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Lefferts JW, Boersma V, Nieuwenhuijze NDA, Suen SWF, Hajo K, Collantes NS, Vermeulen C, Groeneweg T, Hagemeijer MC, de Jonge HR, van der Ent CK, Splinter E, Beekman JM. Targeted locus amplification reveals heterogeneity between and within CFTR genotypes and association with CFTR function in patient-derived intestinal organoids. J Cyst Fibros 2023; 22:538-547. [PMID: 37100706 DOI: 10.1016/j.jcf.2023.04.003] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) disease severity can be highly variable, even between people with CF (pwCF) with similar genotypes. Here we use patient-derived intestinal organoids to study the influence of genetic variation within the cystic fibrosis transmembrane conductance regulator (CFTR) gene on CFTR function. METHODS Organoids of F508del/class I, F508del/S1251N and pwCF with only one detected CF-causing mutation were cultured. Allele-specific CFTR variation was investigated using targeted locus amplification (TLA), CFTR function was measured using the forskolin-induced swelling assay and mRNA levels were quantified using RT-qPCR. RESULTS We were able to distinguish CFTR genotypes based on TLA data. Additionally, we observed heterogeneity within genotypes, which we were able to link to CFTR function for S1251N alleles. CONCLUSIONS Our results indicate that the paired analysis of CFTR intragenic variation and CFTR function can gain insights in the underlying CFTR defect for individuals where the disease phenotype does not match the CFTR mutations detected during diagnosis.
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Affiliation(s)
- J W Lefferts
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands
| | - V Boersma
- Cergentis BV., Utrecht, the Netherlands
| | - N D A Nieuwenhuijze
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands; Gastroenterology & Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - S W F Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands; Xilis BV, Utrecht, the Netherlands
| | - K Hajo
- Cergentis BV., Utrecht, the Netherlands
| | - N Sanchez Collantes
- Oncode Institute, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - C Vermeulen
- Oncode Institute, Utrecht, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - T Groeneweg
- Gastroenterology & Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - M C Hagemeijer
- Current affiliation: Center for Lysosomal and Metabolic Diseases, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - H R de Jonge
- Gastroenterology & Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - C K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - J M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Regenerative Medicine Center, Center for Living Technologies, University Medical Center Utrecht, Utrecht, the Netherlands; Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, the Netherlands.
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Feitsma H, Yilmaz M, Swennenhuis J, Rakszewska A, Hajo K, Splinter E, Simonis M, Van Min M, Van Wezel T. Targeted proximity ligation assays combined with sequencing for robust detection of translocations in FFPE samples. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz413.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ferrero S, Genuardi E, Klous P, Drandi D, Mantoan B, Monitillo L, Barbero D, Yilmaz M, Cattellino F, Vasta M, Cavallo F, Cortelazzo S, Vitolo U, Luminari S, Federico M, Boccadoro M, Splinter E, Ladetto M. NOVEL MOLECULAR MARKERS FOR MINIMAL RESIDUAL DISEASE (MRD) MONITORING IN MANTLE CELL AND FOLLICULAR LYMPHOMA: THE TARGETED LOCUS AMPLIFICATION (TLA) NGS STRATEGY. Hematol Oncol 2017. [DOI: 10.1002/hon.2438_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- S. Ferrero
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - E. Genuardi
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - P. Klous
- B.V., Cergentis B.V.; Utrecht Netherlands
| | - D. Drandi
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - B. Mantoan
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - L. Monitillo
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - D. Barbero
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - M. Yilmaz
- B.V., Cergentis B.V.; Utrecht Netherlands
| | - F. Cattellino
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - M. Vasta
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - F. Cavallo
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | - S. Cortelazzo
- Oncology Unit; Humanitas/Gavazzeni Clinic; Bergamo Italy
| | - U. Vitolo
- Department of Oncology, Division of Hematology; AOU Città della Salute e della Scienza di Torino; Torino Italy
| | - S. Luminari
- Clinics and Public Health, “Arcispedale S.Maria Nuova”; University of Modena e Reggio Emilia, Hematology Division, Department of Diagnostic Medicine; Reggio Emilia Italy
| | - M. Federico
- Department of Diagnostic, Clinical and Public Health Medicine; University of Modena and Reggio Emilia; Modena Italy
| | - M. Boccadoro
- Department of Molecular Biotechnology and Health Sciences; University of Torino; Torino Italy
| | | | - M. Ladetto
- Division of Hematology; Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo; Alessandria Italy
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