1
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Jaramillo AM, Vladar EK, Holguin F, Dickey BF, Evans CM. Emerging cell and molecular targets for treating mucus hypersecretion in asthma. Allergol Int 2024; 73:375-381. [PMID: 38692992 DOI: 10.1016/j.alit.2024.04.002] [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: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 05/03/2024] Open
Abstract
Mucus provides a protective barrier that is crucial for host defense in the lungs. However, excessive or abnormal mucus can have pathophysiological consequences in many pulmonary diseases, including asthma. Patients with asthma are treated with agents that relax airway smooth muscle and reduce airway inflammation, but responses are often inadequate. In part, this is due to the inability of existing therapeutic agents to directly target mucus. Accordingly, there is a critical need to better understand how mucus hypersecretion and airway plugging are affected by the epithelial cells that synthesize, secrete, and transport mucus components. This review highlights recent advances in the biology of mucin glycoproteins with a specific focus on MUC5AC and MUC5B, the chief macromolecular components of airway mucus. An improved mechanistic understanding of key steps in mucin production and secretion will help reveal novel potential therapeutic strategies.
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Affiliation(s)
- Ana M Jaramillo
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Eszter K Vladar
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Burton F Dickey
- Department of Pulmonary Medicine, Anderson Cancer Center, University of Texas M.D., Houston, TX, USA
| | - Christopher M Evans
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
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2
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Lei L, Pan W, Shou X, Shao Y, Ye S, Zhang J, Kolliputi N, Shi L. Nanomaterials-assisted gene editing and synthetic biology for optimizing the treatment of pulmonary diseases. J Nanobiotechnology 2024; 22:343. [PMID: 38890749 PMCID: PMC11186260 DOI: 10.1186/s12951-024-02627-w] [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: 03/06/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
The use of nanomaterials in gene editing and synthetic biology has emerged as a pivotal strategy in the pursuit of refined treatment methodologies for pulmonary disorders. This review discusses the utilization of nanomaterial-assisted gene editing tools and synthetic biology techniques to promote the development of more precise and efficient treatments for pulmonary diseases. First, we briefly outline the characterization of the respiratory system and succinctly describe the principal applications of diverse nanomaterials in lung ailment treatment. Second, we elaborate on gene-editing tools, their configurations, and assorted delivery methods, while delving into the present state of nanomaterial-facilitated gene-editing interventions for a spectrum of pulmonary diseases. Subsequently, we briefly expound on synthetic biology and its deployment in biomedicine, focusing on research advances in the diagnosis and treatment of pulmonary conditions against the backdrop of the coronavirus disease 2019 pandemic. Finally, we summarize the extant lacunae in current research and delineate prospects for advancement in this domain. This holistic approach augments the development of pioneering solutions in lung disease treatment, thereby endowing patients with more efficacious and personalized therapeutic alternatives.
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Affiliation(s)
- Lanjie Lei
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Wenjie Pan
- Department of Pharmacy, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325200, China
| | - Xin Shou
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Yunyuan Shao
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Shuxuan Ye
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Junfeng Zhang
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, 210046, China
| | - Narasaiah Kolliputi
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Liyun Shi
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China.
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3
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Hussen BM, Najmadden ZB, Abdullah SR, Rasul MF, Mustafa SA, Ghafouri-Fard S, Taheri M. CRISPR/Cas9 gene editing: a novel strategy for fighting drug resistance in respiratory disorders. Cell Commun Signal 2024; 22:329. [PMID: 38877530 PMCID: PMC11179281 DOI: 10.1186/s12964-024-01713-8] [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: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024] Open
Abstract
Respiratory disorders are among the conditions that affect the respiratory system. The healthcare sector faces challenges due to the emergence of drug resistance to prescribed medications for these illnesses. However, there is a technology called CRISPR/Cas9, which uses RNA to guide DNA targeting. This technology has revolutionized our ability to manipulate and visualize the genome, leading to advancements in research and treatment development. It can effectively reverse epigenetic alterations that contribute to drug resistance. Some studies focused on health have shown that targeting genes using CRISPR/Cas9 can be challenging when it comes to reducing drug resistance in patients with respiratory disorders. Nevertheless, it is important to acknowledge the limitations of this technology, such as off-target effects, immune system reactions to Cas9, and challenges associated with delivery methods. Despite these limitations, this review aims to provide knowledge about CRISPR/Cas9 genome editing tools and explore how they can help overcome resistance in patients with respiratory disorders. Additionally, this study discusses concerns related to applications of CRISPR and provides an overview of successful clinical trial studies.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Biomedical Sciences, College of Science, Cihan University-Erbil, Erbil, 44001, Kurdistan Region, Iraq
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Zana Baqi Najmadden
- Research Center, University of Halabja, Halabja, 46018, Kurdistan region, Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, College of Health Sciences, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Tishk International University, Kurdistan Region, Iraq
| | - Suhad A Mustafa
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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4
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Sarno F, Koncz M, Eilers RE, Verschure PJ, Rots MG. Generation of Cell Lines Stably Expressing a dCas9-Fusion or sgRNA to Address Dynamics of Long-Term Effects of Epigenetic Editing. Methods Mol Biol 2024; 2842:289-307. [PMID: 39012602 DOI: 10.1007/978-1-0716-4051-7_15] [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] [Indexed: 07/17/2024]
Abstract
Epigenetic modifications play a crucial role in regulating gene expression patterns. Through epigenetic editing approaches, the chromatin structure is modified and the activity of the targeted gene can be reprogrammed without altering the DNA sequence. By using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic repeats) platform with nuclease-deactivated dCas9 proteins to direct epigenetic effector domains (EDs) to genomic regulatory regions, the expression of the targeted gene can be modulated. However, the long-term stability of these effects, although demonstrated, remains unpredictable. The versatility and flexibility of (co-)targeting different genes with multiple epigenetic effectors has made the CRISPR/dCas9 platform the most widely used gene modulating technology currently available. Efficient delivery of large dCas9-ED fusion constructs into target cells, however, is challenging. An approach to overcome this limitation is to generate cells that stably express sgRNA(s) or dCas9-ED constructs. The sgRNA(s) or dCas9-ED stable cell lines can be used to study the mechanisms underlying sustained gene expression reprogramming by transiently expressing the other of the two constructs. Here, we describe a detailed protocol for the engineering of cells that stably express CRISPR/dCas9 or sgRNA. Creating a system where one component of the CRISPR/dCas9 is stably expressed while the other is transiently expressed offers a versatile platform for investigating the dynamics of epigenetic reprogramming.
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Affiliation(s)
- Federica Sarno
- Department of Pathology and Medical Biology, Epigenetic Editing Research Group, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology and Medical Biology, MATRIX Research Group, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mihaly Koncz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Roos E Eilers
- Department of Pathology and Medical Biology, Epigenetic Editing Research Group, University Medical Center Groningen, Groningen, The Netherlands
| | - Pernette J Verschure
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Marianne G Rots
- Department of Pathology and Medical Biology, Epigenetic Editing Research Group, University Medical Center Groningen, Groningen, The Netherlands.
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5
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Wu DD, Lau ATY, Xu YM, Reinders-Luinge M, Koncz M, Kiss A, Timens W, Rots MG, Hylkema MN. Targeted epigenetic silencing of UCHL1 expression suppresses collagen-1 production in human lung epithelial cells. Epigenetics 2023; 18:2175522. [PMID: 38016026 PMCID: PMC9980648 DOI: 10.1080/15592294.2023.2175522] [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: 09/02/2022] [Revised: 12/17/2022] [Accepted: 01/11/2023] [Indexed: 02/24/2023] Open
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) is highly expressed in smokers, but little is known about the molecular mechanism of UCHL1 in airway epithelium and its possible role in affecting extracellular matrix (ECM) remodelling in the underlying submucosa. Since cigarette smoking is a major cause of lung diseases, we studied its effect on UCHL1 expression and DNA methylation patterns in human bronchial epithelial cells, obtained after laser capture micro-dissection (LCM) or isolated from residual tracheal/main stem bronchial tissue. Targeted regulation of UCHL1 expression via CRISPR/dCas9 based-epigenetic editing was used to explore the function of UCHL1 in lung epithelium. Our results show that cigarette smoke extract (CSE) stimulated the expression of UCHL1 in vitro. The methylation status of the UCHL1 gene was negatively associated with UCHL1 transcription in LCM-obtained airway epithelium at specific sites. Treatment with a UCHL1 inhibitor showed that the TGF-β1-induced upregulation of the ECM gene COL1A1 can be prevented by the inhibition of UCHL1 activity in cell lines. Furthermore, upon downregulation of UCHL1 by epigenetic editing using CRISPR/dCas-EZH2, mRNA expression of COL1A1 and fibronectin was reduced. In conclusion, we confirmed higher UCHL1 expression in current smokers compared to non- and ex-smokers, and induced downregulation of UCHL1 by epigenetic editing. The subsequent repression of genes encoding ECM proteins suggest a role for UCHL1 as a therapeutic target in fibrosis-related disease.
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Affiliation(s)
- Dan-Dan Wu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Marjan Reinders-Luinge
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihaly Koncz
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Machteld N. Hylkema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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6
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Zhang M, Lu H, Xie L, Liu X, Cun D, Yang M. Inhaled RNA drugs to treat lung diseases: Disease-related cells and nano-bio interactions. Adv Drug Deliv Rev 2023; 203:115144. [PMID: 37995899 DOI: 10.1016/j.addr.2023.115144] [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: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
In recent years, RNA-based therapies have gained much attention as biomedicines due to their remarkable therapeutic effects with high specificity and potency. Lung diseases offer a variety of currently undruggable but attractive targets that could potentially be treated with RNA drugs. Inhaled RNA drugs for the treatment of lung diseases, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and acute respiratory distress syndrome, have attracted more and more attention. A variety of novel nanoformulations have been designed and attempted for the delivery of RNA drugs to the lung via inhalation. However, the delivery of RNA drugs via inhalation poses several challenges. It includes protection of the stability of RNA molecules, overcoming biological barriers such as mucus and cell membrane to the delivery of RNA molecules to the targeted cytoplasm, escaping endosomal entrapment, and circumventing unwanted immune response etc. To address these challenges, ongoing researches focus on developing innovative nanoparticles to enhance the stability of RNA molecules, improve cellular targeting, enhance cellular uptake and endosomal escape to achieve precise delivery of RNA drugs to the intended lung cells while avoiding unwanted nano-bio interactions and off-target effects. The present review first addresses the pathologic hallmarks of different lung diseases, disease-related cell types in the lung, and promising therapeutic targets in these lung cells. Subsequently we highlight the importance of the nano-bio interactions in the lung that need to be addressed to realize disease-related cell-specific delivery of inhaled RNA drugs. This is followed by a review on the physical and chemical characteristics of inhaled nanoformulations that influence the nano-bio interactions with a focus on surface functionalization. Finally, the challenges in the development of inhaled nanomedicines and some key aspects that need to be considered in the development of future inhaled RNA drugs are discussed.
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Affiliation(s)
- Mengjun Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road No. 103, 110016 Shenyang, China; School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Haoyu Lu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road No. 103, 110016 Shenyang, China
| | - Liangkun Xie
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road No. 103, 110016 Shenyang, China
| | - Xulu Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road No. 103, 110016 Shenyang, China
| | - Dongmei Cun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road No. 103, 110016 Shenyang, China.
| | - Mingshi Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road No. 103, 110016 Shenyang, China; Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
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7
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Xu HJ, Bai J, Tian Y, Feng X, Chen AP, Wang J, Wu J, Jin XR, Zhang F, Quan MY, Chen C, Lee KY, Zhang JS. ESE1/AGR2 axis antagonizes TGF-β-induced epithelial-mesenchymal transition in low-grade pancreatic cancer. Cancer Med 2023; 12:5979-5993. [PMID: 36329620 PMCID: PMC10028153 DOI: 10.1002/cam4.5397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Epithelium-specific ETS transcription factor 1 (ESE1) has been implicated in epithelial homeostasis, inflammation, as well as tumorigenesis, and cancer progression. However, numerous studies have reported contradictory roles-as an oncogene or a tumor suppressor of ESE1 in different cancers, and its function in the development and progression of pancreatic ductal adenocarcinoma (PDAC) has remained largely unexplored. Herein, we report that ESE1 was found upregulated in primary PDAC compared to normal pancreatic tissue, but high expression of ESE1 correlated to better relapse-free survival in patients with PDAC. Interestingly, ESE1 was found to exhibit dual roles in regulation of malignant properties of PDAC cells in that its overexpression promoted cell proliferation, whereas its downregulation enhanced epithelial-mesenchymal transition (EMT) phenotype. In the context of TGF-β-induced EMT, ESE1 is markedly downregulated at post-transcriptional level, and reconstituted ESE1 expression partially reversed TGF-β-induced EMT marker expression. Furthermore, we identify AGR2 as a novel transcriptional target of ESE1 that participates in TGF-β-induced EMT in PDAC. Collectively, our findings reveal an ESE1/AGR2 axis that interacts with TGF-β signaling to modulate EMT phenotype in PDAC.
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Affiliation(s)
- Hui-Jing Xu
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Jing Bai
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Ye Tian
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Xiao Feng
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Ai-Ping Chen
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Jie Wang
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Jin Wu
- International Collaborative Center on Growth Factor Research, and School of Pharmaceutical Sciences, Wenzhou Medical University, Zhejiang, China
| | - Xu-Ru Jin
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Feng Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Mei-Yu Quan
- Medical Research Center, and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
| | - Kwang-Youl Lee
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Zhejiang, China
- Medical Research Center, and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
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8
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Koh KD, Bonser LR, Eckalbar WL, Yizhar-Barnea O, Shen J, Zeng X, Hargett KL, Sun DI, Zlock LT, Finkbeiner WE, Ahituv N, Erle DJ. Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma. CELL GENOMICS 2023; 3:100229. [PMID: 36777184 PMCID: PMC9903679 DOI: 10.1016/j.xgen.2022.100229] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/02/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Epithelial responses to the cytokine interleukin-13 (IL-13) cause airway obstruction in asthma. Here we utilized multiple genomic techniques to identify IL-13-responsive regulatory elements in bronchial epithelial cells and used these data to develop a CRISPR interference (CRISPRi)-based therapeutic approach to downregulate airway obstruction-inducing genes in a cell type- and IL-13-specific manner. Using single-cell RNA sequencing (scRNA-seq) and acetylated lysine 27 on histone 3 (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) in primary human bronchial epithelial cells, we identified IL-13-responsive genes and regulatory elements. These sequences were functionally validated and optimized via massively parallel reporter assays (MPRAs) for IL-13-inducible activity. The top secretory cell-selective sequence from the MPRA, a novel, distal enhancer of the sterile alpha motif pointed domain containing E-26 transformation-specific transcription factor (SPDEF) gene, was utilized to drive CRISPRi and knock down SPDEF or mucin 5AC (MUC5AC), both involved in pathologic mucus production in asthma. Our work provides a catalog of cell type-specific genes and regulatory elements involved in IL-13 bronchial epithelial response and showcases their use for therapeutic purposes.
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Affiliation(s)
- Kyung Duk Koh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Luke R. Bonser
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Walter L. Eckalbar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ofer Yizhar-Barnea
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiangshan Shen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xiaoning Zeng
- Department of Pulmonary & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kirsten L. Hargett
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dingyuan I. Sun
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorna T. Zlock
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Walter E. Finkbeiner
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nadav Ahituv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David J. Erle
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
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9
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Functional Validation of the Putative Oncogenic Activity of PLAU. Biomedicines 2022; 11:biomedicines11010102. [PMID: 36672610 PMCID: PMC9856075 DOI: 10.3390/biomedicines11010102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Plasminogen activator, urokinase (PLAU) is involved in cell migration, proliferation and tissue remodeling. PLAU upregulation is associated with an increase in aggressiveness, metastasis, and invasion of several cancer types, including breast cancer. In patients, this translates into decreased sensitivity to hormonal treatment, and poor prognosis. These clinical findings have led to the examination of PLAU as a biomarker for predicting breast cancer prognosis and therapy responses. In this study, we investigated the functional ability of PLAU to act as an oncogene in breast cancers by modulating its expression using CRISPR-deactivated Cas9 (CRISPR-dCas9) tools. Different effector domains (e.g., transcription modulators (VP64, KRAB)) alone or in combination with epigenetic writers (DNMT3A/3L, MSssI) were fused to dCas9 and targeted to the PLAU promoter. In MDA-MB-231 cells characterized by high PLAU expression downregulation of PLAU expression by CRISPR-dCas9-DNMT3A/3L-KRAB, resulted in decreased cell proliferation. Conversely, CRISPR-dCas9-VP64 induced PLAU upregulation in low PLAU expressing MCF-7 cells and significantly increased aggressiveness and invasion. In conclusion, modulation of PLAU expression affected metastatic related properties of breast cancer cells, thus further validating its oncogenic activity in breast cancer cells.
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10
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Agache I, Zemelka-Wiącek M, Shamji MH, Jutel M. Immunotherapy: State-of-the-art review of therapies and theratypes. J Allergy Clin Immunol 2022; 150:1279-1288. [PMID: 36328808 DOI: 10.1016/j.jaci.2022.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/02/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Through its disease-modifying potential, immunotherapy is the keystone to curing allergic diseases. Allergen immunotherapy, applied for more than a century, is currently supported by novel modalities such as mAb-based therapies or small molecules targeting the key nodes of the allergic inflammation network. In this review, a summary of the most significant advances in immunotherapy is presented, addressing not only novel approaches to stratifying patients but also major controlled clinical trials and real-world evidence that strengthen the role of immunotherapy in the treatment of allergies.
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Affiliation(s)
- Ioana Agache
- Faculty of Medicine, Transylvania University, Brasov, Romania.
| | | | - Mohamed H Shamji
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Marek Jutel
- Department of Clinical Immunology, Wroclaw Medical University, Wroclaw, Poland; ALL-MED Medical Research Institute, Wroclaw, Poland
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11
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Namous H, Braz CU, Wang Y, Khatib H. The Activation of Protamine 1 Using Epigenome Editing Decreases the Proliferation of Tumorigenic Cells. Front Genome Ed 2022; 4:844904. [PMID: 35783678 PMCID: PMC9244402 DOI: 10.3389/fgeed.2022.844904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methyltransferases (DNMT) and histone deacetylases (HDAC) inhibitors are used as cancer epigenome drugs. However, these epigenetic drugs lack targeting specificity and could risk inducing genome instability and the expression of oncogenes. Therefore, there is a need to develop new therapeutic strategies where specific cancer genes can be targeted for silencing or activation. The CRISPR/dCas9 system represents a promising, powerful therapeutic tool because of its simplicity and specificity. Protamine 1 (PRM1) is exclusively expressed in sperm and has a vital role in the tight packaging of DNA, thus inducing transcriptional silencing in sperm cells. We hypothesized that the activation of the PRM1 gene in tumorigenic cells would lead to DNA condensation and reduce the proliferation of these cells. To test our hypothesis, we transfected human embryonic kidney cells 293T with a dCas9-P300 plasmid that adds acetyl groups to the promoter region of PRM1 via specific gRNAs plasmids. RNA-Seq analysis of transfected cells revealed high specificity of targeted gene activation. PRM1 expression resulted in a significant decrease in cell proliferation as measured by the BrdU ELISA assay. To confirm that the activation of PRM1 was due to acetyl groups deposited to H3K27, a ChIP-qPCR was performed. The acetylation of the PRM1 promoter region targeted by dCas9-p300 in transfected cells was higher than that of the control cells. Interestingly, the targeted promoter region for acetylation showed reduced DNA methylation. These findings demonstrate the efficacy of epigenome editing in activating PRM1 in non-expressing tumorigenic cells, which could be used as a promising therapeutic strategy in cancer treatment.
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Avci E, Sarvari P, Savai R, Seeger W, Pullamsetti SS. Epigenetic Mechanisms in Parenchymal Lung Diseases: Bystanders or Therapeutic Targets? Int J Mol Sci 2022; 23:ijms23010546. [PMID: 35008971 PMCID: PMC8745712 DOI: 10.3390/ijms23010546] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 12/17/2022] Open
Abstract
Epigenetic responses due to environmental changes alter chromatin structure, which in turn modifies the phenotype, gene expression profile, and activity of each cell type that has a role in the pathophysiology of a disease. Pulmonary diseases are one of the major causes of death in the world, including lung cancer, idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), pulmonary hypertension (PH), lung tuberculosis, pulmonary embolism, and asthma. Several lines of evidence indicate that epigenetic modifications may be one of the main factors to explain the increasing incidence and prevalence of lung diseases including IPF and COPD. Interestingly, isolated fibroblasts and smooth muscle cells from patients with pulmonary diseases such as IPF and PH that were cultured ex vivo maintained the disease phenotype. The cells often show a hyper-proliferative, apoptosis-resistant phenotype with increased expression of extracellular matrix (ECM) and activated focal adhesions suggesting the presence of an epigenetically imprinted phenotype. Moreover, many abnormalities observed in molecular processes in IPF patients are shown to be epigenetically regulated, such as innate immunity, cellular senescence, and apoptotic cell death. DNA methylation, histone modification, and microRNA regulation constitute the most common epigenetic modification mechanisms.
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MESH Headings
- Animals
- Biomarkers
- Combined Modality Therapy
- DNA Methylation
- Diagnosis, Differential
- Disease Management
- Disease Susceptibility
- Epigenesis, Genetic
- Gene Expression Regulation
- Histones/metabolism
- Humans
- Idiopathic Pulmonary Fibrosis/diagnosis
- Idiopathic Pulmonary Fibrosis/etiology
- Idiopathic Pulmonary Fibrosis/metabolism
- Idiopathic Pulmonary Fibrosis/therapy
- Lung Diseases, Interstitial/diagnosis
- Lung Diseases, Interstitial/etiology
- Lung Diseases, Interstitial/metabolism
- Lung Diseases, Interstitial/therapy
- Pulmonary Disease, Chronic Obstructive/diagnosis
- Pulmonary Disease, Chronic Obstructive/etiology
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/therapy
- Treatment Outcome
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Affiliation(s)
- Edibe Avci
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
| | - Pouya Sarvari
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
- Department of Internal Medicine, Justus Liebig University, 35392 Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Werner Seeger
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
- Department of Internal Medicine, Justus Liebig University, 35392 Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Soni S. Pullamsetti
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
- Department of Internal Medicine, Justus Liebig University, 35392 Giessen, Germany
- Correspondence: ; Tel.: +49-603-270-5380; Fax: +49-603-270-5385
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Recent developments with advancing gene therapy to treat chronic infection with hepatitis B virus. Curr Opin HIV AIDS 2021; 15:200-207. [PMID: 32141890 DOI: 10.1097/coh.0000000000000623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW The available vaccine and therapies against hepatitis B virus (HBV) rarely eliminate chronic infection with the virus. High mortality resulting from complicating cirrhosis and hepatocellular carcinoma makes improving anti-HBV therapy an important priority. Recent advances with using gene therapy to counter HBV have potential and are the focus of this review. RECENT FINDINGS The stable replication-competent HBV intermediate comprising covalently closed circular DNA (cccDNA) is the template for expression of all viral genes. Inactivating cccDNA has thus been a focus of research aimed at achieving cure for HBV infection. Many studies have reported profound inhibition of replication of the virus using silencing and editing techniques. Therapeutic gene silencing with synthetic short interfering RNA is now in clinical trials. Ability to mutate and permanently inactivate cccDNA with engineered gene editors, such as those derived from CRISPR/Cas or TALENs, is particularly appealing but has not yet reached clinical evaluation. SUMMARY Gene silencing and gene editing potentially provide the means to cure HBV infection. However, achieving efficient delivery of therapeutic sequences, ensuring their specificity of action and progress with other antiviral strategies are likely to determine utility of gene therapy for chronic HBV infection.
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Pacheco MB, Camilo V, Henrique R, Jerónimo C. Epigenetic Editing in Prostate Cancer: Challenges and Opportunities. Epigenetics 2021; 17:564-588. [PMID: 34130596 DOI: 10.1080/15592294.2021.1939477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Epigenome editing consists of fusing a predesigned DNA recognition unit to the catalytic domain of a chromatin modifying enzyme leading to the introduction or removal of an epigenetic mark at a specific locus. These platforms enabled the study of the mechanisms and roles of epigenetic changes in several research domains such as those addressing pathogenesis and progression of cancer. Despite the continued efforts required to overcome some limitations, which include specificity, off-target effects, efficacy, and longevity, these tools have been rapidly progressing and improving.Since prostate cancer is characterized by multiple genetic and epigenetic alterations that affect different signalling pathways, epigenetic editing constitutes a promising strategy to hamper cancer progression. Therefore, by modulating chromatin structure through epigenome editing, its conformation might be better understood and events that drive prostate carcinogenesis might be further unveiled.This review describes the different epigenome engineering tools, their mechanisms concerning gene's expression and regulation, highlighting the challenges and opportunities concerning prostate cancer research.
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Affiliation(s)
- Mariana Brütt Pacheco
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Vânia Camilo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. DR. António Bernardino De Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
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Sheikhpour M, Maleki M, Ebrahimi Vargoorani M, Amiri V. A review of epigenetic changes in asthma: methylation and acetylation. Clin Epigenetics 2021; 13:65. [PMID: 33781317 PMCID: PMC8008616 DOI: 10.1186/s13148-021-01049-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
Several studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.
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Affiliation(s)
- Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Mobina Maleki
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Ebrahimi Vargoorani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, College of Basic Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Vahid Amiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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Cañas JA, Rodrigo-Muñoz JM, Sastre B, Gil-Martinez M, Redondo N, del Pozo V. MicroRNAs as Potential Regulators of Immune Response Networks in Asthma and Chronic Obstructive Pulmonary Disease. Front Immunol 2021; 11:608666. [PMID: 33488613 PMCID: PMC7819856 DOI: 10.3389/fimmu.2020.608666] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Chronic respiratory diseases (CRDs) are an important factor of morbidity and mortality, accounting for approximately 6% of total deaths worldwide. The main CRDs are asthma and chronic obstructive pulmonary disease (COPD). These complex diseases have different triggers including allergens, pollutants, tobacco smoke, and other risk factors. It is important to highlight that although CRDs are incurable, various forms of treatment improve shortness of breath and quality of life. The search for tools that can ensure accurate diagnosis and treatment is crucial. MicroRNAs (miRNAs) are small non-coding RNAs and have been described as promising diagnostic and therapeutic biomarkers for CRDs. They are implicated in multiple processes of asthma and COPD, regulating pathways associated with inflammation, thereby showing that miRNAs are critical regulators of the immune response. Indeed, miRNAs have been found to be deregulated in several biofluids (sputum, bronchoalveolar lavage, and serum) and in both structural lung and immune cells of patients in comparison to healthy subjects, showing their potential role as biomarkers. Also, miRNAs play a part in the development or termination of histopathological changes and comorbidities, revealing the complexity of miRNA regulation and opening up new treatment possibilities. Finally, miRNAs have been proposed as prognostic tools in response to both conventional and biologic treatments for asthma or COPD, and miRNA-based treatment has emerged as a potential approach for clinical intervention in these respiratory diseases; however, this field is still in development. The present review applies a systems biology approach to the understanding of miRNA regulatory networks in asthma and COPD, summarizing their roles in pathophysiology, diagnosis, and treatment.
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Affiliation(s)
- José A. Cañas
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - José M. Rodrigo-Muñoz
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Beatriz Sastre
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Marta Gil-Martinez
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Natalia Redondo
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Victoria del Pozo
- Immunoallergy Laboratory, Immunology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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17
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Li J, Ye Z. The Potential Role and Regulatory Mechanisms of MUC5AC in Chronic Obstructive Pulmonary Disease. Molecules 2020; 25:molecules25194437. [PMID: 32992527 PMCID: PMC7582261 DOI: 10.3390/molecules25194437] [Citation(s) in RCA: 20] [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: 08/10/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is associated with high morbidity and mortality globally. Studies show that airway mucus hypersecretion strongly compromises lung function, leading to frequent hospitalization and mortality, highlighting an urgent need for effective COPD treatments. MUC5AC is known to contribute to severe muco-obstructive lung diseases, worsening COPD pathogenesis. Various pathways are implicated in the aberrant MUC5AC production and secretion MUC5AC. These include signaling pathways associated with mucus-secreting cell differentiation [nuclear factor-κB (NF-κB)and IL-13-STAT6- SAM pointed domain containing E26 transformation-specific transcription factor (SPDEF), as well as epithelial sodium channel (ENaC) and cystic fibrosis transmembrane conductance regulator (CFTR)], and signaling pathways related to mucus transport and excretion-ciliary beat frequency (CBF). Various inhibitors of mucus hypersecretion are in clinical use but have had limited benefits against COPD. Thus, novel therapies targeting airway mucus hypersecretion should be developed for effective management of muco-obstructive lung disease. Here, we systematically review the mechanisms and pathogenesis of airway mucus hypersecretion, with emphasis on multi-target and multi-link intervention strategies for the elucidation of novel inhibitors of airway mucus hypersecretion.
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Affiliation(s)
- Jingyuan Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China;
| | - Zuguang Ye
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China;
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Correspondence: ; Tel./Fax: +86-10-8425-2805
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18
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Moses C, Hodgetts SI, Nugent F, Ben-Ary G, Park KK, Blancafort P, Harvey AR. Transcriptional repression of PTEN in neural cells using CRISPR/dCas9 epigenetic editing. Sci Rep 2020; 10:11393. [PMID: 32647121 PMCID: PMC7347541 DOI: 10.1038/s41598-020-68257-y] [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: 02/27/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
After damage to the adult mammalian central nervous system (CNS), surviving neurons have limited capacity to regenerate and restore functional connectivity. Conditional genetic deletion of PTEN results in robust CNS axon regrowth, while PTEN repression with short hairpin RNA (shRNA) improves regeneration but to a lesser extent, likely due to suboptimal PTEN mRNA knockdown using this approach. Here we employed the CRISPR/dCas9 system to repress PTEN transcription in neural cells. We targeted the PTEN proximal promoter and 5' untranslated region with dCas9 fused to the repressor protein Krüppel-associated box (KRAB). dCas9-KRAB delivered in a lentiviral vector with one CRISPR guide RNA (gRNA) achieved potent and specific PTEN repression in human cell line models and neural cells derived from human iPSCs, and induced histone (H)3 methylation and deacetylation at the PTEN promoter. The dCas9-KRAB system outperformed a combination of four shRNAs targeting the PTEN transcript, a construct previously used in CNS injury models. The CRISPR system also worked more effectively than shRNAs for Pten repression in rat neural crest-derived PC-12 cells, and enhanced neurite outgrowth after nerve growth factor stimulation. PTEN silencing with CRISPR/dCas9 epigenetic editing may provide a new option for promoting axon regeneration and functional recovery after CNS trauma.
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Affiliation(s)
- C Moses
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
| | - S I Hodgetts
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia
| | - F Nugent
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - G Ben-Ary
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - K K Park
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - P Blancafort
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia.
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - A R Harvey
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia.
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Gjaltema RAF, Goubert D, Huisman C, del Pilar García Tobilla C, Koncz M, Jellema PG, Wu D, Brouwer U, Kiss A, Verschure PJ, Bank RA, Rots MG. KRAB-Induced Heterochromatin Effectively Silences PLOD2 Gene Expression in Somatic Cells and is Resilient to TGFβ1 Activation. Int J Mol Sci 2020; 21:ijms21103634. [PMID: 32455614 PMCID: PMC7279273 DOI: 10.3390/ijms21103634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenetic editing, an emerging technique used for the modulation of gene expression in mammalian cells, is a promising strategy to correct disease-related gene expression. Although epigenetic reprogramming results in sustained transcriptional modulation in several in vivo models, further studies are needed to develop this approach into a straightforward technology for effective and specific interventions. Important goals of current research efforts are understanding the context-dependency of successful epigenetic editing and finding the most effective epigenetic effector(s) for specific tasks. Here we tested whether the fibrosis- and cancer-associated PLOD2 gene can be repressed by the DNA methyltransferase M.SssI, or by the non-catalytic Krüppel associated box (KRAB) repressor directed to the PLOD2 promoter via zinc finger- or CRISPR-dCas9-mediated targeting. M.SssI fusions induced de novo DNA methylation, changed histone modifications in a context-dependent manner, and led to 50%–70% reduction in PLOD2 expression in fibrotic fibroblasts and in MDA-MB-231 cancer cells. Targeting KRAB to PLOD2 resulted in the deposition of repressive histone modifications without DNA methylation and in almost complete PLOD2 silencing. Interestingly, both long-term TGFβ1-induced, as well as unstimulated PLOD2 expression, was completely repressed by KRAB, while M.SssI only prevented the TGFβ1-induced PLOD2 expression. Targeting transiently expressed dCas9-KRAB resulted in sustained PLOD2 repression in HEK293T and MCF-7 cells. Together, these findings point to KRAB outperforming DNA methylation as a small potent targeting epigenetic effector for silencing TGFβ1-induced and uninduced PLOD2 expression.
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Affiliation(s)
- Rutger A. F. Gjaltema
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Désirée Goubert
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Christian Huisman
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Consuelo del Pilar García Tobilla
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Mihály Koncz
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (M.K.); (A.K.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Pytrick G. Jellema
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Dandan Wu
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Uilke Brouwer
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (M.K.); (A.K.)
| | - Pernette J. Verschure
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Ruud A. Bank
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Marianne G. Rots
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- Correspondence: ; Tel.: +31-50-3610153
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Abstract
PURPOSE OF REVIEW Allergic diseases are prototypic examples for gene × environment-wide interactions. This review considers the current evidence for genetic and epigenetic mechanisms in allergic diseases and highlights barriers and facilitators for the implementation of these novel tools both for research and clinical practice. RECENT FINDINGS The value of whole-genome sequencing studies and the use of polygenic risk score analysis in homogeneous well characterized populations are currently being tested. Epigenetic mechanisms are known to play a crucial role in the pathogenesis of allergic disorders, especially through mediating the effects of the environmental factors, well recognized risk modifiers. There is emerging evidence for the immune-modulatory role of probiotics through epigenetic changes. Direct or indirect targeting of epigenetic mechanisms affect expression of the genes favouring the development of allergic diseases and can improve tissue biology. The ability to specifically edit the epigenome, especially using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology, holds the promise of enhancing understanding of how epigenetic modifications function and enabling manipulation of cell phenotype for research or therapeutic purposes. SUMMARY Additional research in the role of genetic and epigenetic mechanisms in relation to allergic diseases' endotypes is needed. An international project characterizing the human epigenome in relation to allergic diseases is warranted.
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Hiemstra PS, Tetley TD, Janes SM. Airway and alveolar epithelial cells in culture. Eur Respir J 2019; 54:13993003.00742-2019. [DOI: 10.1183/13993003.00742-2019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/13/2019] [Indexed: 12/29/2022]
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22
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Tan Q, Tschumperlin DJ. Epigenome Editing Enters the Arena. A New Tool to Reveal (and Reverse?) Pathologic Gene Regulation. Am J Respir Crit Care Med 2019; 198:549-551. [PMID: 30016116 DOI: 10.1164/rccm.201807-1239ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Qi Tan
- 1 Department of Physiology & Biomedical Engineering Mayo Clinic College of Medicine and Science Rochester Minnesota
| | - Daniel J Tschumperlin
- 1 Department of Physiology & Biomedical Engineering Mayo Clinic College of Medicine and Science Rochester Minnesota
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23
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Nikolić MZ, Garrido-Martin EM, Greiffo FR, Fabre A, Heijink IH, Boots A, Greene CM, Hiemstra PS, Bartel S. From the pathophysiology of the human lung alveolus to epigenetic editing: Congress 2018 highlights from ERS Assembly 3 "Basic and Translational Science.". ERJ Open Res 2019; 5:00194-2018. [PMID: 31111040 PMCID: PMC6513036 DOI: 10.1183/23120541.00194-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/23/2019] [Indexed: 12/16/2022] Open
Abstract
The European Respiratory Society (ERS) International Congress is the largest respiratory congress and brings together leading experts in all fields of respiratory medicine and research. ERS Assembly 3 shapes the basic and translational science aspects of this congress, aiming to combine cutting-edge novel developments in basic research with novel clinical findings. In this article, we summarise a selection of the scientific highlights from the perspective of the three groups within Assembly 3. In particular, we discuss new insights into the pathophysiology of the human alveolus, novel tools in organoid development and (epi)genome editing, as well as insights from the presented abstracts on novel therapeutic targets being identified for idiopathic pulmonary fibrosis. The amount of basic and translational science presented at #ERSCongress is steadily increasing, showing novel cutting-edge technologies and models.http://bit.ly/2GgXIJi
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Affiliation(s)
- Marko Z Nikolić
- University College London, Division of Medicine, London, UK.,These contributed equally to this work
| | - Eva M Garrido-Martin
- H12O-CNIO Lung Cancer Clinical Research Unit, Research Institute Hospital 12 Octubre - Spanish National Cancer Research Centre (CNIO), and Biomedical Research Networking Centre Consortium of Cancer (CIBERONC), Madrid, Spain.,These contributed equally to this work
| | - Flavia R Greiffo
- Comprehensive Pneumology Center, Ludwig-Maximilians University (LMU), University Hospital Grosshadern, and Helmholtz Zentrum München; Member of the German Center for Lung Research (DZL), Munich, Germany.,These contributed equally to this work
| | - Aurélie Fabre
- University College Dublin, St Vincent's University Hospital, Elm Park, Dublin, Ireland
| | - Irene H Heijink
- University of Groningen, University Medical Center Groningen, Depts of Pathology and Medical Biology and Pulmonology, GRIAC Research Institute, Groningen, The Netherlands
| | - Agnes Boots
- Dept of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Catherine M Greene
- Lung Biology Group, Dept of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Pieter S Hiemstra
- Dept of Pulmonology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Sabine Bartel
- Early Life Origins of Chronic Lung Disease, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
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24
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Willyard C. The epigenome editors: How tools such as CRISPR offer new details about epigenetics. Nat Med 2019; 23:900-903. [PMID: 28777784 DOI: 10.1038/nm0817-900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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25
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Chen G, Volmer AS, Wilkinson KJ, Deng Y, Jones LC, Yu D, Bustamante-Marin XM, Burns KA, Grubb BR, O'Neal WK, Livraghi-Butrico A, Boucher RC. Role of Spdef in the Regulation of Muc5b Expression in the Airways of Naive and Mucoobstructed Mice. Am J Respir Cell Mol Biol 2019; 59:383-396. [PMID: 29579396 DOI: 10.1165/rcmb.2017-0127oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Understanding how expression of airway secretory mucins MUC5B and MUC5AC is regulated in health and disease is important to elucidating the pathogenesis of mucoobstructive respiratory diseases. The transcription factor SPDEF (sterile α-motif pointed domain epithelial specific transcription factor) is a key regulator of MUC5AC, but its role in regulating MUC5B in health and in mucoobstructive lung diseases is unknown. Characterization of Spdef-deficient mice upper and lower airways demonstrated region-specific, Spdef-dependent regulation of basal Muc5b expression. Neonatal Spdef-deficient mice exhibited reductions in BAL Muc5ac and Muc5b. Adult Spdef-deficient mice partially phenocopied Muc5b-deficient mice as they exhibited reduced Muc5b in nasopharyngeal and airway epithelia but not in olfactory Bowman glands, 75% incidence of nasopharyngeal hair/mucus plugs, and mild bacterial otitis media, without defective mucociliary clearance in the nasopharynx. In contrast, tracheal mucociliary clearance was reduced in Spdef-deficient mice in the absence of lung disease. To evaluate the role of Spdef in the development and persistence of Muc5b-predominant mucoobstructive lung disease, Spdef-deficient mice were crossed with Scnn1b-transgenic (Scnn1b-Tg) mice, which exhibit airway surface dehydration-induced airway mucus obstruction and inflammation. Spdef-deficient Scnn1b-Tg mice exhibited reduced Muc5ac, but not Muc5b, expression and BAL content. Airway mucus obstruction was not decreased in Spdef-deficient Scnn1b-Tg mice, consistent with Muc5b-dominant Scnn1b disease, but increased airway neutrophilia was observed compared with Spdef-sufficient Scnn1b-Tg mice. Collectively, these results indicate that Spdef regulates baseline Muc5b expression in respiratory epithelia but does not contribute to Muc5b regulation in a mouse model of Muc5b-predominant mucus obstruction caused by airway dehydration.
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Affiliation(s)
- Gang Chen
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Allison S Volmer
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kristen J Wilkinson
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yangmei Deng
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lisa C Jones
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Dongfang Yu
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ximena M Bustamante-Marin
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kimberlie A Burns
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Barbara R Grubb
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wanda K O'Neal
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alessandra Livraghi-Butrico
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Richard C Boucher
- Marsico Lung Institute and University of North Carolina Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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26
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Moses C, Kaur P. Applications of CRISPR systems in respiratory health: Entering a new 'red pen' era in genome editing. Respirology 2019; 24:628-637. [PMID: 30883991 DOI: 10.1111/resp.13527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 12/16/2022]
Abstract
Respiratory diseases, such as influenza infection, acute tracheal bronchitis, pneumonia, tuberculosis, chronic obstructive pulmonary disease, asthma, lung cancer and nasopharyngeal carcinoma, continue to significantly impact human health. Diseases of the lung and respiratory tract are influenced by environmental conditions and socio-economic factors; however, many of these serious respiratory disorders are also rooted in genetic or epigenetic causes. Clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, isolated from the immune system of prokaryotes, provide a tool to manipulate gene sequences and gene expression with significant implications for respiratory research. CRISPR/Cas systems allow preclinical modelling of causal factors involved in many respiratory diseases, providing new insights into their underlying mechanisms. CRISPR can also be used to screen for genes involved in respiratory processes, development and pathology, identifying novel disease drivers or drug targets. Finally, CRISPR/Cas systems can potentially correct genetic mutations and edit epigenetic marks that contribute to respiratory disorders, providing a form of personalized medicine that could be used in conjunction with other technologies such as stem cell reprogramming and transplantation. CRISPR gene editing is a young field of research, and concerns regarding its specificity, as well as the need for efficient and safe delivery methods, need to be addressed further. However, CRISPR/Cas systems represent a significant step forward for research and therapy in respiratory health, and it is likely we will see the breakthroughs generated from this technology continue.
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Affiliation(s)
| | - Parwinder Kaur
- Faculty of Science, School of Human Sciences and School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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27
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Zakarya R, Adcock I, Oliver BG. Epigenetic impacts of maternal tobacco and e-vapour exposure on the offspring lung. Clin Epigenetics 2019; 11:32. [PMID: 30782202 PMCID: PMC6381655 DOI: 10.1186/s13148-019-0631-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/11/2019] [Indexed: 12/15/2022] Open
Abstract
In utero exposure to tobacco products, whether maternal or environmental, have harmful effects on first neonatal and later adult respiratory outcomes. These effects have been shown to persist across subsequent generations, regardless of the offsprings' smoking habits. Established epigenetic modifications induced by in utero exposure are postulated as the mechanism underlying the inherited poor respiratory outcomes. As e-cigarette use is on the rise, their potential to induce similar functional respiratory deficits underpinned by an alteration in the foetal epigenome needs to be explored. This review will focus on the functional and epigenetic impact of in utero exposure to maternal cigarette smoke, maternal environmental tobacco smoke, environmental tobacco smoke and e-cigarette vapour on foetal respiratory outcomes.
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Affiliation(s)
- Razia Zakarya
- Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, The University of Sydney, Sydney, Australia
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Ian Adcock
- Airway Diseases Section, National Heart and Lung Institute, Imperial College London, London, UK
- Biomedical Research Unit, Section of Respiratory Diseases, Royal Brompton and Harefield NHS Trust, London, UK
| | - Brian G Oliver
- Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, The University of Sydney, Sydney, Australia.
- School of Life Sciences, University of Technology Sydney, Sydney, Australia.
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28
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Hussain SS, George S, Singh S, Jayant R, Hu CA, Sopori M, Chand HS. A Small Molecule BH3-mimetic Suppresses Cigarette Smoke-Induced Mucous Expression in Airway Epithelial Cells. Sci Rep 2018; 8:13796. [PMID: 30218002 PMCID: PMC6138652 DOI: 10.1038/s41598-018-32114-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/03/2018] [Indexed: 01/07/2023] Open
Abstract
Cigarette smoke (CS) exposure is one of the primary risk factors associated with the chronic mucous hypersecretion (CMH). The antiapoptotic protein, Bcl-2 sustains hyperplastic mucous cells, and the airway epithelium of ex-smokers with CMH as well as mice exposed to chronic CS showed increased Bcl-2 expression. Therefore, we investigated whether Bcl-2 plays a role in CS-induced mucous expression. Primary airway epithelial cells (AECs) of murine and human origin were treated with CS extract (CSE), and there was a concentration- and time-dependent increase in secretory mucin (MUC5AC), mucous regulator (SPDEF) and Bcl-2 expression. Using differentiated human AECs cultured on air-liquid interface, EGFR and ERK1/2 pathways were interrogated. Bcl-2 activity was blocked using a small molecule BH3 mimetic ABT-263 that disrupts the Bcl-2 interaction with pro-apoptotic proteins. The ABT-263 treatment resulted in the downregulation of CSE-induced mucus expression and disrupted the EGFR-signaling while inducing the apoptosis and the pro-apoptotic protein, Bik expression. This strategy significantly suppressed the mainstream CS-induced mucous phenotype in a 3-D human airway epithelium model. Therefore, the present study suggests that CS induces Bcl-2 expression to help promote mucous cell survival; and small molecule BH3 mimetics targeting Bcl-2 could be useful in suppressing the CS-induced mucous response.
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Affiliation(s)
- Shah S Hussain
- Department of Immunology & Nano-Medicine, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL - 33199, USA
| | - Shebin George
- Department of Immunology & Nano-Medicine, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL - 33199, USA
| | - Shashi Singh
- Lovelace Respiratory Research Institute, Albuquerque, NM - 87108, USA
| | - Rahul Jayant
- Department of Immunology & Nano-Medicine, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL - 33199, USA
| | - Chien-An Hu
- Department of Biochemistry and Molecular Biology, University of New Mexico, Albuquerque, NM - 87131, USA
| | - Mohan Sopori
- Lovelace Respiratory Research Institute, Albuquerque, NM - 87108, USA
| | - Hitendra S Chand
- Department of Immunology & Nano-Medicine, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL - 33199, USA.
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29
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Wu J, Qin W, Wang Y, Sadik A, Liu J, Wang Y, Song P, Wang X, Sun K, Zeng J, Wang L. SPDEF is overexpressed in gastric cancer and triggers cell proliferation by forming a positive regulation loop with FoxM1. J Cell Biochem 2018; 119:9042-9054. [PMID: 30076647 DOI: 10.1002/jcb.27161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/14/2018] [Indexed: 12/20/2022]
Abstract
The SAM-pointed domain-containing ETS transcription factor (SPDEF) is an epithelial-specific transcription factor of the E26 transformation-specific (ETS) family, which binds the target gene through the high-affinity sequence of GGAT. It is suggested that SPDEF targets the promoter activity of Forkhead Box M1 (FoxM1), which has been proven to be highly expressed in gastric cancer. We found that SPDEF was overexpressed both at the messenger RNA (mRNA) and at the protein level in human gastric cancer species. The gastric cancer cells transfected with the SPDEF expression plasmid or SPDEF small interfering RNA (siRNA) led to observations on the clone genetics assay that indicated the promotion or the inhibition of gastric cancer cell proliferation, respectively. Both mRNA and protein levels of FoxM1 were regulated by SPDEF in gastric cancer cells and FoxM1 was also overexpressed in the corresponding human gastric cancer species. The overexpression and inhibition of FoxM1 could upregulate and downregulate the mRNA and protein levels of SPDEF expression, respectively. The recovery experiments verified that the overexpression of FoxM1 could at least partially revert both the expression of SPDEF and the proliferation of the cell lines even with the siRNA inhibition of SPDEF. The result of the dual luciferase activity assay showed that SPDEF bound to the promoter of FoxM1 and activated it. FoxM1 might also bind to the promoter of SPDEF to affect its expression. The results were checked in vivo. In conclusion, SPDEF is overexpressed in gastric cancer, which can form a positive regulation loop with FoxM1 to promote gastric carcinogenesis.
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Affiliation(s)
- Jing Wu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Wen Qin
- Department of Medical Administration, Shandong University Hospital, Shandong University, Jinan, China
| | - Ying Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Arsil Sadik
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Jilan Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yangyang Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ping Song
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Xiaoyun Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Kaiyue Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Jiping Zeng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Lixiang Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
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30
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Saco TV, Breitzig MT, Lockey RF, Kolliputi N. Epigenetics of Mucus Hypersecretion in Chronic Respiratory Diseases. Am J Respir Cell Mol Biol 2018; 58:299-309. [PMID: 29096066 DOI: 10.1165/rcmb.2017-0072tr] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Asthma, chronic obstructive pulmonary disease, and cystic fibrosis are three chronic pulmonary diseases that affect an estimated 420 million individuals across the globe. A key factor contributing to each of these conditions is mucus hypersecretion. Although management of these diseases is vastly studied, researchers have only begun to scratch the surface of the mechanisms contributing to mucus hypersecretion. Epigenetic regulation of mucus hypersecretion, other than microRNA post-translational modification, is even more scarcely researched. Detailed study of epigenetic mechanisms, such as DNA methylation and histone modification, could not only help to better the understanding of these respiratory conditions but also reveal new treatments for them. Because mucus hypersecretion is such a complex event, there are innumerable genes involved in the process, which are beyond the scope of a single review. Therefore, the purpose of this review is to narrow the focus and summarize specific epigenetic research that has been conducted on a few aspects of mucus hypersecretion in asthma, chronic obstructive pulmonary disease, cystic fibrosis, and some cancers. Specifically, this review emphasizes the contribution of DNA methylation and histone modification of particular genes involved in mucus hypersecretion to identify possible targets for the development of future therapies for these conditions. Elucidating the role of epigenetics in these respiratory diseases may provide a breath of fresh air to millions of affected individuals around the world.
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Affiliation(s)
- Tara V Saco
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Mason T Breitzig
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Richard F Lockey
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Narasaiah Kolliputi
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
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31
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Wu DD, Song J, Bartel S, Krauss-Etschmann S, Rots MG, Hylkema MN. The potential for targeted rewriting of epigenetic marks in COPD as a new therapeutic approach. Pharmacol Ther 2018; 182:1-14. [PMID: 28830839 DOI: 10.1016/j.pharmthera.2017.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is an age and smoking related progressive, pulmonary disorder presenting with poorly reversible airflow limitation as a result of chronic bronchitis and emphysema. The prevalence, disease burden for the individual, and mortality of COPD continues to increase, whereas no effective treatment strategies are available. For many years now, a combination of bronchodilators and anti-inflammatory corticosteroids has been most widely used for therapeutic management of patients with persistent COPD. However, this approach has had disappointing results as a large number of COPD patients are corticosteroid resistant. In patients with COPD, there is emerging evidence showing aberrant expression of epigenetic marks such as DNA methylation, histone modifications and microRNAs in blood, sputum and lung tissue. Therefore, novel therapeutic approaches may exist using epigenetic therapy. This review aims to describe and summarize current knowledge of aberrant expression of epigenetic marks in COPD. In addition, tools available for restoration of epigenetic marks are described, as well as delivery mechanisms of epigenetic editors to cells. Targeting epigenetic marks might be a very promising tool for treatment and lung regeneration in COPD in the future.
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Affiliation(s)
- Dan-Dan Wu
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands; Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Juan Song
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands; Tianjin Medical University, School of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Department of Immunology, Tianjin, China
| | - Sabine Bartel
- Early Life Origins of Chronic Lung Disease, Priority Area Asthma & Allergy, Leibnitz Center for Medicine and Biosciences, Research Center Borstel and Christian Albrechts University Kiel; Airway Research Center North, member of the German Center for Lung Research (DZL), Germany
| | - Susanne Krauss-Etschmann
- Early Life Origins of Chronic Lung Disease, Priority Area Asthma & Allergy, Leibnitz Center for Medicine and Biosciences, Research Center Borstel and Christian Albrechts University Kiel; Airway Research Center North, member of the German Center for Lung Research (DZL), Germany
| | - Marianne G Rots
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Machteld N Hylkema
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.
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32
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Goubert D, Koncz M, Kiss A, Rots MG. Establishment of Cell Lines Stably Expressing dCas9-Fusions to Address Kinetics of Epigenetic Editing. Methods Mol Biol 2018; 1767:395-415. [PMID: 29524148 DOI: 10.1007/978-1-4939-7774-1_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Epigenetic editing is a promising approach to modulate the local chromatin environment of target genes with the ultimate goal of stable gene expression reprogramming. Epigenetic editing tools minimally consist of a DNA-binding domain and an effector domain. The CRISPR/dCas9 platform, where mutations in the nuclease domains render the Cas9 protein inactive, is widely used to guide epigenetic effectors to their intended genomic loci. Its flexible nature, simple use, and relatively low cost have revolutionized the research field of epigenetic editing. Although effective expression modulation is readily achieved, only a few studies have addressed the maintenance of the induced effects on endogenous loci. Here, we describe a detailed protocol to engineer cells that stably express the CRISPR/dCas9-effectors. The protocol involves modification of published dCas9-based plasmid vectors for easy transfer of the effector domain between the vector designed for transient transfection and the vector used for establishing cell lines stably expressing the dCas9-effector fusion protein. Transient transfection of the dCas9-effector-producing cells with sgRNA-expressing plasmids allows studying of the maintenance of epigenetic editing. Targeting various genes in different chromatin contexts and/or co-targeting multiple CRISPR/dCas9-effectors can be used to unravel rules underlying maintained gene expression reprogramming.
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Affiliation(s)
- Désirée Goubert
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical CenterGroningen, Groningen, The Netherlands
| | - Mihály Koncz
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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33
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Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol 2018. [PMID: 29524128 DOI: 10.1007/978-1-4939-7774-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
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Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
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Reid AT, Veerati PC, Gosens R, Bartlett NW, Wark PA, Grainge CL, Stick SM, Kicic A, Moheimani F, Hansbro PM, Knight DA. Persistent induction of goblet cell differentiation in the airways: Therapeutic approaches. Pharmacol Ther 2017; 185:155-169. [PMID: 29287707 DOI: 10.1016/j.pharmthera.2017.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dysregulated induction of goblet cell differentiation results in excessive production and retention of mucus and is a common feature of several chronic airways diseases. To date, therapeutic strategies to reduce mucus accumulation have focused primarily on altering the properties of the mucus itself, or have aimed to limit the production of mucus-stimulating cytokines. Here we review the current knowledge of key molecular pathways that are dysregulated during persistent goblet cell differentiation and highlights both pre-existing and novel therapeutic strategies to combat this pathology.
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Affiliation(s)
- Andrew T Reid
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia.
| | - Punnam Chander Veerati
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Nathan W Bartlett
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Peter A Wark
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia; Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Chris L Grainge
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia; Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Stephen M Stick
- School of Paediatrics and Child Health, University of Western Australia, Nedlands 6009, Western Australia, Australia; Telethon Kids Institute, University of Western Australia, Nedlands 6009, Western Australia, Australia; Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth 6001, Western Australia, Australia; Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, University of Western Australia, Nedlands 6009, Western Australia, Australia
| | - Anthony Kicic
- School of Paediatrics and Child Health, University of Western Australia, Nedlands 6009, Western Australia, Australia; Telethon Kids Institute, University of Western Australia, Nedlands 6009, Western Australia, Australia; Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth 6001, Western Australia, Australia; Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, University of Western Australia, Nedlands 6009, Western Australia, Australia; Occupation and Environment, School of Public Health, Curtin University, Bentley 6102, Western Australia, Australia
| | - Fatemeh Moheimani
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Philip M Hansbro
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Darryl A Knight
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia; Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, Canada
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Bonser LR, Erle DJ. Airway Mucus and Asthma: The Role of MUC5AC and MUC5B. J Clin Med 2017; 6:jcm6120112. [PMID: 29186064 PMCID: PMC5742801 DOI: 10.3390/jcm6120112] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/25/2017] [Accepted: 11/27/2017] [Indexed: 11/16/2022] Open
Abstract
Asthma is characterized by mucus abnormalities. Airway epithelial hyperplasia and metaplasia result in changes in stored and secreted mucin and the production of a pathologic mucus gel. Mucus transport is impaired, culminating in mucus plugging and airway obstruction—a major cause of morbidity in asthma. The polymeric mucins MUC5AC and MUC5B are integral components of airway mucus. MUC5AC and MUC5B gene expression is altered in asthma, and recent work sheds light on their contribution to asthma pathogenesis. Herein, we review our current understanding of the role of MUC5AC and MUC5B in mucus dysfunction in asthma.
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Affiliation(s)
- Luke R Bonser
- Lung Biology Center, University of California San Francisco, San Francisco, CA 94143, USA.
| | - David J Erle
- Lung Biology Center, University of California San Francisco, San Francisco, CA 94143, USA.
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Cancer induction and suppression with transcriptional control and epigenome editing technologies. J Hum Genet 2017; 63:187-194. [PMID: 29215091 DOI: 10.1038/s10038-017-0377-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/27/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
Cancer epigenetics is one of the most important research subjects in dissecting cancer mechanisms and therapeutic targets because the emergence and malignant transformation of various cancers are caused by unnatural expression of cancer-related genes attributed to their epigenetic errors. The original concept of cancer epigenetics basically stands on the analysis of the epigenetic status in naturally occurring cancer cells; however, the rapidly emerging technology called epigenome editing would change this situation drastically. Epigenome editing, the most promising derivative technology of genome editing, can modify the epigenetic states at the pre-defined genomic locus using the programmable effectors, consisting of various epigenetic factors combined with site-specific DNA-binding domains. This technology can be utilized in a reversible manner; i.e., cancer modeling can be achieved by introducing aberrant epigenetic marks in normal cells, and cancer suppression can be achieved by correcting the epigenetic errors in cancer cells. In this review, we summarize the basics of epigenome editing and cancer epigenetics, followed by the current examples of cancer induction and suppression with the transcriptional control and epigenome editing technologies.
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Song J, Heijink IH, Kistemaker LEM, Reinders-Luinge M, Kooistra W, Noordhoek JA, Gosens R, Brandsma CA, Timens W, Hiemstra PS, Rots MG, Hylkema MN. Aberrant DNA methylation and expression of SPDEF and FOXA2 in airway epithelium of patients with COPD. Clin Epigenetics 2017; 9:42. [PMID: 28450970 PMCID: PMC5404321 DOI: 10.1186/s13148-017-0341-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 04/12/2017] [Indexed: 12/20/2022] Open
Abstract
Background Goblet cell metaplasia, a common feature of chronic obstructive pulmonary disease (COPD), is associated with mucus hypersecretion which contributes to the morbidity and mortality among patients. Transcription factors SAM-pointed domain-containing Ets-like factor (SPDEF) and forkhead box protein A2 (FOXA2) regulate goblet cell differentiation. This study aimed to (1) investigate DNA methylation and expression of SPDEF and FOXA2 during goblet cell differentiation and (2) compare this in airway epithelial cells from patients with COPD and controls during mucociliary differentiation. Methods To assess DNA methylation and expression of SPDEF and FOXA2 during goblet cell differentiation, primary airway epithelial cells, isolated from trachea (non-COPD controls) and bronchial tissue (patients with COPD), were differentiated by culture at the air-liquid interface (ALI) in the presence of cytokine interleukin (IL)-13 to promote goblet cell differentiation. Results We found that SPDEF expression was induced during goblet cell differentiation, while FOXA2 expression was decreased. Importantly, CpG number 8 in the SPDEF promoter was hypermethylated upon differentiation, whereas DNA methylation of FOXA2 promoter was not changed. In the absence of IL-13, COPD-derived ALI-cultured cells displayed higher SPDEF expression than control-derived ALI cultures, whereas no difference was found for FOXA2 expression. This was accompanied with hypomethylation of CpG number 6 in the SPDEF promoter and also hypomethylation of CpG numbers 10 and 11 in the FOXA2 promoter. Conclusions These findings suggest that aberrant DNA methylation of SPDEF and FOXA2 is one of the factors underlying mucus hypersecretion in COPD, opening new avenues for epigenetic-based inhibition of mucus hypersecretion. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0341-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Song
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - I H Heijink
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - L E M Kistemaker
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - M Reinders-Luinge
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - W Kooistra
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J A Noordhoek
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - R Gosens
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - C A Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - W Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - M G Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - M N Hylkema
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology EA10, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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