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

Marne C Hagemeijer; Annelotte M Vonk; Nikhil T Awatade; Iris A L Silva; Christian Tischer; Volker Hilsenstein; Jeffrey M Beekman; Margarida D Amaral; Hugo M Botelho

doi:10.1093/bioinformatics/btaa1073

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

Bioinformatics. 2021 Apr 5;36(24):5686-5694. doi: 10.1093/bioinformatics/btaa1073.

Authors

Affiliations

¹ Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, The Netherlands.
² Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA Utrecht, The Netherlands.
³ BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal.
⁴ European Molecular Biology Laboratory (EMBL), Centre for Bioimage Analysis (CBA), 69117 Heidelberg, Germany.
⁵ European Molecular Biology Laboratory (EMBL), Advanced Light Microscopy Facility (ALMF), 69117 Heidelberg, Germany.

PMID: 33367496
DOI: 10.1093/bioinformatics/btaa1073

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.

Abstract

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