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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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2
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Ghigo A, De Santi C, Hart M, Mitash N, Swiatecka-Urban A. Cell signaling and regulation of CFTR expression in cystic fibrosis cells in the era of high efficiency modulator therapy. J Cyst Fibros 2023; 22 Suppl 1:S12-S16. [PMID: 36621372 DOI: 10.1016/j.jcf.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/26/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP- and protein kinase A (PKA)-regulated channel, expressed on the luminal surface of secretory and absorptive epithelial cells. CFTR has a complex, cell-specific regulatory network playing a major role in cAMP- and Ca2+-activated secretion of electrolytes. It secretes intracellular Cl- and bicarbonate and regulates absorption of electrolytes by differentially controlling the activity of the epithelial Na+ channel (ENaC) in colon, airways, and sweat ducts. The CFTR gene expression is regulated by cell-specific, time-dependent mechanisms reviewed elsewhere [1]. This review will focus on the transcriptional, post-transcriptional, and translational regulation of CFTR by cAMP-PKA, non-coding (nc)RNAs, and TGF-β signaling pathways in cystic fibrosis (CF) cells.
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Affiliation(s)
- Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Torino, Via Nizza 52, Torino 10126, Italy.
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, 111St Stephen's Green, Dublin 2, Ireland
| | - Merrill Hart
- Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, United States
| | - Nilay Mitash
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, United States
| | - Agnieszka Swiatecka-Urban
- Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, United States
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3
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Yousif Hamdan AH, Zakaria F, Lourdes Pormento MK, Lawal OS, Opiegbe A, Zahid S, Guntipalli P, Nasr U, Hasan Rizvi SA. Cystic Fibrosis Transmembrane Conductance Regulator Protein Modulators in Children and Adolescents with different CF Genotypes - Systematic Review and Meta-Analysis. Curr Rev Clin Exp Pharmacol 2023; 19:CRCEP-EPUB-129191. [PMID: 36722487 DOI: 10.2174/2772432818666230201094115] [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: 05/28/2022] [Revised: 11/12/2022] [Accepted: 12/01/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To determine the efficacy of the first triple CFTR protein modulators in children and adolescents with cystic fibrosis. METHODS Systematic review and meta-analysis were conducted, following PRISMA guidelines. The following databases were searched extensively: PubMed/Medline, Clinical trials.gov, Google Scholar, Scopus, Embase, and Europe PMC using the keywords: "Ivacaftor," "Elexacaftor," "Tezacaftor," VX_661", VX_770", "VX_445", "cystic fibrosis". A total of ten randomized clinical trials were included in our analysis. Primary outcomes included: Absolute change in predicted FEV1 from baseline, Absolute change in sweat chloride test from baseline, Absolute change in BMI from baseline, Absolute change in CF-QR from baseline, and Adverse Events. RESULTS Among primary findings, significant absolute change in predictive FEV1 from baseline through 4 weeks favoured the triple CFTR protein modulators. [MD=11.80,95%CI=8.47_15.12, p value=<0.00001]; as well as CF_QR score [MD=0.00,95%CI=-2.50_2.50, p value=1.00], and BMI kg/m² change [MD=16.90,95%CI=12.73_21.06, p value=<0.00001]. No significant change was noted for CFTR channels activity in the treatment group when compared to placebo or VX_770/VX_661 [MD= -12.57,95%CI=-94.46_69.32, p value=0.76]. CONCLUSION In children aged ≥ 6 y old and adolescents with F508del_CFTR mutation, Elexacaftor-Tezacaftor-Ivacaftor tend to be more effective than first-generation therapy, demonstrating promising results by exhibiting significant improvement in lung function, body weight, and respiratory-related quality of life.
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Affiliation(s)
- Alaa Hassan Yousif Hamdan
- Larkin Community Hospital, Division of Clinical and Transitional Research, South Miami, Florida, USA
- Department of Paediatrics, Sudan Medical Specialization Board, Sudan
| | - Faiza Zakaria
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | | | | | | | | | - Prathima Guntipalli
- Larkin Community Hospital, South Miami, Florida
- Texas Woman's University, Dallas, Texas
| | - Ujala Nasr
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
- Nazareth Hospital, Philadelphia, PA
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4
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Matthaiou EI, Chiu W, Conrad C, Hsu J. Macrophage Lysosomal Alkalinization Drives Invasive Aspergillosis in a Mouse Cystic Fibrosis Model of Airway Transplantation. J Fungi (Basel) 2022; 8:751. [PMID: 35887506 PMCID: PMC9321820 DOI: 10.3390/jof8070751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 01/25/2023] Open
Abstract
Cystic fibrosis (CF) lung transplant recipients (LTRs) exhibit a disproportionately high rate of life-threatening invasive aspergillosis (IA). Loss of the cystic fibrosis transmembrane conductance regulator (CFTR-/-) in macrophages (mφs) has been associated with lyosomal alkalinization. We hypothesize that this alkalinization would persist in the iron-laden post-transplant microenvironment increasing the risk of IA. To investigate our hypothesis, we developed a murine CF orthotopic tracheal transplant (OTT) model. Iron levels were detected by immunofluorescence staining and colorimetric assays. Aspergillus fumigatus (Af) invasion was evaluated by Grocott methenamine silver staining. Phagocytosis and killing of Af conidia were examined by flow cytometry and confocal microscopy. pH and lysosomal acidification were measured by LysoSensorTM and LysotrackerTM, respectively. Af was more invasive in the CF airway transplant recipient compared to the WT recipient (p < 0.05). CFTR-/- mφs were alkaline at baseline, a characteristic that was increased with iron-overload. These CFTR-/- mφs were unable to phagocytose and kill Af conidia (p < 0.001). Poly(lactic-co-glycolic acid) (PLGA) nanoparticles acidified lysosomes, restoring the CFTR-/- mφs’ ability to clear conidia. Our results suggest that CFTR-/- mφs’ alkalinization interacts with the iron-loaded transplant microenvironment, decreasing the CF-mφs’ ability to kill Af conidia, which may explain the increased risk of IA. Therapeutic pH modulation after transplantation could decrease the risk of IA.
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Affiliation(s)
- Efthymia Iliana Matthaiou
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA; (E.I.M.); (W.C.)
| | - Wayland Chiu
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA; (E.I.M.); (W.C.)
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carol Conrad
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA;
| | - Joe Hsu
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA; (E.I.M.); (W.C.)
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5
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Molecular mechanisms of Cystic Fibrosis - how mutations lead to misfunction and guide therapy. Biosci Rep 2022; 42:231430. [PMID: 35707985 PMCID: PMC9251585 DOI: 10.1042/bsr20212006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Cystic fibrosis, the most common autosomal recessive disorder in Caucasians, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a cAMP-activated chloride and bicarbonate channel that regulates ion and water transport in secretory epithelia. Although all mutations lead to the lack or reduction in channel function, the mechanisms through which this occurs are diverse – ranging from lack of full-length mRNA, reduced mRNA levels, impaired folding and trafficking, targeting to degradation, decreased gating or conductance, and reduced protein levels to decreased half-life at the plasma membrane. Here, we review the different molecular mechanisms that cause cystic fibrosis and detail how these differences identify theratypes that can inform the use of directed therapies aiming at correcting the basic defect. In summary, we travel through CFTR life cycle from the gene to function, identifying what can go wrong and what can be targeted in terms of the different types of therapeutic approaches.
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6
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Bhattacharya R, Blankenheim Z, Scott PM, Cormier RT. CFTR and Gastrointestinal Cancers: An Update. J Pers Med 2022; 12:868. [PMID: 35743652 PMCID: PMC9224611 DOI: 10.3390/jpm12060868] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Cystic Fibrosis (CF) is a disease caused by mutations in the CFTR gene that severely affects the lungs as well as extra-pulmonary tissues, including the gastrointestinal (GI) tract. CFTR dysfunction resulting from either mutations or the downregulation of its expression has been shown to promote carcinogenesis. An example is the enhanced risk for several types of cancer in patients with CF, especially cancers of the GI tract. CFTR also acts as a tumor suppressor in diverse sporadic epithelial cancers in many tissues, primarily due to the silencing of CFTR expression via multiple mechanisms, but especially due to epigenetic regulation. This review provides an update on the latest research linking CFTR-deficiency to GI cancers, in both CF patients and in sporadic GI cancers, with a particular focus on cancer of the intestinal tract. It will discuss changes in the tissue landscape linked to CFTR-deficiency that may promote cancer development such as breakdowns in physical barriers, microbial dysbiosis and inflammation. It will also discuss molecular pathways and mechanisms that act upstream to modulate CFTR expression, such as by epigenetic silencing, as well as molecular pathways that act downstream of CFTR-deficiency, such as the dysregulation of the Wnt/β-catenin and NF-κB signaling pathways. Finally, it will discuss the emerging CFTR modulator drugs that have shown promising results in improving CFTR function in CF patients. The potential impact of these modulator drugs on the treatment and prevention of GI cancers can provide a new example of personalized cancer medicine.
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Affiliation(s)
| | | | - Patricia M. Scott
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA or (R.B.); (Z.B.)
| | - Robert T. Cormier
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA or (R.B.); (Z.B.)
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7
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Yin S, Mazumdar MN, Paranjapye A, Harris A. Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene. Genomics 2022; 114:110350. [PMID: 35346781 PMCID: PMC9509493 DOI: 10.1016/j.ygeno.2022.110350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 01/14/2023]
Abstract
Robust protocols to examine 3D chromatin structure have greatly advanced knowledge of gene regulatory mechanisms. Here we focus on the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which provides a paradigm for validating models of gene regulation built upon genome-wide analysis. We examine the mechanisms by which multiple cis-regulatory elements (CREs) at the CFTR gene coordinate its expression in intestinal epithelial cells. Using CRISPR/Cas9 to remove CREs, individually and in tandem, followed by assays of gene expression and higher-order chromatin structure (4C-seq), we reveal the cross-talk and dependency of two cell-specific intronic enhancers. The results suggest a mechanism whereby the locus responds when CREs are lost, which may involve activating transcription factors such as FOXA2. Also, by removing the 5' topologically-associating domain (TAD) boundary, we illustrate its impact on CFTR gene expression and architecture. These data suggest a multi-layered regulatory hierarchy that is highly sensitive to perturbations.
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8
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Farinha CM, Gentzsch M. Revisiting CFTR Interactions: Old Partners and New Players. Int J Mol Sci 2021; 22:13196. [PMID: 34947992 PMCID: PMC8703571 DOI: 10.3390/ijms222413196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/07/2023] Open
Abstract
Remarkable progress in CFTR research has led to the therapeutic development of modulators that rescue the basic defect in cystic fibrosis. There is continuous interest in studying CFTR molecular disease mechanisms as not all cystic fibrosis patients have a therapeutic option available. Addressing the basis of the problem by comprehensively understanding the critical molecular associations of CFTR interactions remains key. With the availability of CFTR modulators, there is interest in comprehending which interactions are critical to rescue CFTR and which are altered by modulators or CFTR mutations. Here, the current knowledge on interactions that govern CFTR folding, processing, and stability is summarized. Furthermore, we describe protein complexes and signal pathways that modulate the CFTR function. Primary epithelial cells display a spatial control of the CFTR interactions and have become a common system for preclinical and personalized medicine studies. Strikingly, the novel roles of CFTR in development and differentiation have been recently uncovered and it has been revealed that specific CFTR gene interactions also play an important role in transcriptional regulation. For a comprehensive understanding of the molecular environment of CFTR, it is important to consider CFTR mutation-dependent interactions as well as factors affecting the CFTR interactome on the cell type, tissue-specific, and transcriptional levels.
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Affiliation(s)
- Carlos M. Farinha
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Martina Gentzsch
- Marsico Lung Institute and Cystic Fibrosis Research Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pediatrics, Division of Pediatric Pulmonology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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9
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Dutta RK, Chinnapaiyan S, Santiago MJ, Rahman I, Unwalla HJ. Gene-specific MicroRNA antagonism protects against HIV Tat and TGF-β-mediated suppression of CFTR mRNA and function. Biomed Pharmacother 2021; 142:112090. [PMID: 34463266 PMCID: PMC9100877 DOI: 10.1016/j.biopha.2021.112090] [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: 06/30/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND MicroRNAs play an important role in health and disease. TGF-β signaling, upregulated by HIV Tat, and in chronic airway diseases and smokers upregulates miR-145-5p to suppress cystic fibrosis transmembrane conductance regulator (CFTR). CFTR suppression in chronic airway diseases like Cystic Fibrosis, COPD and smokers has been associated with suppressed MCC and recurrent lung infections and inflammation. This can explain the emergence of recurrent lung infections and inflammation in people living with HIV. METHODS Tat-induced aberrant microRNAome was identified by miRNA expression analysis. microRNA mimics and antagomirs were used to validate the identified miRNAs involved in Tat mediated CFTR mRNA suppression. CRISPR-based editing of the miRNA target sites in CFTR 3'UTR was used to determine rescue of CFTR mRNA and function in airway epithelial cell lines and in primary human bronchial epithelial cells exposed to TGF-β and Tat. FINDINGS HIV Tat upregulates miR-145-5p and miR-509-3p. The two miRNAs demonstrate co-operative effects in suppressing CFTR. CRISPR-based editing of the miRNA target site preserves CFTR mRNA and function in airway epithelial cells INTERPRETATION: Given the important roles of TGF-β signaling and the multitude of genes regulated by miRNAs, we demonstrate that CRISPR-based gene-specific microRNA antagonism approach can preserve CFTR mRNA and function in the context of HIV Tat and TGF-β signaling without suppressing expression of other genes regulated by miR-145-5p.
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Affiliation(s)
- R K Dutta
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - S Chinnapaiyan
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - M J Santiago
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - I Rahman
- University of Rochester Medical Center, Departments of Environmental Medicine and Pulmonary Medicine, Rochester, NY 14642, USA
| | - H J Unwalla
- Department of Immunology and Nanomedicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
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10
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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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11
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Kerschner JL, Paranjapye A, NandyMazumdar M, Yin S, Leir SH, Harris A. OTX2 regulates CFTR expression during endoderm differentiation and occupies 3' cis-regulatory elements. Dev Dyn 2021; 250:684-700. [PMID: 33386644 PMCID: PMC11227118 DOI: 10.1002/dvdy.293] [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: 10/05/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Cell-specific and developmental mechanisms contribute to expression of the cystic fibrosis transmembrane conductance regulator (CFTR) gene; however, its developmental regulation is poorly understood. Here we use human induced pluripotent stem cells differentiated into pseudostratified airway epithelial cells to study these mechanisms. RESULTS Changes in gene expression and open chromatin profiles were investigated by RNA-seq and ATAC-seq, and revealed that alterations in CFTR expression are associated with differences in stage-specific open chromatin. Additionally, two novel open chromatin regions, at +19.6 kb and +22.6 kb 3' to the CFTR translational stop signal, were observed in definitive endoderm (DE) cells, prior to an increase in CFTR expression in anterior foregut endoderm (AFE) cells. Chromatin studies in DE and AFE cells revealed enrichment of active enhancer marks and occupancy of OTX2 at these sites in DE cells. Loss of OTX2 in DE cells alters histone modifications across the CFTR locus and results in a 2.5-fold to 5-fold increase in CFTR expression. However, deletion of the +22.6 kb site alone does not affect CFTR expression in DE or AFE cells. CONCLUSIONS These results suggest that a network of interacting cis-regulatory elements recruit OTX2 to the locus to impact CFTR expression during early endoderm differentiation.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Monali NandyMazumdar
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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12
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Collobert M, Bocher O, Le Nabec A, Génin E, Férec C, Moisan S. CFTR Cooperative Cis-Regulatory Elements in Intestinal Cells. Int J Mol Sci 2021; 22:ijms22052599. [PMID: 33807548 PMCID: PMC7961337 DOI: 10.3390/ijms22052599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 11/16/2022] Open
Abstract
About 8% of the human genome is covered with candidate cis-regulatory elements (cCREs). Disruptions of CREs, described as "cis-ruptions" have been identified as being involved in various genetic diseases. Thanks to the development of chromatin conformation study techniques, several long-range cystic fibrosis transmembrane conductance regulator (CFTR) regulatory elements were identified, but the regulatory mechanisms of the CFTR gene have yet to be fully elucidated. The aim of this work is to improve our knowledge of the CFTR gene regulation, and to identity factors that could impact the CFTR gene expression, and potentially account for the variability of the clinical presentation of cystic fibrosis as well as CFTR-related disorders. Here, we apply the robust GWAS3D score to determine which of the CFTR introns could be involved in gene regulation. This approach highlights four particular CFTR introns of interest. Using reporter gene constructs in intestinal cells, we show that two new introns display strong cooperative effects in intestinal cells. Chromatin immunoprecipitation analyses further demonstrate fixation of transcription factors network. These results provide new insights into our understanding of the CFTR gene regulation and allow us to suggest a 3D CFTR locus structure in intestinal cells. A better understand of regulation mechanisms of the CFTR gene could elucidate cases of patients where the phenotype is not yet explained by the genotype. This would thus help in better diagnosis and therefore better management. These cis-acting regions may be a therapeutic challenge that could lead to the development of specific molecules capable of modulating gene expression in the future.
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Affiliation(s)
- Mégane Collobert
- Univ. Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (O.B.); (A.L.N.); (E.G.); (C.F.)
- Correspondence: (M.C.); (S.M.); Tel.: +33-298-0165-67 (M.C.)
| | - Ozvan Bocher
- Univ. Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (O.B.); (A.L.N.); (E.G.); (C.F.)
| | - Anaïs Le Nabec
- Univ. Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (O.B.); (A.L.N.); (E.G.); (C.F.)
| | - Emmanuelle Génin
- Univ. Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (O.B.); (A.L.N.); (E.G.); (C.F.)
| | - Claude Férec
- Univ. Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (O.B.); (A.L.N.); (E.G.); (C.F.)
- Department of Molecular Genetics and Reproduction Biology, CHRU Brest, F-29200 Brest, France
| | - Stéphanie Moisan
- Univ. Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; (O.B.); (A.L.N.); (E.G.); (C.F.)
- Department of Molecular Genetics and Reproduction Biology, CHRU Brest, F-29200 Brest, France
- Correspondence: (M.C.); (S.M.); Tel.: +33-298-0165-67 (M.C.)
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13
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Minso R, Schulz A, Dopfer C, Alfeis N, Barneveld AV, Makartian-Gyulumyan L, Hansen G, Junge S, Müller C, Ringshausen FCC, Sauer-Heilborn A, Stanke F, Stolpe C, Tamm S, Welte T, Dittrich AM, Tümmler B. Intestinal current measurement and nasal potential difference to make a diagnosis of cases with inconclusive CFTR genetics and sweat test. BMJ Open Respir Res 2020; 7:e000736. [PMID: 33020115 PMCID: PMC7537139 DOI: 10.1136/bmjresp-2020-000736] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/31/2020] [Accepted: 09/05/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Nasal potential difference (NPD) and intestinal current measurements (ICM) are cystic fibrosis transmembrane conductance regulator (CFTR) biomarkers recommended to make a diagnosis in individuals with inconclusive sweat test and CFTR genetics and a clinical suspicion for cystic fibrosis (CF) or CFTR-related disorder (CFTR-RD). METHODS NPD and ICM were measured according to standard operating procedures of the European Cystic Fibrosis Society Diagnostic Network Working Group. RESULTS We assessed 219 individuals by NPD or ICM who had been referred to our laboratory due to clinical symptoms suggestive of CF, but inconclusive sweat test and CFTR genetics (median age: 16.3 years, range 0.4 to 76 years). CF or CFTR-related disorder was diagnosed in 22 of 29 patients (76%) with a CFTR genotype of unknown or variable clinical significance and in 51 of 190 carriers (27%) of one (35/42) or no (16/148) identified CFTR mutation. If two CFTR sequence variants had been identified, the outcome of NPD and ICM was consistent with the classification of the CFTR2 database. Moreover, a suspected false-positive diagnosis of CF was confirmed in seven and withdrawn in eight patients. Of 26 individuals assessed by both NPD and ICM, eleven individuals exhibited discordant tracings of ICM and NPD, with one measurement being in the CF range and the other in the normal range. CONCLUSION The majority of patients whom we diagnosed with CF or CFTR-RD by extended electrophysiology are carriers of the wild-type CFTR coding sequence on at least one of their CF alleles. The disease-causing genetic lesions should reside in the non-coding region of CFTR or elsewhere in the genome, affecting the regulation of CFTR expression in a tissue-depending fashion which may explain the large within-group variability of CFTR activity in the respiratory and intestinal epithelium seen in this group.
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Affiliation(s)
- Rebecca Minso
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Angela Schulz
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Christian Dopfer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research DZL, Hannover, Germany
| | - Nadine Alfeis
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Andrea van Barneveld
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Hannover, Germany
| | - Lena Makartian-Gyulumyan
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Hannover, Germany
| | - Gesine Hansen
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research DZL, Hannover, Germany
| | - Sibylle Junge
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Carsten Müller
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Felix C C Ringshausen
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research DZL, Hannover, Germany
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | | | - Frauke Stanke
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research DZL, Hannover, Germany
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Hannover, Germany
| | - Cornelia Stolpe
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Stephanie Tamm
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Hannover, Germany
| | - Tobias Welte
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research DZL, Hannover, Germany
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Anna-Maria Dittrich
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research DZL, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research DZL, Hannover, Germany
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Hannover, Germany
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14
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Suzuki S, Crane AM, Anirudhan V, Barillà C, Matthias N, Randell SH, Rab A, Sorscher EJ, Kerschner JL, Yin S, Harris A, Mendel M, Kim K, Zhang L, Conway A, Davis BR. Highly Efficient Gene Editing of Cystic Fibrosis Patient-Derived Airway Basal Cells Results in Functional CFTR Correction. Mol Ther 2020; 28:1684-1695. [PMID: 32402246 DOI: 10.1016/j.ymthe.2020.04.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/01/2020] [Accepted: 04/23/2020] [Indexed: 12/26/2022] Open
Abstract
There is a strong rationale to consider future cell therapeutic approaches for cystic fibrosis (CF) in which autologous proximal airway basal stem cells, corrected for CFTR mutations, are transplanted into the patient's lungs. We assessed the possibility of editing the CFTR locus in these cells using zinc-finger nucleases and have pursued two approaches. The first, mutation-specific correction, is a footprint-free method replacing the CFTR mutation with corrected sequences. We have applied this approach for correction of ΔF508, demonstrating restoration of mature CFTR protein and function in air-liquid interface cultures established from bulk edited basal cells. The second is targeting integration of a partial CFTR cDNA within an intron of the endogenous CFTR gene, providing correction for all CFTR mutations downstream of the integration and exploiting the native CFTR promoter and chromatin architecture for physiologically relevant expression. Without selection, we observed highly efficient, site-specific targeted integration in basal cells carrying various CFTR mutations and demonstrated restored CFTR function at therapeutically relevant levels. Significantly, Omni-ATAC-seq analysis revealed minimal impact on the positions of open chromatin within the native CFTR locus. These results demonstrate efficient functional correction of CFTR and provide a platform for further ex vivo and in vivo editing.
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Affiliation(s)
- Shingo Suzuki
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ana M Crane
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Varada Anirudhan
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Cristina Barillà
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nadine Matthias
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Andras Rab
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Kenneth Kim
- Sangamo Therapeutics, Richmond, CA 94804, USA
| | - Lei Zhang
- Sangamo Therapeutics, Richmond, CA 94804, USA
| | | | - Brian R Davis
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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15
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Scott P, Anderson K, Singhania M, Cormier R. Cystic Fibrosis, CFTR, and Colorectal Cancer. Int J Mol Sci 2020; 21:E2891. [PMID: 32326161 PMCID: PMC7215855 DOI: 10.3390/ijms21082891] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF), caused by biallelic inactivating mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, has recently been categorized as a familial colorectal cancer (CRC) syndrome. CF patients are highly susceptible to early, aggressive colorectal tumor development. Endoscopic screening studies have revealed that by the age of forty 50% of CF patients will develop adenomas, with 25% developing aggressive advanced adenomas, some of which will have already advanced to adenocarcinomas. This enhanced risk has led to new CF colorectal cancer screening recommendations, lowering the initiation of endoscopic screening to age forty in CF patients, and to age thirty in organ transplant recipients. The enhanced risk for CRC also extends to the millions of people (more than 10 million in the US) who are heterozygous carriers of CFTR gene mutations. Further, lowered expression of CFTR is reported in sporadic CRC, where downregulation of CFTR is associated with poor survival. Mechanisms underlying the actions of CFTR as a tumor suppressor are not clearly understood. Dysregulation of Wnt/β-catenin signaling and disruption of intestinal stem cell homeostasis and intestinal barrier integrity, as well as intestinal dysbiosis, immune cell infiltration, stress responses, and intestinal inflammation have all been reported in human CF patients and in animal models. Notably, the development of new drug modalities to treat non-gastrointestinal pathologies in CF patients, especially pulmonary disease, offers hope that these drugs could be repurposed for gastrointestinal cancers.
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Affiliation(s)
| | | | | | - Robert Cormier
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; (P.S.); (K.A.); (M.S.)
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16
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NandyMazumdar M, Yin S, Paranjapye A, Kerschner JL, Swahn H, Ge A, Leir SH, Harris A. Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells. Nucleic Acids Res 2020; 48:3513-3524. [PMID: 32095812 PMCID: PMC7144911 DOI: 10.1093/nar/gkaa089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/14/2020] [Accepted: 02/03/2020] [Indexed: 12/14/2022] Open
Abstract
The CFTR gene lies within an invariant topologically associated domain (TAD) demarcated by CTCF and cohesin, but shows cell-type specific control mechanisms utilizing different cis-regulatory elements (CRE) within the TAD. Within the respiratory epithelium, more than one cell type expresses CFTR and the molecular mechanisms controlling its transcription are likely divergent between them. Here, we determine how two extragenic CREs that are prominent in epithelial cells in the lung, regulate expression of the gene. We showed earlier that these CREs, located at -44 and -35 kb upstream of the promoter, have strong cell-type-selective enhancer function. They are also responsive to inflammatory mediators and to oxidative stress, consistent with a key role in CF lung disease. Here, we use CRISPR/Cas9 technology to remove these CREs from the endogenous locus in human bronchial epithelial cells. Loss of either site extinguished CFTR expression and abolished long-range interactions between these sites and the gene promoter, suggesting non-redundant enhancers. The deletions also greatly reduced promoter interactions with the 5' TAD boundary. We show substantial recruitment of RNAPII to the -35 kb element and identify CEBPβ as a key activator of airway expression of CFTR, likely through occupancy at this CRE and the gene promoter.
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Affiliation(s)
- Monali NandyMazumdar
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Hannah Swahn
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Alex Ge
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44116, USA
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17
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Di W, Clark HA. Optical Nanosensors for in vivo Physiological Chloride Detection for Monitoring Cystic Fibrosis Treatment. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:1441-1448. [PMID: 32226484 PMCID: PMC7100910 DOI: 10.1039/c9ay02717c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Personalized approaches for continuous monitoring of chloride levels are potentially valuable for evaluating the efficacy of new treatments of genetic disorders such as cystic fibrosis. In this report, we validated optode-based nanosensors for real-time chloride monitoring in the interstitial fluid of living animals. These nanosensors take advantage of a ratiometric sensing scheme which demonstrates reversible and selective chloride detection in the physiological range. We further investigate how skin pigmentation affects the sensor performance during in vivo fluorescence imaging. We successfully monitored endogenous chloride changes using nanosensors during pharmacological treatment in a cystic fibrosis mouse model. We believe this platform is a valuable tool for chloride detection which could assess the efficacy of new treatments for cystic fibrosis.
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Affiliation(s)
- Wenjun Di
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115, United States
| | - Heather A Clark
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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18
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Paranjapye A, Ruffin M, Harris A, Corvol H. Genetic variation in CFTR and modifier loci may modulate cystic fibrosis disease severity. J Cyst Fibros 2020; 19 Suppl 1:S10-S14. [PMID: 31734115 PMCID: PMC7036019 DOI: 10.1016/j.jcf.2019.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
In patients with cystic fibrosis (CF), genetic variants within and outside the CFTR locus contribute to the variability of the disease severity. CFTR transcription is tightly regulated by cis-regulatory elements (CREs) that control the three-dimensional structure of the locus, chromatin accessibility and transcription factor recruitment. Variants within these CREs may contribute to the pathophysiology and to the phenotypic heterogeneity by altering CFTR transcript abundance. In addition to the CREs, variants outside the CFTR locus, namely "modifiers genes", may also be associated with the clinical variability. This review addresses variants at the CFTR locus itself and CFTR CREs, together with the outcomes of the latest modifier gene studies with respect to the different CF phenotypes.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA
| | - Manon Ruffin
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA.
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France; AP-HP, Hôpital Trousseau, Service de Pneumologie Pédiatrique, Paris, France.
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19
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Mithal A, Capilla A, Heinze D, Berical A, Villacorta-Martin C, Vedaie M, Jacob A, Abo K, Szymaniak A, Peasley M, Stuffer A, Mahoney J, Kotton DN, Hawkins F, Mostoslavsky G. Generation of mesenchyme free intestinal organoids from human induced pluripotent stem cells. Nat Commun 2020; 11:215. [PMID: 31924806 PMCID: PMC6954238 DOI: 10.1038/s41467-019-13916-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Efficient generation of human induced pluripotent stem cell (hiPSC)-derived human intestinal organoids (HIOs) would facilitate the development of in vitro models for a variety of diseases that affect the gastrointestinal tract, such as inflammatory bowel disease or Cystic Fibrosis. Here, we report a directed differentiation protocol for the generation of mesenchyme-free HIOs that can be primed towards more colonic or proximal intestinal lineages in serum-free defined conditions. Using a CDX2eGFP iPSC knock-in reporter line to track the emergence of hindgut progenitors, we follow the kinetics of CDX2 expression throughout directed differentiation, enabling the purification of intestinal progenitors and robust generation of mesenchyme-free organoids expressing characteristic markers of small intestinal or colonic epithelium. We employ HIOs generated in this way to measure CFTR function using cystic fibrosis patient-derived iPSC lines before and after correction of the CFTR mutation, demonstrating their future potential for disease modeling and therapeutic screening applications.
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Affiliation(s)
- Aditya Mithal
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
- The Department of Microbiology at Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Amalia Capilla
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
| | - Dar Heinze
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
- The Department of Surgery at Boston University School of Medicine, 72 E Concord Street, Boston, MA, 02118, USA
| | - Andrew Berical
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
- The Pulmonary Center at Boston University School of Medicine, 72 E Concord Street, Boston, MA, 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
| | - Marall Vedaie
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
| | - Anjali Jacob
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
| | - Kristine Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
| | - Aleksander Szymaniak
- Cystic Fibrosis Foundation Therapeutics Lab, 44 Hartwell Avenue, Lexington, MA, 02421, USA
| | - Megan Peasley
- Cystic Fibrosis Foundation Therapeutics Lab, 44 Hartwell Avenue, Lexington, MA, 02421, USA
| | - Alexander Stuffer
- Cystic Fibrosis Foundation Therapeutics Lab, 44 Hartwell Avenue, Lexington, MA, 02421, USA
| | - John Mahoney
- Cystic Fibrosis Foundation Therapeutics Lab, 44 Hartwell Avenue, Lexington, MA, 02421, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
- The Pulmonary Center at Boston University School of Medicine, 72 E Concord Street, Boston, MA, 02118, USA
| | - Finn Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA
- The Pulmonary Center at Boston University School of Medicine, 72 E Concord Street, Boston, MA, 02118, USA
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine of Boston University and Boston Medical Center, 670 Albany Street, Boston, MA, 02118, USA.
- The Department of Microbiology at Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.
- The Section of Gastroenterology in the Department of Medicine at Boston University School of Medicine, 650 Albany Street, Boston, MA, 02118, USA.
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20
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Favia M, de Bari L, Bobba A, Atlante A. An Intriguing Involvement of Mitochondria in Cystic Fibrosis. J Clin Med 2019; 8:jcm8111890. [PMID: 31698802 PMCID: PMC6912654 DOI: 10.3390/jcm8111890] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 12/16/2022] Open
Abstract
Cystic fibrosis (CF) occurs when the cystic fibrosis transmembrane conductance regulator (CFTR) protein is not synthetized and folded correctly. The CFTR protein helps to maintain the balance of salt and water on many body surfaces, such as the lung surface. When the protein is not working correctly, chloride becomes trapped in cells, then water cannot hydrate the cellular surface and the mucus covering the cells becomes thick and sticky. Furthermore, a defective CFTR appears to produce a redox imbalance in epithelial cells and extracellular fluids and to cause an abnormal generation of reactive oxygen species: as a consequence, oxidative stress has been implicated as a causative factor in the aetiology of the process. Moreover, massive evidences show that defective CFTR gives rise to extracellular GSH level decrease and elevated glucose concentrations in airway surface liquid (ASL), thus encouraging lung infection by pathogens in the CF advancement. Recent research in progress aims to rediscover a possible role of mitochondria in CF. Here the latest new and recent studies on mitochondrial bioenergetics are collected. Surprisingly, they have enabled us to ascertain that mitochondria have a leading role in opposing the high ASL glucose level as well as oxidative stress in CF.
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Affiliation(s)
- Maria Favia
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari—CNR, Via G. Amendola 122/O, 70126 Bari, Italy; (L.d.B.); (A.B.)
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari, Via E. Orabona 4, 70126 Bari, Italy
- Correspondence: (M.F.); (A.A.)
| | - Lidia de Bari
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari—CNR, Via G. Amendola 122/O, 70126 Bari, Italy; (L.d.B.); (A.B.)
| | - Antonella Bobba
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari—CNR, Via G. Amendola 122/O, 70126 Bari, Italy; (L.d.B.); (A.B.)
| | - Anna Atlante
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari—CNR, Via G. Amendola 122/O, 70126 Bari, Italy; (L.d.B.); (A.B.)
- Correspondence: (M.F.); (A.A.)
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