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

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^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

1 Citation (Scopus)

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.

Original language	English
Pages (from-to)	5686-5694
Number of pages	9
Journal	Bioinformatics
Volume	36
Issue number	24
DOIs	https://doi.org/10.1093/bioinformatics/btaa1073
Publication status	Published - 15 Dec 2020

Access to Document

10.1093/bioinformatics/btaa1073

Cite this

@article{56fa70d094604c76a12b425d27aa6b0b,

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

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.",

author = "Hagemeijer, {Marne C.} and Vonk, {Annelotte M.} and Awatade, {Nikhil T.} and Silva, {Iris A.L.} and Christian Tischer and Volker Hilsenstein and Beekman, {Jeffrey M.} and Amaral, {Margarida D.} and Botelho, {Hugo M.}",

note = "Funding Information: This work was supported by UIDB/04046/2020 and UIDP/04046/2020 centre grants from FCT-Funda{\c c}{\~a}o para a Ci{\^e}ncia e a Tecnologia, Portugal (to BioISI) and 'HIT-CF' [H2020-SC1-2017-755021] from EU [to J.M.B. and M.D.A.]. H.M.B. was recipient of post-doctoral fellowship [SFRH/BPD/ 93017/2013] from FCT. J.M.B. received funding from the Dutch Cystic Fibrosis Foundation (Nederlandse Cystic Fibrosis Stichting; HIT-CF program). Software development was performed at Faculty of Sciences of the University of Lisboa Microscopy Facility, a node of the Portuguese Platform of BioImaging (PPBI), PPBI-POCI-01-0145-FEDER-022122 from FCT. Publisher Copyright: {\textcopyright} The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected]",

year = "2020",

month = dec,

day = "15",

doi = "10.1093/bioinformatics/btaa1073",

language = "English",

volume = "36",

pages = "5686--5694",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "24",

}

TY - JOUR

T1 - An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

AU - Hagemeijer, Marne C.

AU - Vonk, Annelotte M.

AU - Awatade, Nikhil T.

AU - Silva, Iris A.L.

AU - Tischer, Christian

AU - Hilsenstein, Volker

AU - Beekman, Jeffrey M.

AU - Amaral, Margarida D.

AU - Botelho, Hugo M.

N1 - Funding Information: This work was supported by UIDB/04046/2020 and UIDP/04046/2020 centre grants from FCT-Fundação para a Ciência e a Tecnologia, Portugal (to BioISI) and 'HIT-CF' [H2020-SC1-2017-755021] from EU [to J.M.B. and M.D.A.]. H.M.B. was recipient of post-doctoral fellowship [SFRH/BPD/ 93017/2013] from FCT. J.M.B. received funding from the Dutch Cystic Fibrosis Foundation (Nederlandse Cystic Fibrosis Stichting; HIT-CF program). Software development was performed at Faculty of Sciences of the University of Lisboa Microscopy Facility, a node of the Portuguese Platform of BioImaging (PPBI), PPBI-POCI-01-0145-FEDER-022122 from FCT. Publisher Copyright: © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected]

PY - 2020/12/15

Y1 - 2020/12/15

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85105052720&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btaa1073

DO - 10.1093/bioinformatics/btaa1073

M3 - Article

AN - SCOPUS:85105052720

SN - 1367-4803

VL - 36

SP - 5686

EP - 5694

JO - Bioinformatics

JF - Bioinformatics

IS - 24

ER -

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

Abstract

Access to Document

Other files and links

Fingerprint

Cite this