Hagemeijer Marne C, Vonk Annelotte M, Awatade Nikhil T, Silva Iris A L, Tischer Christian, Hilsenstein Volker, Beekman Jeffrey M, Amaral Margarida D, Botelho Hugo M
Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, The Netherlands.
Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA Utrecht, The Netherlands.
Bioinformatics. 2021 Apr 5;36(24):5686-5694. doi: 10.1093/bioinformatics/btaa1073.
The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility.
We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids.
All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0.
Supplementary data are available at Bioinformatics online.
福斯可林诱导肿胀（FIS）测定法已成为预测囊性纤维化（CF）患者已批准和正在研究的CFTR调节剂药物疗效的首选测定法。目前，不存在FIS数据的标准化定量方法，从而妨碍了实验室间的可重复性。
我们开发了一个完整的开源工作流程，用于以原始显微镜图像为输入，对肠道类器官中的CFTR功能测量进行标准化的高内涵分析。该工作流程包括用于（i）文件和元数据处理；（ii）图像定量和（iii）统计分析的工具。我们的工作流程重现了已发表的专有分析协议产生的结果，并能够在CF类器官中进行标准化的CFTR功能测量。
所有工作流程组件都是开源且免费提供的：用于文件处理的htmrenamer R包https://github.com/hmbotelho/htmrenamer；CellProfiler和ImageJ分析脚本/管道https://github.com/hmbotelho/FIS_image_analysis；用于统计分析的类器官分析应用程序https://github.com/hmbotelho/organoid_analyst；详细的使用说明和演示数据集https://github.com/hmbotelho/FIS_analysis。根据GPL v3.0分发。
补充数据可在《生物信息学》在线获取。
