1
|
Fainardi V, Cresta F, Sorio C, Melotti P, Pesce E, Deolmi M, Longo F, Karina K, Esposito S, Pisi G. Elexacaftor/tezacaftor/ivacaftor in people with cystic fibrosis and rare mutations. Pediatr Pulmonol 2024. [PMID: 39212240 DOI: 10.1002/ppul.27211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/16/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION The triple combination of elexacaftor/tezacaftor/ivacaftor (ETI) has dramatically improved the outcome of people with Cystic Fibrosis (pwCF) with at least one F508del mutation. However, carriers of rare cystic fibrosis transmembrane conductance regulator (CFTR) variants are not candidates for this innovative treatment. METHODS In this observational study, we report the results of the compassionate use of ETI in 10 pwCF carriers of rare mutations after 2 months of treatment. Rectal organoids and short-term cultures of nasal epithelium obtained from rectal suction biopsies and nasal brushing were obtained from four subjects. RESULTS After 2 months of ETI, all patients (4 males, mean age 30.1 ± 13.3 years) showed a significant increase of FEV1% predicted values [+8.0 (3.5-12.7) %, p < 0.010], body mass index [+0.85 (0-1.22) kg/m2, p < 0.020] and cystic fibrosis questionnaire-revised [+19.5 (6.3-29.2) points, p < 0.009]. A significant decrease of sweat chloride concentration [-11.2 (-1.7 to -34.0) mmol/L, p < 0.020] and exacerbations [-1.5 (-2 to -1), p < 0.008] was also recorded. Overall, 7 out of 10 participants were considered full responders. All patients reported cough disappearance (n = 3) or reduction (n = 7). Long-term oxygen was discontinued in two out of three patients and one also stopped noninvasive ventilation and was removed from the lung transplantation waiting list. CONCLUSIONS Despite the limited number of cases, our results support the use of CFTR modulators in patients with rare CFTR variants that are not currently approved for ETI in Europe.
Collapse
Affiliation(s)
- Valentina Fainardi
- Department of Medicine and Surgery, Cystic Fibrosis Unit, Pediatric Clinic, Parma, Italy
| | - Federico Cresta
- UOSD Centro Fibrosi Cistica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Claudio Sorio
- Cystic Fibrosis Laboratory D. Lissandrini, Department of Medicine, Division of General Pathology, University of Verona, Verona, Italy
| | - Paola Melotti
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Emanuela Pesce
- IRCCS Istituto Giannina Gaslini, UOC Genetica Medica, Genova, Italy
| | - Michela Deolmi
- Cystic Fibrosis Unit, Pediatric Clinics, University Hospital of Parma, Parma, Italy
| | - Francesco Longo
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, Parma, Italy
| | - Kleinfelder Karina
- Cystic Fibrosis Laboratory D. Lissandrini, Department of Medicine, Division of General Pathology, University of Verona, Verona, Italy
| | - Susanna Esposito
- Department of Medicine and Surgery, Cystic Fibrosis Unit, Pediatric Clinic, Parma, Italy
| | - Giovanna Pisi
- Cystic Fibrosis Unit, Pediatric Clinics, University Hospital of Parma, Parma, Italy
| |
Collapse
|
2
|
Cuyx S, Ramalho AS, Fieuws S, Corthout N, Proesmans M, Boon M, Arnauts K, Carlon MS, Munck S, Dupont L, De Boeck K, Vermeulen F. Rectal organoid morphology analysis (ROMA) as a novel physiological assay for diagnostic classification in cystic fibrosis. Thorax 2024; 79:834-841. [PMID: 39004507 DOI: 10.1136/thorax-2023-220964] [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: 09/19/2023] [Accepted: 04/14/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND Diagnosing cystic fibrosis (CF) is not always straightforward, in particular when sweat chloride concentration (SCC) is intermediate and <2 CF-causing CFTR variants are identified. The physiological CFTR assays proposed in the guidelines, nasal potential difference and intestinal current measurement, are not readily available nor feasible at all ages. Rectal organoid morphology analysis (ROMA) was previously shown to discriminate between organoids from subjects with and without CF based on a distinct phenotypical difference: compared with non-CF organoids, CF organoids have an irregular shape and lack a visible lumen. The current study serves to further explore the role of ROMA when a CF diagnosis is inconclusive. METHODS Organoid morphology was analysed using the previously established ROMA protocol. Two indices were calculated: the circularity index to quantify the roundness of organoids and the intensity ratio as a measure of the presence of a central lumen. RESULTS Rectal organoids from 116 subjects were cultured and analysed together with the 189 subjects from the previous study. ROMA almost completely discriminated between CF and non-CF. ROMA indices correlated with SCC, pancreatic status and genetics, demonstrating convergent validity. For cases with an inconclusive diagnosis according to current guidelines, ROMA provided additional diagnostic information, with a diagnostic ROMA classification for 18 of 24 (75%). DISCUSSION ROMA provides additional information to support a CF diagnosis when SCC and genetics are insufficient for diagnostic classification. ROMA is standardised and can be centralised, allowing future inclusion in the diagnostic work-up as first-choice physiological assay in case of an unclear diagnosis.
Collapse
Affiliation(s)
- Senne Cuyx
- Department of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospitals Leuven, Leuven, Belgium
| | - Anabela Santo Ramalho
- Department of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium
| | - Steffen Fieuws
- Interuniversity Center for Biostatistics and Statistical Bioinformatics, KU Leuven, Leuven, Belgium
- Interuniversity Center for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium
| | - Nikky Corthout
- VIB Bio Imaging Core and VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
- Department of Neuroscience, KU Leuven, Leuven, Belgium
| | - Marijke Proesmans
- Department of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospitals Leuven, Leuven, Belgium
| | - Mieke Boon
- Department of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospitals Leuven, Leuven, Belgium
| | - Kaline Arnauts
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Marianne S Carlon
- Center for Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Sebastian Munck
- VIB Bio Imaging Core and VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
- Department of Neuroscience, KU Leuven, Leuven, Belgium
| | - Lieven Dupont
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Kris De Boeck
- Department of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospitals Leuven, Leuven, Belgium
| | - François Vermeulen
- Department of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospitals Leuven, Leuven, Belgium
| |
Collapse
|
3
|
Ramananda Y, Naren AP, Arora K. Functional Consequences of CFTR Interactions in Cystic Fibrosis. Int J Mol Sci 2024; 25:3384. [PMID: 38542363 PMCID: PMC10970640 DOI: 10.3390/ijms25063384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 09/01/2024] Open
Abstract
Cystic fibrosis (CF) is a fatal autosomal recessive disorder caused by the loss of function mutations within a single gene for the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). CFTR is a chloride channel that regulates ion and fluid transport across various epithelia. The discovery of CFTR as the CF gene and its cloning in 1989, coupled with extensive research that went into the understanding of the underlying biological mechanisms of CF, have led to the development of revolutionary therapies in CF that we see today. The highly effective modulator therapies have increased the survival rates of CF patients and shifted the epidemiological landscape and disease prognosis. However, the differential effect of modulators among CF patients and the presence of non-responders and ineligible patients underscore the need to develop specialized and customized therapies for a significant number of patients. Recent advances in the understanding of the CFTR structure, its expression, and defined cellular compositions will aid in developing more precise therapies. As the lifespan of CF patients continues to increase, it is becoming critical to clinically address the extra-pulmonary manifestations of CF disease to improve the quality of life of the patients. In-depth analysis of the molecular signature of different CF organs at the transcriptional and post-transcriptional levels is rapidly advancing and will help address the etiological causes and variability of CF among patients and develop precision medicine in CF. In this review, we will provide an overview of CF disease, leading to the discovery and characterization of CFTR and the development of CFTR modulators. The later sections of the review will delve into the key findings derived from single-molecule and single-cell-level analyses of CFTR, followed by an exploration of disease-relevant protein complexes of CFTR that may ultimately define the etiological course of CF disease.
Collapse
Affiliation(s)
- Yashaswini Ramananda
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anjaparavanda P. Naren
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kavisha Arora
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| |
Collapse
|
4
|
Walker AJ, Graham C, Greenwood M, Woodall M, Maeshima R, O’Hara-Wright M, Sanz DJ, Guerrini I, Aldossary AM, O’Callaghan C, Baines DL, Harrison PT, Hart SL. Molecular and functional correction of a deep intronic splicing mutation in CFTR by CRISPR-Cas9 gene editing. Mol Ther Methods Clin Dev 2023; 31:101140. [PMID: 38027060 PMCID: PMC10661860 DOI: 10.1016/j.omtm.2023.101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CFTR gene. The 10th most common mutation, c.3178-2477C>T (3849+10kb C>T), involves a cryptic, intronic splice site. This mutation was corrected in CF primary cells homozygous for this mutation by delivering pairs of guide RNAs (gRNAs) with Cas9 protein in ribonucleoprotein (RNP) complexes that introduce double-strand breaks to flanking sites to excise the 3849+10kb C>T mutation, followed by DNA repair by the non-homologous end-joining pathway, which functions in all cells of the airway epithelium. RNP complexes were delivered to CF basal epithelial cell by a non-viral, receptor-targeted nanocomplex comprising a formulation of targeting peptides and lipids. Canonical CFTR mRNA splicing was, thus, restored leading to the restoration of CFTR protein expression with concomitant restoration of electrophysiological function in airway epithelial air-liquid interface cultures. Off-target editing was not detected by Sanger sequencing of in silico-selected genomic sites with the highest sequence similarities to the gRNAs, although more sensitive unbiased whole genome sequencing methods would be required for possible translational developments. This approach could potentially be used to correct aberrant splicing signals in several other CF mutations and other genetic disorders where deep-intronic mutations are pathogenic.
Collapse
Affiliation(s)
- Amy J. Walker
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Carina Graham
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Miriam Greenwood
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Maximillian Woodall
- Institute for Infection and Immunity, St. George’s, University of London, London, UK
| | - Ruhina Maeshima
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Michelle O’Hara-Wright
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - David J. Sanz
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Ileana Guerrini
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Ahmad M. Aldossary
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Christopher O’Callaghan
- Infection, Immunity & Inflammation Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Deborah L. Baines
- Institute for Infection and Immunity, St. George’s, University of London, London, UK
| | - Patrick T. Harrison
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Stephen L. Hart
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| |
Collapse
|
5
|
Zlotogora J, Harel T, Meiner V. Explanations for the discrepancy between variant frequency and homozygous disease occurrence: Lessons from Ashkenazi Jewish data. Eur J Med Genet 2023; 66:104765. [PMID: 37028505 DOI: 10.1016/j.ejmg.2023.104765] [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: 09/05/2022] [Revised: 12/28/2022] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Ample data on recessive disorders among Ashkenazi Jews has been gathered and published through the years. The opportunity to integrate molecular records analyzed in actual affected individuals with data derived from population-documented frequencies enables to compare these figures. We reviewed assumed pathogenic variants reported among patients in the Israeli medical genetic database (IMGD) with a carrier frequency of 1% or more among Ashkenazi Jews in gnomAD. Among the 60 assumed pathogenic variants recorded in IMGD, 15 (25%) had either a disease incidence considerably lower than expected by the calculated carrier frequency (12 variants), or the variant was not characterized in Ashkenazi Jewish patients (three variants). Possible explanations for the rarity or absence of affected individuals despite high carrier frequency include embryonic lethality, clinical variability, and incomplete and age-related penetrance, in addition to the existence of additional assumed pathogenic variants on the founder haplotype, hypomorphic variants or digenic inheritance. The discrepancy in actual versus expected number of patients calls for caution upon designing and choosing targeted genes and recessive mutations for carrier screening.
Collapse
Affiliation(s)
- Joël Zlotogora
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel.
| | - Tamar Harel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel; Department of Genetics, Hadassah Medical Organization, Jerusalem, 9112001, Israel
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel; Department of Genetics, Hadassah Medical Organization, Jerusalem, 9112001, Israel
| |
Collapse
|
6
|
Kim YJ, Krainer AR. Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Mol Cells 2023; 46:10-20. [PMID: 36697233 PMCID: PMC9880599 DOI: 10.14348/molcells.2023.2172] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 01/27/2023] Open
Abstract
Antisense oligonucleotide (ASO) technology has become an attractive therapeutic modality for various diseases, including Mendelian disorders. ASOs can modulate the expression of a target gene by promoting mRNA degradation or changing pre-mRNA splicing, nonsense-mediated mRNA decay, or translation. Advances in medicinal chemistry and a deeper understanding of post-transcriptional mechanisms have led to the approval of several ASO drugs for diseases that had long lacked therapeutic options. For instance, an ASO drug called nusinersen became the first approved drug for spinal muscular atrophy, improving survival and the overall disease course. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). Although Trikafta and other CFTR-modulation therapies benefit most CF patients, there is a significant unmet therapeutic need for a subset of CF patients. In this review, we introduce ASO therapies and their mechanisms of action, describe the opportunities and challenges for ASO therapeutics for CF, and discuss the current state and prospects of ASO therapies for CF.
Collapse
Affiliation(s)
- Young Jin Kim
- Department of Pediatrics, Mount Sinai Hospital, New York, NY 10029, USA
| | | |
Collapse
|
7
|
Egan ME. Non-Modulator Therapies: Developing a Therapy for Every Cystic Fibrosis Patient. Clin Chest Med 2022; 43:717-725. [PMID: 36344076 DOI: 10.1016/j.ccm.2022.06.011] [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] [Indexed: 11/06/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy brings hope to most patients with cystic fibrosis (CF), but not all. For approximately 12% of CF patients with premature termination codon mutations, large deletions, insertions, and frameshifts, the CFTR modulator therapy is not effective. Many believe that genetic-based therapies such as RNA therapies, DNA therapies, and gene editing technologies will be needed to treat mutations that are not responsive to modulator therapy. Delivery of these therapeutic agents to affected cells is the major challenge that will need to be overcome if we are to harness the power of these emerging therapies for the treatment of CF.
Collapse
Affiliation(s)
- Marie E Egan
- Division of Pulmonary Allergy Immunology Sleep Medicine, Department of Pediatrics, Pediatric Pulmonary Allergy Immunology and Sleep Medicine, Yale Cystic Fibrosis Center, School of Medicine, Yale University, 333 Cedar Street, PO Box 208064, New Haven, CT 06520, USA.
| |
Collapse
|
8
|
Sermet-Gaudelus I, Girodon E, Vermeulen F, Solomon G, Melotti P, Graeber S, Bronsveld I, Rowe S, Wilschanski M, Tümmler B, Cutting G, Gonska T. ECFS standards of care on CFTR-related disorders: Diagnostic criteria of CFTR dysfunction. J Cyst Fibros 2022; 21:922-936. [DOI: 10.1016/j.jcf.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
|
9
|
Feng J, Zhang Y, Yang X, Zhang Y. Heterogeneous spectrum of CFTR gene mutations in Chinese patients with CAVD and the dilemma of genetic blocking strategy. Reproduction 2022; 164:R47-R56. [PMID: 35913788 DOI: 10.1530/rep-21-0315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 06/17/2022] [Indexed: 01/18/2023]
Abstract
In brief The genetic heterogeneity of CFTR gene mutations in Chinese patients with congenital absence of the vas deferens (CAVD) differs from the hotspot mutation pattern in Caucasians. This paper reviews and suggests a more suitable screening strategy for the Chinese considering the dilemma of CFTR genetic blocking. Abstract Congenital absence of the vas deferens (CAVD) is a major cause of obstructive azoospermia and male infertility, with CFTR gene mutation as the main pathogenesis. Other genes such as ADGRG2, SLC9A3, and PANK2 have been discovered and proven to be associated with CAVD in recent studies. Multiple CFTR hotspot mutations have been found in Caucasians in several foreign countries, and relevant genetic counseling and preimplantation genetic diagnosis (PGD) have been conducted for decades. However, when we examined research on Chinese CAVD, we discovered that CFTR mutations show heterogeneity in the Chinese Han population, and there is currently no well-established screening strategy. Therefore, we have reviewed the literature, combining domestic and international research as well as our own, aiming to review research progress on the CFTR gene in China and discuss the appropriate scope for CFTR gene detection, the detection efficiency of other CAVD-related genes, and the screening strategy applicable to the Chinese Han population. This study provides more valuable information for genetic counseling and a theoretical basis for PGD and treatment for couples with CAVD when seeking reproductive assistance.
Collapse
Affiliation(s)
- Jiarong Feng
- 1Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yanan Zhang
- 1Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaojian Yang
- 1Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yan Zhang
- 1Department of Infertility and Sexual Medicine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| |
Collapse
|
10
|
Kreda SM. Oligonucleotide-based therapies for cystic fibrosis. Curr Opin Pharmacol 2022; 66:102271. [PMID: 35988291 DOI: 10.1016/j.coph.2022.102271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/03/2022]
Abstract
In the clinically successful era of CFTR modulators and Theratyping, 10-20% of individuals with cystic fibrosis (CF) may develop disease due to CFTR mutations that remain undruggable. These individuals produce low levels of CFTR mRNA and/or not enough protein to be rescued with modulator drugs. Alternative therapeutic approaches to correct the CFTR defect at the mRNA level using nucleic acid technologies are currently feasible; e.g., oligonucleotides platforms, which are being rapidly developed to correct genetic disorders. Drug-like properties, great specificity, and predictable off-target effects by design make oligonucleotides a valuable approach with fewer clinical and ethical challenges than genomic editing strategies. Together with personalized and precision medicine approaches, oligonucleotides are ideal therapeutics to target CF-causing mutations that affect only a few individuals resilient to modulator therapies.
Collapse
Affiliation(s)
- Silvia M Kreda
- Marsico Lung Institute / Cystic Fibrosis Center, University of North Carolina at Chapel Hill, 6009 Thurston Bowles Bldg, Chapel Hill, NC, 27599-7248, USA; Department of Medicine, University of North Carolina at Chapel Hill, NC, 27599-7248, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, 27599-7248, USA.
| |
Collapse
|
11
|
Ensinck MM, Carlon MS. One Size Does Not Fit All: The Past, Present and Future of Cystic Fibrosis Causal Therapies. Cells 2022; 11:cells11121868. [PMID: 35740997 PMCID: PMC9220995 DOI: 10.3390/cells11121868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
Cystic fibrosis (CF) is the most common monogenic disorder, caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Over the last 30 years, tremendous progress has been made in understanding the molecular basis of CF and the development of treatments that target the underlying defects in CF. Currently, a highly effective CFTR modulator treatment (Kalydeco™/Trikafta™) is available for 90% of people with CF. In this review, we will give an extensive overview of past and ongoing efforts in the development of therapies targeting the molecular defects in CF. We will discuss strategies targeting the CFTR protein (i.e., CFTR modulators such as correctors and potentiators), its cellular environment (i.e., proteostasis modulation, stabilization at the plasma membrane), the CFTR mRNA (i.e., amplifiers, nonsense mediated mRNA decay suppressors, translational readthrough inducing drugs) or the CFTR gene (gene therapies). Finally, we will focus on how these efforts can be applied to the 15% of people with CF for whom no causal therapy is available yet.
Collapse
Affiliation(s)
- Marjolein M. Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Flanders, Belgium
- Correspondence:
| |
Collapse
|
12
|
Splicing mutations in the CFTR gene as therapeutic targets. Gene Ther 2022; 29:399-406. [PMID: 35650428 PMCID: PMC9385490 DOI: 10.1038/s41434-022-00347-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
The marketing approval, about ten years ago, of the first disease modulator for patients with cystic fibrosis harboring specific CFTR genotypes (~5% of all patients) brought new hope for their treatment. To date, several therapeutic strategies have been approved and the number of CFTR mutations targeted by therapeutic agents is increasing. Although these drugs do not reverse the existing disease, they help to increase the median life expectancy. However, on the basis of their CFTR genotype, ~10% of patients presently do not qualify for any of the currently available CFTR modulator therapies, particularly patients with splicing mutations (~12% of the reported CFTR mutations). Efforts are currently made to develop therapeutic agents that target disease-causing CFTR variants that affect splicing. This highlights the need to fully identify them by scanning non-coding regions and systematically determine their functional consequences. In this review, we present some examples of CFTR alterations that affect splicing events and the different therapeutic options that are currently developed and tested for splice switching.
Collapse
|
13
|
Abstract
Rationale: Ivacaftor’s clinical effects in the residual function mutations 3849 + 10kb C→T and D1152H warrant further characterization. Objectives: To evaluate ivacaftor’s effect in people with cystic fibrosis aged ≥6 years with 3849 + 10kb C→T or D1152H residual function mutations and to explore the correlation between ivacaftor-induced organoid-based cystic fibrosis transmembrane conductance regulator function measurements and clinical response to ivacaftor. Methods: Participants were randomized (1:1) in this placebo-controlled crossover study; each treatment sequence included two 8-week treatments with an 8-week washout period. The primary endpoint was absolute change in lung clearance index2.5 from baseline through Week 8. Additional endpoints included lung function, patient-reported outcomes, and in vitro intestinal organoid–based measurements of ivacaftor-induced cystic fibrosis transmembrane conductance regulator function. Results: Of 38 participants, 37 completed the study. The primary endpoint was met; the Bayesian posterior probability of improvement in lung clearance index2.5 with ivacaftor versus placebo was >99%. Additional endpoints improved with ivacaftor. Safety findings were consistent with ivacaftor’s known safety profile. Dose-dependent swelling was observed in 23 of 25 viable organoid cultures with ivacaftor treatment. Correlations between ivacaftor-induced organoid swelling and clinical endpoints were negligible to low. Conclusions: In people with cystic fibrosis aged ≥6 years with a 3849 + 10kb C→T or D1152H mutation, ivacaftor treatment improved clinical endpoints compared with placebo; however, there was no correlation between organoid swelling and change in clinical endpoints. The organoid assay may assist in identification of ivacaftor-responsive mutations but in this study did not predict magnitude of clinical benefit for individual people with cystic fibrosis with these two mutations. Clinical trial registered with ClinicalTrials.gov (NCT03068312).
Collapse
|
14
|
Antisense oligonucleotide-based drug development for Cystic Fibrosis patients carrying the 3849+10 kb C-to-T splicing mutation. J Cyst Fibros 2021; 20:865-875. [PMID: 34226157 PMCID: PMC8464507 DOI: 10.1016/j.jcf.2021.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/24/2023]
Abstract
Background: Antisense oligonucleotide (ASO)-based drugs for splicing modulation were recently approved for various genetic diseases with unmet need. Here we aimed to develop an ASO-based splicing modulation therapy for Cystic Fibrosis (CF) patients carrying the 3849 + 10 kb C-to-T splicing mutation in the CFTR gene. Methods: We have screened, in FRT cells expressing the 3849 + 10 kb C-to-T splicing mutation, ~30 2ʹ-O-Methyl-modified phosphorothioate ASOs, targeted to prevent the recognition and inclusion of a cryptic exon generated due to the mutation. The effect of highly potent ASO candidates on the splicing pattern, protein maturation and CFTR function was further analyzed in well differentiated primary human nasal and bronchial epithelial cells, derived from patients carrying at least one 3849 + 10 kb C-to-T allele. Results: A highly potent lead ASO, efficiently delivered by free uptake, was able to significantly increase the level of correctly spliced mRNA and completely restore the CFTR function to wild type levels in cells from a homozygote patient. This ASO led to CFTR function with an average of 43% of wild type levels in cells from various heterozygote patients. Optimized efficiency of the lead ASO was further obtained with 2ʹ-Methoxy Ethyl modification (2ʹMOE). Conclusion: The highly efficient splicing modulation and functional correction, achieved by free uptake of the selected lead ASO in various patients, demonstrate the ASO therapeutic potential benefit for CF patients carrying splicing mutations and is aimed to serve as the basis for our current clinical development.
Collapse
|
15
|
Fischer S, Stanke F, Tümmler B. VJ Segment Usage of TCR-Beta Repertoire in Monozygotic Cystic Fibrosis Twins. Front Immunol 2021; 12:599133. [PMID: 33708199 PMCID: PMC7940196 DOI: 10.3389/fimmu.2021.599133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/28/2021] [Indexed: 11/26/2022] Open
Abstract
Sixteen monozygotic cystic fibrosis (CF) twin pairs of whom 14 pairs were homozygous for the most common p.Phe508del CFTR mutation were selected from the European Cystic Fibrosis Twin and Sibling Study Cohort. The monozygotic twins were examined in their T cell receptor (TCR) repertoire in peripheral blood by amplicon sequencing of the CDR3 variable region of the ß-chain. The recruitment of TCR J and V genes for recombination and selection in the thymus showed a strong genetic influence in the CF twin cohort as indicated by the shortest Jensen-Shannon distance to the twin individual. Exceptions were the clinically most discordant and/or most severely affected twin pairs where clonal expansion probably caused by recurrent pulmonary infections overshadowed the impact of the identical genomic blueprint. In general the Simpson clonality was low indicating that the population of TCRß clonotypes of the CF twins was dominated by the naïve T-cell repertoire. Intrapair sharing of clonotypes was significantly more frequent among monozygotic CF twins than among pairs of unrelated CF patients. Complete nucleotide sequence identity was observed in about 0.11% of CDR3 sequences which partially should represent persisting fetal clones derived from the same progenitor T cells. Complete amino acid sequence identity was noted in 0.59% of clonotypes. Of the nearly 40,000 frequent amino acid clonotypes shared by at least two twin siblings 99.8% were already known within the immuneACCESS database and only 73 had yet not been detected indicating that the CDR3ß repertoire of CF children and adolescents does not carry a disease-specific signature but rather shares public clones with that of the non-CF community. Clonotypes shared within twin pairs and between unrelated CF siblings were highly abundant among healthy non-CF people, less represented in individuals with infectious disease and uncommon in patients with cancer. This subset of shared CF clonotypes defines CDR3 amino acid sequences that are more common in health than in disease.
Collapse
Affiliation(s)
- Sebastian Fischer
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Frauke Stanke
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| |
Collapse
|
16
|
Egan ME. Emerging technologies for cystic fibrosis transmembrane conductance regulator restoration in all people with CF. Pediatr Pulmonol 2021; 56 Suppl 1:S32-S39. [PMID: 32681713 PMCID: PMC8114183 DOI: 10.1002/ppul.24965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022]
Abstract
Although effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has the potential to change the lives of many patients with cystic fibrosis (CF), it is unlikely that these drugs will be a game changing therapy for all. There are about 10% of patients with CF who don't produce a mutant protein tomodulate, potentiate, or optimize and for these patients such therapies are unlikely to be of significant benefit. There is a need to develop new therapeutic approaches that can work for this patient population and can advance CF therapies. These new therapies will be genetic-based therapies and each approach will result in functional CFTR protein inpreviously affected CF cells. In this review we will examine the potential of RNA therapies, gene transfer therapies, and gene editing therapies for the treatment of CF as well as the challenges that will need to be facedas we harness the power of these emerging therapies towards a one-time cure.
Collapse
Affiliation(s)
- Marie E Egan
- Division of Pulmonary Allergy Immunology Sleep Medicine, Department of Pediatrics, School of Medicine, Yale University, New Haven, Connecticut
| |
Collapse
|
17
|
Shibata S, Ajiro M, Hagiwara M. Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion. Cell Chem Biol 2020; 27:1472-1482.e6. [DOI: 10.1016/j.chembiol.2020.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/29/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
|
18
|
Michaels WE, Bridges RJ, Hastings ML. Antisense oligonucleotide-mediated correction of CFTR splicing improves chloride secretion in cystic fibrosis patient-derived bronchial epithelial cells. Nucleic Acids Res 2020; 48:7454-7467. [PMID: 32520327 PMCID: PMC7367209 DOI: 10.1093/nar/gkaa490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/22/2020] [Accepted: 06/05/2020] [Indexed: 12/27/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, encoding an anion channel that conducts chloride and bicarbonate across epithelial membranes. Mutations that disrupt pre-mRNA splicing occur in >15% of CF cases. One common CFTR splicing mutation is CFTR c.3718-2477C>T (3849+10 kb C>T), which creates a new 5′ splice site, resulting in splicing to a cryptic exon with a premature termination codon. Splice-switching antisense oligonucleotides (ASOs) have emerged as an effective therapeutic strategy to block aberrant splicing. We test an ASO targeting the CFTR c.3718-2477C>T mutation and show that it effectively blocks aberrant splicing in primary bronchial epithelial (hBE) cells from CF patients with the mutation. ASO treatment results in long-term improvement in CFTR activity in hBE cells, as demonstrated by a recovery of chloride secretion and apical membrane conductance. We also show that the ASO is more effective at recovering chloride secretion in our assay than ivacaftor, the potentiator treatment currently available to these patients. Our findings demonstrate the utility of ASOs in correcting CFTR expression and channel activity in a manner expected to be therapeutic in patients.
Collapse
Affiliation(s)
- Wren E Michaels
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Robert J Bridges
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Michelle L Hastings
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| |
Collapse
|
19
|
Wachs AS, Bohne J. Two sides of the same medal: Noncoding mutations reveal new pathological mechanisms and insights into the regulation of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1616. [PMID: 32633083 DOI: 10.1002/wrna.1616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022]
Abstract
Noncoding sequences constitute the major part of the human genome and also of pre-mRNAs. Single nucleotide variants in these regions are often overlooked, but may be responsible for much of the variation of phenotypes observed. Mutations in the noncoding part of pre-mRNAs often reveal new and meaningful insights into the regulation of cellular gene expression. Thus, the mechanistic analysis of the pathological mechanism of such mutations will both foster a deeper understanding of the disease and the underlying cellular pathways. Even synonymous mutations can cause diseases, since the primary mRNA sequence not only encodes amino acids, but also encrypts information on RNA-binding proteins and secondary structure. In fact, the RNA sequence directs assembly of a specific mRNP complex, which in turn dictates the fate of the mRNA or regulates its biogenesis. The accumulation of genomic sequence information is increasing at a rapid pace. However, much of the diversity uncovered may not explain the phenotype of a certain syndrome or disease. For this reason, we also emphasize the value of mechanistic studies on pathological mechanisms being complementary to genome-wide studies and bioinformatic approaches. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Amelie S Wachs
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, Hanover, Germany
| |
Collapse
|
20
|
Incomplete cryptic splicing by an intronic mutation of OCRL in patients with partial phenotypes of Lowe syndrome. J Hum Genet 2020; 65:831-839. [PMID: 32427950 DOI: 10.1038/s10038-020-0773-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 01/03/2023]
Abstract
Mutations of OCRL cause Lowe syndrome, which is characterised by congenital cataracts, infantile hypotonia with mental retardation, and renal tubular dysfunction and Dent-2 disease, which only affects the kidney. While few patients with an intermediate phenotype between these diseases have been reported, the mechanism underlying variability in the phenotype is unclear. We identified an intronic mutation, c.2257-5G>A, in intron 20 of OCRL in an older brother with atypical Lowe syndrome without eye involvement and a younger brother with renal phenotype alone. This mutation created a splice acceptor motif that was accompanied by a cryptic premature termination codon at the junction of exons 20 and 21. The mutation caused incomplete alternative splicing, which created a small amount of wild-type transcript and a relatively large amount of alternatively spliced transcript with a premature termination codon. In the patients' cells, the alternatively spliced transcript was degraded by nonsense-mediated decay and the wild-type transcript was significantly decreased, but not completely depleted. These findings imply that an intronic mutation creating an incomplete alternative splicing acceptor site results in a relatively low level of wild-type OCRL mRNA expression, leading to partial phenotypes of Lowe syndrome.
Collapse
|
21
|
Vojcek E, Keszthelyi TM, Jávorszky E, Balogh L, Tory K. EPG5
c.1007A > G mutation in a sibling pair with rapidly progressing Vici syndrome. Ann Hum Genet 2019; 84:80-86. [DOI: 10.1111/ahg.12337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/23/2019] [Accepted: 05/22/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Eszter Vojcek
- 1st Department of Pediatrics Semmelweis University Budapest Hungary
| | - Tália Magdolna Keszthelyi
- 1st Department of Pediatrics Semmelweis University Budapest Hungary
- MTA‐SE Lendulet Nephrogenetic Laboratory Budapest Hungary
| | - Eszter Jávorszky
- 1st Department of Pediatrics Semmelweis University Budapest Hungary
- MTA‐SE Lendulet Nephrogenetic Laboratory Budapest Hungary
| | - Lídia Balogh
- 1st Department of Pediatrics Semmelweis University Budapest Hungary
| | - Kálmán Tory
- 1st Department of Pediatrics Semmelweis University Budapest Hungary
- MTA‐SE Lendulet Nephrogenetic Laboratory Budapest Hungary
| |
Collapse
|
22
|
Bergougnoux A, Délétang K, Pommier A, Varilh J, Houriez F, Altieri JP, Koenig M, Férec C, Claustres M, Lalau G, Bienvenu T, Audrézet MP, Pagin A, Girodon E, Raynal C, Taulan-Cadars M. Functional characterization and phenotypic spectrum of three recurrent disease-causing deep intronic variants of the CFTR gene. J Cyst Fibros 2018; 18:468-475. [PMID: 30389601 DOI: 10.1016/j.jcf.2018.10.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND The CFTR genotype remains incomplete in 1% of Cystic Fibrosis (CF) cases, because only one or no disease-causing variants is detected after extended analysis. This fraction is probably higher in CFTR-Related Disorders (CFTR-RD). Deep-intronic CFTR variants are putative candidates to fill this gap. However, the recurrence, phenotypic spectrum and full molecular characterization of newly reported variants are unknown. METHODS Minigenes and analysis of CFTR transcripts in nasal epithelial cells were used to determine the impact on CFTR splicing of intronic variants that we previously identified by next generation sequencing of the whole CFTR locus. Phenotypic data were collected in 19 patients with CF and CFTR-RD, in whom one of the deep intronic variants has been detected. RESULTS Three deep-intronic variants promoted the inclusion of pseudo-exons (PE) in the CFTR transcript, hindering the synthesis of a functional protein. The c.2989-313A > T variant, detected in four patients with CF or CFTR-RD from three different families, led to the inclusion of a 118 bp PE. The c.3469-1304C > G variant promoted the inclusion of a 214 bp-PE and was identified in five patients with CF from four families. Haplotype analysis confirmed that this variant was associated with one CF chromosome of African origin. The most represented variant in our cohort was the c.3874-4522A > G, detected in 10 patients with various phenotypes, from male infertility to CF with pancreatic insufficiency. CONCLUSION These three deep intronic CFTR variants are associated with a large phenotypic spectrum, including typical CF. They should be included in CF diagnostic testing and carrier screening strategies.
Collapse
Affiliation(s)
- A Bergougnoux
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France; Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France.
| | - K Délétang
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - A Pommier
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - J Varilh
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - F Houriez
- AP-HP, HUPC, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France
| | - J P Altieri
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - M Koenig
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France; Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - C Férec
- Inserm, UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, France; Univ Brest, EFS, IBSAM, Brest, France; CHU de Brest, Laboratoire de Génétique Moléculaire, Brest, France
| | - M Claustres
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - G Lalau
- Service de Toxicologie et Génopathies, Institut de Biochimie et Biologie Moléculaire, Centre Hospitalier Régional Universitaire, Lille, France
| | - T Bienvenu
- AP-HP, HUPC, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France
| | - M P Audrézet
- CHU de Brest, Laboratoire de Génétique Moléculaire, Brest, France
| | - A Pagin
- Service de Toxicologie et Génopathies, Institut de Biochimie et Biologie Moléculaire, Centre Hospitalier Régional Universitaire, Lille, France
| | - E Girodon
- AP-HP, HUPC, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France
| | - C Raynal
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - M Taulan-Cadars
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| |
Collapse
|
23
|
Oren YS, Pranke IM, Kerem B, Sermet-Gaudelus I. The suppression of premature termination codons and the repair of splicing mutations in CFTR. Curr Opin Pharmacol 2017; 34:125-131. [PMID: 29128743 DOI: 10.1016/j.coph.2017.09.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022]
Abstract
Premature termination codons (PTC) originate from nucleotide substitution introducing an in-frame PTC. They induce truncated, usually non-functional, proteins, degradation of the PTC containing transcripts by the nonsense-mediated decay (NMD) pathway and abnormal exon skipping. Readthrough compounds facilitate near cognate amino-acyl-tRNA incorporation, leading potentially to restoration of a functional full-length protein. Splicing mutations can lead to aberrantly spliced transcripts by creating a cryptic splice site or destroying a normal site. Most mutations result in disruption of the open reading frame and activation of NMD. Antisense oligonucleotides are single stranded short synthetic RNA-like molecules chemically modified to improve their stability and ability to recognize their target RNAs and modify the splice site. This review focuses on recent developments in therapies aiming to improve the health of CF patients carrying nonsense or splicing mutations.
Collapse
Affiliation(s)
- Yifat S Oren
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel; SpliSense Therapeutics, Givat Ram Campus, Hebrew University, Jerusalem, Israel
| | - Iwona M Pranke
- INSERM U 1151, Institut Necker Enfants Malades, Paris, France; Université Paris Sorbonne, France
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel.
| | - Isabelle Sermet-Gaudelus
- INSERM U 1151, Institut Necker Enfants Malades, Paris, France; Unité de Pneumo-Allergologie Pédiatrique, Centre de Ressources et de Compétence de la Mucoviscidose, Hôpital Necker Enfants Malades, Paris, France; Université Paris Sorbonne, France.
| |
Collapse
|
24
|
Martorell L, Luce E, Vazquez JL, Richaud-Patin Y, Jimenez-Delgado S, Corrales I, Borras N, Casacuberta-Serra S, Weber A, Parra R, Altisent C, Follenzi A, Dubart-Kupperschmitt A, Raya A, Vidal F, Barquinero J. Advanced cell-based modeling of the royal disease: characterization of the mutated F9 mRNA. J Thromb Haemost 2017; 15:2188-2197. [PMID: 28834196 DOI: 10.1111/jth.13808] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Indexed: 11/28/2022]
Abstract
Essentials The Royal disease (RD) is a form of hemophilia B predicted to be caused by a splicing mutation. We generated an iPSC-based model of the disease allowing mechanistic studies at the RNA level. F9 mRNA analysis in iPSC-derived hepatocyte-like cells showed the predicted abnormal splicing. Mutated F9 mRNA level was very low but we also found traces of wild type transcripts. SUMMARY Background The royal disease is a form of hemophilia B (HB) that affected many descendants of Queen Victoria in the 19th and 20th centuries. It was found to be caused by the mutation F9 c.278-3A>G. Objective To generate a physiological cell model of the disease and to study F9 expression at the RNA level. Methods Using fibroblasts from skin biopsies of a previously identified hemophilic patient bearing the F9 c.278-3A>G mutation and his mother, we generated induced pluripotent stem cells (iPSCs). Both the patient's and mother's iPSCs were differentiated into hepatocyte-like cells (HLCs) and their F9 mRNA was analyzed using next-generation sequencing (NGS). Results and Conclusion We demonstrated the previously predicted aberrant splicing of the F9 transcript as a result of an intronic nucleotide substitution leading to a frameshift and the generation of a premature termination codon (PTC). The F9 mRNA level in the patient's HLCs was significantly reduced compared with that of his mother, suggesting that mutated transcripts undergo nonsense-mediated decay (NMD), a cellular mechanism that degrades PTC-containing mRNAs. We also detected small proportions of correctly spliced transcripts in the patient's HLCs, which, combined with genetic variability in splicing and NMD machineries, could partially explain some clinical variability among affected members of the European royal families who had lifespans above the average. This work allowed the demonstration of the pathologic consequences of an intronic mutation in the F9 gene and represents the first bona fide cellular model of HB allowing the study of rare mutations at the RNA level.
Collapse
Affiliation(s)
- L Martorell
- Gene and Cell Therapy Laboratory, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank (BST), Barcelona, Spain
- Molecular Diagnosis and Therapy Unit, VHIR-UAB, Barcelona, Spain
| | - E Luce
- INSERM Unité Mixte de Recherche (UMR_S) 1193, Villejuif, France
- Université Paris-Sud, Villejuif, France
- Département Hospitalo-Universitaire Hepatinov, Paul Brousse Hospital, Villejuif, France
| | - J L Vazquez
- Center of Regenerative Medicine in Barcelona (CMRB), Barcelona, Spain
| | - Y Richaud-Patin
- Center of Regenerative Medicine in Barcelona (CMRB), Barcelona, Spain
| | - S Jimenez-Delgado
- Center of Regenerative Medicine in Barcelona (CMRB), Barcelona, Spain
| | - I Corrales
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank (BST), Barcelona, Spain
| | - N Borras
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank (BST), Barcelona, Spain
| | - S Casacuberta-Serra
- Gene and Cell Therapy Laboratory, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Weber
- INSERM Unité Mixte de Recherche (UMR_S) 1193, Villejuif, France
- Université Paris-Sud, Villejuif, France
- Département Hospitalo-Universitaire Hepatinov, Paul Brousse Hospital, Villejuif, France
| | - R Parra
- Molecular Diagnosis and Therapy Unit, VHIR-UAB, Barcelona, Spain
- Hemophilia Unit, Vall d'Hebron University Hospital, Barcelona, Spain
| | - C Altisent
- Hemophilia Unit, Vall d'Hebron University Hospital, Barcelona, Spain
| | - A Follenzi
- University of Piemonte Orientale, Novara, Italy
| | - A Dubart-Kupperschmitt
- INSERM Unité Mixte de Recherche (UMR_S) 1193, Villejuif, France
- Université Paris-Sud, Villejuif, France
- Département Hospitalo-Universitaire Hepatinov, Paul Brousse Hospital, Villejuif, France
| | - A Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Biomedical Research Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - F Vidal
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank (BST), Barcelona, Spain
- Molecular Diagnosis and Therapy Unit, VHIR-UAB, Barcelona, Spain
- Biomedical Research Networking Center on Cardiovascular Diseases, Madrid, Spain
| | - J Barquinero
- Gene and Cell Therapy Laboratory, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
25
|
Sanz DJ, Hollywood JA, Scallan MF, Harrison PT. Cas9/gRNA targeted excision of cystic fibrosis-causing deep-intronic splicing mutations restores normal splicing of CFTR mRNA. PLoS One 2017; 12:e0184009. [PMID: 28863137 PMCID: PMC5581164 DOI: 10.1371/journal.pone.0184009] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/16/2017] [Indexed: 12/27/2022] Open
Abstract
Cystic Fibrosis is an autosomal recessive disorder caused by mutations in the CFTR gene. CRISPR mediated, template-dependent homology-directed gene editing has been used to correct the most common mutation, c.1521_1523delCTT / p.Phe508del (F508del) which affects ~70% of individuals, but the efficiency was relatively low. Here, we describe a high efficiency strategy for editing of three different rare CFTR mutations which together account for about 3% of individuals with Cystic Fibrosis. The mutations cause aberrant splicing of CFTR mRNA due to the creation of cryptic splice signals that result in the formation of pseudoexons containing premature stop codons c.1679+1634A>G (1811+1.6kbA>G) and c.3718-2477C>T (3849+10kbC>T), or an out-of-frame 5' extension to an existing exon c.3140-26A>G (3272-26A>G). We designed pairs of Cas9 guide RNAs to create targeted double-stranded breaks in CFTR either side of each mutation which resulted in high efficiency excision of the target genomic regions via non-homologous end-joining repair. When evaluated in a mini-gene splicing assay, we showed that targeted excision restored normal splicing for all three mutations. This approach could be used to correct aberrant splicing signals or remove disruptive transcription regulatory motifs caused by deep-intronic mutations in a range of other genetic disorders.
Collapse
Affiliation(s)
- David J. Sanz
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Jennifer A. Hollywood
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Patrick T. Harrison
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| |
Collapse
|
26
|
McGarry ME, Illek B, Ly NP, Zlock L, Olshansky S, Moreno C, Finkbeiner WE, Nielson DW. In vivo and in vitro ivacaftor response in cystic fibrosis patients with residual CFTR function: N-of-1 studies. Pediatr Pulmonol 2017; 52:472-479. [PMID: 28068001 PMCID: PMC5461115 DOI: 10.1002/ppul.23659] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 01/17/2023]
Abstract
RATIONALE Ivacaftor, a cystic fibrosis transmembrane conductance regulator (CFTR) potentiator, decreases sweat chloride concentration, and improves pulmonary function in 6% of cystic fibrosis (CF) patients with specific CFTR mutations. Ivacaftor increases chloride transport in many other CFTR mutations in non-human cells, if CFTR is in the epithelium. Some CF patients have CFTR in the epithelium with residual CFTR function. The effect of ivacaftor in these patients is unknown. METHODS This was a series of randomized, crossover N-of-1 trials of ivacaftor and placebo in CF patients ≥8 years old with potential residual CFTR function (intermediate sweat chloride concentration, pancreatic sufficient, or mild bronchiectasis on chest CT). Human nasal epithelium (HNE) was obtained via nasal brushing and cultured. Sweat chloride concentration change was the in vivo outcome. Chloride current change in HNE cultures with ivacaftor was the in vitro outcome. RESULTS Three subjects had decreased sweat chloride concentration (-14.8 to -40.8 mmol/L, P < 0.01). Two subjects had unchanged sweat chloride concentration. Two subjects had increased sweat chloride concentration (+23.8 and +27.3 mmol/L, P < 0.001); both were heterozygous for A455E and pancreatic sufficient. Only subjects with decreased sweat chloride concentration had increased chloride current in HNE cultures. CONCLUSIONS Some CF patients with residual CFTR function have decreased sweat chloride concentration with ivacaftor. Increased chloride current in HNE cultures among subjects with decreased sweat chloride concentrations may predict clinical response to ivacaftor. Ivacaftor can increase sweat chloride concentration in certain mutations with unclear clinical effect. Pediatr Pulmonol. 2017;52:472-479. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Meghan E McGarry
- Pediatric Pulmonology, Department of Pediatrics, University of California, San Francisco, California
| | - Beate Illek
- Children's Hospital Oakland Research Institute, Oakland, California
| | - Ngoc P Ly
- Pediatric Pulmonology, Department of Pediatrics, University of California, San Francisco, California
| | - Lorna Zlock
- Department of Pathology, University of California, San Francisco, California
| | - Sabrina Olshansky
- Children's Hospital Oakland Research Institute, Oakland, California.,College of Pharmacy, Touro University, Vallejo, California
| | - Courtney Moreno
- Pediatric Pulmonology, Department of Pediatrics, University of California, San Francisco, California
| | - Walter E Finkbeiner
- Department of Pathology, University of California, San Francisco, California
| | - Dennis W Nielson
- Pediatric Pulmonology, Department of Pediatrics, University of California, San Francisco, California
| |
Collapse
|
27
|
The roles of RNA processing in translating genotype to phenotype. NATURE REVIEWS. MOLECULAR CELL BIOLOGY 2016. [PMID: 27847391 DOI: 10.1038/nrm.2016.139.] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.
Collapse
|
28
|
Manning KS, Cooper TA. The roles of RNA processing in translating genotype to phenotype. Nat Rev Mol Cell Biol 2016; 18:102-114. [PMID: 27847391 DOI: 10.1038/nrm.2016.139] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.
Collapse
Affiliation(s)
- Kassie S Manning
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
29
|
Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis. Eur J Hum Genet 2013; 22:784-91. [PMID: 24129438 DOI: 10.1038/ejhg.2013.238] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/06/2013] [Accepted: 09/10/2013] [Indexed: 01/18/2023] Open
Abstract
The major purpose of the present study was to quantify correctly spliced CFTR transcripts in human nasal epithelial cells from cystic fibrosis (CF) patients carrying the splicing mutations c.580-1G>T (712-1G>T) and c.2657+5G>A (2789+5G>A) and to assess the applicability of this model in CFTR therapeutic approaches. We performed the relative quantification of CFTR mRNA by reverse transcription quantitative PCR (RT-qPCR) of these splicing mutations in four groups (wild type, CF-F508del controls, CF patients and CF carriers) of individuals. In addition, in vitro assays using minigene constructs were performed to evaluate the effect of a new CF complex allele c.[2657+5G>A; 2562T>G]. Ex vivo qPCR data show that the primary consequence of both mutations at the RNA level is the skipping of their neighboring exon (6 and 16, respectively). The CFTR minigenes results mimicked the ex vivo data, as exon 16 skipping is the main aberrant transcript, and the correctly spliced transcript level was observed in a similar proportion when the c.2657+5G>A mutation is present. In summary, we provide evidence that ex vivo quantitative transcripts analysis using RT/qPCR is a robust technology that could be useful for measuring the efficacy of therapeutic approaches that attempt to achieve an increase in CFTR gene expression.
Collapse
|
30
|
Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
Collapse
Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | | |
Collapse
|
31
|
Kawoosa MS, Bhat MA, Ali SW, Hafeez I, Shastri S. Clinical and mutation profile of children with cystic fibrosis in Jammu and Kashmir. Indian Pediatr 2013; 51:185-9. [PMID: 24277965 DOI: 10.1007/s13312-014-0381-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 09/05/2013] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To study the clinical and mutation profiles of children with cystic fibrosis in Jammu and Kashmir. METHODS One hundred consecutive patients presenting with one or more phenotypic features suggestive of cystic fibrosis (CF) were screened by quantitative sweat chloride testing. For patients with positive/equivocal test result on two occasions, CFTR gene mutation analysis was done by polymerase chain reaction. RESULTS Of the 100 patients, 18 (10 females) were diagnosed to have CF at a median age of 10.5 y (IQR 4.75-15.25 y) while the median age at the onset of symptoms was 12 mo (IQR 4-63 mo) with a delay in diagnosis by 102.4±80.5 months. Clinical features at presentation included failure to thrive (94.4%), chronic cough (78%), recurrent pneumonia (61%), persistent pneumonia (11%), and chronic diarrhea (50%). Positive sweat chloride (>60 meq/L) was seen in 14 (14%) patients and 4 (4%) patients had equivocal (40-60 meq/L) value on two different occasions. Mutational analysis done in 15 patients showed DeltaF508 mutation in 20% (3/15) patients in homozygous form and in 13% (2/15) patients in heterozygous form. Intron 19 mutation 3849+10kb C>T was found in 40% (6/15) in heterozygous form. One (6.6%) patient had DeltaF508 and 3849+10kbC>T mutations in compound heterozygous form. Patients with equivocal sweat chloride and 3849+10kbC>T mutation had delayed onset of pulmonary involvement. CONCLUSION 3849 +10kbC>T mutation appears to be common in children with cystic fibrosis in Jammu and Kashmir followed by DeltaF508, although the data are quite limited. Although presentation is delayed and sweat chloride is in the equivocal range, severe lung involvement may occur in these patients.
Collapse
Affiliation(s)
- Masarat Sultana Kawoosa
- Department of Pediatrics, Sher-i-Kashmir Institute of Medical Sciences, Srinagar, Jammu and Kashmir, India and *Department of Genetics, All India Institute of Medical Sciences, New Delhi, India. Correspondence to: Prof Mushtaq Ahmad Bhat, Department of Pediatrics, Sheri Kashmir Institute of Medical Sciences, Srinagar Kashmir, India.
| | | | | | | | | |
Collapse
|
32
|
Defective CFTR expression and function are detectable in blood monocytes: development of a new blood test for cystic fibrosis. PLoS One 2011; 6:e22212. [PMID: 21811577 PMCID: PMC3141019 DOI: 10.1371/journal.pone.0022212] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Accepted: 06/21/2011] [Indexed: 12/22/2022] Open
Abstract
Background Evaluation of cystic fibrosis transmembrane conductance regulator (CFTR) functional activity to assess new therapies and define diagnosis of cystic fibrosis (CF) is cumbersome. It is known that leukocytes express detectable levels of CFTR but the molecule has not been characterized in these cells. In this study we aim at setting up and validating a blood test to evaluate CFTR expression and function in leukocytes. Description Western blot, PCR, immunofluorescence and cell membrane depolarization analysis by single-cell fluorescence imaging, using the potential-sensitive DiSBAC2(3) probe were utilized. Expression of PKA phosphorylated, cell membrane-localized CFTR was detected in non-CF monocytes, being undetectable or present in truncated form in monocytes derived from CF patients presenting with nonsense mutations. CFTR agonist administration induced membrane depolarization in monocytes isolated from non-CF donors (31 subjects) and, to a lesser extent, obligate CFTR heterozygous carriers (HTZ: 15 subjects), but it failed in monocytes from CF patients (44 subjects). We propose an index, which values in CF patients are significantly (p<0.001) lower than in the other two groups. Nasal Potential Difference, measured in selected subjects had concordant results with monocytes assay (Kappa statistic 0.93, 95%CI: 0.80–1.00). Results and Significance CFTR is detectable and is functional in human monocytes. We also showed that CFTR-associated activity can be evaluated in 5 ml of peripheral blood and devise an index potentially applicable for diagnostic purposes and both basic and translational research: from drug development to evaluation of functional outcomes in clinical trials.
Collapse
|
33
|
Tan YC, Blumenfeld J, Michaeel A, Donahue S, Balina M, Parker T, Levine D, Rennert H. Aberrant PKD2 splicing due to a presumed novel missense mutation in autosomal-dominant polycystic kidney disease. Clin Genet 2010; 80:287-92. [DOI: 10.1111/j.1399-0004.2010.01555.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
34
|
Faà V, Incani F, Meloni A, Corda D, Masala M, Baffico AM, Seia M, Cao A, Rosatelli MC. Characterization of a disease-associated mutation affecting a putative splicing regulatory element in intron 6b of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. J Biol Chem 2009; 284:30024-31. [PMID: 19759008 DOI: 10.1074/jbc.m109.032623] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cystic fibrosis (CF) is a common recessive disorder caused by >1600 mutations in the CF transmembrane conductance regulator (CFTR) gene. About 13% of CFTR mutations are classified as "splicing mutations," but for almost 40% of these, their role in affecting the pre-mRNA splicing of the gene is not yet defined. In this work, we describe a new splicing mutation detected in three unrelated Italian CF patients. By DNA analyses and mRNA studies, we identified the c.1002-1110_1113delTAAG mutation localized in intron 6b of the CFTR gene. At the mRNA level, this mutation creates an aberrant inclusion of a sequence of 101 nucleotides between exons 6b and 7. This sequence corresponds to a portion of intron 6b and resembles a cryptic exon because it is characterized by an upstream ag and a downstream gt sequence, which are most probably recognized as 5'- and 3'-splice sites by the spliceosome. Through functional analysis of this splicing defect, we show that this mutation abolishes the interaction of the splicing regulatory protein heterogeneous nuclear ribonucleoprotein A2/B1 with an intronic splicing regulatory element and creates a new recognition motif for the SRp75 splicing factor, causing activation of the cryptic exon. Our results show that the c.1002-1110_1113delTAAG mutation creates a new intronic splicing regulatory element in intron 6b of the CFTR gene exclusively recognized by SRp75.
Collapse
Affiliation(s)
- Valeria Faà
- From the Istituto di Neurogenetica e Neurofarmacologia, Consiglio Nazionale delle Ricerche, 09042 Cagliari, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros 2008; 7:179-96. [PMID: 18456578 DOI: 10.1016/j.jcf.2008.03.009] [Citation(s) in RCA: 384] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2007] [Accepted: 03/14/2008] [Indexed: 02/06/2023]
Abstract
It is often challenging for the clinician interested in cystic fibrosis (CF) to interpret molecular genetic results, and to integrate them in the diagnostic process. The limitations of genotyping technology, the choice of mutations to be tested, and the clinical context in which the test is administered can all influence how genetic information is interpreted. This paper describes the conclusions of a consensus conference to address the use and interpretation of CF mutation analysis in clinical settings. Although the diagnosis of CF is usually straightforward, care needs to be exercised in the use and interpretation of genetic tests: genotype information is not the final arbiter of a clinical diagnosis of CF or CF transmembrane conductance regulator (CFTR) protein related disorders. The diagnosis of these conditions is primarily based on the clinical presentation, and is supported by evaluation of CFTR function (sweat testing, nasal potential difference) and genetic analysis. None of these features are sufficient on their own to make a diagnosis of CF or CFTR-related disorders. Broad genotype/phenotype associations are useful in epidemiological studies, but CFTR genotype does not accurately predict individual outcome. The use of CFTR genotype for prediction of prognosis in people with CF at the time of their diagnosis is not recommended. The importance of communication between clinicians and medical genetic laboratories is emphasized. The results of testing and their implications should be reported in a manner understandable to the clinicians caring for CF patients.
Collapse
|
36
|
Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007; 8:749-61. [PMID: 17726481 DOI: 10.1038/nrg2164] [Citation(s) in RCA: 733] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human genes contain a dense array of diverse cis-acting elements that make up a code required for the expression of correctly spliced mRNAs. Alternative splicing generates a highly dynamic human proteome through networks of coordinated splicing events. Cis- and trans-acting mutations that disrupt the splicing code or the machinery required for splicing and its regulation have roles in various diseases, and recent studies have provided new insights into the mechanisms by which these effects occur. An unexpectedly large fraction of exonic mutations exhibit a primary pathogenic effect on splicing. Furthermore, normal genetic variation significantly contributes to disease severity and susceptibility by affecting splicing efficiency.
Collapse
Affiliation(s)
- Guey-Shin Wang
- Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | |
Collapse
|
37
|
MacDonald KD, McKenzie KR, Zeitlin PL. Cystic fibrosis transmembrane regulator protein mutations: 'class' opportunity for novel drug innovation. Paediatr Drugs 2007; 9:1-10. [PMID: 17291132 DOI: 10.2165/00148581-200709010-00001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cystic fibrosis (CF) is the most common autosomal, recessive, life-span shortening disease in Caucasians. Since discovery of the gene for CF (cystic fibrosis transmembrane conductance regulator [CFTR]) in 1989, knowledge of the molecular function of this gene and its interactions has offered new therapeutic targets. New therapeutics aimed at improving mutant CFTR protein function, also known as 'protein repair therapy,' have been proposed but are yet to be successful in clinical trials. Some of the most exciting efforts involve a new field known as small molecule discovery, which entails the identification, evaluation, and optimization of small organic compounds that can alter the function of a selected gene target or cell phenotype. More than 1300 CFTR mutations have been identified. Many of the more common mutations have been organized into five broad classes based on the fate of the mutant CFTR protein. In each of these mutation classes, interventions have been able to restore some level of CFTR function in vitro. While these 'repairs' have yet to be demonstrated clinically, some early clinical trials are underway. Questions regarding the amount of CFTR correction needed, delivery methods, and optimal therapeutic combinations, however, remain outstanding.
Collapse
Affiliation(s)
- Kelvin D MacDonald
- Johns Hopkins University School of Medicine, Eudowood Division of Pediatric Respiratory Sciences, Baltimore, Maryland, USA
| | | | | |
Collapse
|
38
|
Nissim-Rafinia M, Kerem B. Splicing modulation as a modifier of the CFTR function. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2007; 44:233-54. [PMID: 17076271 DOI: 10.1007/978-3-540-34449-0_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
A significant fraction of CF-causing mutations affects pre-mRNA splicing. These mutations can generate both aberrant and correct transcripts, the level of which varies among different patients. An inverse correlation was found between this level and disease severity, suggesting a role for splicing regulation as a genetic modifier. Subsequent studies showed that overexpression of splicing factors modulated the level of correctly spliced RNA, transcribed from minigenes carrying CF-causing splicing mutations. Overexpression of splicing factors also modulated the level of normal CFTR transcripts, transcribed from the endogenous CFTR allele carrying splicing mutations, in CF-derived epithelial cells. Several of the factors promoted higher level of correct CFTR transcripts. The increased level of normal transcripts led to activation of the CFTR channel and restoration of its function. Restoration was also obtained by sodium butyrate, a histone deacetylase inhibitor, known to up-regulate the expression of splicing factors. These results highlight the role of the splicing machinery as a modifier of disease severity in patients carrying splicing mutations and shed a new light on the therapeutic potential of splicing modulation for genetic diseases caused by splicing mutations.
Collapse
Affiliation(s)
- Malka Nissim-Rafinia
- Department of Genetics, Life Sciences Institute, Hebrew University, Jerusalem 91904, Israel
| | | |
Collapse
|
39
|
Venesio T, Balsamo A, Sfiligoi C, Fuso L, Molatore S, Ranzani GN, Risio M. Constitutional high expression of an APC mRNA isoform in a subset of attenuated familial adenomatous polyposis patients. J Mol Med (Berl) 2006; 85:305-12. [PMID: 17143620 DOI: 10.1007/s00109-006-0127-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 09/27/2006] [Accepted: 09/29/2006] [Indexed: 10/23/2022]
Abstract
Familial adenomatous polyposis is an inherited condition associated with hundreds to thousands of colorectal adenomas conferring a very high risk of cancer at a young age. In addition to "classical" form, there is also an attenuated polyposis, with fewer than 100 polyps and a delayed age of cancer onset. Both classical and attenuated polyposis are characterized by a relevant phenotypic heterogeneity. The disease has been linked to constitutive mutations of either APC tumor suppressor gene, or less frequently, MYH base-excision repair gene. However, the genetic cause remains undetected in up to 70-80% of patients with the attenuated form. This analysis was performed on 26 polyposis patients with the attenuated phenotype. All patients had formerly proven to be negative for APC truncating mutations that typically represent the majority of APC gene alterations. We evaluated the APC mRNA constitutional level by real-time quantitative reverse transcription polymerase chain reaction (PCR). Eleven patients (42%) showed an anomalous APC transcription level. One patient with reduced mRNA was a carrier of a whole APC gene deletion. In seven out of the ten remaining cases, we found the increased expression of an APC mRNA isoform resulting from exon 10/15 connection and giving rise to a stable truncated peptide. Mutations neither in the invariant splice sites nor in the known transcription regulatory signals were found. Our results support the notion that in attenuated polyposis patients, a detailed investigation of APC transcription can allow detection of rare alterations. Although functional data are required, the isoform we observed might have some pathogenic role, accounting for the heterogeneous phenotype that characterizes the polyposis syndrome.
Collapse
Affiliation(s)
- Tiziana Venesio
- Unit of Pathology, Institute for Cancer Research and Treatment-IRCC, Strada Provinciale 142, 10060, Candiolo, Torino, Italy.
| | | | | | | | | | | | | |
Collapse
|
40
|
Pros E, Larriba S, López E, Ravella A, Gili ML, Kruyer H, Valls J, Serra E, Lázaro C. NF1mutation rather than individual genetic variability is the main determinant of theNF1-transcriptional profile of mutations affecting splicing. Hum Mutat 2006; 27:1104-14. [PMID: 16937374 DOI: 10.1002/humu.20396] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A significant number of neurofibromatosis type 1 (NF1) mutations result in exon skipping. The majority of these mutations do not occur in the canonical splice sites and can produce different aberrant transcripts whose proportions have not been well studied. It has been hypothesized that differences in the mutation-determined NF1-transcriptional profile could partially explain disease variability among patients bearing the same NF1 splice defect. In order to gain insight into these aspects, we analyzed the proportion of the different transcripts generated by nine NF1-splicing mutations in 30 patients. We assessed the influence of the mutation in the NF1-related transcriptional profiles and investigated the existence of individual differences in a global manner. We analyzed potential differences in tissue-specific transcriptional profiles and evaluated the influence of sample processing and mRNA nonsense-mediated decay (NMD). Small transcriptional differences were found in neurofibromas and neurofibroma-derived Schwann cells (SC) compared to blood. We also detected a higher cell culture-dependent NMD. We observed that mutation per se explains 93.5% of the profile variability among mutations studied. However, despite the importance of mutation in determining the proportion of NF1 transcripts generated, we found certain variability among patients with the same mutation. From our results, it seems that genetic factors influencing RNA processing play a minor role in determining the NF1-transcriptional profile. Nevertheless neurofibromin studies would clarify whether these small differences translate into significant functional changes that could explain the great clinical expressivity observed in the disease or any of the disease-related traits.
Collapse
Affiliation(s)
- Eva Pros
- Centre de Genètica Mèdica i Molecular-Institut de Recerca Oncològica--Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Lucarelli M, Narzi L, Piergentili R, Ferraguti G, Grandoni F, Quattrucci S, Strom R. A 96-well formatted method for exon and exon/intron boundary full sequencing of the CFTR gene. Anal Biochem 2006; 353:226-35. [PMID: 16635477 DOI: 10.1016/j.ab.2006.03.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Revised: 03/03/2006] [Accepted: 03/10/2006] [Indexed: 12/01/2022]
Abstract
Full genotypic characterization of subjects affected by cystic fibrosis (CF) is essential for the definition of the genotype-phenotype correlation as well as for the enhancement of the diagnostic and prognostic value of the genetic investigation. High-sensitivity diagnostic methods, capable of full scanning of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, are needed to enhance the significance of these genetic assays. A method for extensive sequencing of the CFTR gene was optimized. This method was applied to subjects clinically positive for CF and to controls from the general population of central Italy as well as to a single subject heterozygous for a mild mutation and with an uncertain diagnosis. Some points that are crucial for the optimization of the method emerged: a 96-well format, primer project and purification, and amplicon purification. The optimized method displayed a high degree of diagnostic sensitivity; we identified a subset of 13 CFTR mutations that greatly enhanced the diagnostic sensitivity of common methods of mutational analysis. A novel G1244R disease causing mutation, leading to a CF phenotype with pancreatic sufficiency but early onset of pulmonary involvement, was detected in the subject with an uncertain diagnosis. Some discrepancies between our results and previously published CFTR sequence were found.
Collapse
Affiliation(s)
- Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, University of Rome La Sapienza, 00161 Rome, Italy.
| | | | | | | | | | | | | |
Collapse
|
42
|
Charizopoulou N, Wilke M, Dorsch M, Bot A, Jorna H, Jansen S, Stanke F, Hedrich HJ, de Jonge HR, Tümmler B. Spontaneous rescue from cystic fibrosis in a mouse model. BMC Genet 2006; 7:18. [PMID: 16571105 PMCID: PMC1448185 DOI: 10.1186/1471-2156-7-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 03/29/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND From the original CftrTgH(neoim)Hgu mutant mouse model with a divergent genetic background (129P2, C57BL/6, MF1) we have generated two inbred CftrTgH(neoim)Hgu mutant strains named CF/1-CftrTgH(neoim)Hgu and CF/3-CftrTgH(neoim)Hgu, which are fertile and show normal growth and lifespan. Initial genome wide scan analysis with microsatellite markers indicated that the two inbred strains differed on the genetic level. In order to further investigate whether these genetic differences have an impact on the disease phenotype of cystic fibrosis we characterised the phenotype of the two inbred strains. RESULTS Reduced amounts, compared to wild type control animals, of correctly spliced Cftr mRNA were detected in the nasal epithelia, lungs and the intestine of both inbred CftrTgH(neoim)Hgu strains, with higher residual amount observed for CF/1-CftrTgH(neoim)Hgu than CF/3-CftrTgH(neoim)Hgu for every investigated tissue. Accordingly the amounts of wild type Cftr protein in the intestine were 9% for CF/1-CftrTgH(neoim)Hgu and 4% for CF/3-CftrTgH(neoim)Hgu. Unlike the apparent strain and/or tissue specific regulation of Cftr mRNA splicing, short circuit current measurements in the respiratory and intestinal epithelium revealed that both strains have ameliorated the basic defect of cystic fibrosis with a presentation of a normal electrophysiology in both tissues. CONCLUSION Unlike the outbred CftrTgH(neoim)Hgu insertional mouse model, which displayed the electrophysiological defect in the gastrointestinal and respiratory tracts characteristic of cystic fibrosis, both inbred CftrTgH(neoim)Hgu strains have ameliorated the electrophysiological defect. On the basis of these findings both CF/1-CftrTgH(neoim)Hgu and CF/3-CftrTgH(neoim)Hgu offer an excellent model whereby determination of the minimal levels of protein required for the restoration of the basic defect of cystic fibrosis can be studied, along with the modulating factors which may affect this outcome.
Collapse
Affiliation(s)
- Nikoletta Charizopoulou
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
- Zentrales Tierlaboratorium, OE 8600, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
| | - Martina Wilke
- Department of Biochemistry, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Martina Dorsch
- Zentrales Tierlaboratorium, OE 8600, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
| | - Alice Bot
- Department of Biochemistry, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Huub Jorna
- Department of Biochemistry, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Silke Jansen
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
| | - Frauke Stanke
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
| | - Hans J Hedrich
- Zentrales Tierlaboratorium, OE 8600, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
| | - Hugo R de Jonge
- Department of Biochemistry, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Burkhard Tümmler
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
| |
Collapse
|
43
|
Howard B, Panchal H, McCarthy A, Ashworth A. Identification of the scaramanga gene implicates Neuregulin3 in mammary gland specification. Genes Dev 2005; 19:2078-90. [PMID: 16140987 PMCID: PMC1199577 DOI: 10.1101/gad.338505] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The mouse scaramanga (ska) mutation impairs mammary gland development such that both abrogation and stimulation of gland formation occurs. We used positional cloning to narrow the interval containing scaramanga (ska) to a 75.6-kb interval containing the distal part of the Neuregulin3 (Nrg3) gene. Within this region the only sequence difference between ska and wild-type mice is in a microsatellite repeat within intron 7. This alteration correlates with variations in Nrg3 expression profiles both at the whole embryo level and locally in the presumptive mammary region in ska mice. Localized expression of Nrg3 and its receptor, Erbb4, in the presumptive mammary region around the future bud site prior to morphological appearance of buds and the expression of bud epithelial markers further support an inductive role. Finally, Neuregulin3 (Nrg3)-soaked beads can induce expression of the early bud marker Lef1 in mouse embryo explant cultures, and epithelial bud formation can be observed histologically, suggesting that initiation of mammary bud development occurs. Taken together, these results indicate that a Neuregulin signaling pathway is involved in specification of mammary gland morphogenesis and support the long-held view that mesenchymal signal(s) are responsible for mammary gland inductive/initiating events.
Collapse
Affiliation(s)
- Beatrice Howard
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom.
| | | | | | | |
Collapse
|
44
|
Amaral MD. Processing of CFTR: traversing the cellular maze--how much CFTR needs to go through to avoid cystic fibrosis? Pediatr Pulmonol 2005; 39:479-91. [PMID: 15765539 DOI: 10.1002/ppul.20168] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Biosynthesis of the cystic fibrosis transmembrane conductance regulator (CFTR), like other proteins aimed at the cell surface, involves transport through a series of membranous compartments, the first of which is the endoplasmic reticulum (ER), where CFTR encounters the appropriate environment for folding, oligomerization, maturation, and export from the ER. After exiting the ER, CFTR has to traffic through complex pathways until it reaches the cell surface. Although not yet fully understood, the fine details of these pathways are starting to emerge, partially through identification of an increasing number of CFTR-interacting proteins (CIPs) and the clarification of their roles in CFTR trafficking and function. These aspects of CFTR biogenesis/degradation and by membrane traffic and CIPs are discussed in this review. Following this description of complex pathways and multiple checkpoints to which CFTR is subjected in the cell, the basic question remains of how much CFTR has to overcome these barriers and be functionally expressed at the plasma membrane to avoid CF. This question is also discussed here.
Collapse
Affiliation(s)
- Margarida D Amaral
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, and Centre of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.
| |
Collapse
|
45
|
Alfakih K, Lawrance RA, Maqbool A, Walters K, Ball SG, Balmforth AJ, Hall AS. The clinical significance of a common, functional, X-linked angiotensin II type 2-receptor gene polymorphism (-1332 G/A) in a cohort of 509 families with premature coronary artery disease. Eur Heart J 2004; 26:584-9. [PMID: 15618059 DOI: 10.1093/eurheartj/ehi013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS To assess, in families with premature coronary artery disease (CAD), the possible association, with linkage, of the X-linked AT2 receptor (-1332 G/A) gene polymorphism and premature CAD. METHODS AND RESULTS We investigated 509 families with a history of premature CAD that consisted of one sibling affected with premature CAD and two unaffected siblings. Genotyping of subjects was performed using a restriction enzyme digestion of an initial 310 bp polymerase chain reaction fragment that included the AT2 (-1332 G/A) locus. The mean age of the 611 individuals affected by premature CAD at the time of event was 49.5 +/- 8.1 years. Conditional logistic regression analysis confirmed a significant predictive value of premature CAD for the covariates of hypertension, diabetes, dyslipidaemia, history of smoking, and male gender. The genetic data were analysed for these families using the X-linked sibling transmission/deletion test (XS-TDT) statistics program. In hemizygous men we observed evidence for association in the presence of linkage, for the AT2 (-1332 G/A) locus and premature CAD (P-exact value = 0.024) and also a trend towards association, in the presence of linkage, for this polymorphism and hypertension (P-exact value = 0.08). CONCLUSIONS We have observed evidence of association between the presence of linkage for the X-linked AT2 (-1332 G/A) polymorphism and premature CAD in hemizygous males.
Collapse
Affiliation(s)
- Khaled Alfakih
- BHF Heart Research Centre (Clinical), G Floor, Jubilee Wing, Leeds General Infirmary, Great George Street, Leeds LS1 3EX, UK
| | | | | | | | | | | | | |
Collapse
|
46
|
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize the recent approaches using mutation-specific therapy to correct the genetic defect according to the molecular mechanism by which the mutation causes the defects in cystic fibrosis transmembrane conductance regulator (CFTR). Premature stop mutations (class I mutations) account for 5 to 10% of the total mutant alleles in cystic fibrosis patients, and in certain subpopulations the incidence is much higher. RECENT FINDINGS The aminoglycoside antibiotics can suppress premature termination codons by permitting translation to continue to the normal termination of the transcript. The susceptibility to suppression by aminoglycosides depends on the stop codon itself and on the sequence context surrounding it. In vitro studies in cell lines expressing stop mutations and in mice have shown that aminoglycosides caused a dose-dependent increase in CFTR expression and restored functional CFTR to the apical membrane. Clinical studies also provided evidence that the aminoglycoside gentamicin can suppress these CFTR premature stop mutations in affected patients. A recent double-blind, placebo-controlled, crossover study has demonstrated restoration of CFTR function by topical application of gentamicin to the nasal epithelium of cystic fibrosis patients carrying stop mutations. In 21% of the patients there was a complete normalization of all the electrophysiologic abnormalities caused by the CFTR defect, and in 68% there was restoration of either chloride or sodium transport. Furthermore, immunohistochemical staining to the C-terminal part of the CFTR was demonstrated via peripheral staining for CFTR in scraped nasal epithelial cells of patients carrying stop mutations. Inconsistent results were reported regarding the required level of corrected CFTR that has to be reached to achieve normal function. Achieving CFTR activity of 10 to 35% might be needed to prevent significant pulmonary morbidity. SUMMARY It is as yet unknown how much corrected mutant CFTR must reach the apical membrane to induce a clinically relevant beneficial effect. The future goal is to maximize the effect of stop-codon supressors on CFTR while minimizing side effects, but further studies must be performed to find a safer compound that may be administered in small children from the time of diagnosis.
Collapse
Affiliation(s)
- Eitan Kerem
- Department of Pediatrics and Cystic Fibrosis Center, Hadassah University Hospital, Mount Scopus, Jerusalem, Israel.
| |
Collapse
|
47
|
Amaral MD, Clarke LA, Ramalho AS, Beck S, Broackes-Carter F, Rowntree R, Mouchel N, Williams SH, Harris A, Tzetis M, Steiner B, Sanz J, Gallati S, Nissim-Rafinifa M, Kerem B, Hefferon T, Cutting GR, Goina E, Pagani F. Quantitative methods for the analysis of CFTR transcripts/splicing variants. J Cyst Fibros 2004; 3 Suppl 2:17-23. [PMID: 15463919 DOI: 10.1016/j.jcf.2004.05.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In cystic fibrosis (CF), transcript analysis and quantification are important for diagnosis, prognosis and also as surrogate markers for some therapies including gene therapy. Classical RNA-based methods require significant expression levels in target samples for appropriate analysis, thus PCR-based methods are evolving towards reliable quantification. Various protocols for the quantitative analysis of CFTR transcripts (including those resulting from splicing variants) are described and discussed here.
Collapse
Affiliation(s)
- Margarida D Amaral
- Department of Chemistry and Biochemistry, University of Lisboa, Lisboa, Portugal.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
Alternative splicing is the major source of proteome diversity in humans and thus is highly relevant to disease and therapy. For example, recent work suggests that the long-sought-after target of the analgesic acetaminophen is a neural-specific, alternatively spliced isoform of cyclooxygenase 1 (COX-1). Several important diseases, such as cystic fibrosis, have been linked with mutations or variations in either cis-acting elements or trans-acting factors that lead to aberrant splicing and abnormal protein production. Correction of erroneous splicing is thus an important goal of molecular therapies. Recent experiments have used modified oligonucleotides to inhibit cryptic exons or to activate exons weakened by mutations, suggesting that these reagents could eventually lead to effective therapies.
Collapse
Affiliation(s)
- Mariano A Garcia-Blanco
- Department of Molecular Genetics and Microbiology, Center for RNA Biology, Box 3053, Research Drive, Duke University Medical Center, Durham, North Carolina 27710, USA.
| | | | | |
Collapse
|
49
|
Svenson IK, Kloos MT, Gaskell PC, Nance MA, Garbern JY, Hisanaga SI, Pericak-Vance MA, Ashley-Koch AE, Marchuk DA. Intragenic modifiers of hereditary spastic paraplegia due to spastin gene mutations. Neurogenetics 2004; 5:157-64. [PMID: 15248095 DOI: 10.1007/s10048-004-0186-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2004] [Indexed: 11/24/2022]
Abstract
Hereditary spastic paraplegia (HSP) is a genetically heterogeneous neurodegenerative disease characterized by wide variability in phenotypic expression, both within and among families. The most-common cause of autosomal dominant HSP is mutation of the gene encoding spastin, a protein of uncertain function. We report the existence of intragenic polymorphisms of spastin that modify the HSP phenotype. One (S44L) is a previously described recessively acting allele and the second is a novel allele affecting the adjacent amino acid residue (P45Q). In 4 HSP families in which either L44 or Q45 segregates independently of a missense or splicing mutation in the AAA domain of spastin, L44 and Q45 are each associated with a striking decrease in age at onset in the presence of the AAA domain mutations. Using a bioinformatics approach, we found that the highly conserved S44 is predicted to be phosphorylated by a number of family members of the proline-directed serine/threonine cyclin-dependent kinases (Cdks). Cdk1 and Cdk5 showed no kinase activity toward synthetic spastin peptide in an in vitro kinase assay, suggesting that this serine residue may be phosphorylated by a different Cdk. Our identification of S44L and P45Q as modifiers of the HSP phenotype suggests a role for spastin phosphorylation by Cdks in the neurodegeneration of the most-common form of HSP.
Collapse
Affiliation(s)
- Ingrid K Svenson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Abstract
Cystic fibrosis is a common autosomal recessive disorder that primarily affects the epithelial cells in the intestine, respiratory system, pancreas, gall bladder and sweat glands. Over one thousand mutations have currently been identified in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene that are associated with CF disease. There have been many studies on the correlation of the CFTR genotype and CF disease phenotype; however, this relationship is still not well understood. A connection between CFTR genotype and disease manifested in the pancreas has been well described, but pulmonary disease appears to be highly variable even between individuals with the same genotype. This review describes the current classification of CFTR mutation classes and resulting CF disease phenotypes. Complex disease alleles and modifier genes are discussed along with alternative disorders, such as disseminated bronchiectasis and pancreatitis, which are also thought to result from CFTR mutations.
Collapse
Affiliation(s)
- Rebecca K Rowntree
- Paediatric Molecular Genetics, Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | | |
Collapse
|