Molecular Basis and Gene Therapies of Cystic Fibrosis

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (31 March 2020) | Viewed by 76952

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Special Issue Editors


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Guest Editor
Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA 52242, USA
Interests: pathogenesis of cystic fibrosis lung and pancreatic disease; the development of animal models of cystic fibrosis; gene therapy of cystic fibrosis; lung stem cell biology

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Guest Editor
UMR 1078 "Genetics, Functional Genomics and Biotechnologies" INSERM, University of Western Brittany, French Blood Bank, Brest Hospital, F-29200 Brest, France
Interests: genetics of cystic fibrosis; genetics of pancreatitits and pancreatic diseases; genetics of autosomal dominant polycystic kidney disease (ADPKD); genetics of haemochromatosis; genetics of intellectual disability; genetics of hip dysplasia
Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
Interests: gene therapy of cystic fibrosis lung disease; recombinant adeno-associated virus; recombinant Boca virus

Special Issue Information

Dear Colleagues,

The journal Genes is pleased to announce a Special Issue entitled “Molecular Basis and Gene Therapies of Cystic Fibrosis”, which is seeking original research contributions. Topics areas in this Special Issue will include three broad areas relevant to developing molecular therapies for cystic fibrosis (CF): (1) molecular mechanisms of CFTR regulation, (2) disease pathogenesis, and (3) genetic therapies for CF. Research areas may include but are not limited to:

1) Molecular mechanisms of CFTR regulation.

  • CFTR gene regulation
  • Post-transcriptional regulation of CFTR
  • CFTR regulation at the cellular level
  • Regulation of CFTR channel function

2) Disease pathogenesis

  • Genotype/phenotype correlation
  • Molecular epidemiology of CF
  • Animal models of CF
  • Cellular models of CF disease processes
  • Cellular mechanisms of CF disease processes and CFTR function
  • Mechanisms of CF pathogenesis (lung, pancreas, liver, intestine, and other affected organs)
  • Molecular diagnosis, genetic counseling, and penetrance of CFTR variants

3) Genetic therapies for cystic fibrosis.

  • Gene editing
  • Gene replacement
  • Vector development
  • Testing of gene therapies in animal models

Dr. John Engelhardt
Dr. Claude Ferec
Dr. Ziying Yan
Guest Editors

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Keywords

  • CFTR
  • Pathogenesis
  • Gene therapy
  • Animal models
  • Vector development
  • Genotype/phenotype
  • Lung
  • Pancreas
  • CFTR regulation
  • Epidemiology

Published Papers (12 papers)

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Research

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20 pages, 3996 KiB  
Article
Detargeting Lentiviral-Mediated CFTR Expression in Airway Basal Cells Using miR-106b
by Soon H. Choi, Rosie E. Reeves, Guillermo S. Romano Ibarra, Thomas J. Lynch, Weam S. Shahin, Zehua Feng, Grace N. Gasser, Michael C. Winter, T. Idil Apak Evans, Xiaoming Liu, Meihui Luo, Yulong Zhang, David A. Stoltz, Eric J. Devor, Ziying Yan and John F. Engelhardt
Genes 2020, 11(10), 1169; https://doi.org/10.3390/genes11101169 - 06 Oct 2020
Cited by 4 | Viewed by 3002
Abstract
Lentiviral-mediated integration of a CFTR transgene cassette into airway basal cells is a strategy being considered for cystic fibrosis (CF) cell-based therapies. However, CFTR expression is highly regulated in differentiated airway cell types and a subset of intermediate basal cells destined to differentiate. [...] Read more.
Lentiviral-mediated integration of a CFTR transgene cassette into airway basal cells is a strategy being considered for cystic fibrosis (CF) cell-based therapies. However, CFTR expression is highly regulated in differentiated airway cell types and a subset of intermediate basal cells destined to differentiate. Since basal stem cells typically do not express CFTR, suppressing the CFTR expression from the lentiviral vector in airway basal cells may be beneficial for maintaining their proliferative capacity and multipotency. We identified miR-106b as highly expressed in proliferating airway basal cells and extinguished in differentiated columnar cells. Herein, we developed lentiviral vectors with the miR-106b-target sequence (miRT) to both study miR-106b regulation during basal cell differentiation and detarget CFTR expression in basal cells. Given that miR-106b is expressed in the 293T cells used for viral production, obstacles of viral genome integrity and titers were overcome by creating a 293T-B2 cell line that inducibly expresses the RNAi suppressor B2 protein from flock house virus. While miR-106b vectors effectively detargeted reporter gene expression in proliferating basal cells and following differentiation in the air–liquid interface and organoid cultures, the CFTR-miRT vector produced significantly less CFTR-mediated current than the non-miR-targeted CFTR vector following transduction and differentiation of CF basal cells. These findings suggest that miR-106b is expressed in certain airway cell types that contribute to the majority of CFTR anion transport in airway epithelium. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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17 pages, 7820 KiB  
Article
Human Nasal Epithelial Organoids for Therapeutic Development in Cystic Fibrosis
by Zhongyu Liu, Justin D. Anderson, Lily Deng, Stephen Mackay, Johnathan Bailey, Latona Kersh, Steven M. Rowe and Jennifer S. Guimbellot
Genes 2020, 11(6), 603; https://doi.org/10.3390/genes11060603 - 29 May 2020
Cited by 41 | Viewed by 5450
Abstract
We describe a human nasal epithelial (HNE) organoid model derived directly from patient samples that is well-differentiated and recapitulates the airway epithelium, including the expression of cilia, mucins, tight junctions, the cystic fibrosis transmembrane conductance regulator (CFTR), and ionocytes. This model requires few [...] Read more.
We describe a human nasal epithelial (HNE) organoid model derived directly from patient samples that is well-differentiated and recapitulates the airway epithelium, including the expression of cilia, mucins, tight junctions, the cystic fibrosis transmembrane conductance regulator (CFTR), and ionocytes. This model requires few cells compared to airway epithelial monolayer cultures, with multiple outcome measurements depending on the application. A novel feature of the model is the predictive capacity of lumen formation, a marker of baseline CFTR function that correlates with short-circuit current activation of CFTR in monolayers and discriminates the cystic fibrosis (CF) phenotype from non-CF. Our HNE organoid model is amenable to automated measurements of forskolin-induced swelling (FIS), which distinguishes levels of CFTR activity. While the apical side is not easily accessible, RNA- and DNA-based therapies intended for systemic administration could be evaluated in vitro, or it could be used as an ex vivo biomarker of successful repair of a mutant gene. In conclusion, this highly differentiated airway epithelial model could serve as a surrogate biomarker to assess correction of the mutant gene in CF or other diseases, recapitulating the phenotypic and genotypic diversity of the population. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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12 pages, 2678 KiB  
Article
Overcoming Immunological Challenges to Helper-Dependent Adenoviral Vector-Mediated Long-Term CFTR Expression in Mouse Airways
by Huibi Cao, Rongqi Duan and Jim Hu
Genes 2020, 11(5), 565; https://doi.org/10.3390/genes11050565 - 18 May 2020
Cited by 2 | Viewed by 2364
Abstract
Cystic Fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and CF patients require life-long treatment. Although CFTR modulators show a great potential for treating most CF patients, some individuals may not tolerate the treatment. [...] Read more.
Cystic Fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and CF patients require life-long treatment. Although CFTR modulators show a great potential for treating most CF patients, some individuals may not tolerate the treatment. In addition, there is no effective therapy for patients with some rare CFTR mutations, such as class I CF mutations, which lead to a lack of CFTR protein production. Therefore, other therapeutic strategies, such as gene therapy, have to be investigated. Currently, immune responses to gene therapy vectors and transgene products are a major obstacle to applying CF gene therapy to clinical applications. In this study, we examined the effects of cyclophosphamide on the modulation of host immune responses and for the improvement of the CFTR transgene expression in the repeated delivery of helper-dependent adenoviral (HD-Ad) vectors to mouse lungs. We have found that cyclophosphamide significantly decreased the expression of T cell genes, such as CD3 (cluster of differentiation 3) and CD4, and reduced their infiltration into mouse lung tissues. We have also found that the levels of the anti-adenoviral antibody and neutralizing activity as well as B-cell infiltration into the mouse lung tissues were significantly reduced with this treatment. Correspondingly, the expression of the human CFTR transgene has been significantly improved with cyclophosphamide administration compared to the group with no treatment. These data suggest that the sustained expression of the human CFTR transgene in mouse lungs through repeated vector delivery can be achieved by transient immunosuppression. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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14 pages, 593 KiB  
Article
Analysis of CFTR Mutation Spectrum in Ethnic Russian Cystic Fibrosis Patients
by Nika V. Petrova, Nataliya Y. Kashirskaya, Tatyana A. Vasilyeva, Elena I. Kondratyeva, Elena K. Zhekaite, Anna Y. Voronkova, Victoria D. Sherman, Varvara A. Galkina, Eugeny K. Ginter, Sergey I. Kutsev, Andrey V. Marakhonov and Rena A. Zinchenko
Genes 2020, 11(5), 554; https://doi.org/10.3390/genes11050554 - 15 May 2020
Cited by 17 | Viewed by 5178
Abstract
The distribution and frequency of the CFTR gene mutations vary considerably between countries and ethnic groups. Russians are an East Slavic ethnic groups are native to Eastern Europe. Russians, the most numerous people of the Russian Federation (RF), make about 80% of the [...] Read more.
The distribution and frequency of the CFTR gene mutations vary considerably between countries and ethnic groups. Russians are an East Slavic ethnic groups are native to Eastern Europe. Russians, the most numerous people of the Russian Federation (RF), make about 80% of the population. The aim is to reveal the molecular causes of CF in ethnic Russian patients as comprehensively as possible. The analysis of most common CFTR mutations utilized for CF diagnosis in multiethnic RF population accounts for about 83% of all CF-causing mutations in 1384 ethnic Russian patients. Variants c.1521_1523delCTT (F508del), c.54-5940_273+10250del21kb (CFTRdele2,3), c.2012delT (2143delT), c.2052_2053insA (2184insA), and c.3691delT (3821delT) are most typical for CF patients of Russian origin. DNA of 154 CF patients, Russian by origin, in whom at least one mutant allele was not previously identified (164 CF alleles), was analyzed by Sanger sequencing followed by the multiplex ligase-dependent probe amplification (MLPA) method. In addition to the 29 variants identified during the previous test for common mutations, 91 pathogenic CFTR variants were also revealed: 29 missense, 19 nonsense, 14 frame shift in/del, 17 splicing, 1 in frame ins, and 11 copy number variations (CNV). Each of the 61 variants was revealed once, and 17 twice. Each of the variants c.1209G>C (E403D), c.2128A>T (K710X), c.3883delA (4015delA), and c.3884_3885insT (4016insT) were detected for three, c.1766+1G>A (1898+1G>A) and c.2834C>T (S945L) for four, c.1766+1G>C (1898+1G>C) and c.(743+1_744-1)_(1584+1_1585-1)dup (CFTRdup6b-10) for five, c.2353C>T (R785X) and c.4004T>C (L1335P) for six, c.3929G>A (W1310X) for seven, c.580-1G>T (712-1G>T for eight, and c.1240_1244delCAAAA (1365del5) for 11 unrelated patients. A comprehensive analysis of CFTR mutant alleles with sequencing followed by MLPA, allowed not only the identification of 163 of 164 unknown alleles in our patient sample, but also expansion of the mutation spectrum with novel and additional frequent variants for ethnic Russians. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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17 pages, 2635 KiB  
Article
Establishment of a Recombinant AAV2/HBoV1 Vector Production System in Insect Cells
by Xuefeng Deng, Wei Zou, Ziying Yan and Jianming Qiu
Genes 2020, 11(4), 439; https://doi.org/10.3390/genes11040439 - 17 Apr 2020
Cited by 7 | Viewed by 3506
Abstract
We have previously developed an rAAV2/HBoV1 vector in which a recombinant adeno-associated virus 2 (rAAV2) genome is pseudopackaged into a human bocavirus 1 (HBoV1) capsid. Recently, the production of rAAV2/HBoV1 in human embryonic kidney (HEK) 293 cells has been greatly improved in the [...] Read more.
We have previously developed an rAAV2/HBoV1 vector in which a recombinant adeno-associated virus 2 (rAAV2) genome is pseudopackaged into a human bocavirus 1 (HBoV1) capsid. Recently, the production of rAAV2/HBoV1 in human embryonic kidney (HEK) 293 cells has been greatly improved in the absence of any HBoV1 nonstructural proteins (NS). This NS-free production system yields over 16-fold more vectors than the original production system that necessitates NS expression. The production of rAAV with infection of baculovirus expression vector (BEV) in the suspension culture of Sf9 insect cells is highly efficient and scalable. Since the replication of the rAAV2 genome in the BEV system is well established, we aimed to develop a BEV system to produce the rAAV2/HBoV1 vector in Sf9 cells. We optimized the usage of translation initiation signals of the HBoV1 capsid proteins (Cap), and constructed a BEV Bac-AAV2Rep-HBoV1Cap, which expresses the AAV2 Rep78 and Rep52 as well as the HBoV1 VP1, VP2, and VP3 at the appropriate ratios. We found that it is sufficient as a trans helper to the production of rAAV2/HBoV1 in Sf9 cells that were co-infected with the transfer Bac-AAV2ITR-GFP-luc that carried a 5.4-kb oversized rAAV2 genome with dual reporters. Further study found that incorporation of an HBoV1 small NS, NP1, in the system maximized the viral DNA replication and thus the rAAV2/HBoV1 vector production at a level similar to that of the rAAV2 vector in Sf9 cells. However, the transduction potency of the rAAV2/HBoV1 vector produced from BEV-infected Sf9 cells was 5–7-fold lower in polarized human airway epithelia than that packaged in HEK293 cells. Transmission electron microscopy analysis found that the vector produced in Sf9 cells had a high percentage of empty capsids, suggesting the pseudopackage of the rAAV2 genome in HBoV1 capsid is not as efficient as in the capsids of AAV2. Nevertheless, our study demonstrated that the rAAV2/HBoV1 can be produced in insect cells with BEVs at a comparable yield to rAAV, and that the highly efficient expression of the HBoV1 capsid proteins warrants further optimization. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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15 pages, 2385 KiB  
Article
Extracellular Vesicle-Mediated siRNA Delivery, Protein Delivery, and CFTR Complementation in Well-Differentiated Human Airway Epithelial Cells
by Brajesh K. Singh, Ashley L. Cooney, Sateesh Krishnamurthy and Patrick L. Sinn
Genes 2020, 11(4), 351; https://doi.org/10.3390/genes11040351 - 26 Mar 2020
Cited by 10 | Viewed by 3595
Abstract
Extracellular vesicles (EVs) are a class of naturally occurring secreted cellular bodies that are involved in long distance cell-to-cell communication. Proteins, lipids, mRNA, and miRNA can be packaged into these vesicles and released from the cell. This information is then delivered to target [...] Read more.
Extracellular vesicles (EVs) are a class of naturally occurring secreted cellular bodies that are involved in long distance cell-to-cell communication. Proteins, lipids, mRNA, and miRNA can be packaged into these vesicles and released from the cell. This information is then delivered to target cells. Since EVs are naturally adapted molecular messengers, they have emerged as an innovative, inexpensive, and robust method to deliver therapeutic cargo in vitro and in vivo. Well-differentiated primary cultures of human airway epithelial cells (HAE) are refractory to standard transfection techniques. Indeed, common strategies used to overexpress or knockdown gene expression in immortalized cell lines simply have no detectable effect in HAE. Here we use EVs to efficiently deliver siRNA or protein to HAE. Furthermore, EVs can deliver CFTR protein to cystic fibrosis donor cells and functionally correct the Cl channel defect in vitro. EV-mediated delivery of siRNA or proteins to HAE provides a powerful genetic tool in a model system that closely recapitulates the in vivo airways. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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11 pages, 400 KiB  
Article
High Prevalence of Staphylococcus aureus Enterotoxin Gene Cluster Superantigens in Cystic Fibrosis Clinical Isolates
by Anthony J. Fischer, Samuel H. Kilgore, Sachinkumar B. Singh, Patrick D. Allen, Alexis R. Hansen, Dominique H. Limoli and Patrick M. Schlievert
Genes 2019, 10(12), 1036; https://doi.org/10.3390/genes10121036 - 12 Dec 2019
Cited by 24 | Viewed by 3185
Abstract
Background: Staphylococcus aureus is a highly prevalent respiratory pathogen in cystic fibrosis (CF). It is unclear how this organism establishes chronic infections in CF airways. We hypothesized that S. aureus isolates from patients with CF would share common virulence properties that enable chronic [...] Read more.
Background: Staphylococcus aureus is a highly prevalent respiratory pathogen in cystic fibrosis (CF). It is unclear how this organism establishes chronic infections in CF airways. We hypothesized that S. aureus isolates from patients with CF would share common virulence properties that enable chronic infection. Methods: 77 S. aureus isolates were obtained from 45 de-identified patients with CF at the University of Iowa. We assessed isolates phenotypically and used genotyping assays to determine the presence or absence of 18 superantigens (SAgs). Results: We observed phenotypic diversity among S. aureus isolates from patients with CF. Genotypic analysis for SAgs revealed 79.8% of CF clinical isolates carried all six members of the enterotoxin gene cluster (EGC). MRSA and MSSA isolates had similar prevalence of SAgs. We additionally observed that EGC SAgs were prevalent in S. aureus isolated from two geographically distinct CF centers. Conclusions: S. aureus SAgs belonging to the EGC are highly prevalent in CF clinical isolates. The greater prevalence in these SAgs in CF airway specimens compared to skin isolates suggests that these toxins confer selective advantage in the CF airway. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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Review

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16 pages, 1648 KiB  
Review
Molecular Diagnosis and Genetic Counseling of Cystic Fibrosis and Related Disorders: New Challenges
by Thierry Bienvenu, Maureen Lopez and Emmanuelle Girodon
Genes 2020, 11(6), 619; https://doi.org/10.3390/genes11060619 - 04 Jun 2020
Cited by 20 | Viewed by 11365
Abstract
Identification of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and its numerous variants opened the way to fantastic breakthroughs in diagnosis, research and treatment of cystic fibrosis (CF). The current and future challenges of molecular diagnosis of CF and CFTR-related disorders and [...] Read more.
Identification of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and its numerous variants opened the way to fantastic breakthroughs in diagnosis, research and treatment of cystic fibrosis (CF). The current and future challenges of molecular diagnosis of CF and CFTR-related disorders and of genetic counseling are here reviewed. Technological advances have enabled to make a diagnosis of CF with a sensitivity of 99% by using next generation sequencing in a single step. The detection of heretofore unidentified variants and ethnic-specific variants remains challenging, especially for newborn screening (NBS), CF carrier testing and genotype-guided therapy. Among the criteria for assessing the impact of variants, population genetics data are insufficiently taken into account and the penetrance of CF associated with CFTR variants remains poorly known. The huge diversity of diagnostic and genetic counseling indications for CFTR studies makes assessment of variant disease-liability critical. This is especially discussed in the perspective of wide genome analyses for NBS and CF carrier screening in the general population, as future challenges. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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13 pages, 316 KiB  
Review
The Changing Epidemiology of Cystic Fibrosis: Incidence, Survival and Impact of the CFTR Gene Discovery
by Virginie Scotet, Carine L’Hostis and Claude Férec
Genes 2020, 11(6), 589; https://doi.org/10.3390/genes11060589 - 26 May 2020
Cited by 147 | Viewed by 16746
Abstract
Significant advances in the management of cystic fibrosis (CF) in recent decades have dramatically changed the epidemiology and prognosis of this serious disease, which is no longer an exclusively pediatric disease. This paper aims to review the changes in the incidence and survival [...] Read more.
Significant advances in the management of cystic fibrosis (CF) in recent decades have dramatically changed the epidemiology and prognosis of this serious disease, which is no longer an exclusively pediatric disease. This paper aims to review the changes in the incidence and survival of CF and to assess the impact of the discovery of the responsible gene (the CFTR gene) on these changes. The incidence of CF appears to be decreasing in most countries and patient survival, which can be monitored by various indicators, has improved substantially, with an estimated median age of survival of approximately50 years today. Cloning of the CFTR gene 30 years ago and efforts to identify its many mutations have greatly improved the management of CF. Implementation of genetic screening policies has enabled earlier diagnosis (via newborn screening), in addition to prevention within families or in the general population in some areas (via prenatal diagnosis, family testing or population carrier screening). In the past decade, in-depth knowledge of the molecular bases of CF has also enabled the emergence of CFTR modulator therapies which have led to major clinical advances in the treatment of CF. All of these phenomena have contributed to changing the face of CF. The advent of targeted therapies has paved the way for precision medicine and is expected to further improve survival in the coming years. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
27 pages, 1824 KiB  
Review
Transcriptomic and Proteostasis Networks of CFTR and the Development of Small Molecule Modulators for the Treatment of Cystic Fibrosis Lung Disease
by Matthew D. Strub and Paul B. McCray, Jr.
Genes 2020, 11(5), 546; https://doi.org/10.3390/genes11050546 - 13 May 2020
Cited by 15 | Viewed by 6542
Abstract
Cystic fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The diversity of mutations and the multiple ways by which the protein is affected present challenges for therapeutic development. The observation [...] Read more.
Cystic fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The diversity of mutations and the multiple ways by which the protein is affected present challenges for therapeutic development. The observation that the Phe508del-CFTR mutant protein is temperature sensitive provided proof of principle that mutant CFTR could escape proteosomal degradation and retain partial function. Several specific protein interactors and quality control checkpoints encountered by CFTR during its proteostasis have been investigated for therapeutic purposes, but remain incompletely understood. Furthermore, pharmacological manipulation of many CFTR interactors has not been thoroughly investigated for the rescue of Phe508del-CFTR. However, high-throughput screening technologies helped identify several small molecule modulators that rescue CFTR from proteosomal degradation and restore partial function to the protein. Here, we discuss the current state of CFTR transcriptomic and biogenesis research and small molecule therapy development. We also review recent progress in CFTR proteostasis modulators and discuss how such treatments could complement current FDA-approved small molecules. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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17 pages, 918 KiB  
Review
The Microbiome in Cystic Fibrosis Pulmonary Disease
by Alice Françoise and Geneviève Héry-Arnaud
Genes 2020, 11(5), 536; https://doi.org/10.3390/genes11050536 - 11 May 2020
Cited by 57 | Viewed by 6591
Abstract
Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of [...] Read more.
Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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15 pages, 594 KiB  
Review
The Impact of the CFTR Gene Discovery on Cystic Fibrosis Diagnosis, Counseling, and Preventive Therapy
by Philip M. Farrell, Michael J. Rock and Mei W. Baker
Genes 2020, 11(4), 401; https://doi.org/10.3390/genes11040401 - 08 Apr 2020
Cited by 22 | Viewed by 8347
Abstract
Discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene was the long-awaited scientific advance that dramatically improved the diagnosis and treatment of cystic fibrosis (CF). The combination of a first-tier biomarker, immunoreactive trypsinogen (IRT), and, if high, DNA analysis for CF-causing [...] Read more.
Discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene was the long-awaited scientific advance that dramatically improved the diagnosis and treatment of cystic fibrosis (CF). The combination of a first-tier biomarker, immunoreactive trypsinogen (IRT), and, if high, DNA analysis for CF-causing variants, has enabled regions where CF is prevalent to screen neonates and achieve diagnoses within 1–2 weeks of birth when most patients are asymptomatic. In addition, IRT/DNA (CFTR) screening protocols simultaneously contribute important genetic data to determine genotype, prognosticate, and plan preventive therapies such as CFTR modulator selection. As the genomics era proceeds with affordable biotechnologies, the potential added value of whole genome sequencing will probably enhance personalized, precision care that can begin during infancy. Issues remain, however, about the optimal size of CFTR panels in genetically diverse regions and how best to deal with incidental findings. Because prospects for a primary DNA screening test are on the horizon, the debate about detecting heterozygote carriers will likely intensify, especially as we learn more about this relatively common genotype. Perhaps, at that time, concerns about CF heterozygote carrier detection will subside, and it will become recognized as beneficial. We share new perspectives on that issue in this article. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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