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Clausen L, Okarmus J, Voutsinos V, Meyer M, Lindorff-Larsen K, Hartmann-Petersen R. PRKN-linked familial Parkinson's disease: cellular and molecular mechanisms of disease-linked variants. Cell Mol Life Sci 2024; 81:223. [PMID: 38767677 PMCID: PMC11106057 DOI: 10.1007/s00018-024-05262-8] [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: 02/27/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is a common and incurable neurodegenerative disorder that arises from the loss of dopaminergic neurons in the substantia nigra and is mainly characterized by progressive loss of motor function. Monogenic familial PD is associated with highly penetrant variants in specific genes, notably the PRKN gene, where homozygous or compound heterozygous loss-of-function variants predominate. PRKN encodes Parkin, an E3 ubiquitin-protein ligase important for protein ubiquitination and mitophagy of damaged mitochondria. Accordingly, Parkin plays a central role in mitochondrial quality control but is itself also subject to a strict protein quality control system that rapidly eliminates certain disease-linked Parkin variants. Here, we summarize the cellular and molecular functions of Parkin, highlighting the various mechanisms by which PRKN gene variants result in loss-of-function. We emphasize the importance of high-throughput assays and computational tools for the clinical classification of PRKN gene variants and how detailed insights into the pathogenic mechanisms of PRKN gene variants may impact the development of personalized therapeutics.
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Affiliation(s)
- Lene Clausen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
| | - Vasileios Voutsinos
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
- Department of Neurology, Odense University Hospital, 5000, Odense, Denmark
- Department of Clinical Research, BRIDGE, Brain Research Inter Disciplinary Guided Excellence, University of Southern Denmark, 5230, Odense, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark.
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2
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Azoicai AN, Lupu A, Trandafir LM, Alexoae MM, Alecsa M, Starcea IM, Cuciureanu M, Knieling A, Salaru DL, Hanganu E, Mocanu A, Lupu VV, Ioniuc I. Cystic fibrosis management in pediatric population-from clinical features to personalized therapy. Front Pediatr 2024; 12:1393193. [PMID: 38798310 PMCID: PMC11116730 DOI: 10.3389/fped.2024.1393193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations of the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). In 1949, it's been identified as a monogenic disease and was thought to primarily affect individuals of Northern European descent. It was the most prevalent autosomal recessive disease that shortens life. With the availability of multiple testing methodologies nowadays, there is a chance to create novel and enhanced treatment options. Even in the absence of a high sweat chloride test (SCT) result, the discovery of two causal mutations is diagnostic for cystic fibrosis (CF). For a CF diagnosis, however, at least two positive E sweat chloride tests are still required. In order to achieve early and active intervention to manage cystic fibrosis (CF) and its comorbidities, treatment regimens for pediatric patients should be evaluated, improved, and closely monitored. New developments in the treatment of cystic fibrosis (CF) have led to the development of medications derived from molecules that target the pathogenetic pathway of the illness. These options are very efficient and allow pediatric patients to receive individualized care. However, in order to better direct patient care and enhance patient outcomes, it is crucial to research uncommon CF mutations, which can provide crucial information about the prognosis of the disease and the relationships between genotype and phenotype. To ensure the success of creating novel, safer, and more efficient treatment approaches, a deeper understanding of the pathogeny of the illness is required. In the age of customized medicine, genetic research will be essential to improving patient care and quality of life for those with uncommon mutations.
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Affiliation(s)
| | - Ancuta Lupu
- Pediatrics, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | | | | | - Mirabela Alecsa
- Pediatrics, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | | | - Magdalena Cuciureanu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Anton Knieling
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Delia Lidia Salaru
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Elena Hanganu
- Department of Biomedical Sciences, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Adriana Mocanu
- Pediatrics, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Vasile Valeriu Lupu
- Pediatrics, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Ileana Ioniuc
- Pediatrics, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
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Williams D, Glasstetter LM, Jong TT, Kapoor A, Zhu S, Zhu Y, Gehrlein A, Vocadlo DJ, Jagasia R, Marugan JJ, Sidransky E, Henderson MJ, Chen Y. Development of quantitative high-throughput screening assays to identify, validate, and optimize small-molecule stabilizers of misfolded β-glucocerebrosidase with therapeutic potential for Gaucher disease and Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586364. [PMID: 38712038 PMCID: PMC11071283 DOI: 10.1101/2024.03.22.586364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Glucocerebrosidase (GCase) is implicated in both a rare, monogenic disorder (Gaucher disease, GD) and a common, multifactorial condition (Parkinson's disease); hence, it is an urgent therapeutic target. To identify correctors of severe protein misfolding and trafficking obstruction manifested by the pathogenic L444P-variant of GCase, we developed a suite of quantitative, high-throughput, cell-based assays. First, we labeled GCase with a small pro-luminescent HiBiT peptide reporter tag, enabling quantitation of protein stabilization in cells while faithfully maintaining target biology. TALEN-based gene editing allowed for stable integration of a single HiBiT-GBA1 transgene into an intragenic safe-harbor locus in GBA1-knockout H4 (neuroglioma) cells. This GD cell model was amenable to lead discovery via titration-based quantitative high-throughput screening and lead optimization via structure-activity relationships. A primary screen of 10,779 compounds from the NCATS bioactive collections identified 140 stabilizers of HiBiT-GCase-L444P, including both pharmacological chaperones (ambroxol and non-inhibitory chaperone NCGC326) and proteostasis regulators (panobinostat, trans-ISRIB, and pladienolide B). Two complementary high-content imaging-based assays were deployed to triage hits: the fluorescence-quenched substrate LysoFix-GBA captured functional lysosomal GCase activity, while an immunofluorescence assay featuring antibody hGCase-1/23 provided direct visualization of GCase lysosomal translocation. NCGC326 was active in both secondary assays and completely reversed pathological glucosylsphingosine accumulation. Finally, we tested the concept of combination therapy, by demonstrating synergistic actions of NCGC326 with proteostasis regulators in enhancing GCase-L444P levels. Looking forward, these physiologically-relevant assays can facilitate the identification, pharmacological validation, and medicinal chemistry optimization of new chemical matter targeting GCase, ultimately leading to a viable therapeutic for two protein-misfolding diseases.
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Affiliation(s)
- Darian Williams
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Logan M. Glasstetter
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tiffany T. Jong
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Abhijeet Kapoor
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Sha Zhu
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Yanping Zhu
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Alexandra Gehrlein
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - David J. Vocadlo
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Ravi Jagasia
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Juan J. Marugan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Ellen Sidransky
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Mark J. Henderson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Yu Chen
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
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Cao L, Wu Y, Gong Y, Zhou Q. Small molecule modulators of cystic fibrosis transmembrane conductance regulator (CFTR): Structure, classification, and mechanisms. Eur J Med Chem 2024; 265:116120. [PMID: 38194776 DOI: 10.1016/j.ejmech.2023.116120] [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: 11/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/11/2024]
Abstract
The advent of small molecule modulators targeting the cystic fibrosis transmembrane conductance regulator (CFTR) has revolutionized the treatment of persons with cystic fibrosis (CF) (pwCF). Presently, these small molecule CFTR modulators have gained approval for usage in approximately 90 % of adult pwCF. Ongoing drug development endeavors are focused on optimizing the therapeutic benefits while mitigating potential adverse effects associated with this treatment approach. Based on their mode of interaction with CFTR, these drugs can be classified into two distinct categories: specific CFTR modulators and non-specific CFTR modulators. Specific CFTR modulators encompass potentiators and correctors, whereas non-specific CFTR modulators encompass activators, proteostasis modulators, stabilizers, reader-through agents, and amplifiers. Currently, four small molecule modulators, all classified as potentiators and correctors, have obtained marketing approval. Furthermore, numerous novel small molecule modulators, exhibiting diverse mechanisms of action, are currently undergoing development. This review aims to explore the classification, mechanisms of action, molecular structures, developmental processes, and interrelationships among small molecule CFTR modulators.
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Affiliation(s)
- Luyang Cao
- China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yong Wu
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China
| | - Yanchun Gong
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China.
| | - Qingfa Zhou
- China Pharmaceutical University, Nanjing, 210009, PR China.
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Man E, Evran S. Deacetylation of Histones and Non-histone Proteins in Inflammatory Diseases and Cancer Therapeutic Potential of Histone Deacetylase Inhibitors. Curr Genomics 2023; 24:136-145. [PMID: 38178983 PMCID: PMC10761333 DOI: 10.2174/0113892029265046231011100327] [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: 05/31/2023] [Revised: 07/18/2023] [Accepted: 08/26/2023] [Indexed: 01/06/2024] Open
Abstract
Epigenetic changes play an important role in the pathophysiology of autoimmune diseases such as allergic asthma, multiple sclerosis, lung diseases, diabetes, cystic fibrosis, atherosclerosis, rheumatoid arthritis, and COVID-19. There are three main classes of epigenetic alterations: post-translational modifications of histone proteins, control by non-coding RNA and DNA methylation. Since histone modifications can directly affect chromatin structure and accessibility, they can regulate gene expression levels. Abnormal expression and activity of histone deacetylases (HDACs) have been reported in immune mediated diseases. Increased acetylated levels of lysine residues have been suggested to be related to the overexpression of inflammatory genes. This review focuses on the effect of HDAC modifications on histone and non-histone proteins in autoimmune diseases. Furthermore, we discuss the potential therapeutic effect of HDAC inhibitors (HDACi) used in these diseases.
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Affiliation(s)
- Ezgi Man
- Department of Biochemistry, Faculty of Science, Ege University, 35100, İzmir, Türkiye
- EGE SCIENCE PRO Scientific Research Inc., Ege University, IdeEGE Technology Development Zone, 35100, Bornova-Izmir, Türkiye
| | - Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, 35100, İzmir, Türkiye
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Díaz-Anaya AM, Gerard L, Albert M, Gaussin JF, Boonen M, Gillet JP. The β Isoform of Human ATP-Binding Cassette B5 Transporter, ABCB5β, Localizes to the Endoplasmic Reticulum. Int J Mol Sci 2023; 24:15847. [PMID: 37958830 PMCID: PMC10649157 DOI: 10.3390/ijms242115847] [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: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
ABCB5β is a member of the ABC transporter superfamily cloned from melanocytes. It has been reported as a marker of skin progenitor cells and melanoma stem cells. ABCB5β has also been shown to exert an oncogenic activity and promote cancer metastasis. However, this protein remains poorly characterized. To elucidate its subcellular localization, we tested several anti-ABCB5 antibodies and prepared several tagged ABCB5β cDNA constructs. We then used a combination of immunofluorescence and biochemical analyses to investigate the presence of ABCB5β in different subcellular compartments of HeLa and MelJuSo cell lines. Treatment of the cells with the proteasome inhibitor MG132 showed that part of the population of newly synthesized ABCB5β is degraded by the proteasome system. Interestingly, treatment with SAHA, a molecule that promotes chaperone-assisted folding, largely increased the expression of ABCB5β. Nevertheless, the overall protein distribution in the cells remained similar to that of control conditions; the protein extensively colocalized with the endoplasmic reticulum marker calnexin. Taken together with cell surface biotinylation studies demonstrating that the protein does not reach the plasma membrane (even after SAHA treatment), the data indicate that ABCB5β is a microsomal protein predominantly localized to the ER.
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Affiliation(s)
- Adriana María Díaz-Anaya
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium; (A.M.D.-A.); (L.G.)
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium (J.-F.G.)
| | - Louise Gerard
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium; (A.M.D.-A.); (L.G.)
| | - Martine Albert
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium (J.-F.G.)
| | - Jean-François Gaussin
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium (J.-F.G.)
| | - Marielle Boonen
- Laboratory of Intracellular Trafficking Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium (J.-F.G.)
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, University of Namur, 5000 Namur, Belgium; (A.M.D.-A.); (L.G.)
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7
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Kim M, McDonald EF, Sabusap CMP, Timalsina B, Joshi D, Hong JS, Rab A, Sorscher EJ, Plate L. Elexacaftor/VX-445-mediated CFTR interactome remodeling reveals differential correction driven by mutation-specific translational dynamics. J Biol Chem 2023; 299:105242. [PMID: 37690692 PMCID: PMC10579539 DOI: 10.1016/j.jbc.2023.105242] [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: 02/06/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023] Open
Abstract
Cystic fibrosis (CF) is one of the most prevalent lethal genetic diseases with over 2000 identified mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Pharmacological chaperones such as lumacaftor (VX-809), tezacaftor (VX-661), and elexacaftor (VX-445) treat mutation-induced defects by stabilizing CFTR and are called correctors. These correctors improve proper folding and thus facilitate processing and trafficking to increase the amount of functional CFTR on the cell surface. Yet, CFTR variants display differential responses to each corrector. Here, we report that variants P67L and L206W respond similarly to VX-809 but divergently to VX-445 with P67L exhibiting little rescue when treated with VX-445. We investigate the underlying cellular mechanisms of how CFTR biogenesis is altered by correctors in these variants. Affinity purification-mass spectrometry multiplexed with isobaric tandem mass tags was used to quantify CFTR protein-protein interaction changes between variants P67L and L206W. VX-445 facilitates unique proteostasis factor interactions especially in translation, folding, and degradation pathways in a CFTR variant-dependent manner. A number of these interacting proteins knocked down by siRNA, such as ribosomal subunit proteins, moderately rescued fully glycosylated P67L. Importantly, these knockdowns sensitize P67L to VX-445 and further enhance the trafficking correction of this variant. Partial inhibition of protein translation also mildly sensitizes P67L CFTR to VX-445 correction, supporting a role for translational dynamics in the rescue mechanism of VX-445. Our results provide a better understanding of VX-445 biological mechanism of action and reveal cellular targets that may sensitize nonresponsive CFTR variants to known and available correctors.
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Affiliation(s)
- Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Bibek Timalsina
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Disha Joshi
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Jeong S Hong
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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8
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Nimer RM, Abdel Rahman AM. Recent advances in proteomic-based diagnostics of cystic fibrosis. Expert Rev Proteomics 2023; 20:151-169. [PMID: 37766616 DOI: 10.1080/14789450.2023.2258282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/06/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF. AREAS COVERED We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers. EXPERT OPINION Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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9
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Wang Y, Abrol R, Mak JYW, Das Gupta K, Ramnath D, Karunakaran D, Fairlie DP, Sweet MJ. Histone deacetylase 7: a signalling hub controlling development, inflammation, metabolism and disease. FEBS J 2023; 290:2805-2832. [PMID: 35303381 PMCID: PMC10952174 DOI: 10.1111/febs.16437] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/02/2022] [Accepted: 03/16/2022] [Indexed: 12/20/2022]
Abstract
Histone deacetylases (HDACs) catalyse removal of acetyl groups from lysine residues on both histone and non-histone proteins to control numerous cellular processes. Of the 11 zinc-dependent classical HDACs, HDAC4, 5, 7 and 9 are class IIa HDAC enzymes that regulate cellular and developmental processes through both enzymatic and non-enzymatic mechanisms. Over the last two decades, HDAC7 has been associated with key roles in numerous physiological and pathological processes. Molecular, cellular, in vivo and disease association studies have revealed that HDAC7 acts through multiple mechanisms to control biological processes in immune cells, osteoclasts, muscle, the endothelium and epithelium. This HDAC protein regulates gene expression, cell proliferation, cell differentiation and cell survival and consequently controls development, angiogenesis, immune functions, inflammation and metabolism. This review focuses on the cell biology of HDAC7, including the regulation of its cellular localisation and molecular mechanisms of action, as well as its associative and causal links with cancer and inflammatory, metabolic and fibrotic diseases. We also review the development status of small molecule inhibitors targeting HDAC7 and their potential for intervention in different disease contexts.
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Affiliation(s)
- Yizhuo Wang
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Rishika Abrol
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Jeffrey Y. W. Mak
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
| | - Kaustav Das Gupta
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Divya Ramnath
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Denuja Karunakaran
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - David P. Fairlie
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt. LuciaAustralia
| | - Matthew J. Sweet
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt. LuciaAustralia
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10
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Abildgaard AB, Nielsen SV, Bernstein I, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Lynch syndrome, molecular mechanisms and variant classification. Br J Cancer 2023; 128:726-734. [PMID: 36434153 PMCID: PMC9978028 DOI: 10.1038/s41416-022-02059-z] [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: 06/17/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Patients with the heritable cancer disease, Lynch syndrome, carry germline variants in the MLH1, MSH2, MSH6 and PMS2 genes, encoding the central components of the DNA mismatch repair system. Loss-of-function variants disrupt the DNA mismatch repair system and give rise to a detrimental increase in the cellular mutational burden and cancer development. The treatment prospects for Lynch syndrome rely heavily on early diagnosis; however, accurate diagnosis is inextricably linked to correct clinical interpretation of individual variants. Protein variant classification traditionally relies on cumulative information from occurrence in patients, as well as experimental testing of the individual variants. The complexity of variant classification is due to (1) that variants of unknown significance are rare in the population and phenotypic information on the specific variants is missing, and (2) that individual variant testing is challenging, costly and slow. Here, we summarise recent developments in high-throughput technologies and computational prediction tools for the assessment of variants of unknown significance in Lynch syndrome. These approaches may vastly increase the number of interpretable variants and could also provide important mechanistic insights into the disease. These insights may in turn pave the road towards developing personalised treatment approaches for Lynch syndrome.
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Affiliation(s)
- Amanda B Abildgaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Inge Bernstein
- Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Institute of Clinical Medicine, Aalborg University Hospital, Aalborg University, Aalborg, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Kim M, McDonald EF, Sabusap CMP, Timalsina B, Joshi D, Hong JS, Rab A, Sorscher EJ, Plate L. Elexacaftor/VX-445-mediated CFTR interactome remodeling reveals differential correction driven by mutation-specific translational dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.04.527134. [PMID: 36778339 PMCID: PMC9915750 DOI: 10.1101/2023.02.04.527134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cystic fibrosis (CF) is one of the most prevalent lethal genetic diseases with over 2000 identified mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Pharmacological chaperones such as Lumacaftor (VX-809), Tezacaftor (VX-661) and Elexacaftor (VX-445) treat mutation-induced defects by stabilizing CFTR and are called correctors. These correctors improve proper folding and thus facilitate processing and trafficking to increase the amount of functional CFTR on the cell surface. Yet, CFTR variants display differential responses to each corrector. Here, we report variants P67L and L206W respond similarly to VX-809 but divergently to VX-445 with P67L exhibiting little rescue when treated with VX-445. We investigate the underlying cellular mechanisms of how CFTR biogenesis is altered by correctors in these variants. Affinity purification-mass spectrometry (AP-MS) multiplexed with isobaric Tandem Mass Tags (TMT) was used to quantify CFTR protein-protein interaction changes between variants P67L and L206W. VX-445 facilitates unique proteostasis factor interactions especially in translation, folding, and degradation pathways in a CFTR variant-dependent manner. A number of these interacting proteins knocked down by siRNA, such as ribosomal subunit proteins, moderately rescued fully glycosylated P67L. Importantly, these knock-downs sensitize P67L to VX-445 and further enhance the correction of this variant. Our results provide a better understanding of VX-445 biological mechanism of action and reveal cellular targets that may sensitize unresponsive CFTR variants to known and available correctors.
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Affiliation(s)
- Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States of America
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | | | - Bibek Timalsina
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Disha Joshi
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Jeong S. Hong
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Eric J. Sorscher
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
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12
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Barbato E, Darrah R, Kelley TJ. The circadian system in cystic fibrosis mice is regulated by histone deacetylase 6. Am J Physiol Cell Physiol 2022; 323:C1112-C1120. [PMID: 36062879 PMCID: PMC9555305 DOI: 10.1152/ajpcell.00248.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Disordered sleep experienced by people with cystic fibrosis (CF) suggest a possible disruption in circadian regulation being associated with the loss of cystic fibrosis transmembrane conductance regulator (Cftr) function. To test this hypothesis, circadian regulation was assessed in an F508del/F508del CF mouse model. CF mice exhibited significant alterations in both timing of locomotor activity and in mean activity per hour in both light-dark (LD) and dark-dark (DD) photoperiods compared with wild-type (WT) controls. It was also noted that in DD periodicity increased in CF mice, whereas shortening in WT mice as is expected. CF mice also exhibited altered timing of circadian gene expression and a reduction of melatonin production at all time points. Mechanistically, the role of microtubules in regulating these outcomes was explored. Mice lacking expression of tubulin polymerization promoting protein (Tppp) effectively mimicked CF mouse phenotypes with each measured outcome. Depleting expression of the microtubule regulatory protein histone deacetylase 6 (Hdac6) from CF mice (CF/Hdac6) resulted in the reversal of each phenotype to WT profiles. These data demonstrate an innate disruption of circadian regulation in CF mice and identify a novel microtubule-related mechanism leading to this disruption that can be targeted for therapeutic intervention.
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13
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Secretion of functional α1-antitrypsin is cell type dependent: Implications for intramuscular delivery for gene therapy. Proc Natl Acad Sci U S A 2022; 119:e2206103119. [PMID: 35901208 PMCID: PMC9351467 DOI: 10.1073/pnas.2206103119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Heterologous expression of proteins is used widely for the biosynthesis of biologics, many of which are secreted from cells. In addition, gene therapy and messenger RNA (mRNA) vaccines frequently direct the expression of secretory proteins to nonnative host cells. Consequently, it is crucial to understand the maturation and trafficking of proteins in a range of host cells including muscle cells, a popular therapeutic target due to the ease of accessibility by intramuscular injection. Here, we analyzed the production efficiency for α1-antitrypsin (AAT) in Chinese hamster ovary cells, commonly used for biotherapeutic production, and myoblasts (embryonic progenitor cells of muscle cells) and compared it to the production in the major natural cells, liver hepatocytes. AAT is a target protein for gene therapy to address pathologies associated with insufficiencies in native AAT activity or production. AAT secretion and maturation were most efficient in hepatocytes. Myoblasts were the poorest of the cell types tested; however, secretion of active AAT was significantly augmented in myoblasts by treatment with the proteostasis regulator suberoylanilide hydroxamic acid, a histone deacetylase inhibitor. These findings were extended and validated in myotubes (mature muscle cells) where AAT was transduced using an adeno-associated viral capsid transduction method used in gene therapy clinical trials. Overall, our study sheds light on a possible mechanism to enhance the efficacy of gene therapy approaches for AAT and, moreover, may have implications for the production of proteins from mRNA vaccines, which rely on the expression of viral glycoproteins in nonnative host cells upon intramuscular injection.
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14
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van der Knoop MM, Maroofian R, Fukata Y, van Ierland Y, Karimiani EG, Lehesjoki AE, Muona M, Paetau A, Miyazaki Y, Hirano Y, Selim L, de França M, Fock RA, Beetz C, Ruivenkamp CAL, Eaton AJ, Morneau-Jacob FD, Sagi-Dain L, Shemer-Meiri L, Peleg A, Haddad-Halloun J, Kamphuis DJ, Peeters-Scholte CMPCD, Kurul SH, Horvath R, Lochmüller H, Murphy D, Waldmüller S, Spranger S, Overberg D, Muir AM, Rad A, Vona B, Abdulwahad F, Maddirevula S, Povolotskaya IS, Voinova VY, Gowda VK, Srinivasan VM, Alkuraya FS, Mefford HC, Alfadhel M, Haack TB, Striano P, Severino M, Fukata M, Hilhorst-Hofstee Y, Houlden H. Biallelic ADAM22 pathogenic variants cause progressive encephalopathy and infantile-onset refractory epilepsy. Brain 2022; 145:2301-2312. [PMID: 35373813 PMCID: PMC9337806 DOI: 10.1093/brain/awac116] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/31/2022] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Pathogenic variants in A Disintegrin And Metalloproteinase (ADAM) 22, the postsynaptic cell membrane receptor for the glycoprotein leucine-rich repeat glioma-inactivated protein 1 (LGI1), have been recently associated with recessive developmental and epileptic encephalopathy. However, so far, only two affected individuals have been described and many features of this disorder are unknown. We refine the phenotype and report 19 additional individuals harbouring compound heterozygous or homozygous inactivating ADAM22 variants, of whom 18 had clinical data available. Additionally, we provide follow-up data from two previously reported cases. All affected individuals exhibited infantile-onset, treatment-resistant epilepsy. Additional clinical features included moderate to profound global developmental delay/intellectual disability (20/20), hypotonia (12/20) and delayed motor development (19/20). Brain MRI findings included cerebral atrophy (13/20), supported by post-mortem histological examination in patient-derived brain tissue, cerebellar vermis atrophy (5/20), and callosal hypoplasia (4/20). Functional studies in transfected cell lines confirmed the deleteriousness of all identified variants and indicated at least three distinct pathological mechanisms: (i) defective cell membrane expression; (ii) impaired LGI1-binding; and/or (iii) impaired interaction with the postsynaptic density protein PSD-95. We reveal novel clinical and molecular hallmarks of ADAM22 deficiency and provide knowledge that might inform clinical management and early diagnostics.
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Affiliation(s)
- Marieke M van der Knoop
- Department of Child Neurology, Sophia Children’s Hospital, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Yuko Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Ehsan G Karimiani
- Next Generation Genetic Polyclinic, Razavi International Hospital, Mashhad, Iran
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George’s University, London SW17 0RE, UK
| | - Anna Elina Lehesjoki
- Folkhälsan Research Center, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki 00290, Finland
| | - Mikko Muona
- Folkhälsan Research Center, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki 00290, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Finland,00100 Helsinki, Finland
- Blueprint Genetics, 02150 Espoo, Finland
| | - Anders Paetau
- Department of Pathology, Medicum, University of Helsinki, 00100 Helsinki, Finland
| | - Yuri Miyazaki
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yoko Hirano
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-8655, Japan
| | - Laila Selim
- Division of Neurology and Metabolism, Kasr Al Ainy School of Medicine, Cairo University Children Hospital, Cairo, Egypt
| | - Marina de França
- Department of Morphology and Genetics, Clinical Center of Medical Genetics Federal, University of São Paulo, São Paulo, Brazil
| | - Rodrigo Ambrosio Fock
- Department of Morphology and Genetics, Clinical Center of Medical Genetics Federal, University of São Paulo, São Paulo, Brazil
| | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Alison J Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | | | - Lena Sagi-Dain
- Affiliated to the Ruth and Bruce Rappaport Faculty of Medicine Technion-Israel Institute of Technology, Genetics Institute, Carmel Medical Center,Haifa, Israel
| | | | - Amir Peleg
- Affiliated to the Ruth and Bruce Rappaport Faculty of Medicine Technion-Israel Institute of Technology, Genetics Institute, Carmel Medical Center,Haifa, Israel
| | - Jumana Haddad-Halloun
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Daan J Kamphuis
- Department of Neurology, Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | | | - Semra Hiz Kurul
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Hanns Lochmüller
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center–University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Division of Neurology, Department of Medicine, The Ottawa Hospital; and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Stephan Waldmüller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
| | | | - David Overberg
- Department of Pediatrics, Klinikum Bremen-Mitte, Bremen 28205, Germany
| | - Alison M Muir
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, WA 98195, USA
| | - Aboulfazl Rad
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Barbara Vona
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Firdous Abdulwahad
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Victoria Y Voinova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
- Mental Health Research Center, Moscow 107076, Russia
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - Fowzan S Alkuraya
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, WA 98195, USA
| | - Majid Alfadhel
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King AbdulAziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen 72076, Germany
| | - Pasquale Striano
- IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | | | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yvonne Hilhorst-Hofstee
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
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15
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Ensinck MM, Carlon MS. One Size Does Not Fit All: The Past, Present and Future of Cystic Fibrosis Causal Therapies. Cells 2022; 11:cells11121868. [PMID: 35740997 PMCID: PMC9220995 DOI: 10.3390/cells11121868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
Cystic fibrosis (CF) is the most common monogenic disorder, caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Over the last 30 years, tremendous progress has been made in understanding the molecular basis of CF and the development of treatments that target the underlying defects in CF. Currently, a highly effective CFTR modulator treatment (Kalydeco™/Trikafta™) is available for 90% of people with CF. In this review, we will give an extensive overview of past and ongoing efforts in the development of therapies targeting the molecular defects in CF. We will discuss strategies targeting the CFTR protein (i.e., CFTR modulators such as correctors and potentiators), its cellular environment (i.e., proteostasis modulation, stabilization at the plasma membrane), the CFTR mRNA (i.e., amplifiers, nonsense mediated mRNA decay suppressors, translational readthrough inducing drugs) or the CFTR gene (gene therapies). Finally, we will focus on how these efforts can be applied to the 15% of people with CF for whom no causal therapy is available yet.
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Affiliation(s)
- Marjolein M. Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Flanders, Belgium
- Correspondence:
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16
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Lin Y, Qiu T, Wei G, Que Y, Wang W, Kong Y, Xie T, Chen X. Role of Histone Post-Translational Modifications in Inflammatory Diseases. Front Immunol 2022; 13:852272. [PMID: 35280995 PMCID: PMC8908311 DOI: 10.3389/fimmu.2022.852272] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Inflammation is a defensive reaction for external stimuli to the human body and generally accompanied by immune responses, which is associated with multiple diseases such as atherosclerosis, type 2 diabetes, Alzheimer’s disease, psoriasis, asthma, chronic lung diseases, inflammatory bowel disease, and multiple virus-associated diseases. Epigenetic mechanisms have been demonstrated to play a key role in the regulation of inflammation. Common epigenetic regulations are DNA methylation, histone modifications, and non-coding RNA expression; among these, histone modifications embrace various post-modifications including acetylation, methylation, phosphorylation, ubiquitination, and ADP ribosylation. This review focuses on the significant role of histone modifications in the progression of inflammatory diseases, providing the potential target for clinical therapy of inflammation-associated diseases.
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Affiliation(s)
- Yingying Lin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Ting Qiu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Guifeng Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Yueyue Que
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Wenxin Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yichao Kong
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Xiabin Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
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17
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Brusa I, Sondo E, Falchi F, Pedemonte N, Roberti M, Cavalli A. Proteostasis Regulators in Cystic Fibrosis: Current Development and Future Perspectives. J Med Chem 2022; 65:5212-5243. [PMID: 35377645 PMCID: PMC9014417 DOI: 10.1021/acs.jmedchem.1c01897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In cystic fibrosis (CF), the deletion of phenylalanine 508 (F508del) in the CF transmembrane conductance regulator (CFTR) leads to misfolding and premature degradation of the mutant protein. These defects can be targeted with pharmacological agents named potentiators and correctors. During the past years, several efforts have been devoted to develop and approve new effective molecules. However, their clinical use remains limited, as they fail to fully restore F508del-CFTR biological function. Indeed, the search for CFTR correctors with different and additive mechanisms has recently increased. Among them, drugs that modulate the CFTR proteostasis environment are particularly attractive to enhance therapy effectiveness further. This Perspective focuses on reviewing the recent progress in discovering CFTR proteostasis regulators, mainly describing the design, chemical structure, and structure-activity relationships. The opportunities, challenges, and future directions in this emerging and promising field of research are discussed, as well.
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Affiliation(s)
- Irene Brusa
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Elvira Sondo
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | | | | | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
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18
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Kolski-Andreaco A, Balut CM, Bertuccio CA, Wilson AS, Rivers WM, Liu X, Gandley RE, Straub AC, Butterworth MB, Binion D, Devor DC. Histone deacetylase inhibitors (HDACi) increase expression of KCa2.3 (SK3) in primary microvascular endothelial cells. Am J Physiol Cell Physiol 2022; 322:C338-C353. [PMID: 35044858 PMCID: PMC8858676 DOI: 10.1152/ajpcell.00409.2021] [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] [Indexed: 02/06/2023]
Abstract
The small conductance calcium-activated potassium channel (KCa2.3) has long been recognized for its role in mediating vasorelaxation through the endothelium-derived hyperpolarization (EDH) response. Histone deacetylases (HDACs) have been implicated as potential modulators of blood pressure and histone deacetylase inhibitors (HDACi) are being explored as therapeutics for hypertension. Herein, we show that HDACi increase KCa2.3 expression when heterologously expressed in HEK cells and endogenously expressed in primary cultures of human umbilical vein endothelial cells (HUVECs) and human intestinal microvascular endothelial cells (HIMECs). When primary endothelial cells were exposed to HDACi, KCa2.3 transcripts, subunits, and functional current are increased. Quantitative RT-PCR (qPCR) demonstrated increased KCa2.3 mRNA following HDACi, confirming transcriptional regulation of KCa2.3 by HDACs. By using pharmacological agents selective for different classes of HDACs, we discriminated between cytoplasmic and epigenetic modulation of KCa2.3. Biochemical analysis revealed an association between the cytoplasmic HDAC6 and KCa2.3 in immunoprecipitation studies. Specifically inhibiting HDAC6 increases expression of KCa2.3. In addition to increasing the expression of KCa2.3, we show that nonspecific inhibition of HDACs causes an increase in the expression of the molecular chaperone Hsp70 in endothelial cells. When Hsp70 is inhibited in the presence of HDACi, the magnitude of the increase in KCa2.3 expression is diminished. Finally, we show a slower rate of endocytosis of KCa2.3 as a result of exposure of primary endothelial cells to HDACi. These data provide the first demonstrated approach to increase KCa2.3 channel number in endothelial cells and may partially account for the mechanism by which HDACi induce vasorelaxation.
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Affiliation(s)
| | - Corina M. Balut
- 1Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Annette S. Wilson
- 2Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - William M. Rivers
- 2Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Xiaoning Liu
- 1Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robin E. Gandley
- 3Department of Obstetrics and Gynecology and Reproductive Sciences, Magee Womens Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adam C. Straub
- 4Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - David Binion
- 2Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Daniel C. Devor
- 1Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
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19
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20
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Lim SH, Snider J, Birimberg‐Schwartz L, Ip W, Serralha JC, Botelho HM, Lopes‐Pacheco M, Pinto MC, Moutaoufik MT, Zilocchi M, Laselva O, Esmaeili M, Kotlyar M, Lyakisheva A, Tang P, López Vázquez L, Akula I, Aboualizadeh F, Wong V, Grozavu I, Opacak‐Bernardi T, Yao Z, Mendoza M, Babu M, Jurisica I, Gonska T, Bear CE, Amaral MD, Stagljar I. CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system. Mol Syst Biol 2022; 18:e10629. [PMID: 35156780 PMCID: PMC8842165 DOI: 10.15252/msb.202110629] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 12/19/2022] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride and bicarbonate channel in secretory epithelia with a critical role in maintaining fluid homeostasis. Mutations in CFTR are associated with Cystic Fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasians. While remarkable treatment advances have been made recently in the form of modulator drugs directly rescuing CFTR dysfunction, there is still considerable scope for improvement of therapeutic effectiveness. Here, we report the application of a high‐throughput screening variant of the Mammalian Membrane Two‐Hybrid (MaMTH‐HTS) to map the protein–protein interactions of wild‐type (wt) and mutant CFTR (F508del), in an effort to better understand CF cellular effects and identify new drug targets for patient‐specific treatments. Combined with functional validation in multiple disease models, we have uncovered candidate proteins with potential roles in CFTR function/CF pathophysiology, including Fibrinogen Like 2 (FGL2), which we demonstrate in patient‐derived intestinal organoids has a significant effect on CFTR functional expression.
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Affiliation(s)
- Sang Hyun Lim
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | - Jamie Snider
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Liron Birimberg‐Schwartz
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Wan Ip
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
| | - Joana C Serralha
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
- Faculty of Life Sciences and Medicine School of Bioscience Education King’s College London London UK
| | - Hugo M Botelho
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Miquéias Lopes‐Pacheco
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Madalena C Pinto
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Mohamed Taha Moutaoufik
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Mara Zilocchi
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Onofrio Laselva
- Department of Physiology University of Toronto Toronto ON Canada
| | - Mohsen Esmaeili
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto ON Canada
| | - Max Kotlyar
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
| | | | | | | | - Indira Akula
- Donnelly Centre University of Toronto Toronto ON Canada
| | | | - Victoria Wong
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Ingrid Grozavu
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | | | - Zhong Yao
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Meg Mendoza
- Department of Molecular Genetics University of Toronto Toronto ON Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Igor Jurisica
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
- Departments of Medical Biophysics and Computer Science University of Toronto Toronto ON Canada
- Institute of Neuroimmunology Slovak Academy of Sciences Bratislava Slovakia
| | - Tanja Gonska
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Christine E Bear
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Physiology University of Toronto Toronto ON Canada
| | - Margarida D Amaral
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Igor Stagljar
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Molecular Genetics University of Toronto Toronto ON Canada
- Mediterranean Institute for Life Sciences Split Croatia
- School of Medicine University of Split Split Croatia
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21
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Barone S, Cassese E, Alfano AI, Brindisi M, Summa V. Chasing a Breath of Fresh Air in Cystic Fibrosis (CF): Therapeutic Potential of Selective HDAC6 Inhibitors to Tackle Multiple Pathways in CF Pathophysiology. J Med Chem 2022; 65:3080-3097. [PMID: 35148101 PMCID: PMC8883472 DOI: 10.1021/acs.jmedchem.1c02067] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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Compelling new support
has been provided for histone deacetylase
isoform 6 (HDAC6) as a common thread in the generation of the dysregulated
proinflammatory and fibrotic phenotype in cystic fibrosis (CF). HDAC6
also plays a crucial role in bacterial clearance or killing as a direct
consequence of its effects on CF immune responses. Inhibiting HDAC6
functions thus eventually represents an innovative and effective strategy
to tackle multiple aspects of CF-associated lung disease. In this
Perspective, we not only showcase the latest evidence linking HDAC(6)
activity and expression with CF phenotype but also track the new dawn
of HDAC(6) modulators in CF and explore potentialities and future
perspectives in the field.
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Affiliation(s)
- Simona Barone
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Emilia Cassese
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Antonella Ilenia Alfano
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Margherita Brindisi
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
| | - Vincenzo Summa
- Department of Pharmacy, Department of Excellence 2018-2022, School of Medicine and Surgery, University of Naples "Federico II", Via D. Montesano 49, I-80131 Naples, Italy
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22
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Sunil AA, Skaria T. Novel regulators of airway epithelial barrier function during inflammation: potential targets for drug repurposing. Expert Opin Ther Targets 2022; 26:119-132. [PMID: 35085478 DOI: 10.1080/14728222.2022.2035720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Endogenous inflammatory signaling molecules resulting from deregulated immune responses, can impair airway epithelial barrier function and predispose individuals with airway inflammatory diseases to exacerbations and lung infections. Targeting the specific endogenous factors disrupting the airway barrier therefore has the potential to prevent disease exacerbations without affecting the protective immune responses. AREAS COVERED Here, we review the endogenous factors and specific mechanisms disrupting airway epithelial barrier during inflammation and reflect on whether these factors can be specifically targeted by repurposed existing drugs. Literature search was conducted using PubMed, drug database of US FDA and European Medicines Agency until and including September 2021. EXPERT OPINION IL-4 and IL-13 signaling are the major pathways disrupting the airway epithelial barrier during airway inflammation. However, blocking IL-4/IL-13 signaling may adversely affect protective immune responses and increase susceptibility of host to infections. An alternate approach to modulate airway epithelial barrier function involves targeting specific downstream component of IL-4/IL-13 signaling or different inflammatory mediators responsible for regulation of airway epithelial barrier. Airway epithelium-targeted therapy using inhibitors of HDAC, HSP90, MIF, mTOR, IL-17A and VEGF may be a potential strategy to prevent airway epithelial barrier dysfunction in airway inflammatory diseases.
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Affiliation(s)
- Ahsan Anjoom Sunil
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India
| | - Tom Skaria
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India
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23
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Strub MD, Gao L, Tan K, McCray PB. Analysis of multiple gene co-expression networks to discover interactions favoring CFTR biogenesis and ΔF508-CFTR rescue. BMC Med Genomics 2021; 14:258. [PMID: 34717611 PMCID: PMC8557508 DOI: 10.1186/s12920-021-01106-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/20/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND We previously reported that expression of a miR-138 mimic or knockdown of SIN3A in primary cultures of cystic fibrosis (CF) airway epithelia increased ΔF508-CFTR mRNA and protein levels, and partially restored CFTR-dependent chloride transport. Global mRNA transcript profiling in ΔF508-CFBE cells treated with miR-138 mimic or SIN3A siRNA identified two genes, SYVN1 and NEDD8, whose inhibition significantly increased ΔF508-CFTR trafficking, maturation, and function. Little is known regarding the dynamic changes in the CFTR gene network during such rescue events. We hypothesized that analysis of condition-specific gene networks from transcriptomic data characterizing ΔF508-CFTR rescue could help identify dynamic gene modules associated with CFTR biogenesis. METHODS We applied a computational method, termed M-module, to analyze multiple gene networks, each of which exhibited differential activity compared to a baseline condition. In doing so, we identified both unique and shared gene pathways across multiple differential networks. To construct differential networks, gene expression data from CFBE cells were divided into three groups: (1) siRNA inhibition of NEDD8 and SYVN1; (2) miR-138 mimic and SIN3A siRNA; and (3) temperature (27 °C for 24 h, 40 °C for 24 h, and 27 °C for 24 h followed by 40 °C for 24 h). RESULTS Interrogation of individual networks (e.g., NEDD8/SYVN1 network), combinations of two networks (e.g., NEDD8/SYVN1 + temperature networks), and all three networks yielded sets of 1-modules, 2-modules, and 3-modules, respectively. Gene ontology analysis revealed significant enrichment of dynamic modules in pathways including translation, protein metabolic/catabolic processes, protein complex assembly, and endocytosis. Candidate CFTR effectors identified in the analysis included CHURC1, GZF1, and RPL15, and siRNA-mediated knockdown of these genes partially restored CFTR-dependent transepithelial chloride current to ΔF508-CFBE cells. CONCLUSIONS The ability of the M-module to identify dynamic modules involved in ΔF508 rescue provides a novel approach for studying CFTR biogenesis and identifying candidate suppressors of ΔF508.
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Affiliation(s)
- Matthew D Strub
- Department of Pediatrics, University of Iowa, 6320 PBDB, 169 Newton Road, Iowa City, IA, 52242, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52245, USA
| | - Long Gao
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Tan
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul B McCray
- Department of Pediatrics, University of Iowa, 6320 PBDB, 169 Newton Road, Iowa City, IA, 52242, USA. .,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52245, USA.
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24
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SFPQ rescues F508del-CFTR expression and function in cystic fibrosis bronchial epithelial cells. Sci Rep 2021; 11:16645. [PMID: 34404863 PMCID: PMC8371023 DOI: 10.1038/s41598-021-96141-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/05/2021] [Indexed: 01/19/2023] Open
Abstract
Cystic fibrosis (CF) occurs as a result of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which lead to misfolding, trafficking defects, and impaired function of the CFTR protein. Splicing factor proline/glutamine-rich (SFPQ) is a multifunctional nuclear RNA-binding protein (RBP) implicated in the regulation of gene expression pathways and intracellular trafficking. Here, we investigated the role of SFPQ in the regulation of the expression and function of F508del-CFTR in CF lung epithelial cells. We find that the expression of SFPQ is reduced in F508del-CFTR CF epithelial cells compared to WT-CFTR control cells. Interestingly, the overexpression of SFPQ in CF cells increases the expression as well as rescues the function of F508del-CFTR. Further, comprehensive transcriptome analyses indicate that SFPQ plays a key role in activating the mutant F508del-CFTR by modulating several cellular signaling pathways. This is the first report on the role of SFPQ in the regulation of expression and function of F508del-CFTR in CF lung disease. Our findings provide new insights into SFPQ-mediated molecular mechanisms and point to possible novel epigenetic therapeutic targets for CF and related pulmonary diseases.
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25
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Cruz DL, Pipalia N, Mao S, Gadi D, Liu G, Grigalunas M, O'Neill M, Quinn TR, Kipper A, Ekebergh A, Dimmling A, Gartner C, Melancon BJ, Wagner FF, Holson E, Helquist P, Wiest O, Maxfield FR. Inhibition of Histone Deacetylases 1, 2, and 3 Enhances Clearance of Cholesterol Accumulation in Niemann-Pick C1 Fibroblasts. ACS Pharmacol Transl Sci 2021; 4:1136-1148. [PMID: 34151204 PMCID: PMC8204796 DOI: 10.1021/acsptsci.1c00033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Indexed: 11/29/2022]
Abstract
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Niemann-Pick disease type C1 (NPC1) is a rare genetic cholesterol storage disorder
caused by mutations in the NPC1 gene. Mutations in this transmembrane
late endosome protein lead to loss of normal cholesterol efflux from late endosomes and
lysosomes. It has been shown that broad spectrum histone deacetylase inhibitors
(HDACi's) such as Vorinostat correct the cholesterol accumulation phenotype in the
majority of NPC1 mutants tested in cultured cells. In order to determine the optimal
specificity for HDACi correction of the mutant NPC1s, we screened 76 HDACi's of varying
specificity. We tested the ability of these HDACi's to correct the excess accumulation
of cholesterol in patient fibroblast cells that homozygously express
NPC1I1061T, the most common mutation. We
determined that inhibition of HDACs 1, 2, and 3 is important for correcting the defect,
and combined inhibition of all three is needed to achieve the greatest effect,
suggesting a need for multiple effects of the HDACi treatments. Identifying the specific
HDACs involved in the process of regulating cholesterol trafficking in NPC1 will help to
focus the search for more specific druggable targets.
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Affiliation(s)
- Dana L Cruz
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Nina Pipalia
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Shu Mao
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Deepti Gadi
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
| | - Gang Liu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Michael Grigalunas
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Matthew O'Neill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Taylor R Quinn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Andi Kipper
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Andreas Ekebergh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Alexander Dimmling
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Carlos Gartner
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Bruce J Melancon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Florence F Wagner
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Edward Holson
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.,KDAc Therapeutics, Cambridge, Massachusetts 02142, United States
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University, Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Frederick R Maxfield
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, United States
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26
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Elmezayen AD, Al-Obaidi A, Yelekçi K. Discovery of novel isoform-selective histone deacetylases 5 and 9 inhibitors through combined ligand-based pharmacophore modeling, molecular mocking, and molecular dynamics simulations for cancer treatment. J Mol Graph Model 2021; 106:107937. [PMID: 34049193 DOI: 10.1016/j.jmgm.2021.107937] [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: 01/30/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022]
Abstract
Class IIa histone deacetylases (HDACs) 5 and 9 play crucial roles in several human disorders such as cancer, making them important targets for drug design. Continuous research is pursed to overcome the cytotoxicity side effect that comes with the currently available broad-spectrum HDACs inhibitors. Herein, common features of active HDACs inhibitors in clinical trials and use have been calculated to generate the best pharmacophore hypothesis. Guner-Henry scoring system was used to validate the generated hypotheses. Hypo1 of HDAC5 and Hypo2 of HDAC9 exhibited the most statistically significance hypotheses. Compounds with fit value of 3 and more were examined by QuickVina 2 docking tool to calculate their binding affinity toward all class IIa HDACs. A total of 6 potential selective compounds were subjected to 100 molecular dynamics (MD) simulation to examine their binding modes. The free binding energy calculations were computed according to the MM-PBSA method. Proposed selective compounds displayed good stability with their targets and thus they may offer potent leads for the designing of HDAC5 and HDAC9 isoform selective inhibitors.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
| | - Anas Al-Obaidi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
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27
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Hodos RA, Strub MD, Ramachandran S, Meleshkevitch EA, Boudko DY, Bridges RJ, Dudley JT, McCray PB. Integrative chemogenomic analysis identifies small molecules that partially rescue ΔF508-CFTR for cystic fibrosis. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2021; 10:500-510. [PMID: 33934548 PMCID: PMC8129714 DOI: 10.1002/psp4.12626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Rare diseases affect 10% of the first‐world population, yet over 95% lack even a single pharmaceutical treatment. In the present age of information, we need ways to leverage our vast data and knowledge to streamline therapeutic development and lessen this gap. Here, we develop and implement an innovative informatic approach to identify therapeutic molecules, using the Connectivity Map and LINCS L1000 databases and disease‐associated transcriptional signatures and pathways. We apply this to cystic fibrosis (CF), the most common genetic disease in people of northern European ancestry leading to chronic lung disease and reduced lifespan. We selected and tested 120 small molecules in a CF cell line, finding 8 with activity, and confirmed 3 in primary CF airway epithelia. Although chemically diverse, the transcriptional profiles of the hits suggest a common mechanism associated with the unfolded protein response and/or TNFα signaling. This study highlights the power of informatics to help identify new therapies and reveal mechanistic insights while moving beyond target‐centric drug discovery.
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Affiliation(s)
- Rachel A Hodos
- Institute for Next Generation Healthcare, Mount Sinai School of Medicine, New York, NY, USA.,Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Matthew D Strub
- Department of Pediatrics, University of Iowa, Carver College of Medicine, Iowa City, IA, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | | | - Ella A Meleshkevitch
- Department of Physiology and Biophysics, Rosalind Franklin University, North Chicago, IL, USA
| | - Dmitri Y Boudko
- Department of Physiology and Biophysics, Rosalind Franklin University, North Chicago, IL, USA
| | - Robert J Bridges
- Department of Physiology and Biophysics, Rosalind Franklin University, North Chicago, IL, USA
| | - Joel T Dudley
- Institute for Next Generation Healthcare, Mount Sinai School of Medicine, New York, NY, USA
| | - Paul B McCray
- Department of Pediatrics, University of Iowa, Carver College of Medicine, Iowa City, IA, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
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28
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Mak JYW, Wu KC, Gupta PK, Barbero S, McLaughlin MG, Lucke AJ, Tng J, Lim J, Loh Z, Sweet MJ, Reid RC, Liu L, Fairlie DP. HDAC7 Inhibition by Phenacetyl and Phenylbenzoyl Hydroxamates. J Med Chem 2021; 64:2186-2204. [PMID: 33570940 DOI: 10.1021/acs.jmedchem.0c01967] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The zinc-containing histone deacetylase enzyme HDAC7 is emerging as an important regulator of immunometabolism and cancer. Here, we exploit a cavity in HDAC7, filled by Tyr303 in HDAC1, to derive new inhibitors. Phenacetyl hydroxamates and 2-phenylbenzoyl hydroxamates bind to Zn2+ and are 50-2700-fold more selective inhibitors of HDAC7 than HDAC1. Phenylbenzoyl hydroxamates are 30-70-fold more potent HDAC7 inhibitors than phenacetyl hydroxamates, which is attributed to the benzoyl aromatic group interacting with Phe679 and Phe738. Phthalimide capping groups, including a saccharin analogue, decrease rotational freedom and provide hydrogen bond acceptor carbonyl/sulfonamide oxygens that increase inhibitor potency, liver microsome stability, solubility, and cell activity. Despite being the most potent HDAC7 inhibitors to date, they are not selective among class IIa enzymes. These strategies may help to produce tools for interrogating HDAC7 biology related to its catalytic site.
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Affiliation(s)
- Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Praveer K Gupta
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sheila Barbero
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maddison G McLaughlin
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jiahui Tng
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhixuan Loh
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew J Sweet
- Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert C Reid
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Inflammation and Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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29
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Wright MT, Plate L. Revealing functional insights into ER proteostasis through proteomics and interactomics. Exp Cell Res 2020; 399:112417. [PMID: 33301765 DOI: 10.1016/j.yexcr.2020.112417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/23/2020] [Accepted: 11/28/2020] [Indexed: 12/16/2022]
Abstract
The endoplasmic reticulum (ER), responsible for processing approximately one-third of the human proteome including most secreted and membrane proteins, plays a pivotal role in protein homeostasis (proteostasis). Dysregulation of ER proteostasis has been implicated in a number of disease states. As such, continued efforts are directed at elucidating mechanisms of ER protein quality control which are mediated by transient and dynamic protein-protein interactions with molecular chaperones, co-chaperones, protein folding and trafficking factors that take place in and around the ER. Technological advances in mass spectrometry have played a pivotal role in characterizing and understanding these protein-protein interactions that dictate protein quality control mechanisms. Here, we highlight the recent progress from mass spectrometry-based investigation of ER protein quality control in revealing the topological arrangement of the proteostasis network, stress response mechanisms that adjust the ER proteostasis capacity, and disease specific changes in proteostasis network engagement. We close by providing a brief outlook on underexplored areas of ER proteostasis where mass spectrometry is a tool uniquely primed to further expand our understanding of the regulation and coordination of protein quality control processes in diverse diseases.
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Affiliation(s)
- Madison T Wright
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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Shen D, Chen J, Liu D, Shen M, Wang X, Wu Y, Ke S, Macdonald RL, Zhang Q. The GABRG2 F343L allele causes spontaneous seizures in a novel transgenic zebrafish model that can be treated with suberanilohydroxamic acid (SAHA). ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1560. [PMID: 33437759 PMCID: PMC7791267 DOI: 10.21037/atm-20-3745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background Mutations in the γ-aminobutyric acid type A (GABAA) receptor γ2 subunit gene, GABRG2, have been associated frequently with epilepsy syndromes with varying severities. Recently, a de novo GABRG2 mutation, c.T1027C, p.F343L, was identified in a patient with an early onset epileptic encephalopathy (EOEE). In vitro, we demonstrated that GABAA receptors containing the mutant γ2(F343L) subunit have impaired trafficking to the cell surface. Here, we aim to validate an in vivo zebrafish model of EOEE associated with the GABRG2 mutation T1027C. Methods We generated a novel transgenic zebrafish (AB strain) that overexpressed mutant human γ2(F343L) subunits and provided an initial characterization of the transgenic Tg(hGABRG2F343L) zebrafish. Results Real-time quantitative PCR and in situ hybridization identified a significant up-regulation of c-fos in the mutant transgenic zebrafish, which has a well-established role in epileptogenesis. In the larval stage 5 days postfertilization (dpf), freely swimming Tg(hGABRG2F343L) zebrafish displayed spontaneous seizure-like behaviors consisting of whole-body shaking and hyperactivity during automated locomotion video tracking, and seizures can be induced by light stimulation. Using RNA sequencing, we investigated transcriptomic changes due to the presence of mutant γ2L(F343L) subunits and have found 524 genes that are differentially expressed, including up-regulation of 33 genes associated with protein processing. More specifically, protein network analysis indicated histone deacetylases (HDACs) as potential therapeutic targets, and suberanilohydroxamic acid (SAHA), a broad HDACs inhibitor, alleviated seizure-like phenotypes in mutant zebrafish larvae. Conclusions Overall, our Tg(hGABRG2F343L) overexpression zebrafish model provides the first example of a human epilepsy-associated GABRG2 mutation resulting in spontaneous seizures in zebrafish. Moreover, HDAC inhibition may be worth investigating as a therapeutic strategy for genetic epilepsies caused by missense mutations in GABRG2 and possibly in other central nervous system genes that impair surface trafficking.
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Affiliation(s)
- Dingding Shen
- Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Dong Liu
- School of Life Science, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Mi Shen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xin Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Youjia Wu
- Department of Pediatrics, Affiliated Hospital of Nantong University, Nantong, China
| | - Shuan Ke
- Xinglin College, Nantong University, Nantong, China
| | - Robert L Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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Amaral MD. How to determine the mechanism of action of CFTR modulator compounds: A gateway to theranostics. Eur J Med Chem 2020; 210:112989. [PMID: 33190956 DOI: 10.1016/j.ejmech.2020.112989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The greatest challenge of 21st century biology is to fully understand mechanisms of disease to drive new approaches and medical innovation. Parallel to this is the huge biomedical endeavour of treating people through personalized medicine. Until now all CFTR modulator drugs that have entered clinical trials have been genotype-dependent. An emerging alternative is personalized/precision medicine in CF, i.e., to determine whether rare CFTR mutations respond to existing (or novel) CFTR modulator drugs by pre-assessing them directly on patient's tissues ex vivo, an approach also now termed theranostics. To administer the right drug to the right person it is essential to understand how drugs work, i.e., to know their mechanism of action (MoA), so as to predict their applicability, not just in certain mutations but also possibly in other diseases that share the same defect/defective pathway. Moreover, an understanding the MoA of a drug before it is tested in clinical trials is the logical path to drug discovery and can increase its chance for success and hence also approval. In conclusion, the most powerful approach to determine the MoA of a compound is to understand the underlying biology. Novel large datasets of intervenients in most biological processes, namely those emerging from the post-genomic era tools, are available and should be used to help in this task.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Faculty of Sciences, University of Lisboa, Portugal.
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32
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Wei T, Sui H, Su Y, Cheng W, Liu Y, He Z, Ji Q, Xu C. Research advances in molecular mechanisms underlying the pathogenesis of cystic fibrosis: From technical improvement to clinical applications (Review). Mol Med Rep 2020; 22:4992-5002. [PMID: 33173976 PMCID: PMC7646950 DOI: 10.3892/mmr.2020.11607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is a chronic disease causing severe impairment to the respiratory system and digestive tracts. Currently, CF is incurable. As an autosomal recessive disorder, the morbidity of CF is significantly higher among Caucasians of European descent, whereas it is less pervasive among African and Asian populations. The disease is caused by identical mutations (homozygosity) or different mutations (heterozygosity) of an autosomal recessive mutation at position 7q31.2-q31.1 of chromosome 7. Diagnostic criteria and guidelines work concurrently with laboratory detection to facilitate precise CF detection. With technological advances, the understanding of CF pathogenesis has reached an unprecedented level, allowing for increasingly precise carrier screening, more effective early stage CF intervention and improved prognostic outcomes. These advances significantly increase the life quality and expectancy of patients with CF. Given the numerous improvements in the field of CF, the current review summarized the technical advances in the study of the molecular mechanisms underlying CF, as well as how these improvements facilitate the clinical outcomes of CF. Furthermore, challenges and obstacles to overcome are discussed.
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Affiliation(s)
- Tao Wei
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Hongshu Sui
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Yanping Su
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Wanjing Cheng
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Yunhua Liu
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Zilin He
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Qingchao Ji
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Changlong Xu
- Reproductive Medical Center, Nanning Second People's Hospital, Nanning, Guangxi Zhuang Autonomous Region 530031, P.R. China
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Di XJ, Wang YJ, Cotter E, Wang M, Whittsette AL, Han DY, Sangwung P, Brown R, Lynch JW, Keramidas A, Mu TW. Proteostasis Regulators Restore Function of Epilepsy-Associated GABA A Receptors. Cell Chem Biol 2020; 28:46-59.e7. [PMID: 32888501 DOI: 10.1016/j.chembiol.2020.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022]
Abstract
Proteostasis deficiency in mutated ion channels leads to a variety of ion channel diseases that are caused by excessive endoplasmic reticulum-associated degradation (ERAD) and inefficient membrane trafficking. We investigated proteostasis maintenance of γ-aminobutyric acid type A (GABAA) receptors, the primary mediators of neuronal inhibition in the mammalian central nervous system. We screened a structurally diverse, Food and Drug Administration-approved drug library and identified dinoprost (DNP) and dihydroergocristine (DHEC) as highly efficacious enhancers of surface expression of four epilepsy-causing trafficking-deficient mutant receptors. Furthermore, DNP and DHEC restore whole-cell and synaptic currents by incorporating mutated subunits into functional receptors. Mechanistic studies revealed that both drugs reduce subunit degradation by attenuating the Grp94/Hrd1/Sel1L/VCP-mediated ERAD pathway and enhance the subunit folding by promoting subunit interactions with major GABAA receptors-interacting chaperones, BiP and calnexin. In summary, we report that DNP and DHEC remodel the endoplasmic reticulum proteostasis network to restore the functional surface expression of mutant GABAA receptors.
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Affiliation(s)
- Xiao-Jing Di
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ya-Juan Wang
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Center for Proteomics and Bioinformatics and Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Edmund Cotter
- Queensland Brain Institute, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Meng Wang
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Angela L Whittsette
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Dong-Yun Han
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Panjamaporn Sangwung
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Renae Brown
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joseph W Lynch
- Queensland Brain Institute, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Angelo Keramidas
- Queensland Brain Institute, the University of Queensland, Brisbane, QLD 4072, Australia.
| | - Ting-Wei Mu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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Liessi N, Pedemonte N, Armirotti A, Braccia C. Proteomics and Metabolomics for Cystic Fibrosis Research. Int J Mol Sci 2020; 21:ijms21155439. [PMID: 32751630 PMCID: PMC7432297 DOI: 10.3390/ijms21155439] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/18/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
The aim of this review article is to introduce the reader to the state-of-the-art of the contribution that proteomics and metabolomics sciences are currently providing for cystic fibrosis (CF) research: from the understanding of cystic fibrosis transmembrane conductance regulator (CFTR) biology to biomarker discovery for CF diagnosis. Our work particularly focuses on CFTR post-translational modifications and their role in cellular trafficking as well as on studies that allowed the identification of CFTR molecular interactors. We also show how metabolomics is currently helping biomarker discovery in CF. The most recent advances in these fields are covered by this review, as well as some considerations on possible future scenarios for new applications.
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Affiliation(s)
- Nara Liessi
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy;
| | - Andrea Armirotti
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
- Correspondence: ; Tel.: +39-010-2896-938
| | - Clarissa Braccia
- D3PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
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Elmezayen AD, Yelekçi K. Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes. J Biomol Struct Dyn 2020; 39:6396-6414. [PMID: 32715940 DOI: 10.1080/07391102.2020.1798812] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have no crystal structures, such as HDAC5 and HDAC9. Lacking proper and suitable crystal structure is obstructing the designing of appropriate isoform selective inhibitors. Here in this study, we constructed human HDAC5 and HDAC9 protein models using human HDAC4 (PDB:2VQM_A) as a template by the means of homology modeling approach. Based on the Z-score of the built models, model M0014 of HDAC5 and model M0020 of HDAC9 were selected. The models were verified by MODELLER and validated using the Web-based PROCHECK server. All selected known inhibitors displayed reasonable binding modes and equivalent predicted Ki values in comparison to the experimental binding affinities (Ki/IC50). The known inhibitor Rac26 showed the best binding affinity for HDAC5, while TMP269 showed the best binding affinity for HDAC9. The best two compounds, CHEMBL2114980 and CHEMBL217223, had relatively similar inhibition constants against HDAC5 and HDAC9. The built models and their complexes were subjected to molecular dynamic simulations (MD) for 100 ns. Examining the MD simulation results of all studied structures, including the RMSD, RMSF, radius of gyration and potential energy suggested the stability and reliability of the built models. Accordingly, the results obtained in this study could be used for designing de novo inhibitors against HDAC5 and HDAC9. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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36
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Strub MD, McCray, Jr. PB. Transcriptomic and Proteostasis Networks of CFTR and the Development of Small Molecule Modulators for the Treatment of Cystic Fibrosis Lung Disease. Genes (Basel) 2020; 11:genes11050546. [PMID: 32414011 PMCID: PMC7288469 DOI: 10.3390/genes11050546] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022] Open
Abstract
Cystic fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The diversity of mutations and the multiple ways by which the protein is affected present challenges for therapeutic development. The observation that the Phe508del-CFTR mutant protein is temperature sensitive provided proof of principle that mutant CFTR could escape proteosomal degradation and retain partial function. Several specific protein interactors and quality control checkpoints encountered by CFTR during its proteostasis have been investigated for therapeutic purposes, but remain incompletely understood. Furthermore, pharmacological manipulation of many CFTR interactors has not been thoroughly investigated for the rescue of Phe508del-CFTR. However, high-throughput screening technologies helped identify several small molecule modulators that rescue CFTR from proteosomal degradation and restore partial function to the protein. Here, we discuss the current state of CFTR transcriptomic and biogenesis research and small molecule therapy development. We also review recent progress in CFTR proteostasis modulators and discuss how such treatments could complement current FDA-approved small molecules.
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Affiliation(s)
- Matthew D. Strub
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA;
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, IA 52242, USA
| | - Paul B. McCray, Jr.
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA;
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, IA 52242, USA
- Correspondence: ; Tel.: +1-(319)-335-6844
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Synthesis and Therapeutic Applications of Iminosugars in Cystic Fibrosis. Int J Mol Sci 2020; 21:ijms21093353. [PMID: 32397443 PMCID: PMC7247015 DOI: 10.3390/ijms21093353] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
Iminosugars are sugar analogues endowed with a high pharmacological potential. The wide range of biological activities exhibited by these glycomimetics associated with their excellent drug profile make them attractive therapeutic candidates for several medical interventions. The ability of iminosugars to act as inhibitors or enhancers of carbohydrate-processing enzymes suggests their potential use as therapeutics for the treatment of cystic fibrosis (CF). Herein we review the most relevant advances in the field, paying attention to both the chemical synthesis of the iminosugars and their biological evaluations, resulting from in vitro and in vivo assays. Starting from the example of the marketed drug NBDNJ (N-butyl deoxynojirimycin), a variety of iminosugars have exhibited the capacity to rescue the trafficking of F508del-CFTR (deletion of F508 residue in the CF transmembrane conductance regulator), either alone or in combination with other correctors. Interesting results have also been obtained when iminosugars were considered as anti-inflammatory agents in CF lung disease. The data herein reported demonstrate that iminosugars hold considerable potential to be applied for both therapeutic purposes.
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38
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Mohammad Hadi L, Yaghini E, MacRobert AJ, Loizidou M. Synergy between Photodynamic Therapy and Dactinomycin Chemotherapy in 2D and 3D Ovarian Cancer Cell Cultures. Int J Mol Sci 2020; 21:E3203. [PMID: 32366058 PMCID: PMC7247344 DOI: 10.3390/ijms21093203] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/05/2023] Open
Abstract
In this study we explored the efficacy of combining low dose photodynamic therapy using a porphyrin photosensitiser and dactinomycin, a commonly used chemotherapeutic agent. The studies were carried out on compressed collagen 3D constructs of two human ovarian cancer cell lines (SKOV3 and HEY) versus their monolayer counterparts. An amphiphilc photosensitiser was employed, disulfonated tetraphenylporphine, which is not a substrate for ABC efflux transporters that can mediate drug resistance. The combination treatment was shown to be effective in both monolayer and 3D constructs of both cell lines, causing a significant and synergistic reduction in cell viability. Compared to dactinomycin alone or PDT alone, higher cell kill was found using 2D monolayer culture vs. 3D culture for the same doses. In 3D culture, the combination therapy resulted in 10 and 22 times higher cell kill in SKOV3 and HEY cells at the highest light dose compared to dactinomycin monotherapy, and 2.2 and 5.5 times higher cell kill than PDT alone. The combination of low dose PDT and dactinomycin appears to be a promising way to repurpose dactinomycin and widen its therapeutic applications.
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Affiliation(s)
- Layla Mohammad Hadi
- Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London NW3 2QG, UK; (E.Y.); (A.J.M.)
| | | | | | - Marilena Loizidou
- Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London NW3 2QG, UK; (E.Y.); (A.J.M.)
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Subramanian K, Hutt DM, Scott SM, Gupta V, Mao S, Balch WE. Correction of Niemann-Pick type C1 trafficking and activity with the histone deacetylase inhibitor valproic acid. J Biol Chem 2020; 295:8017-8035. [PMID: 32354745 DOI: 10.1074/jbc.ra119.010524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
Niemann-Pick type C (NPC) disease is primarily caused by mutations in the NPC1 gene and is characterized by the accumulation of unesterified cholesterol and lipids in the late endosomal (LE) and lysosomal (Ly) compartments. The most prevalent disease-linked mutation is the I1061T variant of NPC1, which exhibits defective folding and trafficking from the endoplasmic reticulum to the LE/Ly compartments. We now show that the FDA-approved histone deacetylase inhibitor (HDACi) valproic acid (VPA) corrects the folding and trafficking defect associated with I1061T-NPC1 leading to restoration of cholesterol homeostasis, an effect that is largely driven by a reduction in HDAC7 expression. The VPA-mediated trafficking correction is in part associated with an increase in the acetylation of lysine residues in the cysteine-rich domain of NPC1. The HDACi-mediated correction is synergistically improved by combining it with the FDA-approved anti-malarial, chloroquine, a known lysosomotropic compound, which improved the stability of the LE/Ly-localized fraction of the I1061T variant. We posit that combining the activity of VPA, to modulate epigenetically the cellular acetylome, with chloroquine, to alter the lysosomal environment to favor stability of the trafficked I1061T variant protein can have a significant therapeutic benefit in patients carrying at least one copy of the I1061T variant of NPC1, the most common disease-associated mutation leading to NPC disease. Given its ability to cross the blood-brain barrier, we posit VPA provides a potential mechanism to improve the response to 2-hydroxypropyl-β-cyclodextrin, by restoring a functional NPC1 to the cholesterol managing compartment as an adjunct therapy.
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Affiliation(s)
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Samantha M Scott
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Vijay Gupta
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Shu Mao
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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Singh BK, Cooney AL, Krishnamurthy S, Sinn PL. Extracellular Vesicle-Mediated siRNA Delivery, Protein Delivery, and CFTR Complementation in Well-Differentiated Human Airway Epithelial Cells. Genes (Basel) 2020; 11:genes11040351. [PMID: 32224868 PMCID: PMC7230663 DOI: 10.3390/genes11040351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/05/2023] Open
Abstract
Extracellular vesicles (EVs) are a class of naturally occurring secreted cellular bodies that are involved in long distance cell-to-cell communication. Proteins, lipids, mRNA, and miRNA can be packaged into these vesicles and released from the cell. This information is then delivered to target cells. Since EVs are naturally adapted molecular messengers, they have emerged as an innovative, inexpensive, and robust method to deliver therapeutic cargo in vitro and in vivo. Well-differentiated primary cultures of human airway epithelial cells (HAE) are refractory to standard transfection techniques. Indeed, common strategies used to overexpress or knockdown gene expression in immortalized cell lines simply have no detectable effect in HAE. Here we use EVs to efficiently deliver siRNA or protein to HAE. Furthermore, EVs can deliver CFTR protein to cystic fibrosis donor cells and functionally correct the Cl− channel defect in vitro. EV-mediated delivery of siRNA or proteins to HAE provides a powerful genetic tool in a model system that closely recapitulates the in vivo airways.
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Lopes-Pacheco M. CFTR Modulators: The Changing Face of Cystic Fibrosis in the Era of Precision Medicine. Front Pharmacol 2020; 10:1662. [PMID: 32153386 PMCID: PMC7046560 DOI: 10.3389/fphar.2019.01662] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Cystic fibrosis (CF) is a lethal inherited disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which result in impairment of CFTR mRNA and protein expression, function, stability or a combination of these. Although CF leads to multifaceted clinical manifestations, the respiratory disorder represents the major cause of morbidity and mortality of these patients. The life expectancy of CF patients has substantially lengthened due to early diagnosis and improvements in symptomatic therapeutic regimens. Quality of life remains nevertheless limited, as these individuals are subjected to considerable clinical, psychosocial and economic burdens. Since the discovery of the CFTR gene in 1989, tremendous efforts have been made to develop therapies acting more upstream on the pathogenesis cascade, thereby overcoming the underlying dysfunctions caused by CFTR mutations. In this line, the advances in cell-based high-throughput screenings have been facilitating the fast-tracking of CFTR modulators. These modulator drugs have the ability to enhance or even restore the functional expression of specific CF-causing mutations, and they have been classified into five main groups depending on their effects on CFTR mutations: potentiators, correctors, stabilizers, read-through agents, and amplifiers. To date, four CFTR modulators have reached the market, and these pharmaceutical therapies are transforming patients' lives with short- and long-term improvements in clinical outcomes. Such breakthroughs have paved the way for the development of novel CFTR modulators, which are currently under experimental and clinical investigations. Furthermore, recent insights into the CFTR structure will be useful for the rational design of next-generation modulator drugs. This review aims to provide a summary of recent developments in CFTR-directed therapeutics. Barriers and future directions are also discussed in order to optimize treatment adherence, identify feasible and sustainable solutions for equitable access to these therapies, and continue to expand the pipeline of novel modulators that may result in effective precision medicine for all individuals with CF.
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Affiliation(s)
- Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Anglès F, Hutt DM, Balch WE. HDAC inhibitors rescue multiple disease-causing CFTR variants. Hum Mol Genet 2020; 28:1982-2000. [PMID: 30753450 DOI: 10.1093/hmg/ddz026] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/21/2018] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Understanding the role of the epigenome in protein-misfolding diseases remains a challenge in light of genetic diversity found in the world-wide population revealed by human genome sequencing efforts and the highly variable response of the disease population to therapeutics. An ever-growing body of evidence has shown that histone deacetylase (HDAC) inhibitors (HDACi) can have significant benefit in correcting protein-misfolding diseases that occur in response to both familial and somatic mutation. Cystic fibrosis (CF) is a familial autosomal recessive disease, caused by genetic diversity in the CF transmembrane conductance regulator (CFTR) gene, a cyclic Adenosine MonoPhosphate (cAMP)-dependent chloride channel expressed at the apical plasma membrane of epithelial cells in multiple tissues. The potential utility of HDACi in correcting the phenylalanine 508 deletion (F508del) CFTR variant as well as the over 2000 CF-associated variants remains controversial. To address this concern, we examined the impact of US Food and Drug Administration-approved HDACi on the trafficking and function of a panel of CFTR variants. Our data reveal that panobinostat (LBH-589) and romidepsin (FK-228) provide functional correction of Class II and III CFTR variants, restoring cell surface chloride channel activity in primary human bronchial epithelial cells. We further demonstrate a synergistic effect of these HDACi with Vx809, which can significantly restore channel activity for multiple CFTR variants. These data suggest that HDACi can serve to level the cellular playing field for correcting CF-causing mutations, a leveling effect that might also extend to other protein-misfolding diseases.
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Affiliation(s)
- Frédéric Anglès
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, North Torrey Pines Rd, La Jolla, CA, USA.,Skaggs Institute of Chemical Biology, North Torrey Pines Rd, La Jolla, CA, USA
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43
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Tosco A, Villella VR, Raia V, Kroemer G, Maiuri L. Cystic Fibrosis: New Insights into Therapeutic Approaches. CURRENT RESPIRATORY MEDICINE REVIEWS 2020. [DOI: 10.2174/1573398x15666190702151613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the identification of Cystic Fibrosis (CF) as a disease in 1938 until 2012, only
therapies to treat symptoms rather than etiological therapies have been used to treat the disease. Over
the last few years, new technologies have been developed, and gene editing strategies are now
moving toward a one-time cure. This review will summarize recent advances in etiological therapies
that target the basic defect in the CF Transmembrane Receptor (CFTR), the protein that is mutated in
CF. We will discuss how newly identified compounds can directly target mutated CFTR to improve
its function. Moreover, we will discuss how proteostasis regulators can modify the environment in
which the mutant CFTR protein is synthesized and decayed, thus restoring CFTR function. The
future of CF therapies lies in combinatory therapies that may be personalized for each CF patient.
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Affiliation(s)
- Antonella Tosco
- Department of Translational Medical Sciences, Pediatric Unit, Regional Cystic Fibrosis Center, Federico II University, Naples 80131, Italy
| | - Valeria R. Villella
- Division of Genetics and Cell Biology, European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Valeria Raia
- Department of Translational Medical Sciences, Pediatric Unit, Regional Cystic Fibrosis Center, Federico II University, Naples 80131, Italy
| | - Guido Kroemer
- Equipe11 labellisee Ligue Nationale Contrele Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Luigi Maiuri
- Division of Genetics and Cell Biology, European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute, Milan 20132, Italy
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44
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Quantitating the epigenetic transformation contributing to cholesterol homeostasis using Gaussian process. Nat Commun 2019; 10:5052. [PMID: 31699992 PMCID: PMC6838179 DOI: 10.1038/s41467-019-12969-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
To understand the impact of epigenetics on human misfolding disease, we apply Gaussian-process regression (GPR) based machine learning (ML) (GPR-ML) through variation spatial profiling (VSP). VSP generates population-based matrices describing the spatial covariance (SCV) relationships that link genetic diversity to fitness of the individual in response to histone deacetylases inhibitors (HDACi). Niemann-Pick C1 (NPC1) is a Mendelian disorder caused by >300 variants in the NPC1 gene that disrupt cholesterol homeostasis leading to the rapid onset and progression of neurodegenerative disease. We determine the sequence-to-function-to-structure relationships of the NPC1 polypeptide fold required for membrane trafficking and generation of a tunnel that mediates cholesterol flux in late endosomal/lysosomal (LE/Ly) compartments. HDACi treatment reveals unanticipated epigenomic plasticity in SCV relationships that restore NPC1 functionality. GPR-ML based matrices capture the epigenetic processes impacting information flow through central dogma, providing a framework for quantifying the effect of the environment on the healthspan of the individual. How epigenetics coordinate with genetics to impact protein fitness is unknown. Here, using a Variation Spatial Profiling strategy and machine learning, the authors map HDAC impact on a full set of Niemann pick C1 disease variants to quantitate an unanticipated plasticity in central dogma.
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Bioactive Thymosin Alpha-1 Does Not Influence F508del-CFTR Maturation and Activity. Sci Rep 2019; 9:10310. [PMID: 31311979 PMCID: PMC6635361 DOI: 10.1038/s41598-019-46639-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/03/2019] [Indexed: 12/11/2022] Open
Abstract
Deletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is the most frequent mutation causing cystic fibrosis (CF). F508del-CFTR is misfolded and prematurely degraded. Recently thymosin a-1 (Tα-1) was proposed as a single molecule-based therapy for CF, improving both F508del-CFTR maturation and function by restoring defective autophagy. However, three independent laboratories failed to reproduce these results. Lack of reproducibility has been ascribed by the authors of the original paper to the use of DMSO and to improper handling. Here, we address these potential issues by demonstrating that Tα-1 changes induced by DMSO are fully reversible and that Tα-1 peptides prepared from different stock solutions have equivalent biological activity. Considering the negative results here reported, six independent laboratories failed to demonstrate F508del-CFTR correction by Tα-1. This study also calls into question the autophagy modulator cysteamine, since no rescue of mutant CFTR function was detected following treatment with cysteamine, while deleterious effects were observed when bronchial epithelia were exposed to cysteamine plus the antioxidant food supplement EGCG. Although these studies do not exclude the possibility of beneficial immunomodulatory effects of thymosin α-1, they do not support its utility as a corrector of F508del-CFTR.
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46
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Hanrahan JW, Sato Y, Carlile GW, Jansen G, Young JC, Thomas DY. Cystic Fibrosis: Proteostatic correctors of CFTR trafficking and alternative therapeutic targets. Expert Opin Ther Targets 2019; 23:711-724. [PMID: 31169041 DOI: 10.1080/14728222.2019.1628948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Cystic fibrosis (CF) is the most frequent lethal orphan disease and is caused by mutations in the CFTR gene. The most frequent mutation F508del-CFTR affects multiple organs; infections and subsequent infections and complications in the lung lead to death. Areas covered: This review focuses on new targets and mechanisms that are attracting interest for the development of CF therapies. The F508del-CFTR protein is retained in the endoplasmic reticulum (ER) but has some function if it can traffic to the plasma membrane. Cell-based assays have been used to screen chemical libraries for small molecule correctors that restore its trafficking. Pharmacological chaperones are correctors that bind directly to the F508del-CFTR mutant and promote its folding and trafficking. Other correctors fall into a heterogeneous class of proteostasis modulators that act indirectly by altering cellular homeostasis. Expert opinion: Pharmacological chaperones have so far been the most successful correctors of F508del-CFTR trafficking, but their level of correction means that more than one corrector is required. Proteostasis modulators have low levels of correction but hold promise because some can correct several different CFTR mutations. Identification of their cellular targets and the potential for development may lead to new therapies for CF.
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Affiliation(s)
- John W Hanrahan
- a Department of Physiology , McGill University , Montréal , QC , Canada.,c Research Institute of the McGill University Health Centre , McGill University , Montréal , QC , Canada
| | - Yukiko Sato
- a Department of Physiology , McGill University , Montréal , QC , Canada.,b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada
| | - Graeme W Carlile
- b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada.,d Department of Biochemistry , McGill University , Montréal , QC , Canada
| | - Gregor Jansen
- d Department of Biochemistry , McGill University , Montréal , QC , Canada
| | - Jason C Young
- b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada.,d Department of Biochemistry , McGill University , Montréal , QC , Canada
| | - David Y Thomas
- b Cystic Fibrosis Translational Research centre , McGill University , Montréal , QC , Canada.,d Department of Biochemistry , McGill University , Montréal , QC , Canada.,e Department of Human Genetics , McGill University , Montréal , QC , Canada
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47
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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48
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Bose SJ, Bijvelds MJC, Wang Y, Liu J, Cai Z, Bot AGM, de Jonge HR, Sheppard DN. Differential thermostability and response to cystic fibrosis transmembrane conductance regulator potentiators of human and mouse F508del-CFTR. Am J Physiol Lung Cell Mol Physiol 2019; 317:L71-L86. [PMID: 30969810 PMCID: PMC6689747 DOI: 10.1152/ajplung.00034.2019] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cross-species comparative studies have highlighted differences between human and mouse cystic fibrosis transmembrane conductance regulator (CFTR), the epithelial Cl- channel defective in cystic fibrosis (CF). Here, we compare the impact of the most common CF mutation F508del on the function of human and mouse CFTR heterologously expressed in mammalian cells and their response to CFTR modulators using the iodide efflux and patch-clamp techniques. Once delivered to the plasma membrane, human F508del-CFTR exhibited a severe gating defect characterized by infrequent channel openings and was thermally unstable, deactivating within minutes at 37°C. By contrast, the F508del mutation was without effect on the gating pattern of mouse CFTR, and channel activity demonstrated thermostability at 37°C. Strikingly, at all concentrations tested, the clinically approved CFTR potentiator ivacaftor was without effect on the mouse F508del-CFTR Cl- channel. Moreover, eight CFTR potentiators, including ivacaftor, failed to generate CFTR-mediated iodide efflux from CHO cells expressing mouse F508del-CFTR. However, they all produced CFTR-mediated iodide efflux with human F508del-CFTR-expressing CHO cells, while fifteen CFTR correctors rescued the plasma membrane expression of both human and mouse F508del-CFTR. Interestingly, the CFTR potentiator genistein enhanced CFTR-mediated iodide efflux from CHO cells expressing either human or mouse F508del-CFTR, whereas it only potentiated human F508del-CFTR Cl- channels in cell-free membrane patches, suggesting that its action on mouse F508del-CFTR is indirect. Thus, the F508del mutation has distinct effects on human and mouse CFTR Cl- channels.
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Affiliation(s)
- Samuel J Bose
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Marcel J C Bijvelds
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - Yiting Wang
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Jia Liu
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Zhiwei Cai
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
| | - Alice G M Bot
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol , Bristol , United Kingdom
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49
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HDAC Inhibitors: Therapeutic Potential in Fibrosis-Associated Human Diseases. Int J Mol Sci 2019; 20:ijms20061329. [PMID: 30884785 PMCID: PMC6471162 DOI: 10.3390/ijms20061329] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 02/07/2023] Open
Abstract
Fibrosis is characterized by excessive deposition of the extracellular matrix and develops because of fibroblast differentiation during the process of inflammation. Various cytokines stimulate resident fibroblasts, which differentiate into myofibroblasts. Myofibroblasts actively synthesize an excessive amount of extracellular matrix, which indicates pathologic fibrosis. Although initial fibrosis is a physiologic response, the accumulated fibrous material causes failure of normal organ function. Cardiac fibrosis interferes with proper diastole, whereas pulmonary fibrosis results in chronic hypoxia; liver cirrhosis induces portal hypertension, and overgrowth of fibroblasts in the conjunctiva is a major cause of glaucoma surgical failure. Recently, several reports have clearly demonstrated the functional relevance of certain types of histone deacetylases (HDACs) in various kinds of fibrosis and the successful alleviation of the condition in animal models using HDAC inhibitors. In this review, we discuss the therapeutic potential of HDAC inhibitors in fibrosis-associated human diseases using results obtained from animal models.
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50
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Pranke I, Golec A, Hinzpeter A, Edelman A, Sermet-Gaudelus I. Emerging Therapeutic Approaches for Cystic Fibrosis. From Gene Editing to Personalized Medicine. Front Pharmacol 2019; 10:121. [PMID: 30873022 PMCID: PMC6400831 DOI: 10.3389/fphar.2019.00121] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
An improved understanding of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) protein structure and the consequences of CFTR gene mutations have allowed the development of novel therapies targeting specific defects underlying CF. Some strategies are mutation specific and have already reached clinical development; some strategies include a read-through of the specific premature termination codons (read-through therapies, nonsense mediated decay pathway inhibitors for Class I mutations); correction of CFTR folding and trafficking to the apical plasma membrane (correctors for Class II mutations); and an increase in the function of CFTR channel (potentiators therapy for Class III mutations and any mutant with a residual function located at the membrane). Other therapies that are in preclinical development are not mutation specific and include gene therapy to edit the genome and stem cell therapy to repair the airway tissue. These strategies that are directed at the basic CF defects are now revolutionizing the treatment for patients and should positively impact their survival rates.
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Affiliation(s)
- Iwona Pranke
- INSERM U 1151, Institut Necker Enfants Malades, Université Paris Descartes, Paris, France
| | - Anita Golec
- INSERM U 1151, Institut Necker Enfants Malades, Université Paris Descartes, Paris, France
| | - Alexandre Hinzpeter
- INSERM U 1151, Institut Necker Enfants Malades, Université Paris Descartes, Paris, France
| | - Aleksander Edelman
- INSERM U 1151, Institut Necker Enfants Malades, Université Paris Descartes, Paris, France
| | - Isabelle Sermet-Gaudelus
- INSERM U 1151, Institut Necker Enfants Malades, Université Paris Descartes, Paris, France.,Centre de Référence Maladie Rare, Mucoviscidose et Maladies de CFTR, Paris, France.,Faculté de Médecine, Université Paris Descartes, Paris, France
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