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Perdyan A, Jąkalski M, Horbacz M, Beheshti A, Mieczkowski J. Chromosomal positioning and epigenetic architecture influence DNA methylation patterns triggered by galactic cosmic radiation. Sci Rep 2024; 14:1324. [PMID: 38225252 PMCID: PMC10789781 DOI: 10.1038/s41598-024-51756-7] [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: 09/27/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
Despite surging interest in space travel in recent decades, the impacts of prolonged, elevated exposure to galactic cosmic radiation (GCR) on human health remain poorly understood. This form of ionizing radiation causes significant changes to biological systems including damage to DNA structure by altering epigenetic phenotype with emphasis on DNA methylation. Building on previous work by Kennedy et al. (Sci Rep 8(1): 6709. 10.1038/S41598-018-24755-8), we evaluated spatial DNA methylation patterns triggered by high-LET (56Fe, 28Si) and low-LET (X-ray) radiation and the influence of chromosome positioning and epigenetic architecture in distinct radial layers of cell nucleus. Next, we validated our results using gene expression data of mice irradiated with simulated GCR and JAXA astronauts. We showed that primarily 56Fe induces a persistent DNA methylation increase whereas 28Si and X-ray induce a decrease DNA methylation which is not persistent with time. Moreover, we highlighted the role of nuclear chromatin architecture in cell response to external radiation. In summary, our study provides novel insights towards epigenetic and transcriptomic response as well as chromatin multidimensional structure influence on galactic cosmic radiation damage.
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Affiliation(s)
- Adrian Perdyan
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Marcin Jąkalski
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
| | - Monika Horbacz
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
| | - Afshin Beheshti
- Space Biosciences Division, NASA Ames Research Center, Blue Marble Space Institute of Science, Moffett Field, CA, 94035, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jakub Mieczkowski
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland.
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2
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Zhou YH, Gallins PJ, Pace RG, Dang H, Aksit MA, Blue EE, Buckingham KJ, Collaco JM, Faino AV, Gordon WW, Hetrick KN, Ling H, Liu W, Onchiri FM, Pagel K, Pugh EW, Raraigh KS, Rosenfeld M, Sun Q, Wen J, Li Y, Corvol H, Strug LJ, Bamshad MJ, Blackman SM, Cutting GR, Gibson RL, O’Neal WK, Wright FA, Knowles MR. Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients. Am J Respir Crit Care Med 2023; 207:1324-1333. [PMID: 36921087 PMCID: PMC10595435 DOI: 10.1164/rccm.202209-1653oc] [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: 09/02/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influence. Identification of genetic modifiers has prognostic and therapeutic importance. Objectives: Identify genetic modifier loci and genes/pathways associated with pulmonary disease severity. Methods: Whole-genome sequencing data on 4,248 unique pwCF with pancreatic insufficiency and lung function measures were combined with imputed genotypes from an additional 3,592 patients with pancreatic insufficiency from the United States, Canada, and France. This report describes association of approximately 15.9 million SNPs using the quantitative Kulich normal residual mortality-adjusted (KNoRMA) lung disease phenotype in 7,840 pwCF using premodulator lung function data. Measurements and Main Results: Testing included common and rare SNPs, transcriptome-wide association, gene-level, and pathway analyses. Pathway analyses identified novel associations with genes that have key roles in organ development, and we hypothesize that these genes may relate to dysanapsis and/or variability in lung repair. Results confirmed and extended previous genome-wide association study findings. These whole-genome sequencing data provide finely mapped genetic information to support mechanistic studies. No novel primary associations with common single variants or rare variants were found. Multilocus effects at chr5p13 (SLC9A3/CEP72) and chr11p13 (EHF/APIP) were identified. Variant effect size estimates at associated loci were consistently ordered across the cohorts, indicating possible age or birth cohort effects. Conclusions: This premodulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and postmodulator genetic studies and the development of novel therapeutics for CF lung disease.
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Affiliation(s)
- Yi-Hui Zhou
- Bioinformatics Research Center
- Department of Biological Sciences, and
| | | | - Rhonda G. Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Hong Dang
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | | | - Elizabeth E. Blue
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Medical Genetics, Department of Medicine
| | | | | | - Anna V. Faino
- Children’s Core for Biostatistics, Epidemiology and Analytics in Research and
| | | | - Kurt N. Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | - Hua Ling
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | | | - Kymberleigh Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth W. Pugh
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | - Margaret Rosenfeld
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | | | | | - Yun Li
- Department of Biostatistics
- Department of Genetics, and
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau, Paris, France
- Centre de Recherche Saint Antoine, Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health
- Department of Statistical Sciences, and
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; and
- Program in Genetics and Genome Biology and
- The Center for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Genetic Medicine, Department of Pediatrics
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Scott M. Blackman
- McKusick-Nathans Department of Genetic Medicine
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ronald L. Gibson
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Wanda K. O’Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Fred A. Wright
- Bioinformatics Research Center
- Department of Biological Sciences, and
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
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3
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Zhang LY, Tan Y, Luo XJ, Wu JF, Ni YR. The roles of ETS transcription factors in liver fibrosis. Hum Cell 2023; 36:528-539. [PMID: 36547849 DOI: 10.1007/s13577-022-00848-5] [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: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
E26 transformation specific or E twenty-six (ETS) protein family consists of 28 transcription factors, five of which, named ETS1/2, PU.1, ERG and EHF, are known to involve in the development of liver fibrosis, and are expected to become diagnostic markers or therapeutic targets of liver fibrosis. In recent years, some small molecule inhibitors of ETS protein family have been discovered, which might open up a new path for the liver fibrosis therapy targeting ETS. This article reviews the research progress of ETS family members in the development liver fibrosis as well as their prospect of clinical application.
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Affiliation(s)
- Li-Ye Zhang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Yong Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Xiao-Jie Luo
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Jiang-Feng Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
| | - Yi-Ran Ni
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
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4
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Paranjapye A, NandyMazumdar M, Harris A. Krüppel-Like Factor 5 Regulates CFTR Expression Through Repression by Maintaining Chromatin Architecture Coupled with Direct Enhancer Activation. J Mol Biol 2022; 434:167561. [PMID: 35341742 DOI: 10.1016/j.jmb.2022.167561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023]
Abstract
Single cell RNA-sequencing has accurately identified cell types within the human airway that express the Cystic Fibrosis Transmembrane Conductance regulator (CFTR) gene. Low abundance CFTR transcripts are seen in many secretory cells, while high levels are restricted to rare pulmonary ionocytes. Here we focus on the mechanisms coordinating basal CFTR expression in the secretory compartment. Cell-selective regulation of CFTR is achieved within its invariant topologically associating domain by the recruitment of cis-regulatory elements (CREs). CRE activity is coordinated by cell-type-selective transcription factors. One such factor, Krüppel-Like Factor 5 (KLF5), profoundly represses CFTR transcript and protein in primary human airway epithelial cells and airway cell lines. Here we reveal the mechanism of action of KLF5 upon the CFTR gene. We find that depletion or ablation of KLF5 from airway epithelial cells changes higher order chromatin structure at the CFTR locus. Critical looping interactions that are required for normal gene expression are altered, the H3K27ac active chromatin mark is redistributed, and CTCF occupancy is modified. However, mutation of a single KLF5 binding site within a pivotal airway cell CRE abolishes CFTR expression. Hence, KLF5 has both direct activating and indirect repressive effects, which together coordinate CFTR expression in the airway.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Monali NandyMazumdar
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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5
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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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6
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Pineau F, Shumyatsky G, Owuor N, Nalamala N, Kotnala S, Bolla S, Marchetti N, Kelsen S, Criner GJ, Sajjan US. Microarray analysis identifies defects in regenerative and immune response pathways in COPD airway basal cells. ERJ Open Res 2020; 6:00656-2020. [PMID: 33313308 PMCID: PMC7720690 DOI: 10.1183/23120541.00656-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 01/07/2023] Open
Abstract
Background Airway basal cells are specialised stem cells and regenerate airway epithelium. Airway basal cells isolated from patients with COPD regenerate airway epithelium with an abnormal phenotype. We performed gene expression analysis to gain insights into the defective regenerative programme in COPD basal cells. Methods We conducted microarray analysis and compared COPD versus normal basal cells to identify differentially regulated genes (DEGs) and the enriched biological pathways. We determined the correlation of DEGs with cell polarisation and markers of ciliated and goblet cells. HOXB2 was knocked down in 16HBE14o− cells and monitored for polarisation of cells. HOXB2 expression in the lung sections was determined by immunofluorescence. Results Comparison of normal and COPD basal cell transcriptomic profiles highlighted downregulation of genes associated with tissue development, epithelial cell differentiation and antimicrobial humoral response. Expression of one of the tissue development genes, HOXB2 showed strong correlation with transepithelial resistance and this gene was downregulated in COPD basal cells. Knockdown of HOXB2, abrogated polarisation of epithelial cells in normal cells. Finally, HOXB2 expression was substantially reduced in the bronchial epithelium of COPD patients. Conclusions Defect in gene signatures involved in tissue development and epithelial differentiation were implicated in COPD basal cells. One of the tissue developmental genes, HOXB2, is substantially reduced in bronchial epithelium of COPD patients. Since HOXB2 contributes to airway epithelial cell polarisation, we speculate that reduced expression of HOXB2 in COPD may contribute to abnormal airway epithelial regeneration in COPD. COPD airway basal cells show downregulation of gene sets that are involved in intercellular junctions, epithelial differentiation and immune responses, highlighting the possible mechanisms of defective airway epithelial repair in COPDhttps://bit.ly/3kneloj
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Affiliation(s)
- Fanny Pineau
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | | | - Nicole Owuor
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Nisha Nalamala
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Sudhir Kotnala
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Sudhir Bolla
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Nathaniel Marchetti
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Steven Kelsen
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Gerard J Criner
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA
| | - Uma S Sajjan
- Dept of Thoracic Surgery and Medicine, Temple University, Philadelphia, PA, USA.,Dept of Physiology, Lewis Katz Medical School, Temple University, Philadelphia, PA, USA
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7
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Kerschner JL, Paranjapye A, Yin S, Skander DL, Bebek G, Leir SH, Harris A. A functional genomics approach to investigate the differentiation of iPSCs into lung epithelium at air-liquid interface. J Cell Mol Med 2020; 24:9853-9870. [PMID: 32692488 PMCID: PMC7520342 DOI: 10.1111/jcmm.15568] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/02/2020] [Accepted: 06/13/2020] [Indexed: 01/24/2023] Open
Abstract
The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air‐liquid interface (HBE‐ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. Here, we perform open chromatin mapping by ATAC‐seq and transcriptomics by RNA‐seq in parallel, to define the functional genomics of key stages of the iPSC to HBE‐ALI differentiation. Within open chromatin peaks, the overrepresented motifs include the architectural protein CTCF at all stages, while motifs for the FOXA pioneer and GATA factor families are seen more often at early stages, and those regulating key airway epithelial functions, such as EHF, are limited to later stages. The RNA‐seq data illustrate dynamic pathways during the iPSC to HBE‐ALI differentiation, and also the marked functional divergence of different iPSC lines at the ALI stages of differentiation. Moreover, a comparison of iPSC‐derived and lung donor‐derived HBE‐ALI cultures reveals substantial differences between these models.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Shiyi Yin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Dannielle L Skander
- Systems Biology and Bioinformatics Graduate Program, Case Western Reserve University, Cleveland, OH, USA
| | - Gurkan Bebek
- Systems Biology and Bioinformatics Graduate Program, Case Western Reserve University, Cleveland, OH, USA.,Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA.,Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA.,Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
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8
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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: 17] [Impact Index Per Article: 4.3] [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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9
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Swahn H, Sabith Ebron J, Lamar K, Yin S, Kerschner JL, NandyMazumdar M, Coppola C, Mendenhall EM, Leir S, Harris A. Coordinate regulation of ELF5 and EHF at the chr11p13 CF modifier region. J Cell Mol Med 2019; 23:7726-7740. [PMID: 31557407 PMCID: PMC6815777 DOI: 10.1111/jcmm.14646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 12/21/2022] Open
Abstract
E74-like factor 5 (ELF5) and ETS-homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three key cis-regulatory elements (CREs) from the chr11p13 region and also activated multiple open chromatin sites with CRISPRa in airway epithelial cells. Deletion of the CREs caused subtle changes in chromatin architecture and site-specific increases in EHF and ELF5. CRISPRa had most effect on ELF5 transcription. ELF5 levels are low in airway cells but higher in LNCaP (prostate) and T47D (breast) cancer cells. ATAC-seq in these lines revealed novel peaks of open chromatin at the 5' end of chr11p13 associated with an expressed ELF5 gene. Furthermore, 4C-seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP-seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6, and siRNA-mediated depletion of ELF5 enhanced EHF expression. These results define a new role for ELF5 in lung epithelial biology.
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Affiliation(s)
- Hannah Swahn
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jey Sabith Ebron
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Kay‐Marie Lamar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Shiyi Yin
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jenny L. Kerschner
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Monali NandyMazumdar
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Candice Coppola
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Eric M. Mendenhall
- Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleALUSA
| | - Shih‐Hsing Leir
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Ann Harris
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
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10
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Polineni D, Dang H, Gallins PJ, Jones LC, Pace RG, Stonebraker JR, Commander LA, Krenicky JE, Zhou YH, Corvol H, Cutting GR, Drumm ML, Strug LJ, Boyle MP, Durie PR, Chmiel JF, Zou F, Wright FA, O'Neal WK, Knowles MR. Airway Mucosal Host Defense Is Key to Genomic Regulation of Cystic Fibrosis Lung Disease Severity. Am J Respir Crit Care Med 2019; 197:79-93. [PMID: 28853905 DOI: 10.1164/rccm.201701-0134oc] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RATIONALE The severity of cystic fibrosis (CF) lung disease varies widely, even for Phe508del homozygotes. Heritability studies show that more than 50% of the variability reflects non-cystic fibrosis transmembrane conductance regulator (CFTR) genetic variation; however, the full extent of the pertinent genetic variation is not known. OBJECTIVES We sought to identify novel CF disease-modifying mechanisms using an integrated approach based on analyzing "in vivo" CF airway epithelial gene expression complemented with genome-wide association study (GWAS) data. METHODS Nasal mucosal RNA from 134 patients with CF was used for RNA sequencing. We tested for associations of transcriptomic (gene expression) data with a quantitative phenotype of CF lung disease severity. Pathway analysis of CF GWAS data (n = 5,659 patients) was performed to identify novel pathways and assess the concordance of genomic and transcriptomic data. Association of gene expression with previously identified CF GWAS risk alleles was also tested. MEASUREMENTS AND MAIN RESULTS Significant evidence of heritable gene expression was identified. Gene expression pathways relevant to airway mucosal host defense were significantly associated with CF lung disease severity, including viral infection, inflammation/inflammatory signaling, lipid metabolism, apoptosis, ion transport, Phe508del CFTR processing, and innate immune responses, including HLA (human leukocyte antigen) genes. Ion transport and CFTR processing pathways, as well as HLA genes, were identified across differential gene expression and GWAS signals. CONCLUSIONS Transcriptomic analyses of CF airway epithelia, coupled to genomic (GWAS) analyses, highlight the role of heritable host defense variation in determining the pathophysiology of CF lung disease. The identification of these pathways provides opportunities to pursue targeted interventions to improve CF lung health.
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Affiliation(s)
- Deepika Polineni
- 1 Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas.,2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Hong Dang
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Paul J Gallins
- 3 Bioinformatics Research Center, Department of Biological Sciences
| | - Lisa C Jones
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Rhonda G Pace
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Jaclyn R Stonebraker
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Leah A Commander
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Jeanne E Krenicky
- 4 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Yi-Hui Zhou
- 3 Bioinformatics Research Center, Department of Biological Sciences
| | - Harriet Corvol
- 5 Pediatric Pulmonary Department, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Trousseau, Institut National de la Santé et la Recherche Médicale (INSERM) U938, Paris, France.,6 Sorbonne Universités, Université Pierre et Marie Curie (UPMC), Paris 6, Paris, France
| | - Garry R Cutting
- 7 McKusick-Nathans Institute of Genetic Medicine.,8 Department of Pediatrics, and
| | - Mitchell L Drumm
- 4 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Lisa J Strug
- 9 Program in Genetics and Genome Biology.,10 Division of Biostatistics, Dalla Lana School of Public Health, and
| | - Michael P Boyle
- 11 Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter R Durie
- 12 Physiology and Experimental Medicine Research Program, and.,13 Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada; and.,14 Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - James F Chmiel
- 4 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Fei Zou
- 15 Department of Biostatistics, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Fred A Wright
- 16 Department of Statistics, and.,17 Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina
| | - Wanda K O'Neal
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
| | - Michael R Knowles
- 2 Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, School of Medicine, and
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11
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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: 17] [Impact Index Per Article: 3.4] [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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12
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Brettmann EA, Oh IY, de Guzman Strong C. High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq). J Vis Exp 2018. [PMID: 30346381 DOI: 10.3791/58030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The identification of regulatory elements for a given target gene poses a significant technical challenge owing to the variability in the positioning and effect sizes of regulatory elements to a target gene. Some progress has been made with the bioinformatic prediction of the existence and function of proximal epigenetic modifications associated with activated gene expression using conserved transcription factor binding sites. Chromatin conformation capture studies have revolutionized our ability to discover physical chromatin contacts between sequences and even within an entire genome. Circular chromatin conformation capture coupled with next-generation sequencing (4C-seq), in particular, is designed to discover all possible physical chromatin interactions for a given sequence of interest (viewpoint), such as a target gene or a regulatory enhancer. Current 4C-seq strategies directly sequence from within the viewpoint but require numerous and diverse viewpoints to be simultaneously sequenced to avoid the technical challenges of uniform base calling (imaging) with next generation sequencing platforms. This volume of experiments may not be practical for many laboratories. Here, we report a modified approach to the 4C-seq protocol that incorporates both an additional restriction enzyme digest and qPCR-based amplification steps that are designed to facilitate a greater capture of diverse sequence reads and mitigate the potential for PCR bias, respectively. Our modified 4C method is amenable to the standard molecular biology lab for assessing chromatin architecture.
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Affiliation(s)
- Erin A Brettmann
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine
| | - Inez Y Oh
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine
| | - Cristina de Guzman Strong
- Division of Dermatology, Center for Pharmacogenomics, Center for the Study of Itch, Department of Medicine, Washington University School of Medicine;
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13
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O'Neal WK, Knowles MR. Cystic Fibrosis Disease Modifiers: Complex Genetics Defines the Phenotypic Diversity in a Monogenic Disease. Annu Rev Genomics Hum Genet 2018; 19:201-222. [DOI: 10.1146/annurev-genom-083117-021329] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In many respects, genetic studies in cystic fibrosis (CF) serve as a paradigm for a human Mendelian genetic success story. From recognition of the condition as a heritable pathological entity to implementation of personalized treatments based on genetic findings, this multistep pathway of progress has focused on the genetic underpinnings of CF clinical disease. Along this path was the recognition that not all CFTR gene mutations produce the same disease and the recognition of the complex, multifactorial nature of CF genotype–phenotype relationships. The non- CFTR genetic components (gene modifiers) that contribute to variation in phenotype are the focus of this review. A multifaceted approach involving candidate gene studies, genome-wide association studies, and gene expression studies has revealed significant gene modifiers for multiple CF phenotypes. The bold challenges for the future are to integrate the findings into our understanding of CF pathogenesis and to use the knowledge to develop novel therapies.
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Affiliation(s)
- Wanda K. O'Neal
- Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;,
| | - Michael R. Knowles
- Cystic Fibrosis/Pulmonary Research and Treatment Center, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;,
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14
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Strug LJ, Stephenson AL, Panjwani N, Harris A. Recent advances in developing therapeutics for cystic fibrosis. Hum Mol Genet 2018; 27:R173-R186. [PMID: 30060192 PMCID: PMC6061831 DOI: 10.1093/hmg/ddy188] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/23/2022] Open
Abstract
Despite hope that a cure was imminent when the causative gene was cloned nearly 30 years ago, cystic fibrosis (CF [MIM: 219700]) remains a life-shortening disease affecting more than 70 000 individuals worldwide. However, within the last 6 years the Food and Drug Administration's approval of Ivacaftor, the first drug that corrects the defective cystic fibrosis transmembrane conductance regulator protein [CFTR (MIM: 602421)] in patients with the G551D mutation, marks a watershed in the development of novel therapeutics for this devastating disease. Here we review recent progress in diverse research areas, which all focus on curing CF at the genetic, biochemical or physiological level. In the near future it seems probable that development of mutation-specific therapies will be the focus, since it is unlikely that any one approach will be efficient in correcting the more than 2000 disease-associated variants. We discuss the new drugs and combinations of drugs that either enhance delivery of misfolded CFTR protein to the cell membrane, where it functions as an ion channel, or that activate channel opening. Next we consider approaches to correct the causative genetic lesion at the DNA or RNA level, through repressing stop mutations and nonsense-mediated decay, modulating splice mutations, fixing errors by gene editing or using novel routes to gene replacement. Finally, we explore how modifier genes, loci elsewhere in the genome that modify CF disease severity, may be used to restore a normal phenotype. Progress in all of these areas has been dramatic, generating enthusiasm that CF may soon become a broadly treatable disease.
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Affiliation(s)
- Lisa J Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne L Stephenson
- Department of Respirology, Adult Cystic Fibrosis Program, St. Michael’s Hospital, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Naim Panjwani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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15
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Ramnath D, Irvine KM, Lukowski SW, Horsfall LU, Loh Z, Clouston AD, Patel PJ, Fagan KJ, Iyer A, Lampe G, Stow JL, Schroder K, Fairlie DP, Powell JE, Powell EE, Sweet MJ. Hepatic expression profiling identifies steatosis-independent and steatosis-driven advanced fibrosis genes. JCI Insight 2018; 3:120274. [PMID: 30046009 DOI: 10.1172/jci.insight.120274] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022] Open
Abstract
Chronic liver disease (CLD) is associated with tissue-destructive fibrosis. Considering that common mechanisms drive fibrosis across etiologies, and that steatosis is an important cofactor for pathology, we performed RNA sequencing on liver biopsies of patients with different fibrosis stages, resulting from infection with hepatitis C virus (HCV) (with or without steatosis) or fatty liver disease. In combination with enhanced liver fibrosis score correlation analysis, we reveal a common set of genes associated with advanced fibrosis, as exemplified by those encoding the transcription factor ETS-homologous factor (EHF) and the extracellular matrix protein versican (VCAN). We identified 17 fibrosis-associated genes as candidate EHF targets and demonstrated that EHF regulates multiple fibrosis-associated genes, including VCAN, in hepatic stellate cells. Serum VCAN levels were also elevated in advanced fibrosis patients. Comparing biopsies from patients with HCV with or without steatosis, we identified a steatosis-enriched gene set associated with advanced fibrosis, validating follistatin-like protein 1 (FSTL1) as an exemplar of this profile. In patients with advanced fibrosis, serum FSTL1 levels were elevated in those with steatosis (versus those without). Liver Fstl1 mRNA levels were also elevated in murine CLD models. We thus reveal a common gene signature for CLD-associated liver fibrosis and potential biomarkers and/or targets for steatosis-associated liver fibrosis.
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Affiliation(s)
- Divya Ramnath
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Katharine M Irvine
- Centre for Liver Disease Research and.,Faculty of Medicine, Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Samuel W Lukowski
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Leigh U Horsfall
- Centre for Liver Disease Research and.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Zhixuan Loh
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Preya J Patel
- Centre for Liver Disease Research and.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | | | - Abishek Iyer
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Guy Lampe
- Pathology Queensland, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate Schroder
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Joseph E Powell
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia.,Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Elizabeth E Powell
- Centre for Liver Disease Research and.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB) and.,IMB Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland, Australia
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16
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A transcription factor network represses CFTR gene expression in airway epithelial cells. Biochem J 2018; 475:1323-1334. [PMID: 29572268 DOI: 10.1042/bcj20180044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 02/06/2023]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause the inherited disorder cystic fibrosis (CF). Lung disease is the major cause of CF morbidity, though CFTR expression levels are substantially lower in the airway epithelium than in pancreatic duct and intestinal epithelia, which also show compromised function in CF. Recently developed small molecule therapeutics for CF are highly successful for one specific CFTR mutation and have a positive impact on others. However, the low abundance of CFTR transcripts in the airway limits the opportunity for drugs to correct the defective substrate. Elucidation of the transcriptional mechanisms for the CFTR locus has largely focused on intragenic and intergenic tissue-specific enhancers and their activating trans-factors. Here, we investigate whether the low CFTR levels in the airway epithelium result from the recruitment of repressive proteins directly to the locus. Using an siRNA screen to deplete ∼1500 transcription factors (TFs) and associated regulatory proteins in Calu-3 lung epithelial cells, we identified nearly 40 factors that upon depletion elevated CFTR mRNA levels more than 2-fold. A subset of these TFs was validated in primary human bronchial epithelial cells. Among the strongest repressors of airway expression of CFTR were Krüppel-like factor 5 and Ets homologous factor, both of which have pivotal roles in the airway epithelium. Depletion of these factors, which are both recruited to an airway-selective cis-regulatory element at -35 kb from the CFTR promoter, improved CFTR production and function, thus defining novel therapeutic targets for enhancement of CFTR.
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17
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Lim SH, Legere EA, Snider J, Stagljar I. Recent Progress in CFTR Interactome Mapping and Its Importance for Cystic Fibrosis. Front Pharmacol 2018; 8:997. [PMID: 29403380 PMCID: PMC5785726 DOI: 10.3389/fphar.2017.00997] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/26/2017] [Indexed: 12/25/2022] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride channel found in secretory epithelia with a plethora of known interacting proteins. Mutations in the CFTR gene cause cystic fibrosis (CF), a disease that leads to progressive respiratory illness and other complications of phenotypic variance resulting from perturbations of this protein interaction network. Studying the collection of CFTR interacting proteins and the differences between the interactomes of mutant and wild type CFTR provides insight into the molecular machinery of the disease and highlights possible therapeutic targets. This mini review focuses on functional genomics and proteomics approaches used for systematic, high-throughput identification of CFTR-interacting proteins to provide comprehensive insight into CFTR regulation and function.
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Affiliation(s)
- Sang Hyun Lim
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | | - Jamie Snider
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Igor Stagljar
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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