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Rivas MA, Chang C. Efficient storage and regression computation for population-scale genome sequencing studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589062. [PMID: 38659813 PMCID: PMC11042230 DOI: 10.1101/2024.04.11.589062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In the era of big data in human genetics, large-scale biobanks aggregating genetic data from diverse populations have emerged as important for advancing our understanding of human health and disease. However, the computational and storage demands of whole genome sequencing (WGS) studies pose significant challenges, especially for researchers from underfunded institutions or developing countries, creating a disparity in research capabilities. We introduce new approaches that significantly enhance computational efficiency and reduce data storage requirements for WGS studies. By developing algorithms for compressed storage of genetic data, focusing particularly on optimizing the representation of rare variants, and designing regression methods tailored for the scale and complexity of WGS data, we significantly lower computational and storage costs. We integrate our approach into PLINK 2.0. The implementation demonstrates considerable reductions in storage space and computational time without compromising analytical accuracy, as evidenced by the application to the AllofUs project data. We optimized the runtime of an exome-wide association analysis involving 19.4 million variants and the body mass index phenotype of 125,077 individuals, reducing it from 695.35 minutes (approximately 11.5 hours) on a single machine to just 1.57 minutes using 30 GB of memory and 50 threads (or 8.67 minutes with 4 threads). Additionally, we extended this approach to support multi-phenotype analyses. We anticipate that our approach will enable researchers across the globe to unlock the potential of population biobanks, accelerating the pace of discoveries that can improve our understanding of human health and disease.
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Affiliation(s)
- Manuel A. Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA 94305
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2
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Gupta A, Barone C, Quijano E, Piotrowski-Daspit AS, Perera JD, Riccardi A, Jamali H, Turchick A, Zao W, Saltzman WM, Glazer PM, Egan ME. Next generation triplex-forming PNAs for site-specific genome editing of the F508del CFTR mutation. J Cyst Fibros 2024:S1569-1993(24)00795-1. [PMID: 39107154 DOI: 10.1016/j.jcf.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/22/2024] [Accepted: 07/15/2024] [Indexed: 08/09/2024]
Abstract
BACKGROUND Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein for which there is no cure. One approach to cure CF is to correct the underlying mutations in the CFTR gene. We have used triplex-forming peptide nucleic acids (PNAs) loaded into biodegradable nanoparticles (NPs) in combination with donor DNAs as reagents for correcting mutations associated with genetic diseases including CF. Previously, we demonstrated that PNAs induce recombination between a donor DNA and the CFTR gene, correcting the F508del CFTR mutation in human cystic fibrosis bronchial epithelial cells (CFBE cells) and in a CF murine model leading to improved CFTR function with low off-target effects, however the level of correction was still below the threshold for therapeutic cure. METHODS Here, we report the use of next generation, chemically modified gamma PNAs (γPNAs) containing a diethylene glycol substitution at the gamma position for enhanced DNA binding. These modified γPNAs yield enhanced gene correction of F508del mutation in human bronchial epithelial cells (CFBE cells) and in primary nasal epithelial cells from CF mice (NECF cells). RESULTS Treatment of CFBE cells and NECF cells grown at air-liquid interface (ALI) by NPs containing γtcPNAs and donor DNA resulted in increased CFTR function measured by short circuit current and improved gene editing (up to 32 %) on analysis of genomic DNA. CONCLUSIONS These findings provide the basis for further development of PNA and NP technology for editing of the CFTR gene.
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Affiliation(s)
- Anisha Gupta
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Christina Barone
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Elias Quijano
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - J Dinithi Perera
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Adele Riccardi
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Haya Jamali
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Audrey Turchick
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Weixi Zao
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Department of Cellular and Molecular Physiology Yale School of Medicine, New Haven, CT 06520, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Marie E Egan
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cellular and Molecular Physiology Yale School of Medicine, New Haven, CT 06520, USA.
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3
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Waheed N, Waris R, Naseer M, Razzaq A, Haider N, Shah AA, Ullah A. Mutational spectrum of CFTR in cystic fibrosis patients with gastrointestinal and hepatobiliary manifestations. Mol Biol Rep 2024; 51:573. [PMID: 38662334 DOI: 10.1007/s11033-024-09508-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Cystic fibrosis (CF) is a rare and debilitating autosomal recessive disorder. It hampers the normal function of various organs and causes severe damage to the lungs, and digestive system leading to recurring pneumonia. Cf also affects reproductive health eventually may cause infertility. The disease manifests due to genetic aberrations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This study aimed to screen for CFTR gene variants in Pakistani CF patients representing variable phenotypes. METHODS Clinical exome and Sanger sequencing were performed after clinical characterization of 25 suspected cases of CF (CF1-CF25). ACMG guidelines were followed to interpret the clinical significance of the identified variants. RESULTS Clinical investigations revealed common phenotypes such as pancreatic insufficiency, chest infections, chronic liver and lung diseases. Some patients also displayed symptoms like gastroesophageal reflux disease (GERD), neonatal cholestasis, acrodermatitis, diabetes mellitus, and abnormal malabsorptive stools. Genetic analysis of the 25 CF patients identified deleterious variants in the CFTR gene. Notably, 12% of patients showed compound heterozygous variants, while 88% had homozygous variants. The most prevalent variant was p. (Met1Thr or Met1?) at 24%, previously not reported in the Pakistani population. The second most common variant was p. (Phe508del) at 16%. Other variants, including p. (Leu218*), p. (Tyr569Asp), p. (Glu585Ter), and p. (Arg1162*) were also identified in the present study. Genetic analysis of one of the present patients showed a pathogenic variant in G6PD in addition to CFTR. CONCLUSION The study reports novel and reported variants in the CFTR gene in CF patients in Pakistani population having distinct phenotypes. It also emphasizes screening suspected Pakistani CF patients for the p. (Met1Thr) variant because of its increased observance and prevalence in the study. Moreover, the findings also signify searching for additional pathogenic variants in the genome of CF patients, which may modify the phenotypes. The findings contribute valuable information for the diagnosis, genetic counseling, and potential therapeutic strategies for CF patients in Pakistan.
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Affiliation(s)
- Nadia Waheed
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Rehmana Waris
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Maryam Naseer
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Ayesha Razzaq
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Nighat Haider
- Department of Pediatrics, Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
| | - Asmat Ullah
- Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Kerschner JL, Meckler F, Coatti GC, Vaghela N, Paranjapye A, Harris A. The impact of genomic distance on enhancer-promoter interactions at the CFTR locus. J Cell Mol Med 2024; 28:e18142. [PMID: 38372567 PMCID: PMC10875976 DOI: 10.1111/jcmm.18142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
We identified and characterized multiple cell-type selective enhancers of the CFTR gene promoter in previous work and demonstrated active looping of these elements to the promoter. Here we address the impact of genomic spacing on these enhancer:promoter interactions and on CFTR gene expression. Using CRISPR/Cas9, we generated clonal cell lines with deletions between the -35 kb airway enhancer and the CFTR promoter in the 16HBE14o- airway cell line, or between the intron 1 (185 + 10 kb) intestinal enhancer and the promoter in the Caco2 intestinal cell line. The effect of these deletions on CFTR transcript abundance, as well as the 3D looping structure of the locus was investigated in triplicate clones of each modification. Our results indicate that both small and larger deletions upstream of the promoter can perturb CFTR expression and -35 kb enhancer:promoter interactions in the airway cells, though the larger deletions are more impactful. In contrast, the small intronic deletions have no effect on CFTR expression and intron 1 enhancer:promoter interactions in the intestinal cells, whereas larger deletions do. Clonal variation following a specific CFTR modification is a confounding factor particularly in 16HBE14o- cells.
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Affiliation(s)
- Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Frederick Meckler
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Giuliana C. Coatti
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Alekh Paranjapye
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
- Present address:
Department of GeneticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOhioUSA
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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Singh H, Jani C, Marshall DC, Franco R, Bhatt P, Podder S, Shalhoub J, Kurman JS, Nanchal R, Uluer AZ, Salciccioli JD. Cystic fibrosis-related mortality in the United States from 1999 to 2020: an observational analysis of time trends and disparities. Sci Rep 2023; 13:15030. [PMID: 37699961 PMCID: PMC10497589 DOI: 10.1038/s41598-023-41868-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/01/2023] [Indexed: 09/14/2023] Open
Abstract
Cystic fibrosis transmembrane conductance regulator modulators have revolutionized cystic fibrosis (CF) care in the past decade. This study explores the CF-related mortality trends in the US from 1999 to 2020. We extracted CF-related mortality data from the CDC WONDER database. CF age-standardized mortality rates (ASMRs) were identified by ICD-10 code E84 and were stratified by demographic and geographical variables. Temporal trends were analyzed using Joinpoint modeling. CF-related ASMRs decreased from 1.9 to 1.04 per million population (p = 0.013), with a greater reduction in recent years. This trend was replicated in both sexes. The median age of death increased from 24 to 37 years. CF mortality rates decreased across sex, white race, non-Hispanic ethnicity, census regions, and urbanization status. Incongruent trends were reported in non-white races and Hispanic ethnicity. A lower median age of death was observed in women, non-white races, and Hispanic ethnicity. SARS-CoV-2 infection was the primary cause of death in 1.7% of CF decedents in 2020. The national CF-related mortality rates declined and the median age of death among CF decedents increased significantly indicating better survival in the recent years. The changes were relatively slow during the earlier period of the study, followed by a greater decline lately. We observed patterns of sex, ethnic, racial, and geographical disparities associated with the worsening of the gap between ethnicities, narrowing of the gap between races and rural vs. urban counties, and closing of the gap between sexes over the study period.
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Affiliation(s)
- Harpreet Singh
- Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
- Medical Data Research Collaborative, London, UK.
| | - Chinmay Jani
- Department of Medicine, Mount Auburn Hospital/Beth Israel Lahey Health, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Medical Data Research Collaborative, London, UK
| | - Dominic C Marshall
- National Heart and Lung Institute, Imperial College London, London, UK
- Medical Data Research Collaborative, London, UK
| | - Rose Franco
- Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Padmanabh Bhatt
- Department of Medicine, Mount Auburn Hospital/Beth Israel Lahey Health, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Medical Data Research Collaborative, London, UK
| | - Shreya Podder
- Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Joseph Shalhoub
- Imperial College Healthcare NHS Trust, London, UK
- Medical Data Research Collaborative, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jonathan S Kurman
- Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Rahul Nanchal
- Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Ahmet Z Uluer
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Justin D Salciccioli
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Medical Data Research Collaborative, London, UK
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7
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Cuevas-Ocaña S, Yang JY, Aushev M, Schlossmacher G, Bear CE, Hannan NRF, Perkins ND, Rossant J, Wong AP, Gray MA. A Cell-Based Optimised Approach for Rapid and Efficient Gene Editing of Human Pluripotent Stem Cells. Int J Mol Sci 2023; 24:10266. [PMID: 37373413 PMCID: PMC10299534 DOI: 10.3390/ijms241210266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Introducing or correcting disease-causing mutations through genome editing in human pluripotent stem cells (hPSCs) followed by tissue-specific differentiation provide sustainable models of multiorgan diseases, such as cystic fibrosis (CF). However, low editing efficiency resulting in extended cell culture periods and the use of specialised equipment for fluorescence activated cell sorting (FACS) make hPSC genome editing still challenging. We aimed to investigate whether a combination of cell cycle synchronisation, single-stranded oligodeoxyribonucleotides, transient selection, manual clonal isolation, and rapid screening can improve the generation of correctly modified hPSCs. Here, we introduced the most common CF mutation, ΔF508, into the CFTR gene, using TALENs into hPSCs, and corrected the W1282X mutation using CRISPR-Cas9, in human-induced PSCs. This relatively simple method achieved up to 10% efficiency without the need for FACS, generating heterozygous and homozygous gene edited hPSCs within 3-6 weeks in order to understand genetic determinants of disease and precision medicine.
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Affiliation(s)
- Sara Cuevas-Ocaña
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
- Biodiscovery Institute, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Jin Ye Yang
- Programme in Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.Y.); (J.R.); (A.P.W.)
| | - Magomet Aushev
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Biomedicine West Wing, Centre for Life, Times Square, Newcastle upon Tyne NE1 3BZ, UK;
| | - George Schlossmacher
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
| | - Christine E. Bear
- Programme in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
| | - Nicholas R. F. Hannan
- Biodiscovery Institute, Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Neil D. Perkins
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
| | - Janet Rossant
- Programme in Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.Y.); (J.R.); (A.P.W.)
| | - Amy P. Wong
- Programme in Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.Y.); (J.R.); (A.P.W.)
| | - Michael A. Gray
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (G.S.); (N.D.P.); (M.A.G.)
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8
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Mastromatteo S, Chen A, Gong J, Lin F, Thiruvahindrapuram B, Sung WW, Whitney J, Wang Z, Patel RV, Keenan K, Halevy A, Panjwani N, Avolio J, Wang C, Côté-Maurais G, Bégin S, Adam D, Brochiero E, Bjornson C, Chilvers M, Price A, Parkins M, van Wylick R, Mateos-Corral D, Hughes D, Smith MJ, Morrison N, Tullis E, Stephenson AL, Wilcox P, Quon BS, Leung WM, Solomon M, Sun L, Ratjen F, Strug LJ. High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification. HGG ADVANCES 2023; 4:100156. [PMID: 36386424 PMCID: PMC9647008 DOI: 10.1016/j.xhgg.2022.100156] [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: 07/08/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Phasing of heterozygous alleles is critical for interpretation of cis-effects of disease-relevant variation. We sequenced 477 individuals with cystic fibrosis (CF) using linked-read sequencing, which display an average phase block N50 of 4.39 Mb. We use these samples to construct a graph representation of CFTR haplotypes, demonstrating its utility for understanding complex CF alleles. These are visualized in a Web app, CFTbaRcodes, that enables interactive exploration of CFTR haplotypes present in this cohort. We perform fine-mapping and phasing of the chr7q35 trypsinogen locus associated with CF meconium ileus, an intestinal obstruction at birth associated with more severe CF outcomes and pancreatic disease. A 20-kb deletion polymorphism and a PRSS2 missense variant p.Thr8Ile (rs62473563) are shown to independently contribute to meconium ileus risk (p = 0.0028, p = 0.011, respectively) and are PRSS2 pancreas eQTLs (p = 9.5 × 10−7 and p = 1.4 × 10−4, respectively), suggesting the mechanism by which these polymorphisms contribute to CF. The phase information from linked reads provides a putative causal explanation for variation at a CF-relevant locus, which also has implications for the genetic basis of non-CF pancreatitis, to which this locus has been reported to contribute.
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9
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Gong J, He G, Wang C, Bartlett C, Panjwani N, Mastromatteo S, Lin F, Keenan K, Avolio J, Halevy A, Shaw M, Esmaeili M, Côté-Maurais G, Adam D, Bégin S, Bjornson C, Chilvers M, Reisman J, Price A, Parkins M, van Wylick R, Berthiaume Y, Bilodeau L, Mateos-Corral D, Hughes D, Smith MJ, Morrison N, Brusky J, Tullis E, Stephenson AL, Quon BS, Wilcox P, Leung WM, Solomon M, Sun L, Brochiero E, Moraes TJ, Gonska T, Ratjen F, Rommens JM, Strug LJ. Genetic evidence supports the development of SLC26A9 targeting therapies for the treatment of lung disease. NPJ Genom Med 2022; 7:28. [PMID: 35396391 PMCID: PMC8993824 DOI: 10.1038/s41525-022-00299-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/04/2022] [Indexed: 12/19/2022] Open
Abstract
Over 400 variants in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) are CF-causing. CFTR modulators target variants to improve lung function, but marked variability in response exists and current therapies do not address all CF-causing variants highlighting unmet needs. Alternative epithelial ion channel/transporters such as SLC26A9 could compensate for CFTR dysfunction, providing therapeutic targets that may benefit all individuals with CF. We investigate the relationship between rs7512462, a marker of SLC26A9 activity, and lung function pre- and post-treatment with CFTR modulators in Canadian and US CF cohorts, in the general population, and in those with chronic obstructive pulmonary disease (COPD). Rs7512462 CC genotype is associated with greater lung function in CF individuals with minimal function variants (for which there are currently no approved therapies; p = 0.008); and for gating (p = 0.033) and p.Phe508del/ p.Phe508del (p = 0.006) genotypes upon treatment with CFTR modulators. In parallel, human nasal epithelia with CC and p.Phe508del/p.Phe508del after Ussing chamber analysis of a combination of approved and experimental modulator treatments show greater CFTR function (p = 0.0022). Beyond CF, rs7512462 is associated with peak expiratory flow in a meta-analysis of the UK Biobank and Spirometa Consortium (p = 2.74 × 10-44) and provides p = 0.0891 in an analysis of COPD case-control status in the UK Biobank defined by spirometry. These findings support SLC26A9 as a therapeutic target to improve lung function for all people with CF and in individuals with other obstructive lung diseases.
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Affiliation(s)
- Jiafen Gong
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gengming He
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Cheng Wang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Claire Bartlett
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Naim Panjwani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Scott Mastromatteo
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Fan Lin
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Katherine Keenan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julie Avolio
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anat Halevy
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michelle Shaw
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohsen Esmaeili
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Guillaume Côté-Maurais
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Damien Adam
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Stéphanie Bégin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | | | - Mark Chilvers
- British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Joe Reisman
- The Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - April Price
- The Children's Hospital, London Health Science Centre, London, ON, Canada
| | | | | | - Yves Berthiaume
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Lara Bilodeau
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec-Université Laval, Québec City, QC, Canada
| | | | | | - Mary J Smith
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Nancy Morrison
- Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada
| | - Janna Brusky
- Department of Pediatrics, University of Saskatchewan, Saskatoon, SK, Canada
| | | | | | | | | | | | - Melinda Solomon
- Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Lei Sun
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Emmanuelle Brochiero
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Theo J Moraes
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Tanja Gonska
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, Canada
| | - Felix Ratjen
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Johanna M Rommens
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lisa J Strug
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada.
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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10
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Dilernia D, Amin P, Flores J, Stecenko A, Sorscher E. Mutation profiling of the c.1521_1523delCTT (p.Phe508del, F508del) CFTR allele using haplotype-resolved long-read next generation sequencing. Hum Mutat 2022; 43:595-603. [PMID: 35170824 DOI: 10.1002/humu.24352] [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: 01/28/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
Current approaches to characterize the mutational profile of the cystic fibrosis transmembrane conductance regulator (CFTR) gene are based on targeted mutation analysis (TMA) or whole gene studies derived from short-read next generation sequencing (NGS). However, these methods lack phasing capability which, in certain scenarios, can provide clinically valuable information. In the present work, we performed near-full length CFTR using Single-Molecule Real-Time Sequencing to produce haplotype-resolved data from both homozygous and heterozygous individuals for mutation c.1521_1523delCTT (p.Phe508del, F508del). This approach utilizes target enrichment of the CFTR gene using biotinylated probes, facilitates multiplexing samples in the same sequencing run, and utilizes fully-automated bioinformatics pipelines for error correction and variant calling. We show a remarkable conservation of F508del haplotype, consistent with the single gene founder effect, as well as diverse mutational profiles in non-F508del alleles. By the same method, 105 single nucleotide polymorphisms (SNPs) exhibiting invariant linkage to F508del CFTR (which better define the founder haplotype) were identified. High level homology between F508del sequences derived from heterozygotes, and those obtained from homozygous individuals, demonstrate accuracy of this method to produce haplotype resolved sequencing. The studies provide a new diagnostic technology for detailed analysis of complex CFTR alleles linked to disease severity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dario Dilernia
- Department of Pathology, School of Medicine, Emory University.,Emory Vaccine Center, Emory University
| | | | - Julie Flores
- Department of Pediatrics, School of Medicine, Emory University, and the Emory + Children's Center for Cystic Fibrosis and Airways Disease Research
| | - Arlene Stecenko
- Department of Pediatrics, School of Medicine, Emory University, and the Emory + Children's Center for Cystic Fibrosis and Airways Disease Research
| | - Eric Sorscher
- Department of Pediatrics, School of Medicine, Emory University, and the Emory + Children's Center for Cystic Fibrosis and Airways Disease Research
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11
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He G, Panjwani N, Avolio J, Ouyang H, Keshavjee S, Rommens JM, Gonska T, Moraes TJ, Strug LJ. Expression of cystic fibrosis lung disease modifier genes in human airway models. J Cyst Fibros 2022; 21:616-622. [DOI: 10.1016/j.jcf.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/05/2022] [Accepted: 02/09/2022] [Indexed: 12/13/2022]
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12
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Viotti Perisse I, Fan Z, Van Wettere A, Liu Y, Leir S, Keim J, Regouski M, Wilson MD, Cholewa KM, Mansbach SN, Kelley TJ, Wang Z, Harris A, White KL, Polejaeva IA. Sheep models of F508del and G542X cystic fibrosis mutations show cellular responses to human therapeutics. FASEB Bioadv 2021; 3:841-854. [PMID: 34632318 PMCID: PMC8493969 DOI: 10.1096/fba.2021-00043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 02/05/2023] Open
Abstract
Cystic Fibrosis (CF) is a genetic disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The F508del and G542X are the most common mutations found in US patients, accounting for 86.4% and 4.6% of all mutations, respectively. The F508del causes deletion of the phenylalanine residue at position 508 and is associated with impaired CFTR protein folding. The G542X is a nonsense mutation that introduces a stop codon into the mRNA, thus preventing normal CFTR protein synthesis. Here, we describe the generation of CFTRF508del / F508del and CFTRG542X / G542X lambs using CRISPR/Cas9 and somatic cell nuclear transfer (SCNT). First, we introduced either F508del or G542X mutations into sheep fetal fibroblasts that were subsequently used as nuclear donors for SCNT. The newborn CF lambs develop pathology similar to CFTR -/- sheep and CF patients. Moreover, tracheal epithelial cells from the CFTRF508del / F508del lambs responded to a human CFTR (hCFTR) potentiator and correctors, and those from CFTRG542X / G542X lambs showed modest restoration of CFTR function following inhibition of nonsense-mediated decay (NMD) and aminoglycoside antibiotic treatments. Thus, the phenotype and electrophysiology of these novel models represent an important advance for testing new CF therapeutics and gene therapy to improve the health of patients with this life-limiting disorder.
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Affiliation(s)
- Iuri Viotti Perisse
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Zhiqiang Fan
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Arnaud Van Wettere
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Ying Liu
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Shih‐Hsing Leir
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Jacob Keim
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Misha Regouski
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Michael D. Wilson
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Kelly M. Cholewa
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Sara N. Mansbach
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Thomas J. Kelley
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Zhongde Wang
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Kenneth L. White
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
| | - Irina A. Polejaeva
- Department of Animal, Dairy and Veterinary SciencesUtah State UniversityLoganUtahUSA
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13
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Harris A. Human molecular genetics and the long road to treating cystic fibrosis. Hum Mol Genet 2021; 30:R264-R273. [PMID: 34245257 DOI: 10.1093/hmg/ddab191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
The causative gene in cystic fibrosis was identified in 1989, three years before the publication of the first issue of Human Molecular Genetics. CFTR was among the first genes underlying a common inherited disorder to be cloned, and hence its subsequent utilization towards a cure for CF provides a roadmap for other monogenic diseases. Over the past 30 years the advances that built upon knowledge of the gene and the CFTR protein to develop effective therapeutics have been remarkable, and yet the setbacks have also been challenging. Technological progress in other fields has often circumvented the barriers. This review focuses on key aspects of CF diagnostics and current approaches to develop new therapies for all CFTR mutations. It also highlights the major research advances that underpinned progress towards treatments, and considers the remaining obstacles.
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Affiliation(s)
- Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
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14
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Shteinberg M, Haq IJ, Polineni D, Davies JC. Cystic fibrosis. Lancet 2021; 397:2195-2211. [PMID: 34090606 DOI: 10.1016/s0140-6736(20)32542-3] [Citation(s) in RCA: 314] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/03/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
Cystic fibrosis is a monogenic disease considered to affect at least 100 000 people worldwide. Mutations in CFTR, the gene encoding the epithelial ion channel that normally transports chloride and bicarbonate, lead to impaired mucus hydration and clearance. Classical cystic fibrosis is thus characterised by chronic pulmonary infection and inflammation, pancreatic exocrine insufficiency, male infertility, and might include several comorbidities such as cystic fibrosis-related diabetes or cystic fibrosis liver disease. This autosomal recessive disease is diagnosed in many regions following newborn screening, whereas in other regions, diagnosis is based on a group of recognised multiorgan clinical manifestations, raised sweat chloride concentrations, or CFTR mutations. Disease that is less easily diagnosed, and in some cases affecting only one organ, can be seen in the context of gene variants leading to residual protein function. Management strategies, including augmenting mucociliary clearance and aggressively treating infections, have gradually improved life expectancy for people with cystic fibrosis. However, restoration of CFTR function via new small molecule modulator drugs is transforming the disease for many patients. Clinical trial pipelines are actively exploring many other approaches, which will be increasingly needed as survival improves and as the population of adults with cystic fibrosis increases. Here, we present the current understanding of CFTR mutations, protein function, and disease pathophysiology, consider strengths and limitations of current management strategies, and look to the future of multidisciplinary care for those with cystic fibrosis.
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Affiliation(s)
- Michal Shteinberg
- Pulmonology Institute and CF Center, Carmel Medical Center, Haifa, Israel; Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Iram J Haq
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Jane C Davies
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield, Guy's and St Thomas' NHS Foundation Trust, London, UK.
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15
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Liu Y, Liu Z, Wang K. The Ca 2+-activated chloride channel ANO1/TMEM16A: An emerging therapeutic target for epithelium-originated diseases? Acta Pharm Sin B 2021; 11:1412-1433. [PMID: 34221860 PMCID: PMC8245819 DOI: 10.1016/j.apsb.2020.12.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/19/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Anoctamin 1 (ANO1) or TMEM16A gene encodes a member of Ca2+ activated Cl– channels (CaCCs) that are critical for physiological functions, such as epithelial secretion, smooth muscle contraction and sensory signal transduction. The attraction and interest in ANO1/TMEM16A arise from a decade long investigations that abnormal expression or dysfunction of ANO1 is involved in many pathological phenotypes and diseases, including asthma, neuropathic pain, hypertension and cancer. However, the lack of specific modulators of ANO1 has impeded the efforts to validate ANO1 as a therapeutic target. This review focuses on the recent progress made in understanding of the pathophysiological functions of CaCC ANO1 and the current modulators used as pharmacological tools, hopefully illustrating a broad spectrum of ANO1 channelopathy and a path forward for this target validation.
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Key Words
- ANO1
- ANO1, anoctamin-1
- ASM, airway smooth muscle
- Ang II, angiotensin II
- BBB, blood–brain barrier
- CAMK, Ca2+/calmodulin-dependent protein kinase
- CF, cystic fibrosis
- CFTR, cystic fibrosis transmembrane conductance regulator
- Ca2+-activated Cl– channels (CaCCs)
- CaCCinh-A01
- CaCCs, Ca2+ activated chloride channels
- Cancer
- Cystic fibrosis
- DRG, dorsal root ganglion
- Drug target
- EGFR, epidermal growth factor receptor
- ENaC, epithelial sodium channels
- ER, endoplasmic reticulum
- ESCC, esophageal squamous cell carcinoma
- FRT, fisher rat thyroid
- GI, gastrointestinal
- GIST, gastrointestinal stromal tumor
- GPCR, G-protein coupled receptor
- HNSCC, head and neck squamous cell carcinoma
- HTS, high-throughput screening
- ICC, interstitial cells of Cajal
- IPAH, idiopathic pulmonary arterial hypertension
- MAPK, mitogen-activated protein kinase
- NF-κB, nuclear factor κB
- PAH, pulmonary arterial hypertension
- PAR2, protease activated receptor 2
- PASMC, pulmonary artery smooth muscle cells
- PIP2, phosphatidylinositol 4,5-bisphosphate
- PKD, polycystic kidney disease
- T16Ainh-A01
- TGF-β, transforming growth factor-β
- TMEM16A
- VGCC, voltage gated calcium channel
- VRAC, volume regulated anion channel
- VSMC, vascular smooth muscle cells
- YFP, yellow fluorescent protein
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Affiliation(s)
- Yani Liu
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao 266073, China
- Institute of Innovative Drugs, Qingdao University, Qingdao 266021, China
| | - Zongtao Liu
- Department of Clinical Laboratory, Qingdao Third People's Hospital, Qingdao 266041, China
| | - KeWei Wang
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao 266073, China
- Institute of Innovative Drugs, Qingdao University, Qingdao 266021, China
- Corresponding authors.
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16
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Sun L, Conrad D, Hall DA, Benkstein KD, Semancik S, Zaghloul ME. Plasmonic Sensing Studies of a Gas-Phase Cystic Fibrosis Marker in Moisture Laden Air. SENSORS 2021; 21:s21113776. [PMID: 34072374 PMCID: PMC8197828 DOI: 10.3390/s21113776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 11/21/2022]
Abstract
A plasmonic sensing platform was developed as a noninvasive method to monitor gas-phase biomarkers related to cystic fibrosis (CF). The nanohole array (NHA) sensing platform is based on localized surface plasmon resonance (LSPR) and offers a rapid data acquisition capability. Among the numerous gas-phase biomarkers that can be used to assess the lung health of CF patients, acetaldehyde was selected for this investigation. Previous research with diverse types of sensing platforms, with materials ranging from metal oxides to 2-D materials, detected gas-phase acetaldehyde with the lowest detection limit at the µmol/mol (parts-per-million (ppm)) level. In contrast, this work presents a plasmonic sensing platform that can approach the nmol/mol (parts-per-billion (ppb)) level, which covers the required concentration range needed to monitor the status of lung infection and find pulmonary exacerbations. During the experimental measurements made by a spectrometer and by a smartphone, the sensing examination was initially performed in a dry air background and then with high relative humidity (RH) as an interferent, which is relevant to exhaled breath. At a room temperature of 23.1 °C, the lowest detection limit for the investigated plasmonic sensing platform under dry air and 72% RH conditions are 250 nmol/mol (ppb) and 1000 nmol/mol (ppb), respectively.
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Affiliation(s)
- Libin Sun
- School of Engineering and Applied Science, George Washington University, Washington, DC 20052, USA
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (K.D.B.); (S.S.)
- Correspondence: (L.S.); (M.E.Z.)
| | - Douglas Conrad
- Department of Medicine, University of California, San Diego, CA 92037, USA;
| | - Drew A. Hall
- Department of Electrical and Computer Engineering, Jacobs School of Engineering, University of California, San Diego, CA 92093, USA;
| | - Kurt D. Benkstein
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (K.D.B.); (S.S.)
| | - Steve Semancik
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (K.D.B.); (S.S.)
| | - Mona E. Zaghloul
- School of Engineering and Applied Science, George Washington University, Washington, DC 20052, USA
- Correspondence: (L.S.); (M.E.Z.)
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17
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Eastman AC, Pace RG, Dang H, Aksit MA, Vecchio-Pagán B, Lam ATN, O'Neal WK, Blackman SM, Knowles MR, Cutting GR. SLC26A9 SNP rs7512462 is not associated with lung disease severity or lung function response to ivacaftor in cystic fibrosis patients with G551D-CFTR. J Cyst Fibros 2021; 20:851-856. [PMID: 33674211 DOI: 10.1016/j.jcf.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND The CFTR modulator ivacaftor has been variably effective in treating individuals with cystic fibrosis (CF) who harbor CFTR gating variants such as G551D, as well as other classes of CFTR variants when used with other modulators. Because CFTR genotype does not fully explain this variability, defining genetic modifiers of response to modulator therapy is of particular interest to the field of individualized CF drug therapy. Previous studies have proposed that a variant in SLC26A9 (rs7512462) is associated with lung disease severity and with response to treatment with ivacaftor in individuals with CF who carry G551D or gating variants. METHODS Given the implications for CF treatment, we re-examined the reported associations in three cohorts; patients enrolled in the Twin and Siblings study at Johns Hopkins University, the CF modifier study at the University of North Carolina at Chapel Hill, and the prospective G551D Observational (GOAL) study. The GOAL study was specifically designed to measure lung function response to ivacaftor. RESULTS We find no association between SLC26A9 (rs7512462) genotype and lung disease severity (n = 272) or change in lung function at one-, three-, and six-month intervals following ivacaftor treatment(n = 141) in individuals with CF who carry at least one G551D variant. CONCLUSIONS Our inability to replicate this association indicates that rs7512462 genotype should not be used in treatment decisions.
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Affiliation(s)
- Alice C Eastman
- Department of Genetic Medicine, Johns Hopkins University (JHU), Baltimore, MD, 21205, USA
| | - Rhonda G Pace
- University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, 27599, USA
| | - Hong Dang
- University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, 27599, USA
| | - Melis Atalar Aksit
- Department of Genetic Medicine, Johns Hopkins University (JHU), Baltimore, MD, 21205, USA
| | - Briana Vecchio-Pagán
- Department of Genetic Medicine, Johns Hopkins University (JHU), Baltimore, MD, 21205, USA
| | - Anh-Thu N Lam
- Department of Genetic Medicine, Johns Hopkins University (JHU), Baltimore, MD, 21205, USA
| | - Wanda K O'Neal
- University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, 27599, USA
| | - Scott M Blackman
- Department of Genetic Medicine, Johns Hopkins University (JHU), Baltimore, MD, 21205, USA
| | - Michael R Knowles
- University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, 27599, USA.
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins University (JHU), Baltimore, MD, 21205, USA.
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18
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Mackie A, Rascher J, Schmid M, Endriss V, Brand T, Seibold W. First clinical trials of the inhaled epithelial sodium channel inhibitor BI 1265162 in healthy volunteers. ERJ Open Res 2021; 7:00447-2020. [PMID: 33569494 PMCID: PMC7861022 DOI: 10.1183/23120541.00447-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022] Open
Abstract
Background Inhibition of the epithelial sodium channel (ENaC) represents a mutation-agnostic therapeutic approach to restore airway surface liquid hydration and mucociliary clearance in patients with cystic fibrosis. BI 1265162 is an inhaled ENaC inhibitor with demonstrated preclinical efficacy. Methods Three phase I trials of BI 1265162 in healthy male subjects are presented: NCT03349723 (single-rising-dose trial evaluating safety, tolerability and pharmacokinetics (PK)); NCT03576144 (multiple-rising-dose trial evaluating safety, tolerability and PK); and NCT03907280 (absolute bioavailability trial). Results BI 1265162 single doses ≤1200 µg and multiple doses of 600 µg were well tolerated. Adverse events were balanced across treatment groups, were of mainly mild or moderate intensity and resolved by trial-end. One subject discontinued from trial medication on day 7 (asymptomatic hyperkalaemia adverse event; recovered day 8). One subject experienced a serious adverse event (neuropathia vestibularis) leading to hospitalisation and missed one of the four dosing periods. Both events were not considered to be drug-related and subjects recovered. BI 1265162 displayed dose-proportional, time-independent PK; maximum accumulation was 1.6-fold; calculated effective elimination half-life was 3.6–8.7 h over the dose ranges tested. Renal excretion was not a major drug elimination route. Oral and inhaled dosing (±activated oral charcoal) absolute bioavailability was 0.50% and ∼40%, respectively. Conclusion BI 1265162 single or multiple doses up to 6.5 days were well tolerated. Systemic exposures mainly represent drug absorbed through the lungs and not the gastrointestinal tract, with ∼40% of the inhaled dose reaching the systemic circulation. Accumulation was minimal. Twice-daily dosing is supported for future development. Cell and animal studies have demonstrated that BI 1265162 is a potent ENaC inhibitor. Three phase I trials show that single- and multiple-dose BI 1265162 is safe. BI 1265162 is being tested in phase II studies, using twice-daily dosing, in people with CF.https://bit.ly/3nPUkrO
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Affiliation(s)
| | - Juliane Rascher
- SocraMetrics GmbH, Erfurt, Germany, on behalf of Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | | | | | - Tobias Brand
- Boehringer Ingelheim, Biberach an der Riss, Germany
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19
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Delivery of genome-editing biomacromolecules for treatment of lung genetic disorders. Adv Drug Deliv Rev 2021; 168:196-216. [PMID: 32416111 DOI: 10.1016/j.addr.2020.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 02/06/2023]
Abstract
Genome-editing systems based on clustered, regularly interspaced, short palindromic repeat (CRISPR)/associated protein (CRISPR/Cas), are emerging as a revolutionary technology for the treatment of various genetic diseases. To date, the delivery of genome-editing biomacromolecules by viral or non-viral vectors have been proposed as new therapeutic options for lung genetic disorders, such as cystic fibrosis (CF) and α-1 antitrypsin deficiency (AATD), and it has been accepted that these delivery vectors can introduce CRISPR/Cas9 machineries into target cells or tissues in vitro, ex vivo and in vivo. However, the efficient local or systemic delivery of CRISPR/Cas9 elements to the lung, enabled by either viral or by non-viral carriers, still remains elusive. Herein, we first introduce lung genetic disorders and their current treatment options, and then summarize CRISPR/Cas9-based strategies for the therapeutic genome editing of these disorders. We further summarize the pros and cons of different routes of administration for lung genetic disorders. In particular, the potentials of aerosol delivery for therapeutic CRISPR/Cas9 biomacromolecules for lung genome editing are discussed and highlighted. Finally, current challenges and future outlooks in this emerging area are briefly discussed.
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20
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Donegà S, Rogalska ME, Pianigiani G, Igreja S, Amaral MD, Pagani F. Rescue of common exon-skipping mutations in cystic fibrosis with modified U1 snRNAs. Hum Mutat 2020; 41:2143-2154. [PMID: 32935393 DOI: 10.1002/humu.24116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
In cystic fibrosis (CF), the correction of splicing defects represents an interesting therapeutic approach to restore normal CFTR function. In this study, we focused on 10 common mutations/variants 711+3A>G/C, 711+5G>A, TG13T3, TG13T5, TG12T5, 1863C>T, 1898+3A>G, 2789+5G>A, and 3120G>A that induce skipping of the corresponding CFTR exons 5, 10, 13, 16, and 18. To rescue the splicing defects we tested, in a minigene assay, a panel of modified U1 small nuclear RNAs (snRNAs), named Exon Specific U1s (ExSpeU1s), that was engineered to bind to intronic sequences downstream of each defective exon. Using this approach, we show that all 10 splicing mutations analyzed are efficiently corrected by specific ExSpeU1s. Using complementary DNA-splicing competent minigenes, we also show that the ExspeU1-mediated splicing correction at the RNA level recovered the full-length CFTR protein for 1863C>T, 1898+3A>G, 2789+5G>A variants. In addition, detailed mutagenesis experiments performed on exon 13 led us to identify a novel intronic regulatory element involved in the ExSpeU1-mediated splicing rescue. These results provide a common strategy based on modified U1 snRNAs to correct exon skipping in a group of disease-causing CFTR mutations.
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Affiliation(s)
- Stefano Donegà
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Malgorzata Ewa Rogalska
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Susana Igreja
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Margarida Duarte Amaral
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Franco Pagani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
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21
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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.
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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
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22
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Fleischer A, Vallejo-Díez S, Martín-Fernández JM, Sánchez-Gilabert A, Castresana M, Del Pozo A, Esquisabel A, Ávila S, Castrillo JL, Gaínza E, Pedraz JL, Viñas M, Bachiller D. iPSC-Derived Intestinal Organoids from Cystic Fibrosis Patients Acquire CFTR Activity upon TALEN-Mediated Repair of the p.F508del Mutation. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:858-870. [PMID: 32373648 PMCID: PMC7195499 DOI: 10.1016/j.omtm.2020.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis (CF) is the main genetic cause of death among the Caucasian population. The disease is characterized by abnormal fluid and electrolyte mobility across secretory epithelia. The first manifestations occur within hours of birth (meconium ileus), later extending to other organs, generally affecting the respiratory tract. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR encodes a cyclic adenosine monophosphate (cAMP)-dependent, phosphorylation-regulated chloride channel required for transport of chloride and other ions through cell membranes. There are more than 2,000 mutations described in the CFTR gene, but one of them, phenylalanine residue at amino acid position 508 (p.F508del), a recessive allele, is responsible for the vast majority of CF cases worldwide. Here, we present the results of the application of genome-editing techniques to the restoration of CFTR activity in p.F508del patient-derived induced pluripotent stem cells (iPSCs). Gene-edited iPSCs were subsequently used to produce intestinal organoids on which the physiological activity of the restored gene was tested in forskolin-induced swelling tests. The seamless restoration of the p.F508del mutation resulted in normal expression of the mature CFTR glycoprotein, full recovery of CFTR activity, and a normal response of the repaired organoids to treatment with two approved CF therapies: VX-770 and VX-809.
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Affiliation(s)
- Aarne Fleischer
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | - Sara Vallejo-Díez
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
| | | | | | - Mónica Castresana
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | | | - Amaia Esquisabel
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Silvia Ávila
- Genetadi Biotech S.L., Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | | | - José Luis Pedraz
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Miguel Viñas
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, University of Barcelona, 08097 Barcelona, Spain
| | - Daniel Bachiller
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
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23
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Baskurt Z, Mastromatteo S, Gong J, Wintle RF, Scherer SW, Strug LJ. VikNGS: a C++ variant integration kit for next generation sequencing association analysis. Bioinformatics 2020; 36:1283-1285. [PMID: 31580400 PMCID: PMC7703770 DOI: 10.1093/bioinformatics/btz716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/13/2019] [Accepted: 09/25/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Integration of next generation sequencing data (NGS) across different research studies can improve the power of genetic association testing by increasing sample size and can obviate the need for sequencing controls. If differential genotype uncertainty across studies is not accounted for, combining datasets can produce spurious association results. We developed the Variant Integration Kit for NGS (VikNGS), a fast cross-platform software package, to enable aggregation of several datasets for rare and common variant genetic association analysis of quantitative and binary traits with covariate adjustment. VikNGS also includes a graphical user interface, power simulation functionality and data visualization tools. AVAILABILITY AND IMPLEMENTATION The VikNGS package can be downloaded at http://www.tcag.ca/tools/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zeynep Baskurt
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Scott Mastromatteo
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Jiafen Gong
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Richard F Wintle
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Lisa J Strug
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada.,Division of Biostatistics and Department of Statistical Sciences, University of Toronto, Toronto, ON, M5T3M7, Canada
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24
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Jaques R, Shakeel A, Hoyle C. Novel therapeutic approaches for the management of cystic fibrosis. Multidiscip Respir Med 2020; 15:690. [PMID: 33282281 PMCID: PMC7706361 DOI: 10.4081/mrm.2020.690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/06/2020] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic condition characterised by the build-up of thick, sticky mucus that can damage many of the body's organs. It is a life-long disease that results in a shortened life expectancy, often due to the progression of advanced lung disease. Treatment has previously targeted the downstream symptoms such as diminished mucus clearance and recurrent infection. More recently, significant advances have been made in treating the cause of the disease by targeting the faulty gene responsible. Hope for the development of potential therapies lies with ongoing research into new pharmacological agents and gene therapy. This review gives an overview of CF, and summarises the current evidence regarding the disease management and upcoming strategies aimed at treating or potentially curing this condition.
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Affiliation(s)
- Ryan Jaques
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, University of Hull, UK
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25
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Tambuyzer E, Vandendriessche B, Austin CP, Brooks PJ, Larsson K, Miller Needleman KI, Valentine J, Davies K, Groft SC, Preti R, Oprea TI, Prunotto M. Therapies for rare diseases: therapeutic modalities, progress and challenges ahead. Nat Rev Drug Discov 2019; 19:93-111. [PMID: 31836861 DOI: 10.1038/s41573-019-0049-9] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2019] [Indexed: 12/26/2022]
Abstract
Most rare diseases still lack approved treatments despite major advances in research providing the tools to understand their molecular basis, as well as legislation providing regulatory and economic incentives to catalyse the development of specific therapies. Addressing this translational gap is a multifaceted challenge, for which a key aspect is the selection of the optimal therapeutic modality for translating advances in rare disease knowledge into potential medicines, known as orphan drugs. With this in mind, we discuss here the technological basis and rare disease applicability of the main therapeutic modalities, including small molecules, monoclonal antibodies, protein replacement therapies, oligonucleotides and gene and cell therapies, as well as drug repurposing. For each modality, we consider its strengths and limitations as a platform for rare disease therapy development and describe clinical progress so far in developing drugs based on it. We also discuss selected overarching topics in the development of therapies for rare diseases, such as approval statistics, engagement of patients in the process, regulatory pathways and digital tools.
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Affiliation(s)
- Erik Tambuyzer
- BioPontis Alliance for Rare Diseases Foundation fup/son, Brussels, Belgium. .,BioPontis Alliance Rare Disease Foundation, Inc, Raleigh, NC, USA.
| | - Benjamin Vandendriessche
- Byteflies, Antwerp, Belgium.,Department of Electrical, Computer, and Systems Engineering (ECSE), Case Western Reserve University, Cleveland, OH, USA
| | - Christopher P Austin
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Philip J Brooks
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Kristina Larsson
- Orphan Medicines Office, European Medicines Agency, Amsterdam, Netherlands
| | | | | | - Kay Davies
- MDUK Oxford Neuromuscular Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Robert Preti
- Hitachi Chemical Regenerative Medicine Business Sector, Allendale, NJ, USA
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Albuquerque, Albuquerque, NM, USA.,UNM Comprehensive Cancer Center, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Marco Prunotto
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.
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26
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Phuan PW, Tan JA, Rivera AA, Zlock L, Nielson DW, Finkbeiner WE, Haggie PM, Verkman AS. Nanomolar-potency 'co-potentiator' therapy for cystic fibrosis caused by a defined subset of minimal function CFTR mutants. Sci Rep 2019; 9:17640. [PMID: 31776420 PMCID: PMC6881293 DOI: 10.1038/s41598-019-54158-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
Available CFTR modulators provide no therapeutic benefit for cystic fibrosis (CF) caused by many loss-of-function mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel, including N1303K. We previously introduced the concept of ‘co-potentiators’ (combination-potentiators) to rescue CFTR function in some minimal function CFTR mutants. Herein, a screen of ~120,000 drug-like synthetic small molecules identified active co-potentiators of pyrazoloquinoline, piperidine-pyridoindole, tetrahydroquinoline and phenylazepine classes, with EC50 down to ~300 nM following initial structure-activity studies. Increased CFTR chloride conductance by up to 8-fold was observed when a co-potentiator (termed ‘Class II potentiator’) was used with a classical potentiator (‘Class I potentiator’) such as VX-770 or GLPG1837. To investigate the range of CFTR mutations benefitted by co-potentiators, 14 CF-associated CFTR mutations were studied in transfected cell models. Co-potentiator efficacy was found for CFTR missense, deletion and nonsense mutations in nucleotide binding domain-2 (NBD2), including W1282X, N1303K, c.3700A > G and Q1313X (with corrector for some mutations). In contrast, CFTR mutations G85E, R334W, R347P, V520F, R560T, A561E, M1101K and R1162X showed no co-potentiator activity, even with corrector. Co-potentiator efficacy was confirmed in primary human bronchial epithelial cell cultures generated from a N1303K homozygous CF subject. The Class II potentiators identified here may have clinical benefit for CF caused by mutations in the NBD2 domain of CFTR.
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Affiliation(s)
- Puay-Wah Phuan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Joseph-Anthony Tan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amber A Rivera
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lorna Zlock
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Dennis W Nielson
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Walter E Finkbeiner
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter M Haggie
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alan S Verkman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
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27
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Lee L, Smith-Whitley K, Banks S, Puckrein G. Reducing Health Care Disparities in Sickle Cell Disease: A Review. Public Health Rep 2019; 134:599-607. [PMID: 31600481 DOI: 10.1177/0033354919881438] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Sickle cell disease (SCD) is an inherited blood disorder most common among African American and Hispanic American persons. The disease can cause substantial, long-term, and costly health problems, including infections, stroke, and kidney failure, many of which can reduce life expectancy. Disparities in receiving health care among African Americans and other racial/ethnic minority groups in the United States are well known and directly related to poor outcomes associated with SCD. As an orphan disease-one that affects <200 000 persons nationwide-SCD does not receive the research funding and pharmaceutical investment directed to other orphan diseases. For example, cystic fibrosis affects fewer than half the number of persons but receives 3.5 times the funding from the National Institutes of Health and 440 times the funding from national foundations. In this review, we discuss the health inequities affecting persons with SCD, describe programs intended to improve their care, and identify actions that could be taken to further reduce these inequities, improve care, control treatment costs, and ease the burden of disease.
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Affiliation(s)
- LaTasha Lee
- Department of Clinical Research & Leadership, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Kim Smith-Whitley
- Comprehensive Sickle Cell Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sonja Banks
- Sickle Cell Disease Association of America, Baltimore, MD, USA
| | - Gary Puckrein
- National Minority Quality Forum, Washington, DC, USA
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28
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Fabris L, Fiorotto R, Spirli C, Cadamuro M, Mariotti V, Perugorria MJ, Banales JM, Strazzabosco M. Pathobiology of inherited biliary diseases: a roadmap to understand acquired liver diseases. Nat Rev Gastroenterol Hepatol 2019; 16:497-511. [PMID: 31165788 PMCID: PMC6661007 DOI: 10.1038/s41575-019-0156-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bile duct epithelial cells, also known as cholangiocytes, regulate the composition of bile and its flow. Acquired, congenital and genetic dysfunctions in these cells give rise to a set of diverse and complex diseases, often of unknown aetiology, called cholangiopathies. New knowledge has been steadily acquired about genetic and congenital cholangiopathies, and this has led to a better understanding of the mechanisms of acquired cholangiopathies. This Review focuses on findings from studies on Alagille syndrome, polycystic liver diseases, fibropolycystic liver diseases (Caroli disease and congenital hepatic fibrosis) and cystic fibrosis-related liver disease. In particular, knowledge on the role of Notch signalling in biliary repair and tubulogenesis has been advanced by work on Alagille syndrome, and investigations in polycystic liver diseases have highlighted the role of primary cilia in biliary pathophysiology and the concept of biliary angiogenic signalling and its role in cyst growth and biliary repair. In fibropolycystic liver disease, research has shown that loss of fibrocystin generates a signalling cascade that increases β-catenin signalling, activates the NOD-, LRR- and pyrin domain-containing 3 inflammasome, and promotes production of IL-1β and other chemokines that attract macrophages and orchestrate the process of pericystic and portal fibrosis, which are the main mechanisms of progression in cholangiopathies. In cystic fibrosis-related liver disease, lack of cystic fibrosis transmembrane conductance regulator increases the sensitivity of epithelial Toll-like receptor 4 that sustains the secretion of nuclear factor-κB-dependent cytokines and peribiliary inflammation in response to gut-derived products, providing a model for primary sclerosing cholangitis. These signalling mechanisms may be targeted therapeutically and they offer a possibility for the development of novel treatments for acquired cholangiopathies.
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Affiliation(s)
- Luca Fabris
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Romina Fiorotto
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA
| | - Carlo Spirli
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA
| | | | - Valeria Mariotti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Mario Strazzabosco
- Liver Center, Department of Medicine, Yale University, New Haven, CT, USA.
- Department of Molecular Medicine, University of Padova, Padova, Italy.
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29
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Mianné J, Ahmed E, Bourguignon C, Fieldes M, Vachier I, Bourdin A, Assou S, De Vos J. Induced Pluripotent Stem Cells for Primary Ciliary Dyskinesia Modeling and Personalized Medicine. Am J Respir Cell Mol Biol 2019; 59:672-683. [PMID: 30230352 DOI: 10.1165/rcmb.2018-0213tr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare and heterogeneous genetic disorder that affects the structure and function of motile cilia. In the airway epithelium, impaired ciliary motion results in reduced or absent mucociliary clearance that leads to the appearance of chronic airway infection, sinusitis, and bronchiectasis. Currently, there is no effective treatment for PCD, and research is limited by the lack of convenient models to study this disease and investigate innovative therapies. Furthermore, the high heterogeneity of PCD genotypes is likely to hinder the development of a single therapy for all patients. The generation of patient-derived, induced pluripotent stem cells, and their differentiation into airway epithelium, as well as genome editing technologies, could represent major tools for in vitro PCD modeling and for developing personalized therapies. Here, we review PCD pathogenesis and then discuss how human induced pluripotent stem cells could be used to model this disease for the development of innovative, patient-specific biotherapies.
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Affiliation(s)
- Joffrey Mianné
- 1 Institute for Regenerative Medicine and Biotherapy, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | - Engi Ahmed
- 1 Institute for Regenerative Medicine and Biotherapy, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | - Chloé Bourguignon
- 1 Institute for Regenerative Medicine and Biotherapy, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | - Mathieu Fieldes
- 1 Institute for Regenerative Medicine and Biotherapy, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | - Isabelle Vachier
- 2 PhyMedExp, University of Montpellier, INSERM, Centre Hospitalier Universitaire Montpellier, Montpellier, France; and
| | - Arnaud Bourdin
- 2 PhyMedExp, University of Montpellier, INSERM, Centre Hospitalier Universitaire Montpellier, Montpellier, France; and
| | - Said Assou
- 1 Institute for Regenerative Medicine and Biotherapy, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | - John De Vos
- 1 Institute for Regenerative Medicine and Biotherapy, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire Montpellier, Montpellier, France.,3 Centre Hospitalier Universitaire Montpellier, Department of Cell and Tissue Engineering, Hospital Saint-Eloi, Montpellier, France
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30
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Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing. BMC Med Genomics 2019; 12:66. [PMID: 31118097 PMCID: PMC6532208 DOI: 10.1186/s12920-019-0529-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background In cystic fibrosis (CF), impaired immune cell responses, driven by the dysfunctional CF transmembrane conductance regulator (CFTR) gene, may determine the disease severity but clinical heterogeneity remains a major therapeutic challenge. The characterization of molecular mechanisms underlying impaired immune responses in CF may reveal novel targets with therapeutic potential. Therefore, we utilized simultaneous RNA sequencing targeted at identifying differentially expressed genes, transcripts, and miRNAs that characterize impaired immune responses triggered by CF and its phenotypes. Methods Peripheral blood mononuclear cells (PBMCs) extracted from a healthy donor were stimulated with plasma from CF patients (n = 9) and healthy controls (n = 3). The PBMCs were cultured (1 × 105 cells/well) for 9 h at 37 ° C in 5% CO2. After culture, total RNA was extracted from each sample and used for simultaneous total RNA and miRNA sequencing. Results Analysis of expression signatures from peripheral blood mononuclear cells induced by plasma of CF patients and healthy controls identified 151 genes, 154 individual transcripts, and 41 miRNAs differentially expressed in CF compared to HC while the expression signatures of 285 genes, 241 individual transcripts, and seven miRNAs differed due to CF phenotypes. Top immune pathways influenced by CF included agranulocyte adhesion, diapedesis signaling, and IL17 signaling, while those influenced by CF phenotypes included natural killer cell signaling and PI3K signaling in B lymphocytes. Upstream regulator analysis indicated dysregulation of CCL5, NF-κB and IL1A due to CF while dysregulation of TREM1 and TP53 regulators were associated with CF phenotype. Five miRNAs showed inverse expression patterns with three target genes relevant in CF-associated impaired immune pathways while two miRNAs showed inverse expression patterns with two target genes relevant to a dysregulated immune pathway associated with CF phenotypes. Conclusions Our results indicate that miRNAs and individual transcript variants are relevant molecular targets contributing to impaired immune cell responses in CF. Electronic supplementary material The online version of this article (10.1186/s12920-019-0529-0) contains supplementary material, which is available to authorized users.
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31
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Vaughan A, Yang IA. CRISPR-Cas9 technology: A new direction for personalized medicine in respiratory disease? Respirology 2019; 24:614-615. [PMID: 31033105 DOI: 10.1111/resp.13570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Annalicia Vaughan
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Metro North Hospital and Health Service, Brisbane, QLD, Australia
| | - Ian A Yang
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Metro North Hospital and Health Service, Brisbane, QLD, Australia
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32
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Swahn H, Harris A. Cell-Selective Regulation of CFTR Gene Expression: Relevance to Gene Editing Therapeutics. Genes (Basel) 2019; 10:E235. [PMID: 30893953 PMCID: PMC6471542 DOI: 10.3390/genes10030235] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 12/19/2022] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene is an attractive target for gene editing approaches, which may yield novel therapeutic approaches for genetic diseases such as cystic fibrosis (CF). However, for gene editing to be effective, aspects of the three-dimensional (3D) structure and cis-regulatory elements governing the dynamic expression of CFTR need to be considered. In this review, we focus on the higher order chromatin organization required for normal CFTR locus function, together with the complex mechanisms controlling expression of the gene in different cell types impaired by CF pathology. Across all cells, the CFTR locus is organized into an invariant topologically associated domain (TAD) established by the architectural proteins CCCTC-binding factor (CTCF) and cohesin complex. Additional insulator elements within the TAD also recruit these factors. Although the CFTR promoter is required for basal levels of expression, cis-regulatory elements (CREs) in intergenic and intronic regions are crucial for cell-specific and temporal coordination of CFTR transcription. These CREs are recruited to the promoter through chromatin looping mechanisms and enhance cell-type-specific expression. These features of the CFTR locus should be considered when designing gene-editing approaches, since failure to recognize their importance may disrupt gene expression and reduce the efficacy of therapies.
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Affiliation(s)
- Hannah Swahn
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44067, USA.
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44067, USA.
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33
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Liu Y, Wang K. Exploiting the Diversity of Ion Channels: Modulation of Ion Channels for Therapeutic Indications. Handb Exp Pharmacol 2019; 260:187-205. [PMID: 31820177 DOI: 10.1007/164_2019_333] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ion channels are macromolecular proteins that form water-filled pores in cell membranes and they are critical for a variety of physiological and pharmacological functions. Dysfunctional ion channels can cause diseases known as channelopathies. Ion channels are encoded by approximately 400 genes, representing the second largest class of proven drug targets for therapeutic areas including neuropsychiatric disorders, cardiovascular and metabolic diseases, immunological diseases, nephrological diseases, gastrointestinal diseases, pulmonary/respiratory diseases, and many cancers. With more ion channel structures are being solved and functional robust assays are being developed, there are tremendous opportunities for identifying specific modulators targeting ion channels for new therapy.
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Affiliation(s)
- Yani Liu
- Department of Pharmacology, Qingdao University School of Pharmacy, Qingdao, China
| | - KeWei Wang
- Department of Pharmacology, Qingdao University School of Pharmacy, Qingdao, China.
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Hodges CA, Conlon RA. Delivering on the promise of gene editing for cystic fibrosis. Genes Dis 2018; 6:97-108. [PMID: 31193992 PMCID: PMC6545485 DOI: 10.1016/j.gendis.2018.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
In this review, we describe a path for translation of gene editing into therapy for cystic fibrosis (CF). Cystic fibrosis results from mutations in the CFTR gene, with one allele predominant in patient populations. This simple, genetic etiology makes gene editing appealing for treatment of this disease. There already have been success in applying this approach to cystic fibrosis in cell and animal models, although these advances have been modest in comparison to advances for other disease. Less than six years after its first demonstration in animals, CRISPR/Cas gene editing is in early clinical trials for several disorders. Most clinical trials, thus far, attempt to edit genes in cells of the blood lineages. The advantage of the blood is that the stem cells are known, can be isolated, edited, selected, expanded, and returned to the body. The likely next trials will be in the liver, which is accessible to many delivery methods. For cystic fibrosis, the biggest hurdle is to deliver editors to other, less accessible organs. We outline a path by which delivery can be improved. The translation of new therapies doesn't occur in isolation, and the development of gene editors is occurring as advances in gene therapy and small molecule therapeutics are being made. The advances made in gene therapy may help develop delivery vehicles for gene editing, although major improvements are needed. Conversely, the approval of effective small molecule therapies for many patients with cystic fibrosis will raise the bar for translation of gene editing.
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Affiliation(s)
- Craig A Hodges
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Ronald A Conlon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
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