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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] [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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2
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Cuyx S, Ramalho SS, Callebaut I, Cuppens H, Kmit A, Arnauts K, Ferrante M, Verfaillie C, Ensinck M, Carlon MS, Boon M, Proesmans M, Dupont L, De Boeck K, Farinha CM, Vermeulen F, Ramalho AS. Severity of the S1251N allele in cystic fibrosis is affected by the presence of the F508C variant in cis. J Cyst Fibros 2022; 21:644-651. [PMID: 35690578 DOI: 10.1016/j.jcf.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/25/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND In cystic fibrosis (CF), genotype-phenotype correlation is complicated by the large number of CFTR variants, the influence of modifier genes, environmental effects, and the existence of complex alleles. We document the importance of complex alleles, in particular the F508C variant present in cis with the S1251N disease-causing variant, by detailed analysis of a patient with CF, with the [S1251N;F508]/G542X genotype and a very mild phenotype, contrasting it to that of four subjects with the [S1251N;F508C]/F508del genotype and classical CF presentation. METHODS Genetic differences were identified by Sanger sequencing and CFTR function was quantified using rectal organoids in rectal organoid morphology analysis (ROMA) and forskolin-induced swelling (FIS) assays. CFTR variants were further characterised in CF bronchial epithelial (CFBE) cell lines. The impact of involved amino acid changes in the CFTR 3D protein structure was evaluated. RESULTS Organoids of the patient [S1251N;F508] with mild CF phenotype confirmed the CF diagnosis but showed higher residual CFTR function compared to the four others [S1251N;F508C]. CFBE cell lines showed a decrease in [S1251N;F508C]-CFTR function but not in processing when compared to [S1251N;F508]-CFTR. Analysis of the 3D CFTR structure suggested an additive deleterious effect of the combined presence of S1251N and F508C with respect to NBD1-2 dimerisation. CONCLUSIONS In vitro and in silico data show that the presence of F508C in cis with S1251N decreases CFTR function without affecting processing. Complex CFTR alleles play a role in clinical phenotype and their identification is relevant in the context of personalised medicine for each patient with CF.
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Affiliation(s)
- Senne Cuyx
- KU Leuven, Department of Development and Regeneration, Woman and Child Unit, CF research lab, B-3000 Leuven, Belgium; University Hospital Leuven, Department of Pediatrics, Pediatric Pulmonology, B-3000 Leuven, Belgium
| | - Sofia S Ramalho
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, F-75005 Paris, France
| | | | - Arthur Kmit
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Kaline Arnauts
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium; KU Leuven, Department of Development and Regeneration, Stem Cell Institute Leuven (SCIL), B-3000 Leuven, Belgium
| | - Marc Ferrante
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium; KU Leuven, Department of Gastroenterology and Hepatology, University Hospital Leuven, B-3000 Leuven, Belgium
| | - Catherine Verfaillie
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute Leuven (SCIL), B-3000 Leuven, Belgium
| | - Marjolein Ensinck
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium; KU Leuven, Department of Chronic Diseases, Metabolism and Ageing; BREATHE, B-3000 Leuven, Belgium
| | - Marianne S Carlon
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium; KU Leuven, Department of Chronic Diseases, Metabolism and Ageing; BREATHE, B-3000 Leuven, Belgium
| | - Mieke Boon
- KU Leuven, Department of Development and Regeneration, Woman and Child Unit, CF research lab, B-3000 Leuven, Belgium; University Hospital Leuven, Department of Pediatrics, Pediatric Pulmonology, B-3000 Leuven, Belgium
| | - Marijke Proesmans
- KU Leuven, Department of Development and Regeneration, Woman and Child Unit, CF research lab, B-3000 Leuven, Belgium; University Hospital Leuven, Department of Pediatrics, Pediatric Pulmonology, B-3000 Leuven, Belgium
| | - Lieven Dupont
- KU Leuven, Department of Chronic Diseases, Metabolism and Ageing; BREATHE, B-3000 Leuven, Belgium; University Hospital Leuven, Department of Respiratory Diseases, B-3000 Leuven, Belgium
| | - Kris De Boeck
- KU Leuven, Department of Development and Regeneration, Woman and Child Unit, CF research lab, B-3000 Leuven, Belgium; University Hospital Leuven, Department of Pediatrics, Pediatric Pulmonology, B-3000 Leuven, Belgium
| | - Carlos M Farinha
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - François Vermeulen
- KU Leuven, Department of Development and Regeneration, Woman and Child Unit, CF research lab, B-3000 Leuven, Belgium; University Hospital Leuven, Department of Pediatrics, Pediatric Pulmonology, B-3000 Leuven, Belgium
| | - Anabela S Ramalho
- KU Leuven, Department of Development and Regeneration, Woman and Child Unit, CF research lab, B-3000 Leuven, Belgium
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Molina Romero M, Yoldi Chaure A, Gañán Parra M, Navas Bastida P, del Pico Sánchez JL, Vaquero Argüelles Á, de la Fuente Vaquero P, Ramírez López JP, Castilla Alcalá JA. Probability of high-risk genetic matching with oocyte and semen donors: complete gene analysis or genotyping test? J Assist Reprod Genet 2022; 39:341-355. [PMID: 35091964 PMCID: PMC8956772 DOI: 10.1007/s10815-021-02381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To estimate the probability of high-risk genetic matching when assisted reproductive techniques (ART) are applied with double gamete donation, following an NGS carrier test based on a complete study of the genes concerned. We then determine the results that would have been obtained if the genotyping tests most widely used in Spanish gamete banks had been applied. METHODS In this descriptive observational study, 1818 gamete donors were characterised by NGS. The pathogenic variants detected were analysed to estimate the probability of high-risk genetic matching and to determine the results that would have been obtained if the three most commonly used genotyping tests in ART had been applied. RESULTS The probability of high-risk genetic matching with gamete donation, screened by NGS and complete gene analysis, was 5.5%, versus the 0.6-2.7% that would have been obtained with the genotyping test. A total of 1741 variants were detected, including 607 different variants, of which only 22.6% would have been detected by all three genotyping tests considered and 44.7% of which would not have been detected by any of these tests. CONCLUSION Our study highlights the considerable heterogeneity of the genotyping tests, which present significant differences in their ability to detect pathogenic variants. The complete study of the genes by NGS considerably reduces reproductive risks when genetic matching is performed with gamete donors. Accordingly, we recommend that carrier screening in gamete donors be carried out using NGS and a complete study with nontargeted analysis of the variants of the screened genes.
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Affiliation(s)
- Marta Molina Romero
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain
| | | | | | | | | | | | | | | | - José Antonio Castilla Alcalá
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain ,U. Reproducción, UGC Obstetricia y Ginecología, HU Virgen de Las Nieves, Granada, Spain ,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
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Kellermann G, Anastasiadis AG, Dräger DL, Prall F, Hakenberg OW. Urinary Retention Due to Severe Pseudocystic Mucoid Degeneration of the Prostatic Matrix: A Rare Urologic Manifestation of Cystic Fibrosis. Urol Int 2015; 95:486-8. [PMID: 25721099 DOI: 10.1159/000368911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 10/06/2014] [Indexed: 11/19/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disease, which is characterized by the production of thick mucus in exocrine glands. The main cause for morbidity and mortality in CF patients is respiratory failure. The gastrointestinal system is also commonly affected. Urologic manifestations of CF include infertility and azoospermia, nephrolithiasis, and stress urinary incontinence. In this report, we describe a 33-year-old male, who presented with recurrent urinary retention due to prostatic enlargement despite his young age. After transurethral resection, the voiding problems resolved. Histopathological examination, however, revealed a severe pseudocystic mucoid degeneration of the prostatic matrix as a cause of his subvesical obstruction. Although these structural changes are most probably due to his underlying disease, detailed histologic features have not been described in the literature.
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Affiliation(s)
- Gesa Kellermann
- Helios Clinic Berlin-Buch, University of Rostock, Rostock, Germany
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