1
|
Lefferts JW, Kroes S, Smith MB, Niemöller PJ, Nieuwenhuijze NDA, Sonneveld van Kooten HN, van der Ent CK, Beekman JM, van Beuningen SFB. OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion. Commun Biol 2024; 7:319. [PMID: 38480810 PMCID: PMC10937908 DOI: 10.1038/s42003-024-05966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Epithelial ion and fluid transport studies in patient-derived organoids (PDOs) are increasingly being used for preclinical studies, drug development and precision medicine applications. Epithelial fluid transport properties in PDOs can be measured through visual changes in organoid (lumen) size. Such organoid phenotypes have been highly instrumental for the studying of diseases, including cystic fibrosis (CF), which is characterized by genetic mutations of the CF transmembrane conductance regulator (CFTR) ion channel. Here we present OrgaSegment, a MASK-RCNN based deep-learning segmentation model allowing for the segmentation of individual intestinal PDO structures from bright-field images. OrgaSegment recognizes spherical structures in addition to the oddly-shaped organoids that are a hallmark of CF organoids and can be used in organoid swelling assays, including the new drug-induced swelling assay that we show here. OrgaSegment enabled easy quantification of organoid swelling and could discriminate between organoids with different CFTR mutations, as well as measure responses to CFTR modulating drugs. The easy-to-apply label-free segmentation tool can help to study CFTR-based fluid secretion and possibly other epithelial ion transport mechanisms in organoids.
Collapse
Affiliation(s)
- Juliet W Lefferts
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Suzanne Kroes
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Matthew B Smith
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Paul J Niemöller
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Natascha D A Nieuwenhuijze
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Heleen N Sonneveld van Kooten
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands.
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands.
| | - Sam F B van Beuningen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands.
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands.
| |
Collapse
|
2
|
Lefferts JW, Bierlaagh MC, Kroes S, Nieuwenhuijze NDA, Sonneveld van Kooten HN, Niemöller PJ, Verburg TF, Janssens HM, Muilwijk D, van Beuningen SFB, van der Ent CK, Beekman JM. CFTR Function Restoration upon Elexacaftor/Tezacaftor/Ivacaftor Treatment in Patient-Derived Intestinal Organoids with Rare CFTR Genotypes. Int J Mol Sci 2023; 24:14539. [PMID: 37833986 PMCID: PMC10572896 DOI: 10.3390/ijms241914539] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. The combination of the CFTR modulators elexacaftor, tezacaftor, and ivacaftor (ETI) enables the effective rescue of CFTR function in people with the most prevalent F508del mutation. However, the functional restoration of rare CFTR variants remains unclear. Here, we use patient-derived intestinal organoids (PDIOs) to identify rare CFTR variants and potentially individuals with CF that might benefit from ETI. First, steady-state lumen area (SLA) measurements were taken to assess CFTR function and compare it to the level observed in healthy controls. Secondly, the forskolin-induced swelling (FIS) assay was performed to measure CFTR rescue within a lower function range, and to further compare it to ETI-mediated CFTR rescue in CFTR genotypes that have received market approval. ETI responses in 30 PDIOs harboring the F508del mutation served as reference for ETI responses of 22 PDIOs with genotypes that are not currently eligible for CFTR modulator treatment, following European Medicine Agency (EMA) and/or U.S. Food and Drug Administration (FDA) regulations. Our data expand previous datasets showing a correlation between in vitro CFTR rescue in organoids and corresponding in vivo ppFEV1 improvement upon a CFTR modulator treatment in published clinical trials, and suggests that the majority of individuals with rare CFTR variants could benefit from ETI. CFTR restoration was further confirmed on protein levels using Western blot. Our data support that CFTR function measurements in PDIOs with rare CFTR genotypes can help to select potential responders to ETI, and suggest that regulatory authorities need to consider providing access to treatment based on the principle of equality for people with CF who do not have access to treatment.
Collapse
Affiliation(s)
- Juliet W. Lefferts
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Marlou C. Bierlaagh
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Suzanne Kroes
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Natascha D. A. Nieuwenhuijze
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| | - Heleen N. Sonneveld van Kooten
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| | - Paul J. Niemöller
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Tibo F. Verburg
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Hettie M. Janssens
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus Medical Center-Sophia Children’s Hospital, University Hospital Rotterdam, 3015 CN Rotterdam, The Netherlands
| | - Danya Muilwijk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Sam F. B. van Beuningen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| | - Cornelis K. van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| |
Collapse
|
3
|
van Coevorden-Hameete MH, van Beuningen SFB, Perrenoud M, Will LM, Hulsenboom E, Demonet JF, Sabater L, Kros JM, Verschuuren JJGM, Titulaer MJ, de Graaff E, Sillevis Smitt PAE, Hoogenraad CC. Antibodies to TRIM46 are associated with paraneoplastic neurological syndromes. Ann Clin Transl Neurol 2017; 4:680-686. [PMID: 28904989 PMCID: PMC5590547 DOI: 10.1002/acn3.396] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 01/25/2017] [Indexed: 11/09/2022] Open
Abstract
Paraneoplastic neurological syndromes (PNS) are often characterized by the presence of antineuronal antibodies in patient serum or cerebrospinal fluid. The detection of antineuronal antibodies has proven to be a useful tool in PNS diagnosis and the search for an underlying tumor. Here, we describe three patients with autoantibodies to several epitopes of the axon initial segment protein tripartite motif 46 (TRIM46). We show that anti‐TRIM46 antibodies are easy to detect in routine immunohistochemistry screening and can be confirmed by western blotting and cell‐based assay. Anti‐TRIM46 antibodies can occur in patients with diverse neurological syndromes and are associated with small‐cell lung carcinoma.
Collapse
Affiliation(s)
- Marleen H van Coevorden-Hameete
- Cell Biology Department of Biology Faculty of Science Utrecht University Padualaan 83584 CH Utrecht The Netherlands.,Department of Neurology Erasmus University Medical Center Dr. Molewaterplein 403015 GD Rotterdam The Netherlands
| | - Sam F B van Beuningen
- Cell Biology Department of Biology Faculty of Science Utrecht University Padualaan 83584 CH Utrecht The Netherlands
| | - Matthieu Perrenoud
- Service of Neurology Centre Hospitalier Universitaire Vaudois (CHUV) Chemin du Mont-Paisible 16CH 1011 Lausanne Switzerland
| | - Lena M Will
- Cell Biology Department of Biology Faculty of Science Utrecht University Padualaan 83584 CH Utrecht The Netherlands
| | - Esther Hulsenboom
- Department of Neurology Erasmus University Medical Center Dr. Molewaterplein 403015 GD Rotterdam The Netherlands
| | - Jean-Francois Demonet
- Leenaards Memory Centre Department of Clinical Neurosciences Centre Hospitalier Universitaire Vaudois (CHUV) Chemin du Mont-Paisible 16CH 1011 Lausanne Switzerland
| | - Lidia Sabater
- Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS) Carrer del Rosselló 14908036 Barcelona Spain
| | - Johan M Kros
- Department of Pathology Erasmus University Medical Center Dr. Molewaterplein 403015 GD Rotterdam The Netherlands
| | - Jan J G M Verschuuren
- Department of Neurology Leiden University Medical Center Albinusdreef 22333 ZA Leiden The Netherlands
| | - Maarten J Titulaer
- Department of Neurology Erasmus University Medical Center Dr. Molewaterplein 403015 GD Rotterdam The Netherlands
| | - Esther de Graaff
- Cell Biology Department of Biology Faculty of Science Utrecht University Padualaan 83584 CH Utrecht The Netherlands
| | - Peter A E Sillevis Smitt
- Department of Neurology Erasmus University Medical Center Dr. Molewaterplein 403015 GD Rotterdam The Netherlands
| | - Casper C Hoogenraad
- Cell Biology Department of Biology Faculty of Science Utrecht University Padualaan 83584 CH Utrecht The Netherlands
| |
Collapse
|
4
|
Yau KW, van Beuningen SFB, Cunha-Ferreira I, Cloin BMC, van Battum EY, Will L, Schätzle P, Tas RP, van Krugten J, Katrukha EA, Jiang K, Wulf PS, Mikhaylova M, Harterink M, Pasterkamp RJ, Akhmanova A, Kapitein LC, Hoogenraad CC. Microtubule minus-end binding protein CAMSAP2 controls axon specification and dendrite development. Neuron 2014; 82:1058-73. [PMID: 24908486 DOI: 10.1016/j.neuron.2014.04.019] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2014] [Indexed: 01/09/2023]
Abstract
In neurons, most microtubules are not associated with a central microtubule-organizing center (MTOC), and therefore, both the minus and plus-ends of these non-centrosomal microtubules are found throughout the cell. Microtubule plus-ends are well established as dynamic regulatory sites in numerous processes, but the role of microtubule minus-ends has remained poorly understood. Using live-cell imaging, high-resolution microscopy, and laser-based microsurgery techniques, we show that the CAMSAP/Nezha/Patronin family protein CAMSAP2 specifically localizes to non-centrosomal microtubule minus-ends and is required for proper microtubule organization in neurons. CAMSAP2 stabilizes non-centrosomal microtubules and is required for neuronal polarity, axon specification, and dendritic branch formation in vitro and in vivo. Furthermore, we found that non-centrosomal microtubules in dendrites are largely generated by γ-Tubulin-dependent nucleation. We propose a two-step model in which γ-Tubulin initiates the formation of non-centrosomal microtubules and CAMSAP2 stabilizes the free microtubule minus-ends in order to control neuronal polarity and development.
Collapse
Affiliation(s)
- Kah Wai Yau
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands; Department of Neuroscience, Erasmus Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Sam F B van Beuningen
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Inês Cunha-Ferreira
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Bas M C Cloin
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Eljo Y van Battum
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Lena Will
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Philipp Schätzle
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Roderick P Tas
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Jaap van Krugten
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Eugene A Katrukha
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Kai Jiang
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Phebe S Wulf
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Marina Mikhaylova
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Martin Harterink
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Anna Akhmanova
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.
| | - Casper C Hoogenraad
- Cell Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands; Department of Neuroscience, Erasmus Medical Center, 3015 GE Rotterdam, The Netherlands.
| |
Collapse
|