we present drug mechanism enrichment analysis (DMEA), an adaptation of gene set enrichment analysis (GSEA), which groups drugs with shared MOAs to improve the prioritization of drug repurposing candidates. RESULTS: First, we tested DMEA on simulated data and showed that it can sensitively and robustly identify an enriched drug MOA. Next, we used DMEA on three types of rank-ordered drug lists: (1) perturbagen signatures based on gene expression data, (2) drug sensitivity scores based on high-throughput cancer cell line screening, and (3) molecular classification scores of intrinsic and acquired drug resistance. In each case, DMEA detected the expected MOA as well as other relevant MOAs. Furthermore, the rankings of MOAs generated by DMEA were better than the original single-drug rankings in all tested data sets. Finally, in a drug discovery experiment, we identified potential senescence-inducing and senolytic drug MOAs for primary human mammary epithelial cells and then experimentally validated the senolytic effects of EGFR inhibitors. CONCLUSIONS: DMEA is a versatile bioinformatic tool that can improve the prioritization of candidates for drug repurposing. By grouping drugs with a shared MOA, DMEA increases on-target signal and reduces off-target effects compared to analysis of individual drugs. DMEA is publicly available as both a web application and an R package at https://belindabgarana.github.io/DMEA .

摘要

背景:目前迫切需要改进的方法来鉴定针对疾病的有效疗法。已经开发了许多计算方法来重新利用现有药物来满足这一需求。然而,这些工具通常会输出大量候选药物的列表,这些列表难以解释,而且个别候选药物可能存在未知的脱靶效应。我们认为,一种汇总具有共同作用机制(MOA)的多种药物信息的方法,与逐个评估药物相比,可增加针对目标的信号。在这项研究中,我们提出了药物机制富集分析(DMEA),这是基因集富集分析(GSEA)的一种改编,它将具有共同 MOA 的药物分组,以提高药物重新定位候选药物的优先级。

结果:首先,我们在模拟数据上测试了 DMEA,并表明它可以灵敏且稳健地识别富集的药物 MOA。接下来,我们在三种类型的排序药物列表上使用了 DMEA:(1)基于基因表达数据的扰动基因特征,(2)基于高通量癌细胞系筛选的药物敏感性评分,以及(3)内在和获得性药物耐药性的分子分类评分。在每种情况下,DMEA 都检测到了预期的 MOA 以及其他相关的 MOA。此外,DMEA 生成的 MOA 排名在所有测试数据集都优于原始单药排名。最后,在药物发现实验中,我们确定了潜在的诱导衰老和衰老细胞溶解的药物 MOA,用于原代人乳腺上皮细胞,并通过实验验证了 EGFR 抑制剂的衰老细胞溶解作用。

结论:DMEA 是一种通用的生物信息学工具,可以提高药物重新定位候选药物的优先级。通过将具有共同 MOA 的药物分组,DMEA 与分析单个药物相比,增加了针对目标的信号并减少了脱靶效应。DMEA 可在 https://belindabgarana.github.io/DMEA 作为网络应用程序和 R 包获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/98370de3a940/12859_2023_5343_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/b65efe7c84a4/12859_2023_5343_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/f122d4c082b2/12859_2023_5343_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/416980a983bb/12859_2023_5343_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/8ef59c56e00a/12859_2023_5343_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/60c61c1666c9/12859_2023_5343_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/ccebecc5e043/12859_2023_5343_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/98370de3a940/12859_2023_5343_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/b65efe7c84a4/12859_2023_5343_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/f122d4c082b2/12859_2023_5343_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/416980a983bb/12859_2023_5343_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/8ef59c56e00a/12859_2023_5343_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/60c61c1666c9/12859_2023_5343_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/ccebecc5e043/12859_2023_5343_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/001e/10207828/98370de3a940/12859_2023_5343_Fig7_HTML.jpg

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引用本文的文献

[1]
Reconciling multiple connectivity-based systems biology methods for drug repurposing.

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[2]
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本文引用的文献

[1]
ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs.

Nat Commun. 2023-2-22

[2]
Loss of NF1 in Melanoma Confers Sensitivity to SYK Kinase Inhibition.

Cancer Res. 2023-1-18

[3]
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Nucleic Acids Res. 2023-1-6

[4]
DRviaSPCN: a software package for drug repurposing in cancer via a subpathway crosstalk network.

Bioinformatics. 2022-10-31

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Front Pharmacol. 2022-6-20

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J Proteome Res. 2021-11-5

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Ann Oncol. 2021-7

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Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning.

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