An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

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.; Xu, ed., Jinbo

doi:10.1093/bioinformatics/btaa1073

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Journal Article · Sat Dec 26 00:00:00 EST 2020 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btaa1073· OSTI ID:1774691

Hagemeijer, Marne C.; Vonk, Annelotte M.; ; ; ; ; Beekman, Jeffrey M.; ; ; Xu, ed., Jinbo

Abstract Motivation

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.

Results

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.

Availability and implementation

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 information

Supplementary data are available at Bioinformatics online.

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Sponsoring Organization:: USDOE Office of Nuclear Energy (NE), Nuclear Fuel Cycle and Supply Chain

OSTI ID:: 1774691

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 24 Vol. 36; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

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